$ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages
All Classes All Packages
All Classes All Packages
$
- $3D_atom_query - Static variable in class com.actelion.research.util.Sketch
- $3D_basis_objs - Static variable in class com.actelion.research.util.Sketch
- $3D_dihed_chiral - Static variable in class com.actelion.research.util.Sketch
- $3D_exclus_dradius - Static variable in class com.actelion.research.util.Sketch
- $3D_exclus_ignore - Static variable in class com.actelion.research.util.Sketch
- $3D_exclus_radius - Static variable in class com.actelion.research.util.Sketch
- $3D_marker_rf - Static variable in class com.actelion.research.util.Sketch
- $3D_maxval - Static variable in class com.actelion.research.util.Sketch
- $3D_minval - Static variable in class com.actelion.research.util.Sketch
- $3D_name - Static variable in class com.actelion.research.util.Sketch
- $3D_num_basis_objs - Static variable in class com.actelion.research.util.Sketch
- $3D_point_ddist - Static variable in class com.actelion.research.util.Sketch
- $3D_point_dir - Static variable in class com.actelion.research.util.Sketch
- $3D_point_dist - Static variable in class com.actelion.research.util.Sketch
- $3D_tolerance - Static variable in class com.actelion.research.util.Sketch
- $Abbrev_atch - Static variable in class com.actelion.research.util.Sketch
- $Arc_endpts - Static variable in class com.actelion.research.util.Sketch
- $ArrowDir - Static variable in class com.actelion.research.util.Sketch
- $ArrowShaftSp - Static variable in class com.actelion.research.util.Sketch
- $ArrowSize - Static variable in class com.actelion.research.util.Sketch
- $ArrowStyle - Static variable in class com.actelion.research.util.Sketch
- $ArrowType - Static variable in class com.actelion.research.util.Sketch
- $Atom_aamap_num - Static variable in class com.actelion.research.util.Sketch
- $Atom_aamapped - Static variable in class com.actelion.research.util.Sketch
- $Atom_alias - Static variable in class com.actelion.research.util.Sketch
- $Atom_AttachLen - Static variable in class com.actelion.research.util.Sketch
- $Atom_can_reverse - Static variable in class com.actelion.research.util.Sketch
- $Atom_chg - Static variable in class com.actelion.research.util.Sketch
- $Atom_coords - Static variable in class com.actelion.research.util.Sketch
- $Atom_dispflags - Static variable in class com.actelion.research.util.Sketch
- $Atom_DotWidth - Static variable in class com.actelion.research.util.Sketch
- $Atom_exact_change - Static variable in class com.actelion.research.util.Sketch
- $Atom_fixed - Static variable in class com.actelion.research.util.Sketch
- $Atom_h0bit - Static variable in class com.actelion.research.util.Sketch
- $Atom_hpos - Static variable in class com.actelion.research.util.Sketch
- $Atom_hshow - Static variable in class com.actelion.research.util.Sketch
- $Atom_list - Static variable in class com.actelion.research.util.Sketch
- $Atom_margin_width - Static variable in class com.actelion.research.util.Sketch
- $Atom_msdif - Static variable in class com.actelion.research.util.Sketch
- $Atom_npos - Static variable in class com.actelion.research.util.Sketch
- $Atom_number - Static variable in class com.actelion.research.util.Sketch
- $Atom_NumSize - Static variable in class com.actelion.research.util.Sketch
- $Atom_Orig_coords - Static variable in class com.actelion.research.util.Sketch
- $Atom_rad - Static variable in class com.actelion.research.util.Sketch
- $Atom_rbcount - Static variable in class com.actelion.research.util.Sketch
- $Atom_rgroupAtch - Static variable in class com.actelion.research.util.Sketch
- $Atom_rxn_stereo - Static variable in class com.actelion.research.util.Sketch
- $Atom_stereo_care - Static variable in class com.actelion.research.util.Sketch
- $Atom_substcount - Static variable in class com.actelion.research.util.Sketch
- $Atom_symbol - Static variable in class com.actelion.research.util.Sketch
- $Atom_tplatchpt - Static variable in class com.actelion.research.util.Sketch
- $Atom_type - Static variable in class com.actelion.research.util.Sketch
- $Atom_unsat - Static variable in class com.actelion.research.util.Sketch
- $Atom_valence - Static variable in class com.actelion.research.util.Sketch
- $Atom_value - Static variable in class com.actelion.research.util.Sketch
- $Atom_zcoord - Static variable in class com.actelion.research.util.Sketch
- $Begsketch - Static variable in class com.actelion.research.util.Sketch
- $BigMetaData - Static variable in class com.actelion.research.util.Sketch
- $Bond_alt_stereo - Static variable in class com.actelion.research.util.Sketch
- $Bond_atoms - Static variable in class com.actelion.research.util.Sketch
- $Bond_bond_spacing - Static variable in class com.actelion.research.util.Sketch
- $Bond_crossed - Static variable in class com.actelion.research.util.Sketch
- $Bond_dbl_side - Static variable in class com.actelion.research.util.Sketch
- $Bond_dbl_width - Static variable in class com.actelion.research.util.Sketch
- $Bond_hash_spacing - Static variable in class com.actelion.research.util.Sketch
- $Bond_qtopo - Static variable in class com.actelion.research.util.Sketch
- $Bond_rxn_center - Static variable in class com.actelion.research.util.Sketch
- $Bond_stereo_care - Static variable in class com.actelion.research.util.Sketch
- $Bond_stereo_type - Static variable in class com.actelion.research.util.Sketch
- $Bond_topo - Static variable in class com.actelion.research.util.Sketch
- $Bond_type - Static variable in class com.actelion.research.util.Sketch
- $Circ_Arc_Points - Static variable in class com.actelion.research.util.Sketch
- $Comment - Static variable in class com.actelion.research.util.Sketch
- $Crop_coords - Static variable in class com.actelion.research.util.Sketch
- $Endsketch - Static variable in class com.actelion.research.util.Sketch
- $Fill_color - Static variable in class com.actelion.research.util.Sketch
- $Fill_RGB2Color - Static variable in class com.actelion.research.util.Sketch
- $Fill_style - Static variable in class com.actelion.research.util.Sketch
- $Font - Static variable in class com.actelion.research.util.Sketch
- $Is_A_Model - Static variable in class com.actelion.research.util.Sketch
- $Locked - Static variable in class com.actelion.research.util.Sketch
- $MDLEditText - Static variable in class com.actelion.research.util.Sketch
- $MetaData - Static variable in class com.actelion.research.util.Sketch
- $Model_Rotated - Static variable in class com.actelion.research.util.Sketch
- $Mol_type - Static variable in class com.actelion.research.util.Sketch
- $Name - Static variable in class com.actelion.research.util.Sketch
- $Nostruct_label - Static variable in class com.actelion.research.util.Sketch
- $Nostruct_regno - Static variable in class com.actelion.research.util.Sketch
- $Obj - Static variable in class com.actelion.research.util.Sketch
- $Obj_Atom - Static variable in class com.actelion.research.util.Sketch
- $Obj_Bond - Static variable in class com.actelion.research.util.Sketch
- $Obj_Chiral - Static variable in class com.actelion.research.util.Sketch
- $Obj_coords - Static variable in class com.actelion.research.util.Sketch
- $Obj_Mol - Static variable in class com.actelion.research.util.Sketch
- $Parent - Static variable in class com.actelion.research.util.Sketch
- $Pen_color - Static variable in class com.actelion.research.util.Sketch
- $Pen_RGB2Color - Static variable in class com.actelion.research.util.Sketch
- $Pen_style - Static variable in class com.actelion.research.util.Sketch
- $Pen_style_token - Static variable in class com.actelion.research.util.Sketch
- $Pen_width - Static variable in class com.actelion.research.util.Sketch
- $Pen_widthUnit - Static variable in class com.actelion.research.util.Sketch
- $Poly_points - Static variable in class com.actelion.research.util.Sketch
- $Poly_smoothed - Static variable in class com.actelion.research.util.Sketch
- $RGroupNo - Static variable in class com.actelion.research.util.Sketch
- $RLogic - Static variable in class com.actelion.research.util.Sketch
- $Roundrect_curve - Static variable in class com.actelion.research.util.Sketch
- $RxnAtch - Static variable in class com.actelion.research.util.Sketch
- $SGroupAtch - Static variable in class com.actelion.research.util.Sketch
- $SGroupAtchPt - Static variable in class com.actelion.research.util.Sketch
- $SGroupBracketLen - Static variable in class com.actelion.research.util.Sketch
- $SGroupContext - Static variable in class com.actelion.research.util.Sketch
- $SGroupLinkVal - Static variable in class com.actelion.research.util.Sketch
- $SGroupName - Static variable in class com.actelion.research.util.Sketch
- $SGroupNewAtch - Static variable in class com.actelion.research.util.Sketch
- $SGroupType - Static variable in class com.actelion.research.util.Sketch
- $Totobjs - Static variable in class com.actelion.research.util.Sketch
- $Transparent - Static variable in class com.actelion.research.util.Sketch
- $Version - Static variable in class com.actelion.research.util.Sketch
A
- a - Variable in class com.actelion.research.chem.forcefield.mmff.SortedPair
- a - Variable in class com.actelion.research.util.BurtleHasherABC
- A - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- a_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'A-i' from the table.
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- a1t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a1t - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- a2t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a2t - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- a3 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- a3 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- a3 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a3t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a4 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a4t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- aat() - Method in interface smile.math.matrix.DenseMatrix
- aat() - Method in class smile.math.matrix.JMatrix
- aat() - Method in interface smile.math.matrix.Matrix
-
Returns A * A'
- abmm(B) - Method in interface smile.math.matrix.MatrixMultiplication
-
Returns the result of matrix multiplication A * B.
- abmm(DenseMatrix) - Method in class smile.math.matrix.JMatrix
- abs() - Method in class smile.math.Complex
-
Returns abs/modulus/magnitude.
- abs(double) - Static method in class smile.math.Math
-
Returns the absolute value of a double value.
- abs(float) - Static method in class smile.math.Math
-
Returns the absolute value of a float value.
- abs(int) - Static method in class smile.math.Math
-
Returns the absolute value of an int value.
- abs(long) - Static method in class smile.math.Math
-
Returns the absolute value of a long value.
- AbstractDepictor<T> - Class in com.actelion.research.chem
- AbstractDepictor(StereoMolecule) - Constructor for class com.actelion.research.chem.AbstractDepictor
- AbstractDepictor(StereoMolecule, int) - Constructor for class com.actelion.research.chem.AbstractDepictor
- AbstractDepictor.DepictorDot - Class in com.actelion.research.chem
- AbstractDepictor.DepictorLine - Class in com.actelion.research.chem
- AbstractDescriptorHandlerFP<U> - Class in com.actelion.research.chem.descriptor
- AbstractDescriptorHandlerFP() - Constructor for class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- AbstractDescriptorHandlerLongFP<U> - Class in com.actelion.research.chem.descriptor
- AbstractDescriptorHandlerLongFP() - Constructor for class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- AbstractDistribution - Class in smile.stat.distribution
-
This is the base class of univariate distributions.
- AbstractDistribution() - Constructor for class smile.stat.distribution.AbstractDistribution
- AbstractDrawingObject - Class in com.actelion.research.chem
- AbstractDrawingObject() - Constructor for class com.actelion.research.chem.AbstractDrawingObject
- AbstractExtendedDepictor<T,C> - Class in com.actelion.research.share.gui.editor.chem
- AbstractExtendedDepictor(Reaction, List<IDrawingObject>, boolean, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- AbstractExtendedDepictor(StereoMolecule[], int, List<IDrawingObject>, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
-
Use this constructor for markush structures.
- AbstractExtendedDepictor(StereoMolecule[], List<IDrawingObject>, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- AbstractExtendedDepictor(StereoMolecule, List<IDrawingObject>, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- AbstractForceField - Class in com.actelion.research.chem.forcefield
- AbstractForceField(StereoMolecule) - Constructor for class com.actelion.research.chem.forcefield.AbstractForceField
- AbstractParser - Class in com.actelion.research.chem.io
-
A parser is used to load and save molecules from the filesystem.
- AbstractParser() - Constructor for class com.actelion.research.chem.io.AbstractParser
- AbstractScoringEngine - Class in com.actelion.research.chem.docking.scoring
-
this class is not thread safe!
- AbstractScoringEngine(StereoMolecule, Set<Integer>, MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- abtmm(B) - Method in interface smile.math.matrix.MatrixMultiplication
-
Returns the result of matrix multiplication A * B'.
- abtmm(DenseMatrix) - Method in class smile.math.matrix.JMatrix
- accept(double, double) - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
- accept(File) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Return true if this file should be shown in the directory pane, false if it shouldn't.
- ACCEPTOR - com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint.Functionality
- ACCEPTOR_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- AcceptorPoint - Class in com.actelion.research.chem.phesa.pharmacophore.pp
- AcceptorPoint(AcceptorPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- AcceptorPoint(StereoMolecule, int, List<Integer>, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- AcceptorPoint(StereoMolecule, int, List<Integer>, int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- acos(double) - Static method in class smile.math.Math
-
Returns the arc cosine of an angle, in the range of 0.0 through pi.
- Action - Interface in com.actelion.research.share.gui.editor.actions
-
Basic Interface for all editor actions
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.dock.JDockingPanel
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.editor.SwingEditorDialog
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JAtomLabelDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JAtomQueryFeatureDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JBondQueryFeatureDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JChemistryView
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JImagePanel
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JProgressDialog
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JProgressPanel
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JStructureView
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JTextDrawingObjectDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.swing.SwingCheckBox
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.swing.SwingDialog
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.swing.SwingPopupMenu
- ACTIVATION_FCT_LOG - Static variable in class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkParameterHelper
- ACTIVATION_FCT_TAN - Static variable in class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkParameterHelper
- add(byte[]) - Method in class com.actelion.research.util.datamodel.IntArray
- add(byte, byte) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
-
Adds a pair of nodes to this solution.
- add(double) - Method in class com.actelion.research.calc.Matrix
- add(double) - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- add(double) - Method in class com.actelion.research.util.Angle
- add(double) - Method in class com.actelion.research.util.datamodel.DoubleArray
- add(double) - Method in interface smile.math.matrix.DenseMatrix
-
In place element-wise addition A = A + x
- add(double) - Method in class smile.math.matrix.JMatrix
- add(double[]) - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- add(double[]) - Method in class com.actelion.research.util.datamodel.DoubleArray
- add(double[]) - Method in class smile.data.AttributeDataset
- add(double[], double) - Method in class smile.data.AttributeDataset
- add(double[], double, double) - Method in class smile.data.AttributeDataset
- add(double[], int) - Method in class smile.data.AttributeDataset
- add(double[], int, double) - Method in class smile.data.AttributeDataset
- add(double, double, double) - Method in class com.actelion.research.chem.Coordinates
- add(double, DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
Element-wise addition C = A + x
- add(double, DenseMatrix) - Method in class smile.math.matrix.JMatrix
- add(double, JMatrix) - Method in class smile.math.matrix.JMatrix
- add(float[]) - Method in class com.actelion.research.util.datamodel.DoubleArray
- add(int) - Method in class com.actelion.research.calc.histogram.IntegerHistogram
-
Added to the bin where fullfilling the criteria v >= lower bound and v < higher bound.
- add(int) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- add(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
Caution! After finishing all adding's realize() has to be called!
- add(int) - Method in class com.actelion.research.util.datamodel.IntArray
- add(int) - Method in class com.actelion.research.util.hash.HashSetInt
-
If the key is already present nothing will happen.
- add(int) - Method in class smile.sort.IntHeapSelect
-
Assimilate a new value from the stream.
- add(int[]) - Method in class com.actelion.research.calc.histogram.IntegerHistogram
- add(int[]) - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- add(int[]) - Method in class com.actelion.research.util.datamodel.IntArray
- add(int[]) - Method in class com.actelion.research.util.hash.HashSetInt
- add(int, int) - Method in class com.actelion.research.chem.coords.FragmentAssociation
- add(int, int, double) - Method in interface smile.math.matrix.DenseMatrix
-
A[i][j] += x
- add(int, int, double) - Method in class smile.math.matrix.JMatrix
- add(int, long) - Method in class com.actelion.research.chem.CanonizerBaseValue
- add(int, T) - Method in class com.actelion.research.util.UniqueList
- add(long) - Method in class com.actelion.research.chem.CanonizerBaseValue
- add(PrecisionAndRecall) - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- add(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- add(SubFlexophoreGenerator.ViolatedConditionsCount) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- add(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Adds two vectors together by component.
- add(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- add(IBitArray) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- add(ListWithIntVecIdCode) - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- add(GenericComponent, int, int) - Method in interface com.actelion.research.gui.generic.GenericDialog
- add(GenericComponent, int, int) - Method in class com.actelion.research.gui.swing.SwingDialog
- add(GenericComponent, int, int, int, int) - Method in interface com.actelion.research.gui.generic.GenericDialog
- add(GenericComponent, int, int, int, int) - Method in class com.actelion.research.gui.swing.SwingDialog
- add(Angle) - Method in class com.actelion.research.util.Angle
- add(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
- add(DoubleArray) - Method in class com.actelion.research.util.datamodel.DoubleArray
- add(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
- add(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
- add(ErrorHashMap) - Method in class com.actelion.research.util.ErrorHashMap
- add(E) - Method in class smile.data.Dataset
-
Add a datum item into the dataset.
- add(E, double) - Method in class smile.data.Dataset
-
Add a datum item into the dataset.
- add(E, double, double) - Method in class smile.data.Dataset
-
Add a datum item into the dataset.
- add(E, int) - Method in class smile.data.Dataset
-
Add a datum item into the dataset.
- add(E, int, double) - Method in class smile.data.Dataset
-
Add a datum item into the dataset.
- add(Component) - Method in class com.actelion.research.gui.JScrollableMenu
- add(Component, int) - Method in class com.actelion.research.gui.JScrollableMenu
- add(Point2D) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- add(Point2D) - Method in class com.actelion.research.share.gui.Polygon
- add(Exception) - Method in class com.actelion.research.util.ErrorHashMap
- add(String, int) - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
- add(String, String) - Method in class com.actelion.research.util.CommandLineParser
- add(List<Integer>) - Method in class com.actelion.research.calc.histogram.IntegerHistogram
- add(List<Integer>) - Method in class com.actelion.research.util.datamodel.IntArray
- add(List<Integer>) - Method in class com.actelion.research.util.hash.HashSetInt
- add(JComponent, String) - Method in class com.actelion.research.gui.JMultiPanelView
- add(JComponent, String, int) - Method in class com.actelion.research.gui.JMultiPanelView
- add(JMenuItem) - Method in class com.actelion.research.gui.JScrollableMenu
- add(AttributeDataset.Row) - Method in class smile.data.AttributeDataset
-
Add a datum item into the dataset.
- add(Datum<double[]>) - Method in class smile.data.AttributeDataset
- add(Datum<E>) - Method in class smile.data.Dataset
-
Add a datum item into the dataset.
- add(DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
In place addition A = A + B
- add(DenseMatrix) - Method in class smile.math.matrix.JMatrix
- add(DenseMatrix, DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
C = A + B
- add(DenseMatrix, DenseMatrix) - Method in class smile.math.matrix.JMatrix
- add(JMatrix) - Method in class smile.math.matrix.JMatrix
- add(JMatrix, JMatrix) - Method in class smile.math.matrix.JMatrix
- add(T) - Method in class com.actelion.research.util.SortedList
-
Adds object to the list provided that it doesn't contain an object being considered equal by compareTo().
- add(T) - Method in class com.actelion.research.util.UniqueList
- add2CompleteCol(Matrix) - Method in class com.actelion.research.calc.Matrix
-
The value in the col from the input matrix is added to all values in the corresponding col in the matrix.
- add2DCoordinatesColumn(int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Creates a new column to hold encoded 2-dimensional atom coordinates for the structures stored in the associated structure column.
- add2Row(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
- add3DCoordinatesColumn(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Creates a new column to hold encoded 3-dimensional atom coordinates for the structures stored in the associated structure column.
- addAll(List<Exception>) - Method in class com.actelion.research.util.ErrorHashMap
- addAllBits(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- addAlphanumericalColumn(String) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Creates a new standard column to hold any alphanumerical content.
- addArrOriginalAtomIndexRGroups(AtomIndexLinkerId) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- addAtom(double, double) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addAtom(double, double, double) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addAtom(int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addAtom(int) - Method in class com.actelion.research.chem.Molecule3D
-
Add an atom with the given atomicNo
- addAtom(Molecule3D, int) - Method in class com.actelion.research.chem.Molecule3D
-
Add an atom by copying its properties from the given Molecule3D This has to be overriden by subclasses
- addAtom(String) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addAtomIndices(HashSetInt, List<SubGraphIndices>) - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
-
Adds the atom indices to the hash set.
- addAtomList(StringBuilder) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- addAtoms(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
Only atoms are added that are not yet in the list, check PPAtom.equals for comparison.
- addAtoms(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
-
Only atoms are added that are not yet in the list, check PPAtom.equals for comparison.
- addAtomVolume(AtomicGaussian) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- addBit(int) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
-
Dont't forget to calculate the hash!
- addBits(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- addBond(int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addBond(int, int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addC(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- addCatalyst(StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reaction
- addCatalyst(StereoMolecule, int) - Method in class com.actelion.research.chem.reaction.Reaction
- addChangeListener(IChangeListener) - Method in class com.actelion.research.share.gui.editor.Model
- addColumnProperty(int, String, String) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
This method may be used to define column properties, e.g.
- addCompound(int, T) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addCompound(int, T) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addCompound(T) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addCompound(T) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addCompoundCollectionListener(CompoundCollectionListener) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addCompoundCollectionListener(CompoundCollectionListener) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addCompoundList(Collection<T>) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addCompoundList(Collection<T>) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addConstraint(PositionConstraint) - Method in class com.actelion.research.chem.docking.LigandPose
- addConstraint(PotentialEnergyTerm) - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- addContent(Dockable, boolean) - Method in class com.actelion.research.gui.dock.TreeLeaf
- addCoord(Coordinates) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- addCore(StereoMolecule) - Method in class com.actelion.research.chem.MarkushStructure
- addData(List<T>) - Method in class com.actelion.research.util.Pipeline
- addData(T) - Method in class com.actelion.research.util.Pipeline
- addDescription(String) - Method in class com.actelion.research.chem.io.CompoundFileFilter
- addDescriptorColumn(String, String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Creates a new column to hold a chemical descriptor for the structures stored in the associated structure column.
- addDividerChangeLister(DividerChangeListener) - Method in class com.actelion.research.gui.dock.JDockingPanel
- addDrawAreaListener(DrawAreaListener) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- addDrawAreaListener(DrawAreaListener) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- addDrawingObject(IDrawingObject) - Method in class com.actelion.research.share.gui.editor.Model
- addElement(String, double) - Method in class com.actelion.research.chem.prediction.IncrementTable
- addElement(String, long[], double) - Method in class com.actelion.research.chem.prediction.IncrementTableWithIndex
- addEnergyTerm(EnergyTerm) - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- addExtension(String) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Adds a filetype "dot" extension to filter against.
- addFacultative(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
-
The fragment is added if it is not already in the hash map.
- addFeatureMatch(TreeMatcher.FeatureMatch) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- addFragment(ExtendedMolecule, int, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
This adds a fragment from sourceMol to this molecule by first copying rootAtom and then all connected atoms and bonds by traversing the graph breadth first.
- addGradient(double[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- addHandle() - Method in class com.actelion.research.gui.wmf.WMF
- addHydrogenAtoms(StereoMolecule) - Static method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Adds explicit hydrogen atoms where they are implicit by filling valences and adapting for atom charges.
- addHydrogens(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Add the missing hydrogens for the ligand
- addHydrogens(Molecule3D, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Adds the missing hydrogens (no optimization)
- addHydrogensAroundLigand(Molecule3D, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- addImpl(Component, Object, int) - Method in class com.actelion.research.gui.JScrollablePopupMenu
- addImplicitHydrogens() - Method in class com.actelion.research.chem.conf.AtomAssembler
- addImplicitHydrogens(int) - Method in class com.actelion.research.chem.conf.AtomAssembler
- addImplicitHydrogens(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.HydrogenHandler
- addImplicitHydrogens(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingUtils
- addImplicitHydrogens(StereoMolecule, int) - Static method in class com.actelion.research.chem.contrib.HydrogenHandler
- addIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- addIndex(int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- addIndexOriginalAtom(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- addInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- addInteraction(int, int, double) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- addItem(String) - Method in interface com.actelion.research.gui.generic.GenericComboBox
- addItem(String) - Method in class com.actelion.research.gui.JComboBoxWithColor
- addItem(String) - Method in class com.actelion.research.gui.swing.SwingComboBox
- addItem(String, Color) - Method in class com.actelion.research.gui.JComboBoxWithColor
- addItem(String, String) - Method in class com.actelion.research.gui.JPopupButton
- addItem(String, String, boolean) - Method in interface com.actelion.research.gui.generic.GenericPopupMenu
- addItem(String, String, boolean) - Method in class com.actelion.research.gui.swing.SwingPopupMenu
- addLayoutComponent(String, Component) - Method in class com.actelion.research.gui.JScrollablePopupMenu.ScrollPopupMenuLayout
- addLayoutComponent(String, Component) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Adds a feature to the LayoutComponent attribute of the VerticalFlowLayout object
- addListener(ForceFieldChangeListener) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
-
Return the variance across all atoms in a molecule for the specified coordinate.
- addListener(ForceFieldChangeListener) - Method in interface com.actelion.research.chem.forcefield.ForceField
- addListener(GenericKeyListener) - Method in class com.actelion.research.gui.swing.SwingKeyHandler
- addListener(GenericMouseListener) - Method in class com.actelion.research.gui.swing.SwingMouseHandler
- addMatching(TreeMatcher.TreeMatching) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- addMissingChirality(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
- addMissingChirality(StereoMolecule, int) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
-
The problem is that sometimes we need to add chiral bond that was not planned because it is the same group This is the case for example for the valine where the 2 C of the methyl groups are diastereotopic
- addMolecule(int, StereoMolecule) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
- addMolecule(Molecule) - Method in class com.actelion.research.chem.Molecule
-
Copies all atoms and bonds of mol to the end of this Molecule's atom and bond tables.
- addMolecule(Molecule, int, int) - Method in class com.actelion.research.chem.Molecule
-
Copies first atoms and first bonds of mol to the end of this Molecule's atom and bond tables.
- addMolecule(StereoMolecule, double, double) - Method in class com.actelion.research.share.gui.editor.Model
- addMoleculeList(Collection<StereoMolecule>) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addMoleculeList(Collection<StereoMolecule>) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addNode(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- addNode(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- addNode(PharmacophoreNode, List<PharmacophoreNode>, Map<Integer, List<Integer>>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- addNoise(double, double, double) - Method in class com.actelion.research.util.DoubleVec
- addNotify() - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- addOrChangeAtom(double, double, int, int, int, int, String) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addOrChangeBond(int, int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addOriginalAtomIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- addOriginalAtomIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- addOriginalAtomIndex(int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- addPastedOrDropped(StereoMolecule, Point) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- addPharmacophorePoint(PPGaussian) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- addPoint(double, double) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- addPoint(double, double) - Method in class com.actelion.research.gui.generic.GenericPolygon
- addPoint(PointDouble) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- addPoint(Point) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
-
add a point to the vector of points
- addPositionalConstraints(double) - Method in class com.actelion.research.chem.docking.LigandPose
- addProduct(StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reaction
- addProduct(StereoMolecule, int) - Method in class com.actelion.research.chem.reaction.Reaction
- addProgressListener(ProgressListener) - Method in class com.actelion.research.calc.DataProcessor
- addPruningBarListener(PruningBarListener) - Method in class com.actelion.research.gui.JPruningBar
- addRadioButtonItem(String, String, Color, boolean) - Method in interface com.actelion.research.gui.generic.GenericPopupMenu
- addRadioButtonItem(String, String, Color, boolean) - Method in class com.actelion.research.gui.swing.SwingPopupMenu
- addReactant(StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reaction
- addReactant(StereoMolecule, int) - Method in class com.actelion.research.chem.reaction.Reaction
- addReaction(String, int) - Method in class com.actelion.research.chem.combinatorialspace.Synthon
- addRenderingHints(Map<?, ?>) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- addResidue(Molecule3D) - Method in class com.actelion.research.chem.io.pdb.parser.ProteinSynthesizer
-
an amino acid is added to the protein structure and a peptide coupling is performed, if coupling cannot be performed, the function results false and the residue is not added
- addRGroup(StereoMolecule) - Method in class com.actelion.research.chem.MarkushStructure
-
This adds a substituent list representing one R-group as multiple fragments within one StereoMolecule.
- addRing(double, double, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- AddRingAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:03 PM
- AddRingAction(Model, int, boolean) - Constructor for class com.actelion.research.share.gui.editor.actions.AddRingAction
- addRingToAtom(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addRingToBond(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addRNDvalue(double) - Method in class com.actelion.research.util.DoubleVec
-
Adds aor subtracts a random value to the original value.
- addRow(double[]) - Method in class com.actelion.research.calc.Matrix
- addRow(int[]) - Method in class com.actelion.research.calc.Matrix
- addSeparator() - Method in interface com.actelion.research.gui.generic.GenericPopupMenu
- addSeparator() - Method in class com.actelion.research.gui.JScrollableMenu
- addSeparator() - Method in class com.actelion.research.gui.swing.SwingPopupMenu
- addShift(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- addStateInfo(ArrayList<String>, String) - Method in class com.actelion.research.gui.dock.TreeFork
- addStateInfo(ArrayList<String>, String) - Method in class com.actelion.research.gui.dock.TreeLeaf
-
adds docking state entries of this leaf's Dockables
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.DistanceRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.PlaneRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.StraightLineRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.TorsionRule
- addString(String) - Method in class com.actelion.research.chem.SortedStringList
- addString(String) - Method in class com.actelion.research.chem.UniqueStringList
- addStructureColumn(String, String) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
This adds a column to host canonical structure representations (idcodes).
- addStructureListener(StructureListener) - Method in class com.actelion.research.gui.editor.SwingEditorDialog
- addStructureListener(StructureListener) - Method in class com.actelion.research.gui.JChemistryView
- addStructureListener(StructureListener) - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- addStructureListener(StructureListener) - Method in class com.actelion.research.gui.JStructureView
- addSubstituent(Molecule, int) - Method in class com.actelion.research.chem.Molecule
-
Adds and connects the substituent molecule to the connectionAtom of this molecule.
- addSubstituent(Molecule, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Adds and connects the substituent molecule to the connectionAtom of this molecule.
- addToElement(int, int, double) - Method in class com.actelion.research.calc.Matrix
- addToExistingSet(long[]) - Method in class com.actelion.research.chem.DiversitySelector
- addToIntArray(int[], int) - Static method in class com.actelion.research.chem.CanonizerMesoHelper
- addTransformation(Transformation) - Method in class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- addValidationListener(IValidationListener) - Method in class com.actelion.research.share.gui.editor.Model
- advanceToNext() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Dont't call this method directly.
- advanceToNext() - Method in class com.actelion.research.chem.io.DWARFileParser
- advanceToNext() - Method in class com.actelion.research.chem.io.ODEFileParser
- advanceToNext() - Method in class com.actelion.research.chem.io.SDFileParser
- alamda - Variable in class com.actelion.research.util.FittingFunction
- align() - Method in class com.actelion.research.chem.alignment3d.KabschAlignment
- align() - Method in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- align(Coordinates, Matrix, Coordinates) - Method in class com.actelion.research.chem.alignment3d.KabschAlignment
- align(PheSAMolecule, PheSAMolecule, StereoMolecule[], double, boolean) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
- AlignmentResult(double, TransformationSequence, int, int) - Constructor for class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer.AlignmentResult
- alignToNegRecImg(ShapeVolume, List<? extends ShapeVolume>, double, boolean) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
- alignTwoMolsInPlace(StereoMolecule, StereoMolecule) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
- alignTwoMolsInPlace(StereoMolecule, StereoMolecule, double) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
- AliphaticPoint - Class in com.actelion.research.chem.phesa.pharmacophore.pp
- AliphaticPoint(AliphaticPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- AliphaticPoint(StereoMolecule, int, List<Integer>) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- all(boolean[]) - Static method in class smile.math.Math
-
Given a set of boolean values, are all of the values true?
- allFieldsEquals(int) - Method in class com.actelion.research.util.datamodel.IntVec
- allowDrag(boolean) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- allowDrag(boolean) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- ALLOWED_DRAG_DROP_ACTIONS - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- ALMOST_ZERO - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- alpha - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- ALPHA - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- alpha_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'alpha-i' from the table.
- alpha_pref - Static variable in class com.actelion.research.chem.phesa.MolecularVolume
- ALTERNATE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- AMemorizedObject - Class in com.actelion.research.util.graph.complete
-
AMemorizedObject
- AMemorizedObject() - Constructor for class com.actelion.research.util.graph.complete.AMemorizedObject
- AMERICAN - com.actelion.research.util.Formatter.LocaleFormat
- AMIDE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- AMIDINE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- AMINO_ACIDS - Static variable in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
- AminoAcidLabeled - Class in com.actelion.research.chem.io.pdb.converter
-
AminoAcidLabeled
- AminoAcidLabeled(StereoMolecule, String, String) - Constructor for class com.actelion.research.chem.io.pdb.converter.AminoAcidLabeled
- AminoAcidsLabeledContainer - Enum in com.actelion.research.chem.io.pdb.converter
-
AminoAcidsLabeledContainer The txt file was generated with com.actelion.research.chem.parsers.pdb.ProcessLabeledAminoAcids
- analyse(String) - Method in class com.actelion.research.util.DateAnalysis
-
Checks, whether entry consists of three elements separated by one or more non-word characters (neither digit nor letter) that might be day, month and year.
- AnalyticalParameterCalculatorSVM - Class in com.actelion.research.calc.regression.svm
-
AnalyticalParameterCalculatorSVM
- AnalyticalParameterCalculatorSVM() - Constructor for class com.actelion.research.calc.regression.svm.AnalyticalParameterCalculatorSVM
- analyzeFragmentMembership() - Method in class com.actelion.research.share.gui.editor.Model
- analyzeMolecule(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- analyzeReaction() - Method in class com.actelion.research.share.gui.editor.Model
- AND(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Makes an logical AND and calculates the hash code.
- angle - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- angle(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns the angle between this vector and that vector.
- Angle - Class in com.actelion.research.chem.forcefield.mmff.table
-
Angle table, corresponds to the MMFFANG.PAR parameters table provided in the MMFF literature.
- Angle - Class in com.actelion.research.chem.forcefield.mmff.type
-
The angle type class provides static functions for getting angle and stretch bend MMFF type.
- Angle - Class in com.actelion.research.util
-
This class provides various operations on angles, while making sure that the values is always in the rangle from -pi >= v > pi.
- Angle() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Angle
- Angle() - Constructor for class com.actelion.research.util.Angle
- Angle(double) - Constructor for class com.actelion.research.util.Angle
- Angle(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Angle
- Angle(Angle) - Constructor for class com.actelion.research.util.Angle
- AngleBend - Class in com.actelion.research.chem.forcefield.mmff
-
Angle bending energy term class.
- AngleBend(Tables, MMFFMolecule, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.AngleBend
-
Construct a new angle bend energy term.
- AngleConstraint - Class in com.actelion.research.chem.potentialenergy
- AngleConstraint(Conformer, int[], double) - Constructor for class com.actelion.research.chem.potentialenergy.AngleConstraint
- AnimatedGIFWriter - Class in com.actelion.research.util
- AnimatedGIFWriter() - Constructor for class com.actelion.research.util.AnimatedGIFWriter
- AnimatedGIFWriter(boolean) - Constructor for class com.actelion.research.util.AnimatedGIFWriter
- AnimatedGIFWriter.GIFFrame - Class in com.actelion.research.util
- ANSI_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- any(boolean[]) - Static method in class smile.math.Math
-
Given a set of boolean values, is at least one of the values true?
- append(int, double) - Method in class smile.math.SparseArray
-
Append an entry to the array, optimizing for the case where the index is greater than all existing indices in the array.
- append(String) - Method in class com.actelion.research.util.datamodel.ByteVec
- appendCols(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- appendRows(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- appendRows(ModelXY, ModelXY) - Static method in class com.actelion.research.util.datamodel.ModelXY
- appendRows(List<Matrix>) - Static method in class com.actelion.research.calc.MatrixFunctions
- APPLICATION_EXTENSION_LABEL - Static variable in class com.actelion.research.util.AnimatedGIFWriter
- apply(double[]) - Method in class com.actelion.research.chem.alignment3d.transformation.Rotation
- apply(double[]) - Method in class com.actelion.research.chem.alignment3d.transformation.Scaling
- apply(double[]) - Method in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- apply(double[]) - Method in class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- apply(double[]) - Method in class com.actelion.research.chem.alignment3d.transformation.Translation
- apply(int, int) - Method in interface smile.math.matrix.Matrix
-
Returns the entry value at row i and column j.
- apply(Conformer) - Method in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.DistanceRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.PlaneRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.StraightLineRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.TorsionRule
- apply(Coordinates) - Method in class com.actelion.research.chem.alignment3d.transformation.Rotation
- apply(Coordinates) - Method in class com.actelion.research.chem.alignment3d.transformation.Scaling
- apply(Coordinates) - Method in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- apply(Coordinates) - Method in class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- apply(Coordinates) - Method in class com.actelion.research.chem.alignment3d.transformation.Translation
- apply(DistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.SlidingWindowDistHist
- apply(StereoMolecule) - Method in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- apply(StereoMolecule) - Method in class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- apply(StereoMolecule, int[]) - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRule
- applyComponentOrientation(ComponentOrientation) - Method in class com.actelion.research.gui.JScrollableMenu
- applyInfluences(Object, Point) - Method in class com.actelion.research.calc.BinarySOM
- applyInfluences(Object, Point) - Method in class com.actelion.research.calc.SelfOrganizedMap
- applyInfluencesSMP(Object, Point) - Method in class com.actelion.research.calc.SelfOrganizedMap
- applyTo(AbstractDrawingObject) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTo(DepictorTransformation) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTo(Molecule) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTo(Point2D.Double) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTo(Rectangle2D.Double) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTransformation(Transformation) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- applyTransformation(DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDepictor
- approveSelection() - Method in class com.actelion.research.gui.JFileChooserOverwrite
- arc(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- arc(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- arccos(double) - Static method in class com.actelion.research.util.Angle
- arcsin(double) - Static method in class com.actelion.research.util.Angle
- arctan(double, double) - Static method in class com.actelion.research.util.Angle
- area - Variable in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- areAllFinite() - Method in class com.actelion.research.calc.statistics.ModelStatisticsOverview
- areAllFinite() - Method in class com.actelion.research.calc.statistics.ModelStatisticsOverviewMedian
- areAtomsSimilar(int, int) - Method in class com.actelion.research.chem.SSSearcher
- areBonded(Residue) - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- areBondsSimilar(int, int) - Method in class com.actelion.research.chem.SSSearcher
- ARegressionMethod<T extends ParameterRegressionMethod> - Class in com.actelion.research.calc.regression
-
ARegressionMethod
- ARegressionMethod() - Constructor for class com.actelion.research.calc.regression.ARegressionMethod
- areNodesMapping(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
-
Dynamic calculation of similarity threshold.
- areNodesMapping(int, int) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- areRowsEqual(int, int) - Method in class com.actelion.research.calc.Matrix
- areSynthonsCompatible(Synthon, Synthon) - Method in class com.actelion.research.chem.combinatorialspace.Synthon
- arom(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the Arom bool of an atom given its MMFF type.
- AROM - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- AROM_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- AROM_RING - com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint.Functionality
- AROM_RING_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- AromaticityResolver - Class in com.actelion.research.chem
- AromaticityResolver(ExtendedMolecule) - Constructor for class com.actelion.research.chem.AromaticityResolver
-
Creates a new AromaticityResolver for molecule mol.
- aromatize(StereoMolecule, ArrayList<Integer>[], RingCollection, Set<Integer>, Set<Integer>) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
- aromatize(StereoMolecule, Set<Integer>, Set<Integer>) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
- AromRingPoint - Class in com.actelion.research.chem.phesa.pharmacophore.pp
- AromRingPoint(AromRingPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- AromRingPoint(StereoMolecule, int, List<Integer>) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- ARR_BINS_EXAMPLE - Static variable in class com.actelion.research.calc.histogram.IntegerHistogram
- ARR_MODEL - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- ARR_MODEL_CODE - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- ARR_RESULT_EVALUATOR - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- ARR_TAGS - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- arrange(double, boolean) - Method in class com.actelion.research.chem.coords.FragmentAssociation
- arrangeReaction(Reaction, Dimension) - Static method in class com.actelion.research.chem.ChemistryHelper
- arrangeWith(InventorFragment) - Method in class com.actelion.research.chem.coords.InventorFragment
- arrAtomLabelRGroups - Static variable in class com.actelion.research.util.ConstantsDWAR
- array() - Method in interface smile.math.matrix.DenseMatrix
-
Return the two-dimensional array of matrix.
- ArrayUtils - Class in com.actelion.research.util
- ArrayUtils() - Constructor for class com.actelion.research.util.ArrayUtils
- ArrayUtilsCalc - Class in com.actelion.research.calc
- ArrayUtilsCalc() - Constructor for class com.actelion.research.calc.ArrayUtilsCalc
- arrDistHists - Variable in class com.actelion.research.chem.descriptor.flexophore.DistHist
- Arrow - Class in com.actelion.research.share.gui
- Arrow(DrawConfig, double, double, double, double) - Constructor for class com.actelion.research.share.gui.Arrow
- ArrowAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/16/13 Time: 3:46 PM
- ArrowAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ArrowAction
- arrRGroupsAtomicNo - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
- arrRGroupsSymbol - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
- asin(double) - Static method in class smile.math.Math
-
Returns the arc sine of an angle, in the range of -pi/2 through pi/2.
- aspec(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the ASPEC type of an atom given its MMFF type.
- assemble() - Method in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- assessCLogP(StereoMolecule) - Method in class com.actelion.research.chem.prediction.CLogPPredictor
-
Ambiguous bonds are normalized.
- assessComplexity(StereoMolecule) - Static method in class com.actelion.research.chem.prediction.FastMolecularComplexityCalculator
-
Ambiguous bonds are normalized.
- assessDruglikeness(StereoMolecule, long[], ThreadMaster) - Method in class com.actelion.research.chem.prediction.DruglikenessPredictorWithIndex
- assessDruglikeness(StereoMolecule, ThreadMaster) - Method in class com.actelion.research.chem.prediction.DruglikenessPredictor
- assessGlobularity(ConformerSet) - Static method in class com.actelion.research.chem.prediction.GlobularityCalculator
-
Generates conformers from a 2D- or 3D-molecule and then calculates the globularity (flat=0, round=1) from the conformer's atom coordinates.
- assessGlobularity(StereoMolecule, int) - Static method in class com.actelion.research.chem.prediction.GlobularityCalculator
-
Generates conformers from a 2D- or 3D-molecule and then calculates the globularity (flat=0, round=1) from the conformer's atom coordinates.
- assessGlobularityFromSVD(Conformer) - Static method in class com.actelion.research.chem.prediction.GlobularityCalculator
-
Calculates the globularity of a conformer (flat=0, round=1) from 3D coordinates
- assessNonPolarSurfaceArea(StereoMolecule) - Method in class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
-
Calculates the topological non-polar surface area (TPSA) of a molecule as a sum of contributions of its non-polar atom-types.
- assessPolarSurfaceArea(StereoMolecule) - Method in class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
-
Calculates the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.
- assessPSA(StereoMolecule) - Method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
-
Calculates the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.
- assessRelativePolarSurfaceArea(StereoMolecule) - Method in class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
-
Calculates the relative (fractional) polar surface area from polar and non-polar atom contributions.
- assessRisk(StereoMolecule, int, ThreadMaster) - Method in class com.actelion.research.chem.prediction.ToxicityPredictor
- assessShape(StereoMolecule) - Static method in class com.actelion.research.chem.prediction.MolecularShapeCalculator
-
Returns the number of bonds of the shortest path between those two atoms with the largest topological distance divided by the number of non-hydrogen atoms.
- assessSolubility(StereoMolecule) - Method in class com.actelion.research.chem.prediction.SolubilityPredictor
- assessTotalSurfaceArea(StereoMolecule) - Method in class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
-
Calculates the topological total surface area (TPSA) of a molecule as a sum of contributions of its polar and non-atom-types.
- ASSIGN_PARITIES_TO_TETRAHEDRAL_N - Static variable in class com.actelion.research.chem.Canonizer
- assignCol(int, Matrix) - Method in class com.actelion.research.calc.Matrix
- assignCol(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
- assignLikelyProtonationStates(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingUtils
- assignRow(int, double[]) - Method in class com.actelion.research.calc.Matrix
- assignRow(int, int[]) - Method in class com.actelion.research.calc.Matrix
- assignRow(int, DoubleVec) - Method in class com.actelion.research.calc.Matrix
- assignRow(int, Vector<Double>) - Method in class com.actelion.research.calc.Matrix
- ata() - Method in interface smile.math.matrix.DenseMatrix
- ata() - Method in class smile.math.matrix.JMatrix
- ata() - Method in interface smile.math.matrix.Matrix
-
Returns A' * A
- atan(double) - Static method in class smile.math.Math
-
Returns the arc tangent of an angle, in the range of -pi/2 through pi/2.
- atan2(double, double) - Static method in class smile.math.Math
-
Converts rectangular coordinates (x, y) to polar (r, theta).
- atbmm(B) - Method in interface smile.math.matrix.MatrixMultiplication
-
Returns the result of matrix multiplication A' * B.
- atbmm(DenseMatrix) - Method in class smile.math.matrix.JMatrix
- atom - Variable in class com.actelion.research.chem.coords.InventorCharge
- atom - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Atom - Class in com.actelion.research.chem.forcefield.mmff.table
-
Atom table, corresponds to the MMFFPROP.PAR parameters table provided in the MMFF literature.
- Atom - Class in com.actelion.research.chem.forcefield.mmff.type
-
The Atom type class provides static functions to perform atom typing on atoms in a Molecule.
- Atom() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Atom
- Atom(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Atom
- ATOM_LABEL_R1 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R10 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R11 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R12 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R13 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R14 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R15 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R16 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R2 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R3 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R4 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R5 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R6 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R7 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R8 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R9 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_TYPE - Static variable in class com.actelion.research.chem.prediction.CLogPPredictor
- AtomAssembler - Class in com.actelion.research.chem.conf
- AtomAssembler(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.AtomAssembler
- atomAtomSubStrucMatch(StereoMolecule, int, StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- AtomComparator - Class in com.actelion.research.chem
- AtomComparator() - Constructor for class com.actelion.research.chem.AtomComparator
- AtomFunctionAnalyzer - Class in com.actelion.research.chem
- AtomFunctionAnalyzer() - Constructor for class com.actelion.research.chem.AtomFunctionAnalyzer
- AtomHighlightAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
- ATOMIC_NO - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- AtomicFloat - Class in com.actelion.research.util.concurrent
- AtomicFloat() - Constructor for class com.actelion.research.util.concurrent.AtomicFloat
- AtomicFloat(float) - Constructor for class com.actelion.research.util.concurrent.AtomicFloat
- AtomicGaussian - Class in com.actelion.research.chem.phesa
- AtomicGaussian(int, int, Coordinates) - Constructor for class com.actelion.research.chem.phesa.AtomicGaussian
- AtomicGaussian(AtomicGaussian) - Constructor for class com.actelion.research.chem.phesa.AtomicGaussian
- atomicGaussians - Variable in class com.actelion.research.chem.phesa.ShapeVolume
- atomicNo - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- atomId - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- AtomIndexLinkerId - Class in com.actelion.research.chem.descriptor.flexophore.entity
-
AtomIndexLinkerId
- AtomIndexLinkerId() - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- AtomIndexLinkerId(int, int, int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- AtomLabelDialogBuilder - Class in com.actelion.research.gui.editor
- AtomLabelDialogBuilder(GenericDialogHelper, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.editor.AtomLabelDialogBuilder
- AtomMapAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/22/13 Time: 4:00 PM
- AtomMapAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.AtomMapAction
- AtomQueryFeatureDialogBuilder - Class in com.actelion.research.gui.editor
- AtomQueryFeatureDialogBuilder(GenericDialogHelper, ExtendedMolecule, int, boolean) - Constructor for class com.actelion.research.gui.editor.AtomQueryFeatureDialogBuilder
- AtomRecord - Class in com.actelion.research.chem.io.pdb.parser
-
ModelAtom
- AtomRecord(int, String, String, String, String, int, String, double, double, double, double, double, String) - Constructor for class com.actelion.research.chem.io.pdb.parser.AtomRecord
- AtomTypeCalculator - Class in com.actelion.research.chem
- AtomTypeCalculator() - Constructor for class com.actelion.research.chem.AtomTypeCalculator
- AtomTypeList - Class in com.actelion.research.chem
- AtomTypeList(int) - Constructor for class com.actelion.research.chem.AtomTypeList
-
Creates an empty AtomTypeList, which must be populated by multiply calling processMolecule() and finally calling finalizeProcessMolecules() once.
- AtomTypeList(String, int) - Constructor for class com.actelion.research.chem.AtomTypeList
-
Creates a new AtomTypeList from a given file using the given mode.
- AtomTypeMap - Class in com.actelion.research.chem.descriptor.flexophore.generator
- ATTACHED_HYDROGEN_COUNT - Static variable in class com.actelion.research.chem.Molecule3D
- ATTACHED_HYDROGEN_COUNT_SHIFT - Static variable in class com.actelion.research.chem.Molecule3D
- ATTR_ACCEPTOR - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_ALIPHATIC - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_AROMATIC - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_DONOR - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_FN - Static variable in class com.actelion.research.calc.classification.PrecisionAndRecall
- ATTR_FP - Static variable in class com.actelion.research.calc.classification.PrecisionAndRecall
- ATTR_NEGATIVE_CHARGE - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_NO - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATTR_POSITIVE_CHARGE - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_TN - Static variable in class com.actelion.research.calc.classification.PrecisionAndRecall
- ATTR_TP - Static variable in class com.actelion.research.calc.classification.PrecisionAndRecall
- ATTR_YES - Static variable in class com.actelion.research.util.ConstantsDWAR
- attribute() - Method in class smile.data.AttributeVector
-
Returns the attribute.
- Attribute - Class in smile.data
-
Generic class to represent a named attribute/variable.
- Attribute(Attribute.Type, String) - Constructor for class smile.data.Attribute
-
Constructor.
- Attribute(Attribute.Type, String, double) - Constructor for class smile.data.Attribute
-
Constructor.
- Attribute(Attribute.Type, String, String) - Constructor for class smile.data.Attribute
-
Constructor.
- Attribute(Attribute.Type, String, String, double) - Constructor for class smile.data.Attribute
-
Constructor.
- Attribute.Type - Enum in smile.data
-
The type of attributes.
- AttributeDataset - Class in smile.data
-
A dataset of fixed number of attributes.
- AttributeDataset(String, double[][], double[]) - Constructor for class smile.data.AttributeDataset
-
Constructor.
- AttributeDataset(String, Attribute[]) - Constructor for class smile.data.AttributeDataset
-
Constructor.
- AttributeDataset(String, Attribute[], double[][], Attribute, double[]) - Constructor for class smile.data.AttributeDataset
-
Constructor.
- AttributeDataset(String, Attribute[], Attribute) - Constructor for class smile.data.AttributeDataset
-
Constructor.
- AttributeDataset.Row - Class in smile.data
- attributes() - Method in class smile.data.AttributeDataset
-
Returns the list of attributes in this dataset.
- AttributeVector - Class in smile.data
-
A vector with attribute information.
- AttributeVector(Attribute, double[]) - Constructor for class smile.data.AttributeVector
-
Constructor.
- AttributeVector(Attribute, double[], String[]) - Constructor for class smile.data.AttributeVector
-
Constructor.
- atx(double[], double[]) - Method in class smile.math.matrix.JMatrix
- atx(double[], double[]) - Method in interface smile.math.matrix.Matrix
-
y = A' * x
- atxpy(double[], double[]) - Method in class smile.math.matrix.JMatrix
- atxpy(double[], double[]) - Method in interface smile.math.matrix.Matrix
-
y = A' * x + y
- atxpy(double[], double[], double) - Method in class smile.math.matrix.JMatrix
- atxpy(double[], double[], double) - Method in interface smile.math.matrix.Matrix
-
y = A' * x + b * y
- autoMap() - Method in interface com.actelion.research.chem.reaction.AutoMapper
- autoMap() - Method in class com.actelion.research.chem.reaction.MoleculeAutoMapper
- AutoMapper - Interface in com.actelion.research.chem.reaction
-
Project: User: rufenec Date: 6/17/2014 Time: 10:04 AM
- autoScroll() - Method in class com.actelion.research.gui.ScrollPaneAutoScrollerWhenDragging
- avr - Variable in class com.actelion.research.calc.statistics.ModelStatisticsOverview
- avr() - Method in class com.actelion.research.util.datamodel.DoubleArray
- ax(double[], double[]) - Method in class smile.math.matrix.JMatrix
- ax(double[], double[]) - Method in interface smile.math.matrix.Matrix
-
y = A * x
- AxialStereoRule - Class in org.openmolecules.chem.conf.so
-
Handles attropisomery as well as chiral allenes
- AxialStereoRule(StereoMolecule, int[], int[], boolean, boolean) - Constructor for class org.openmolecules.chem.conf.so.AxialStereoRule
- axpy(double[], double[]) - Method in class smile.math.matrix.JMatrix
- axpy(double[], double[]) - Method in interface smile.math.matrix.Matrix
-
y = A * x + y
- axpy(double[], double[], double) - Method in class smile.math.matrix.JMatrix
- axpy(double[], double[], double) - Method in interface smile.math.matrix.Matrix
-
y = A * x + b * y
- axpy(double, double[], double[]) - Static method in class smile.math.Math
-
Update an array by adding a multiple of another array y = a * x + y.
B
- b - Variable in class com.actelion.research.chem.forcefield.mmff.SortedPair
- b - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- b - Variable in class com.actelion.research.util.BurtleHasherABC
- B - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- B - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- B_sq - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- back(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
- back(S) - Method in class com.actelion.research.util.graph.complete.ContainerMemory
- BACKBONE - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- BACKBONE - Static variable in class com.actelion.research.chem.Molecule3D
- BACKGROUND_COLOR - Static variable in class com.actelion.research.gui.JImagePanel
- BadAtomTypeException - Exception in com.actelion.research.chem.forcefield.mmff
-
The BadAtomTypeException is thrown when there is a bad atom type in a molecule.
- BadAtomTypeException() - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadAtomTypeException
- BadAtomTypeException(String) - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadAtomTypeException
- BadRingAromException - Exception in com.actelion.research.chem.forcefield.mmff
-
The BadRingAromException is thrown when there is a problem with the MMFF ring aromaticity assignment.
- BadRingAromException() - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadRingAromException
- BadRingAromException(String) - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadRingAromException
- BASE_LOG - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- Base64 - Class in com.actelion.research.util
- Base64.InputStream - Class in com.actelion.research.util
-
A
Base64.InputStream
will read data from another java.io.InputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly. - Base64.OutputStream - Class in com.actelion.research.util
-
A
Base64.OutputStream
will write data to another java.io.OutputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly. - BASIC - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- BASIC_ATOM_FLAG_COUNT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
- BBDTree - Class in smile.clustering
-
Balanced Box-Decomposition Tree.
- BBDTree(double[][]) - Constructor for class smile.clustering.BBDTree
-
Constructs a tree out of the given n data data living in R^d.
- bcc() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.Graph
- bccutil(int, int[], int[], LinkedList<Graph.Edge>, int[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.Graph
- bci_binary_search(int, int, int, int, boolean) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
-
Binary search in the bci table.
- beta - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- between(Coordinates, Coordinates, double) - Method in class com.actelion.research.chem.Coordinates
-
Updates this to contain a point on the straight line through c1 and c2.
- bic(double[]) - Method in class smile.stat.distribution.Mixture
-
BIC score of the mixture for given data.
- BiGramInt(int[]) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- BiGramInt(int[], int) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- BiGramInt(int, int) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- BIN_SIZE - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- BIN_SIZE - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- binary(int[], int[], Searchable) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
-
Binary search on a collection of values in columns in a table.
- binary(int, int, int, int, boolean, Searchable) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
-
Binary searches for a value and returns the index to it.
- binary(int, int, Searchable) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
-
Helper function that acts like Search.binary(int[], int[], Searchable) but takes a single int for cols and vals to search just one column.
- BinaryDecoder - Class in com.actelion.research.util
- BinaryDecoder(BufferedReader) - Constructor for class com.actelion.research.util.BinaryDecoder
- BinaryDecoder(BufferedReader, int, int) - Constructor for class com.actelion.research.util.BinaryDecoder
- BinaryEncoder - Class in com.actelion.research.util
- BinaryEncoder(BufferedWriter) - Constructor for class com.actelion.research.util.BinaryEncoder
-
Creates an encoder to make a BufferedWriter write byte/int arrays as Strings.
- BinaryEncoder(BufferedWriter, int, int, int) - Constructor for class com.actelion.research.util.BinaryEncoder
-
Instantiates an encoder for byte/int arrays to String.
- BinarySOM - Class in com.actelion.research.calc
- BinarySOM() - Constructor for class com.actelion.research.calc.BinarySOM
- BinarySOM(int, int, int) - Constructor for class com.actelion.research.calc.BinarySOM
- bindingSiteAtoms - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- BINS_HISTOGRAM - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
-
Defines the resolution for the range.
- BitArray128 - Class in com.actelion.research.chem.properties.complexity
- BitArray128() - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128
- BitArray128(int) - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128
- BitArray128(BitArray128) - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128
-
Deep copy
- BitArray128Factory - Class in com.actelion.research.chem.properties.complexity
- BitArray128Factory() - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128Factory
- bitCount(int) - Static method in class com.actelion.research.util.BitUtils
-
Deprecated.use Integer.bitCount() instead.
- bitCount(long) - Static method in class com.actelion.research.util.BitUtils
- BitUtils - Class in com.actelion.research.util
- BitUtils() - Constructor for class com.actelion.research.util.BitUtils
- BLACK - Static variable in class com.actelion.research.gui.hidpi.ColorUtils
- BLACK - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- BLACKNESS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BLUE - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- blurrSingleBinHistograms() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- bndk - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Bndk - Class in com.actelion.research.chem.forcefield.mmff.table
-
Bndk table, corresponds to the MMFFBNDK.PAR parameters table provided in the MMFF literature.
- Bndk(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Bndk
- BOMSkipper - Class in com.actelion.research.io
- BOMSkipper() - Constructor for class com.actelion.research.io.BOMSkipper
- bond - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Bond - Class in com.actelion.research.chem.forcefield.mmff.table
-
Bond table, corresponds to the MMFFBOND.PAR parameters table provided in the MMFF literature.
- Bond - Class in com.actelion.research.chem.forcefield.mmff.type
-
The bond type class provides static functions for getting the MMFF bond type (either by bond or by the atoms of a bond).
- Bond() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Bond
- Bond(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Bond
- BOND_CUTOFF_SQ - Static variable in class com.actelion.research.chem.io.pdb.parser.Residue
- BondAngleSet - Class in com.actelion.research.chem.conf
- BondAngleSet(StereoMolecule, BondLengthSet) - Constructor for class com.actelion.research.chem.conf.BondAngleSet
-
Calculates and caches a list of bond angle estimates for any two neighbours of any atom of the molecule.
- BondBaseAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:07 PM
- BondBaseAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.BondBaseAction
- BondConstraint - Class in com.actelion.research.chem.potentialenergy
- BondConstraint(Conformer, int[], double) - Constructor for class com.actelion.research.chem.potentialenergy.BondConstraint
- BondHighlightAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:07 PM
- BondHighlightAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- BondLengthSet - Class in com.actelion.research.chem.conf
- BondLengthSet(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.BondLengthSet
-
Calculates and caches a list of bond length estimates from molecule.
- BondQueryFeatureDialogBuilder - Class in com.actelion.research.gui.editor
- BondQueryFeatureDialogBuilder(GenericDialogHelper, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.editor.BondQueryFeatureDialogBuilder
- BondRotationHelper - Class in com.actelion.research.chem.conf
- BondRotationHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.BondRotationHelper
- BondRotationHelper(StereoMolecule, boolean) - Constructor for class com.actelion.research.chem.conf.BondRotationHelper
- bondsAreParallel(double, double) - Method in class com.actelion.research.chem.ExtendedMolecule
- BondsCalculator - Class in com.actelion.research.chem.io.pdb.converter
-
BondsCalculator is used to recreate the bonds and / or calculate the bonds orders based on the 3D coordinates of the atoms
- BondsCalculator() - Constructor for class com.actelion.research.chem.io.pdb.converter.BondsCalculator
- BondStretch - Class in com.actelion.research.chem.forcefield.mmff
-
Bond stretching energy term class.
- BondStretch(Tables, MMFFMolecule, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Creates a new bond stretch given a force field and a bond.
- BondStretch(Tables, MMFFMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Creates a new bond stretch given a force field and two bonded atoms.
- BondVector2IdCode - Class in com.actelion.research.chem.mcs
- BondVector2IdCode(StereoMolecule) - Constructor for class com.actelion.research.chem.mcs.BondVector2IdCode
- borrowContent() - Method in class com.actelion.research.gui.dock.Dockable
-
Removes the content temporarily to be added to another container Must be followed later by a endBorrowContent() call.
- BOTTOM - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- BoxCox - Class in com.actelion.research.calc
-
BoxCox
- BoxCox(double) - Constructor for class com.actelion.research.calc.BoxCox
- brighter(Color, float) - Static method in class com.actelion.research.util.ColorHelper
-
Creates a new
Color
that is a brighter version of thisColor
. - Bromine - Static variable in class com.actelion.research.chem.PeriodicTable
- BrowserControl - Class in com.actelion.research.util
- BrowserControl() - Constructor for class com.actelion.research.util.BrowserControl
- BS_DIBPATTERN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_HATCHED - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_HOLLOW - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_NULL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_PATTERN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_SOLID - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- build() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- buildImagePath(String, String, boolean) - Static method in class com.actelion.research.gui.JImagePanel
- BURIED_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- BurtleHasher - Class in com.actelion.research.util
-
http://burtleburtle.net/bob/c/lookup3.c ------------------------------------------------------------------------------- lookup3.c, by Bob Jenkins, May 2006, Public Domain.
- BurtleHasher() - Constructor for class com.actelion.research.util.BurtleHasher
- BurtleHasherABC - Class in com.actelion.research.util
- BurtleHasherABC(long, long, long) - Constructor for class com.actelion.research.util.BurtleHasherABC
- buttonPressed(int) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- buttonPressed(int) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- ByteArray - Class in com.actelion.research.util
- ByteArrayArrayComparator - Class in com.actelion.research.util
- ByteArrayArrayComparator() - Constructor for class com.actelion.research.util.ByteArrayArrayComparator
- ByteArrayComparator - Class in com.actelion.research.util
- ByteArrayComparator() - Constructor for class com.actelion.research.util.ByteArrayComparator
- byteArrayToDouble(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- byteArrayToDoubleArray(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- byteArrayToInt(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- byteArrayToIntArray(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- ByteVec - Class in com.actelion.research.util.datamodel
-
ByteVec:
- ByteVec(byte[]) - Constructor for class com.actelion.research.util.datamodel.ByteVec
- ByteVec(int) - Constructor for class com.actelion.research.util.datamodel.ByteVec
- ByteVec(int[]) - Constructor for class com.actelion.research.util.datamodel.ByteVec
- ByteVec(ByteVec) - Constructor for class com.actelion.research.util.datamodel.ByteVec
-
Deep copy
- ByteVec(String) - Constructor for class com.actelion.research.util.datamodel.ByteVec
-
Hash code is calculated.
C
- c - Variable in class com.actelion.research.util.BurtleHasherABC
- c(double...) - Static method in class smile.math.Math
-
Combines the arguments to form a vector.
- c(double[]...) - Static method in class smile.math.Math
-
Merges multiple vectors into one.
- c(float...) - Static method in class smile.math.Math
-
Combines the arguments to form a vector.
- c(float[]...) - Static method in class smile.math.Math
-
Merges multiple vectors into one.
- c(int...) - Static method in class smile.math.Math
-
Combines the arguments to form a vector.
- c(int[]...) - Static method in class smile.math.Math
-
Merges multiple vectors into one.
- c(String...) - Static method in class smile.math.Math
-
Combines the arguments to form a vector.
- c(String[]...) - Static method in class smile.math.Math
-
Merges multiple vectors into one.
- C - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- C - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- C_SVC - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- cache_size - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- CacheEntry(Coordinates[][], double[]) - Constructor for class org.openmolecules.chem.conf.gen.RigidFragmentCache.CacheEntry
- calcCOM() - Method in class com.actelion.research.chem.phesa.MolecularVolume
-
calculates volume weighted center of mass of the molecular Volume
- calcCOM() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- calcFeatureSim(int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- calcFragmentCenter(Molecule3D, List<MultCoordFragIndex>) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
-
Calculates the center of the fragments and stores the coordinates in MultCoordFragIndex.
- calcMin(StereoMolecule) - Method in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- calcScore(StereoMolecule, int, Coordinates, int[]) - Static method in class com.actelion.research.chem.docking.ScoringTask
-
calculate interaction of probe atom with receptor
- calcScore(StereoMolecule, StereoMolecule, int[], int[]) - Static method in class com.actelion.research.chem.docking.ScoringTask
- calculate() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- calculate() - Method in class com.actelion.research.chem.conf.SymmetryCorrectedRMSDCalculator
- calculate() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- calculate() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.FeatureCalculator
- calculate() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
-
calculates the total volume and size of the node from its elements
- calculate() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- calculate() - Method in class com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage
- calculate(double, double, double, double, int[]) - Static method in class com.actelion.research.chem.prediction.DrugScoreCalculator
- calculate(int[]) - Method in interface smile.regression.RegressionTree.NodeOutput
-
Calculate the node output.
- calculate(StereoMolecule) - Method in class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
- calculate(ModelXYIndex) - Static method in class com.actelion.research.calc.regression.svm.AnalyticalParameterCalculatorSVM
- calculate(List<PharmacophoreNode>, List<PharmacophoreNode>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- calculateAccuracy() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- calculateAverageBondLength() - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- calculateBondOrders(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
-
Calculate the bond orders of the molecule (without knowing the hydrogens).
- calculateCohensKappa() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- calculateCollisionTolerance() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- calculateCorrelation(INumericalDataColumn, INumericalDataColumn, int) - Method in class com.actelion.research.calc.CorrelationCalculator
-
Calculates the correlation coefficient between two columns of data.
- calculateDescriptor(int[]) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
-
Calculates the torsion descriptor for the current coordinates.
- calculateError(Matrix, Matrix) - Static method in class com.actelion.research.calc.regression.ModelError
-
Calculates the absolute and the relative error.
- calculateError(Matrix, Matrix, double, boolean) - Static method in class com.actelion.research.calc.regression.ModelError
- calculateHarmonicMean() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
-
F1 score
- calculateHash() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- calculateHash(BitArray128) - Method in class com.actelion.research.chem.properties.complexity.BitArray128Factory
- calculateHash(BitArray128) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsHasher
- calculateHash(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- calculateHash(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- calculateHash(T) - Method in interface com.actelion.research.chem.properties.complexity.IBitArrayFactory
-
Stores the hash in f.
- calculateHashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- calculateHashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- calculateHashCode() - Method in class com.actelion.research.util.datamodel.IntArray
- calculateHashCode() - Method in class com.actelion.research.util.datamodel.IntVec
- calculateHashCode(IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- calculateHeight() - Method in class com.actelion.research.chem.phesa.AtomicGaussian
- calculateHeight() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- calculateHeight() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- calculateHeight() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- calculateInfluences(double) - Method in class com.actelion.research.calc.BinarySOM
- calculateInfluences(double) - Method in class com.actelion.research.calc.SelfOrganizedMap
- calculateMassCovarianceMatrix(Conformer) - Static method in class com.actelion.research.chem.docking.DockingUtils
- calculateMatrix(INumericalDataColumn[], int) - Method in class com.actelion.research.calc.CorrelationCalculator
-
Calculates a half correlation matrix of all passed numerical columns
- calculateMaxSimilarity(Matrix, double[]) - Static method in class com.actelion.research.calc.MatrixFunctions
- calculateMaxSimilarity(Matrix, double[], int) - Static method in class com.actelion.research.calc.MatrixFunctions
- calculateMaxSimilarity(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- calculateMedianTestError() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLSLMOValidation
-
Deprecated.
- calculateModel(ModelXYIndex, int, int) - Method in class com.actelion.research.calc.regression.linear.pls.RegressionModelCalculatorOptimumFactors
-
Calculates the PLS regression model for the given data set.
- calculateModelErrorTest(Matrix, Matrix) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- calculateMolecularFlexibility(StereoMolecule) - Method in class com.actelion.research.chem.conf.MolecularFlexibilityCalculator
-
Calculates a molecular flexibility as a value from 0.0 to 1.0 considering torsion statistics derived from the CSD database (torsion maxima, frequencies, and 50% intervals) of rotatable bonds.
- calculatePrecision() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- calculatePreferredAttachmentAngle(double, double, int, double) - Method in class com.actelion.research.chem.coords.InventorFragment
- calculateProbabilities() - Method in class com.actelion.research.chem.AtomTypeList
- calculateProperty(StereoMolecule, int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- calculateRecall() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.AxialStereoRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.DistanceRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.PlaneRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.StraightLineRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.TorsionRule
- calculateScore(ResultFragmentsStatistic) - Method in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
-
28.08.2013
- calculateSimilarity() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- calculateSimilarityMatrixRowWise(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- calculateStrain(ArrayList<ConformationRule>) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- calculateTorsion(int[]) - Method in class com.actelion.research.chem.conf.Conformer
-
Calculates a signed torsion as an exterior spherical angle from a valid 4-atom strand.
- calculateTorsion(int[]) - Method in class com.actelion.research.chem.Molecule
-
Calculates a signed torsion as an exterior spherical angle from a valid 4-atom strand.
- calculateTorsionExtended(Conformer, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Calculates a signed torsion like calculateTorsion().
- calculateTorsionExtended(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Calculates a signed torsion like calculateTorsion().
- calculateVolume() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- calculateWidth() - Method in class com.actelion.research.chem.phesa.AtomicGaussian
- calculateWidth() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- calculateWidth() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- calculateWidth() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- calculateYHat(byte[]) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- calculateYHat(double[]) - Method in class com.actelion.research.calc.regression.gaussianprocess.GaussianProcessRegression
- calculateYHat(double[]) - Method in interface com.actelion.research.calc.regression.ICalculateYHat
- calculateYHat(double[]) - Method in class com.actelion.research.calc.regression.knn.KNNRegression
-
Thread save method.
- calculateYHat(double[]) - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- calculateYHat(double[]) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- calculateYHat(double[]) - Method in class com.actelion.research.calc.regression.median.MedianRegression
- calculateYHat(double[]) - Method in class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkRegression
- calculateYHat(double[]) - Method in class com.actelion.research.calc.regression.randomforest.RandomForestRegression
- calculateYHat(double[]) - Method in class com.actelion.research.calc.regression.svm.SVMRegression
- calculateYHat(int[]) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- calculateYHat(Matrix) - Method in class com.actelion.research.calc.regression.gaussianprocess.GaussianProcessRegression
- calculateYHat(Matrix) - Method in interface com.actelion.research.calc.regression.ICalculateYHat
- calculateYHat(Matrix) - Method in class com.actelion.research.calc.regression.knn.KNNRegression
-
Not thread save.
- calculateYHat(Matrix) - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- calculateYHat(Matrix) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
-
With centering of Xtest with Xtrain.
- calculateYHat(Matrix) - Method in class com.actelion.research.calc.regression.median.MedianRegression
- calculateYHat(Matrix) - Method in class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkRegression
- calculateYHat(Matrix) - Method in class com.actelion.research.calc.regression.randomforest.RandomForestRegression
- calculateYHat(Matrix) - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- calculateYHat(Matrix) - Method in class com.actelion.research.calc.regression.svm.SVMRegression
- calculateYHatWithoutDeCentering(Matrix) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- calculationFailed(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- calculationFailed(int[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- calculationFailed(int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- calculationFailed(int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- calculationFailed(long[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- calculationFailed(PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- calculationFailed(PheSAMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- calculationFailed(Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- calculationFailed(T) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- cAllowedAtomicNo - Static variable in class com.actelion.research.chem.Mutation
- cAllowLogModeForNegativeOrZeroValues - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cancel() - Method in class com.actelion.research.gui.JProgressPanel
- candidatePose - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- canDrop() - Method in class com.actelion.research.gui.JChemistryView
- canDrop() - Method in class com.actelion.research.gui.JStructureView
- canonize() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- canonizeCharge(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Normalizes charge distribution in single- and multifragment molecules.
- canonizeCharge(boolean, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Normalizes charge distribution in single- and multifragment molecules.
- Canonizer - Class in com.actelion.research.chem
- Canonizer(StereoMolecule) - Constructor for class com.actelion.research.chem.Canonizer
-
Runs a canonicalization procedure for the given molecule that creates unique atom ranks, which takes stereo features, ESR settings and query features into account.
- Canonizer(StereoMolecule, int) - Constructor for class com.actelion.research.chem.Canonizer
-
Runs a canonicalization procedure for the given molecule that creates unique atom ranks, which takes stereo features, ESR settings and query features into account.
- CanonizerBaseValue - Class in com.actelion.research.chem
- CanonizerBaseValue(int) - Constructor for class com.actelion.research.chem.CanonizerBaseValue
- CanonizerMesoHelper - Class in com.actelion.research.chem
- CanonizerMesoHelper(ExtendedMolecule, int[], boolean[], byte[], byte[], byte[], byte[], byte[], byte[], boolean[], boolean[], boolean[]) - Constructor for class com.actelion.research.chem.CanonizerMesoHelper
- CanonizerUtil - Class in com.actelion.research.chem
- CanonizerUtil() - Constructor for class com.actelion.research.chem.CanonizerUtil
- CanonizerUtil.IDCODE_TYPE - Enum in com.actelion.research.chem
- CanonizerUtil.StrongHasher - Class in com.actelion.research.chem
-
64 bit hash, derived from numerical recipes Will move this class later to dd_core.
- canWriteAndDeleteInPath(File) - Static method in class com.actelion.research.util.IO
- CAPACITY_INEVITABLE_PPPOINTS - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- CapacityReachedError(String) - Constructor for exception com.actelion.research.chem.properties.complexity.ContainerBitArray.CapacityReachedError
- Carbon - Static variable in class com.actelion.research.chem.PeriodicTable
- CARBOXYL - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- cartesianProduct(List<List<T>>) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
-
https://en.wikipedia.org/wiki/Cartesian_product generates all possible combinations of elements from a list of lists
- cat(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- CATALYST_DELIMITER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- cAtomCIPParityNone - Static variable in class com.actelion.research.chem.Molecule
- cAtomCIPParityProblem - Static variable in class com.actelion.research.chem.Molecule
- cAtomCIPParityRorM - Static variable in class com.actelion.research.chem.Molecule
- cAtomCIPParitySorP - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorBlue - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorDarkGreen - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorDarkRed - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorGreen - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorMagenta - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorNone - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorOrange - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorRed - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagAllylic - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagAromatic - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagConfigurationUnknown - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagMarked - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlags2RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlags3RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlags4RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsESR - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsHelper - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsHelper2 - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsHelper3 - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagSmallRing - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsParity - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsRingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagStabilized - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagStereoProblem - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsValence - Static variable in class com.actelion.research.chem.Molecule
- cAtomLabel - Static variable in class com.actelion.research.chem.Molecule
- cAtomParity1 - Static variable in class com.actelion.research.chem.Molecule
- cAtomParity2 - Static variable in class com.actelion.research.chem.Molecule
- cAtomParityIsPseudo - Static variable in class com.actelion.research.chem.Molecule
- cAtomParityNone - Static variable in class com.actelion.research.chem.Molecule
- cAtomParityUnknown - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAny - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAromatic - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAromState - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAromStateBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAromStateShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFCharge - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFChargeBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFChargeShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFExcludeGroup - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFFlatNitrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFHydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFHydrogenBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFHydrogenShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFMatchStereo - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFMoreNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNarrowing - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNeighbourBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNeighbourShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNoMoreNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNoOfBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot0Hydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot0Neighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot0PiElectrons - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot1Hydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot1Neighbour - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot1PiElectron - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot2Hydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot2Neighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot2PiElectrons - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot2RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot3Hydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot3Neighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot3RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot4Neighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot4RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotAromatic - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotChain - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotCharge0 - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotChargeNeg - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotChargePos - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFPiElectronBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFPiElectrons - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFPiElectronShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingSize - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingSizeBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingSizeShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingState - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingStateBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingStateShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityHint - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityInvert - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityRacemize - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityRetain - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFSimpleFeatures - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalState - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateD - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateNone - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateS - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateT - Static variable in class com.actelion.research.chem.Molecule
- cAtomValence - Static variable in class com.actelion.research.chem.Molecule
- cAutoStartMacro - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cbind(double[]...) - Static method in class smile.math.Math
-
Take a sequence of vector arguments and combine by columns.
- cbind(float[]...) - Static method in class smile.math.Math
-
Take a sequence of vector arguments and combine by columns.
- cbind(int[]...) - Static method in class smile.math.Math
-
Take a sequence of vector arguments and combine by columns.
- cbind(String[]...) - Static method in class smile.math.Math
-
Take a sequence of vector arguments and combine by columns.
- cBondCIPParityEorP - Static variable in class com.actelion.research.chem.Molecule
- cBondCIPParityNone - Static variable in class com.actelion.research.chem.Molecule
- cBondCIPParityProblem - Static variable in class com.actelion.research.chem.Molecule
- cBondCIPParityZorM - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagAromatic - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagDelocalized - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagRing - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsCIPParityShift - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsESR - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsHelper2 - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsHelper3 - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagSmallRing - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsParity - Static variable in class com.actelion.research.chem.Molecule
- cBondParityEor1 - Static variable in class com.actelion.research.chem.Molecule
- cBondParityNone - Static variable in class com.actelion.research.chem.Molecule
- cBondParityUnknown - Static variable in class com.actelion.research.chem.Molecule
- cBondParityZor2 - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAllFeatures - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAromatic - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAromState - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAromStateBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAromStateShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBondTypes - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBondTypesBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBondTypesShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridge - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeMin - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeMinBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeMinShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeSpan - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeSpanBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeSpanShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFDelocalized - Static variable in class com.actelion.research.chem.Molecule
- cBondQFDouble - Static variable in class com.actelion.research.chem.Molecule
- cBondQFMatchStereo - Static variable in class com.actelion.research.chem.Molecule
- cBondQFMetalLigand - Static variable in class com.actelion.research.chem.Molecule
- cBondQFNarrowing - Static variable in class com.actelion.research.chem.Molecule
- cBondQFNoOfBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFNotAromatic - Static variable in class com.actelion.research.chem.Molecule
- cBondQFNotRing - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRing - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingSize - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingSizeBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingSizeShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingState - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingStateBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingStateShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFSimpleFeatures - Static variable in class com.actelion.research.chem.Molecule
- cBondQFSingle - Static variable in class com.actelion.research.chem.Molecule
- cBondQFTriple - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeCross - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeDeleted - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeDelocalized - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeDouble - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeDown - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeIncreaseOrder - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeMaskSimple - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeMaskStereo - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeMetalLigand - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeSingle - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeTriple - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeUp - Static variable in class com.actelion.research.chem.Molecule
- cbrt(double) - Static method in class smile.math.Math
-
Returns the cube root of a double value.
- cButtonBorder - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cButtonBorder - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cButtonCleanStructure - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cButtonCleanStructure - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cButtonClear - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cButtonClear - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cButtonSize - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cButtonSize - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cButtonsPerColumn - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cButtonsPerColumn - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cButtonUndo - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cButtonUndo - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cChainCursor - Static variable in class com.actelion.research.util.CursorHelper
- cChiralityDiastereomers - Static variable in class com.actelion.research.chem.Molecule
- cChiralityEpimers - Static variable in class com.actelion.research.chem.Molecule
- cChiralityIsomerCountMask - Static variable in class com.actelion.research.chem.Molecule
- cChiralityKnownEnantiomer - Static variable in class com.actelion.research.chem.Molecule
- cChiralityMeso - Static variable in class com.actelion.research.chem.Molecule
- cChiralityNotChiral - Static variable in class com.actelion.research.chem.Molecule
- cChiralityRacemic - Static variable in class com.actelion.research.chem.Molecule
- cChiralityUnknown - Static variable in class com.actelion.research.chem.Molecule
- cChiralityUnknownEnantiomer - Static variable in class com.actelion.research.chem.Molecule
- cCLogPUnknown - Static variable in class com.actelion.research.chem.prediction.CLogPPredictor
- cColorGray - Static variable in class com.actelion.research.chem.AbstractDepictor
- cColumnName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnNameRowList - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnProperty - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnProperty3DFragmentSplit - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyBinBase - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyBinIsDate - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyBinIsLog - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyBinSize - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyCalculated - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyCommentDepartment - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyCommentUploadStatus - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyCyclicDataMax - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDataMax - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDataMin - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDescriptorVersion - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailSource - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDisplayGroup - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyFormula - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyGroupName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyImagePath - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyIsClusterNo - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyIsDisplayable - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyIsFragment - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchAllowMultiple - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchCommand - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchDecoration - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchOption - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupDetailURL - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupEncode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupFilter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupFilterRemoveMinus - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupURL - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyNaturalLigand - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyOpenExternalName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyOpenExternalPath - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyOrbitType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyParentColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyProteinCavity - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReactionPart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferencedColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferenceStrengthColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferenceType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferenceTypeRedundant - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferenceTypeTopDown - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyRelatedCatalystColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyRelatedIdentifierColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyShowNaturalLigand - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertySpecialType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertySuperpose - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertySuperposeAlign - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertySuperposeMolecule - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyUseThumbNail - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnRelationTypes - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnType2DCoordinates - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnType3DCoordinates - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeAtomColorInfo - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeFlagColors - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeIDCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeNegRecImage - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeReactionMapping - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeReactionObjects - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeRXNCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeTransformation - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnUnassignedCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnUnassignedItemText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cCommonOxidationState - Static variable in class com.actelion.research.chem.Molecule
- cCountModeExistance - Static variable in class com.actelion.research.chem.SSSearcher
- cCountModeFirstMatch - Static variable in class com.actelion.research.chem.SSSearcher
- cCountModeOverlapping - Static variable in class com.actelion.research.chem.SSSearcher
- cCountModeRigorous - Static variable in class com.actelion.research.chem.SSSearcher
- cCountModeSeparated - Static variable in class com.actelion.research.chem.SSSearcher
- cCountModeUnique - Static variable in class com.actelion.research.chem.SSSearcher
- cDataDependentPropertiesEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataDependentPropertiesStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeAutomatic - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeDate - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeFloat - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeInteger - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeString - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDefaultAtomValence - Static variable in class com.actelion.research.chem.Molecule
- cDefaultDetailSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDefaultImageExtension - Static variable in class com.actelion.research.gui.JImagePanel
- cDefaultMatchMode - Static variable in class com.actelion.research.chem.SSSearcher
- cDeleteCursor - Static variable in class com.actelion.research.util.CursorHelper
- cDetailDataEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDetailDataStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDetailID - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDetailIndexSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cdf(double) - Method in interface smile.stat.distribution.Distribution
-
Cumulative distribution function.
- cdf(double) - Method in class smile.stat.distribution.GaussianDistribution
- cdf(double) - Method in class smile.stat.distribution.Mixture
- cDModeAtomNo - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeBondNo - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeHiliteAllQueryFeatures - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeNoColorOnESRAndCIP - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeNoImplicitAtomLabelColors - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeNoImplicitHydrogen - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeNoStereoProblem - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeNoTabus - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeShowMapping - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeShowSymmetryDiastereotopic - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeShowSymmetryEnantiotopic - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeShowSymmetrySimple - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeSuppressChiralText - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeSuppressCIPParity - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeSuppressESR - Static variable in class com.actelion.research.chem.AbstractDepictor
- CDPBondAttach(int, int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondAttach
- CDPBondBegin(int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondBegin
- CDPBondEnd(int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondEnd
- CDPElement(short) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPElement
- CDPPoint2D(int, int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPPoint2D
- cDruglikenessUnknown - Static variable in class com.actelion.research.chem.prediction.DruglikenessPredictor
- cDruglikenessUnknown - Static variable in class com.actelion.research.chem.prediction.DruglikenessPredictorWithIndex
- CDXConstants - Class in com.actelion.research.gui.clipboard.external
- CDXConstants() - Constructor for class com.actelion.research.gui.clipboard.external.CDXConstants
- CDXDocument() - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
- CDXPage() - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXPage
- CDXReactionStep(int[], int[]) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXReactionStep
- ceil(double) - Static method in class smile.math.Math
-
Returns the smallest (closest to negative infinity) double value that is greater than or equal to the argument and is equal to a mathematical integer.
- center - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- center() - Method in class com.actelion.research.chem.conf.Conformer
-
Translate this conformer's coordinates such that its center of gravity is moved to P(0,0,0) assuming all atoms have the same mass.
- center() - Method in class com.actelion.research.chem.Molecule
-
Translate this molecule's 3D-coordinates such that its center of gravity is moved to P(0,0,0) assuming all atoms have the same mass.
- center(Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Calculates the center point between this and c and sets this to the center point.
- center(Coordinates, Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Updates this to contains the center between c1 and c2.
- CENTER - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- CENTER_DATA - Static variable in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- centroids() - Method in class smile.clustering.KMeans
-
Returns the centroids.
- cEntrySeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cEntrySeparatorBytes - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cError2AlphasInSameStrand - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorCCBondCleavageLimit - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorCCBondCreationLimit - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorComplexReaction - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorCRClassifyError - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorDRClassifyError - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorDupProdMapNoDifEd - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorEductMapNoOverused - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorEduFragPartMapped - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorForkedOrLongStrand - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorFragmentAtomLimit - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorHRClassifyError - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorIncoOrLeavMissing - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorMapNoNotInEduct - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorMapNoNotInProduct - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorNoChangeNorEFG - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorNoChangingAtoms - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorNoDatabaseReaction - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorNoError - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorProdFragPartMapped - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorProdMapNoOverused1 - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorProdMapNoOverused2 - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorProdRemapFailed - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorRAClassifyError - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorREClassifyError - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorUnexpected - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorUnitReactionLimit - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cErrorUnMappedCInConOrFr - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cESRGroupBits - Static variable in class com.actelion.research.chem.Molecule
- cESRMaxGroups - Static variable in class com.actelion.research.chem.Molecule
- cESRMenuBorder - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cESRMenuBorder - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cESRMenuX - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cESRMenuX - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cESRMenuY - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cESRMenuY - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cESRTypeAbs - Static variable in class com.actelion.research.chem.Molecule
- cESRTypeAnd - Static variable in class com.actelion.research.chem.Molecule
- cESRTypeOr - Static variable in class com.actelion.research.chem.Molecule
- cExtensionNameFileExplanation - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cExtensionNameMacroList - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cFileExplanationEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cFileExplanationStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cFileTypeDataWarrior - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorCompatibleData - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorMacro - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorQuery - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorTemplate - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorTemplateContaining - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDirectory - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeGIF - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeJPG - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeMask - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeMMTF - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeMOL - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeMOL2 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypePDB - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypePictureFile - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypePNG - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeProtein - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeRD - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeRDV2 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeRDV3 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeRXN - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSD - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSDGZ - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSDV2 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSDV3 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSOM - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSVG - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeText - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeTextCommaSeparated - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeTextTabDelimited - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeUnknown - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFistCursor - Static variable in class com.actelion.research.util.CursorHelper
- cFlagColor - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cGZipExtention - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- chainHiliteColor() - Static method in class com.actelion.research.gui.editor.GenericDrawArea
- chainHiliteColor() - Static method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- cHandCursor - Static variable in class com.actelion.research.util.CursorHelper
- cHandPlusCursor - Static variable in class com.actelion.research.util.CursorHelper
- changeAtom(int, int, int, int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- ChangeAtomAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
- ChangeAtomAction(Model, int) - Constructor for class com.actelion.research.share.gui.editor.actions.ChangeAtomAction
- changeAtomCharge(double, double, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- changeAtomCharge(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- ChangeAtomPropertiesAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
- ChangeAtomPropertiesAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ChangeAtomPropertiesAction
- changeBond(int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- ChangeChargeAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
- ChangeChargeAction(Model, boolean) - Constructor for class com.actelion.research.share.gui.editor.actions.ChangeChargeAction
- changed() - Method in class com.actelion.research.share.gui.editor.Model
- changed(Action) - Method in interface com.actelion.research.share.gui.editor.actions.ToolbarSelectionChange
- changeTitle(String, String) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
changes a title of a docked Dockable
- changeTitle(String, String) - Method in class com.actelion.research.gui.dock.TreeLeaf
- charge - Variable in class com.actelion.research.chem.coords.InventorCharge
- Charge - Class in com.actelion.research.chem.forcefield.mmff.table
- Charge - Class in com.actelion.research.chem.forcefield.mmff.type
-
The charge class provides static functions for calculating formal and partial charges on a molecule.
- Charge() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Charge
- Charge(Tables, String, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Charge
- CHARGE_NEG_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- CHARGE_POS_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- charge_term - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- ChargedGroupDetector - Class in com.actelion.research.chem.phesa.pharmacophore
-
derives charged groups
- ChargedGroupDetector(StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.ChargedGroupDetector
- ChargePoint - Class in com.actelion.research.chem.phesa.pharmacophore.pp
- ChargePoint(ChargePoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- ChargePoint(StereoMolecule, int, List<Integer>, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- CHARSET_ENCODING - Static variable in class com.actelion.research.util.ConstantsDWAR
- check() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- check() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- check(String, String) - Method in interface com.actelion.research.chem.forcefield.mmff.Sdf.OnMolecule
- checkBiggestFragmentForUnwanted(StereoMolecule, List<Integer>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- checkCommandWithValue(String) - Method in class com.actelion.research.util.CommandLineParser
- checkForEigenvaluesAndEigenvectors() - Static method in class com.actelion.research.calc.MatrixTests
-
Checks for the correctness of the Eigenvector and Eigenvalues calculation.
- checkHiliting(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- checkHiliting(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- checkHiliting(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- cHelperBitCIP - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitIncludeNitrogenParities - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitParities - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitRings - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitRingsSimple - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitsStereo - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitSymmetryDiastereotopic - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitSymmetryEnantiotopic - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitSymmetrySimple - Static variable in class com.actelion.research.chem.Molecule
- cHelperCIP - Static variable in class com.actelion.research.chem.Molecule
- cHelperNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cHelperNone - Static variable in class com.actelion.research.chem.Molecule
- cHelperParities - Static variable in class com.actelion.research.chem.Molecule
- cHelperRings - Static variable in class com.actelion.research.chem.Molecule
- cHelperRingsSimple - Static variable in class com.actelion.research.chem.Molecule
- cHelperSymmetryDiastereotopic - Static variable in class com.actelion.research.chem.Molecule
- cHelperSymmetryEnantiotopic - Static variable in class com.actelion.research.chem.Molecule
- cHelperSymmetrySimple - Static variable in class com.actelion.research.chem.Molecule
- CHEM_SIM_WEIGHT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- ChemDrawCDX - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX() - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- ChemDrawCDX.CDPAtomCharge - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomCIP - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomEnhGroup - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomEnhStereoType - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomIsotope - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomRadical - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondAttach - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondBegin - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondDisplay - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondEnd - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondType - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPElement - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPPoint2D - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPProducts - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPReactants - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPShowAtomStereo - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPShowBondStereo - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPShowEnhAtomStereo - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPText - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDXDocument - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDXPage - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDXReactionStep - Class in com.actelion.research.gui.clipboard.external
- ChemicalRule - Class in com.actelion.research.chem.reaction.mapping
-
A ChemicalRule is basically a chemical reaction (transformation) defined by a reaction substructure and a product substructure with full stoichiometry and completely mapped atoms.
- ChemicalRule(String, String, float) - Constructor for class com.actelion.research.chem.reaction.mapping.ChemicalRule
- ChemicalRuleEnhancedReactionMapper - Class in com.actelion.research.chem.reaction.mapping
- ChemicalRuleEnhancedReactionMapper() - Constructor for class com.actelion.research.chem.reaction.mapping.ChemicalRuleEnhancedReactionMapper
- ChemicalSpaceCreator - Class in com.actelion.research.chem.chemicalspaces
- ChemicalSpaceCreator(Set<String>, List<Reaction>, File) - Constructor for class com.actelion.research.chem.chemicalspaces.ChemicalSpaceCreator
- ChemistryCellRenderer - Class in com.actelion.research.gui.table
- ChemistryCellRenderer() - Constructor for class com.actelion.research.gui.table.ChemistryCellRenderer
- ChemistryCellRenderer(Dimension) - Constructor for class com.actelion.research.gui.table.ChemistryCellRenderer
- ChemistryDataFormats - Class in com.actelion.research.chem.dnd
- ChemistryDataFormats() - Constructor for class com.actelion.research.chem.dnd.ChemistryDataFormats
- ChemistryFlavors - Class in com.actelion.research.chem.dnd
- ChemistryFlavors() - Constructor for class com.actelion.research.chem.dnd.ChemistryFlavors
- ChemistryHelper - Class in com.actelion.research.chem
- ChemistryRenderPanel - Class in com.actelion.research.gui.table
- ChemistryRenderPanel() - Constructor for class com.actelion.research.gui.table.ChemistryRenderPanel
- ChemPLP - Class in com.actelion.research.chem.docking.scoring
-
Implementation of ChemPLP scoring function as described in: doi: 10.1021/ci800298z THIS SCORING FUNCTION REQUIRES EXPLICIT HYDROGENS TO BE PRESENT!
- ChemPLP(Molecule3D, Set<Integer>, MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.ChemPLP
- CHEMPLP - com.actelion.research.chem.docking.DockingEngine.ScoringFunction
- chge - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- chi(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
-
Returns the 'chi' (or pauEle) parameter from the table at the given index.
- CHI - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- CHI - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- cHighRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- chisq - Variable in class com.actelion.research.util.FittingFunction
- cHitlistData - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cHitlistDataEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cHitlistDataStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cHitlistName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- Chlorine - Static variable in class com.actelion.research.chem.PeriodicTable
- cholesky() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the Cholesky decomposition.
- cholesky() - Method in class smile.math.matrix.JMatrix
-
Cholesky decomposition for symmetric and positive definite matrix.
- cholesky(boolean) - Method in interface smile.math.matrix.DenseMatrix
-
Returns the Cholesky decomposition.
- cholesky(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- Cholesky - Class in smile.math.matrix
-
Cholesky decomposition is a decomposition of a symmetric, positive-definite matrix into a lower triangular matrix L and the transpose of the lower triangular matrix such that A = L*L'.
- Cholesky(DenseMatrix) - Constructor for class smile.math.matrix.Cholesky
-
Constructor.
- CholeskyOfAtA() - Method in class smile.math.matrix.QR
-
Returns the Cholesky decomposition of A'A.
- CholeskyOfAtA() - Method in class smile.math.matrix.SVD
-
Returns the Cholesky decomposition of A'A.
- choose(int, int) - Static method in class smile.math.Math
-
n choose k.
- chooseDropFlavor(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- chooseDropFlavor(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- chooseDropFlavor(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- cIDCodeCurrentVersion - Static variable in class com.actelion.research.chem.Canonizer
- cIDCodeVersion2 - Static variable in class com.actelion.research.chem.Canonizer
- cIDCodeVersion3 - Static variable in class com.actelion.research.chem.Canonizer
- cIndexFullPermutation - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cIndexMatchMode - Static variable in class com.actelion.research.chem.SSSearcher
- cIndexNone - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cIndexOnePermToFile - Static variable in class com.actelion.research.chem.reaction.ReactionClassifier
- cIndexVersion - Static variable in class com.actelion.research.chem.SSSearcherWithIndex
- cInvisibleCursor - Static variable in class com.actelion.research.util.CursorHelper
- cKeyIDCode - Static variable in class com.actelion.research.chem.SSSearcherWithIndex
- CLARANS<T> - Class in smile.clustering
-
Clustering Large Applications based upon RANdomized Search.
- CLARANS(T[], Distance<T>, int) - Constructor for class smile.clustering.CLARANS
-
Constructor.
- CLARANS(T[], Distance<T>, int, int) - Constructor for class smile.clustering.CLARANS
-
Constructor.
- CLARANS(T[], Distance<T>, int, int, int) - Constructor for class smile.clustering.CLARANS
-
Constructor.
- classification - Variable in class com.actelion.research.calc.regression.ModelError
- Classification - Class in com.actelion.research.chem.reaction
- Classification() - Constructor for class com.actelion.research.chem.reaction.Classification
- ClassificationAttr - Enum in com.actelion.research.calc.classification
-
Modest v.
- ClassificationData - Class in com.actelion.research.chem.reaction
- classify(int, Reaction) - Method in class com.actelion.research.chem.reaction.ReactionClassifier
- classify(Reaction) - Method in class com.actelion.research.chem.reaction.ReactionClassifier
- classify(StereoMolecule, int) - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Determines uniquely an identifying name for the rotatable bond and its vicinity.
- cLassoCursor - Static variable in class com.actelion.research.util.CursorHelper
- cLassoPlusCursor - Static variable in class com.actelion.research.util.CursorHelper
- CleanAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 10:09 AM
- CleanAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CleanAction
- cleanDate(String) - Static method in class com.actelion.research.util.Formatter
- cleanDateTime(String) - Static method in class com.actelion.research.util.Formatter
- cleanMolecule(boolean, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- cleanReaction(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- cleanStructure() - Method in class com.actelion.research.gui.editor.SwingEditorPanel
- cleanStructure() - Method in class com.actelion.research.gui.JDrawPanel
-
Deprecated.
- cleanupCoordinates(boolean, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- clear() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- clear() - Method in class com.actelion.research.chem.DepictorTransformation
- clear() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- clear() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- clear() - Method in class com.actelion.research.chem.Molecule
-
Empties the molecule to serve as container for constructing a new molecule, e.g.
- clear() - Method in class com.actelion.research.chem.Molecule3D
- clear() - Method in class com.actelion.research.chem.reaction.Reaction
- clear() - Method in interface com.actelion.research.gui.CompoundCollectionModel
- clear() - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- clear() - Method in class com.actelion.research.gui.generic.GenericPolygon
- clear() - Method in class com.actelion.research.util.datamodel.DoubleArray
- clear() - Method in class com.actelion.research.util.datamodel.IntArray
- clear() - Method in class com.actelion.research.util.datamodel.IntVec
- clear() - Method in class com.actelion.research.util.ErrorHashMap
- clear() - Method in class com.actelion.research.util.hash.HashSetInt
- clear() - Method in class com.actelion.research.util.IntQueue
- clear() - Method in class com.actelion.research.util.Pipeline
- clear() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- ClearAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/24/13 Time: 5:09 PM
- ClearAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ClearAction
- clearAll() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- clearAll() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- clearCovers(int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- clearHiliting() - Method in class com.actelion.research.chem.AbstractDrawingObject
- clearHiliting() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- clearHiliting() - Method in class com.actelion.research.chem.TextDrawingObject
- clearInfo() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- clearOriginalAtomIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- clearRect(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- clearRect(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- clearRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- clearRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- clearStateInfo() - Method in class com.actelion.research.gui.dock.TreeElement
- clearStateInfo() - Method in class com.actelion.research.gui.dock.TreeFork
- clearStateInfo() - Method in class com.actelion.research.gui.dock.TreeLeaf
- clearStateInfo() - Method in class com.actelion.research.gui.dock.TreeRoot
- cLineSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cLineSeparatorByte - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- clip(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- CLIP_CHARACTER_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_DEFAULT_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_LH_ANGLES - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_MASK - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_STROKE_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_TT_ALWAYS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- ClipboardHandler - Class in com.actelion.research.gui.clipboard
-
Title: Actelion Library
- ClipboardHandler() - Constructor for class com.actelion.research.gui.clipboard.ClipboardHandler
- ClipboardHelper - Class in com.actelion.research.jfx.gui.misc
-
Created by baerr on 7/28/14.
- clipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- clipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- cLoginCancel - Static variable in class com.actelion.research.gui.JLoginDialog
- cLoginOK - Static variable in class com.actelion.research.gui.JLoginDialog
- CLogPPredictor - Class in com.actelion.research.chem.prediction
- CLogPPredictor() - Constructor for class com.actelion.research.chem.prediction.CLogPPredictor
- clone() - Method in class com.actelion.research.chem.AbstractDrawingObject
- clone() - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- clone() - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- clone() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- clone() - Method in class com.actelion.research.chem.TextDrawingObject
- clone() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- clone() - Method in class com.actelion.research.util.DoubleVec
- clone() - Method in class org.machinelearning.svm.libsvm.svm_parameter
- clone() - Method in class smile.regression.NeuralNetwork
- clone(double[][]) - Static method in class smile.math.Math
-
Deep clone a two-dimensional array.
- clone(float[][]) - Static method in class smile.math.Math
-
Deep clone a two-dimensional array.
- clone(int[][]) - Static method in class smile.math.Math
-
Deep clone a two-dimensional array.
- close() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Closes the underlying reader.
- close() - Method in class com.actelion.research.gui.JProgressDialog
-
Closes and disposes the dialog.
- close() - Method in class com.actelion.research.io.StringReadChannel
- close() - Method in class com.actelion.research.util.Base64.OutputStream
-
Flushes and closes (I think, in the superclass) the stream.
- close() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- close() - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- close(Frame) - Method in class com.actelion.research.gui.JProgressDialog
-
Disposes of the progress dialog and optionally moves the specified frame to the front.
- cLowRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cluster(double, int) - Method in class com.actelion.research.chem.Clusterer
-
Defines the criteria for stopping the clustering.
- Clusterer<T> - Class in com.actelion.research.chem
- Clusterer(DescriptorHandler<T, ?>, T[]) - Constructor for class com.actelion.research.chem.Clusterer
- clustering(double[][], double[][], int[], int[]) - Method in class smile.clustering.BBDTree
-
Given k cluster centroids, this method assigns data to nearest centroids.
- Clustering<T> - Interface in smile.clustering
-
Clustering interface.
- ClusteringDistance - Enum in smile.clustering
-
Clustering distance measure.
- ClusterNode - Class in com.actelion.research.chem.descriptor.flexophore
- ClusterNode(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- cMacroListEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cMacroListStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cMatchAromDBondToDelocalized - Static variable in class com.actelion.research.chem.SSSearcher
- cMatchAtomCharge - Static variable in class com.actelion.research.chem.SSSearcher
- cMatchAtomMass - Static variable in class com.actelion.research.chem.SSSearcher
- cMatchDBondToDelocalized - Static variable in class com.actelion.research.chem.SSSearcher
- cMaxAtomicNo - Static variable in class com.actelion.research.chem.Molecule
- cMaxConnAtoms - Static variable in class com.actelion.research.chem.ExtendedMolecule
- cMaxDateOrDoubleCategoryCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cMaxTextCategoryCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- CMNT_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- cModeChiralTextAboveMolecule - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeChiralTextBelowMolecule - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeChiralTextOnFrameBottom - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeChiralTextOnFrameTop - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeFastBestMatchFinding - Static variable in class com.actelion.research.calc.SelfOrganizedMap
- cModeGrowDuringOptimization - Static variable in class com.actelion.research.calc.SelfOrganizedMap
- cModeInflateToAVBL - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeInflateToHighResAVBL - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeInflateToMaxAVBL - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeMaxBondLength - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeNeighbourhoodGaussean - Static variable in class com.actelion.research.calc.SelfOrganizedMap
- cModeNeighbourhoodLinear - Static variable in class com.actelion.research.calc.SelfOrganizedMap
- cModeNeighbourhoodMexicanHat - Static variable in class com.actelion.research.calc.SelfOrganizedMap
- cModeTopologyUnlimited - Static variable in class com.actelion.research.calc.SelfOrganizedMap
- cMoleculeColorDefault - Static variable in class com.actelion.research.chem.Molecule
- cMoleculeColorNeutral - Static variable in class com.actelion.research.chem.Molecule
- cNastyFunctionsUnknown - Static variable in class com.actelion.research.chem.NastyFunctionDetector
- cNativeFileCreated - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNativeFileHeaderEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNativeFileHeaderStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNativeFileRowCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNativeFileVersion - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNewLineString - Static variable in class com.actelion.research.chem.io.RDFileParser
- cNewLineString - Static variable in class com.actelion.research.chem.io.SDFileParser
- cNonPolarAtomTypeName - Static variable in class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
- cNoRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- coef0 - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- coeff - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- coefficients() - Method in class smile.regression.GaussianProcessRegression
-
Returns the coefficients.
- collectionUpdated(int, int) - Method in interface com.actelion.research.gui.CompoundCollectionListener
- collectionUpdated(int, int) - Method in class com.actelion.research.gui.CompoundCollectionPane
- colMax(double[][]) - Static method in class smile.math.Math
-
Returns the column maximum for a matrix.
- colMeans() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the mean of each column for a matrix.
- colMeans(double[][]) - Static method in class smile.math.Math
-
Returns the column means for a matrix.
- colMin(double[][]) - Static method in class smile.math.Math
-
Returns the column minimum for a matrix.
- color - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorDot
- COLOR_BLUE - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_DARK_GREEN - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_DARK_RED - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_FOR_CENTER_SELECTION - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
- COLOR_GREEN - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_MAGENTA - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_ORANGE - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_RED - Static variable in class com.actelion.research.chem.AbstractDepictor
- ColorHelper - Class in com.actelion.research.util
- ColorHelper() - Constructor for class com.actelion.research.util.ColorHelper
- COLORS - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Colors for visualization of the Flexophore mapping.
- colorToString(Color) - Static method in class com.actelion.research.gui.hidpi.ColorUtils
- ColorUtils - Class in com.actelion.research.gui.hidpi
-
Defines a color with some utility methods.
- ColorUtils() - Constructor for class com.actelion.research.gui.hidpi.ColorUtils
- cols() - Method in class com.actelion.research.calc.Matrix
- colSds(double[][]) - Static method in class smile.math.Math
-
Returns the column deviations for a matrix.
- colSums() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the sum of each column for a matrix.
- colSums(double[][]) - Static method in class smile.math.Math
-
Returns the column sums for a matrix.
- column(int) - Method in class smile.data.AttributeDataset
-
Returns a column.
- column(String) - Method in class smile.data.AttributeDataset
-
Returns a column.
- columnIntoDoubleArray(Matrix, int, DoubleArray) - Static method in class com.actelion.research.calc.MatrixFunctions
- columns(String...) - Method in class smile.data.AttributeDataset
-
Returns a dataset with selected columns.
- com - Variable in class com.actelion.research.chem.phesa.ShapeVolume
- com.actelion.research.calc - package com.actelion.research.calc
- com.actelion.research.calc.classification - package com.actelion.research.calc.classification
- com.actelion.research.calc.combinatorics - package com.actelion.research.calc.combinatorics
- com.actelion.research.calc.distance - package com.actelion.research.calc.distance
- com.actelion.research.calc.filter - package com.actelion.research.calc.filter
- com.actelion.research.calc.geometry - package com.actelion.research.calc.geometry
- com.actelion.research.calc.graph - package com.actelion.research.calc.graph
- com.actelion.research.calc.histogram - package com.actelion.research.calc.histogram
- com.actelion.research.calc.regression - package com.actelion.research.calc.regression
- com.actelion.research.calc.regression.gaussianprocess - package com.actelion.research.calc.regression.gaussianprocess
- com.actelion.research.calc.regression.knn - package com.actelion.research.calc.regression.knn
- com.actelion.research.calc.regression.linear.pls - package com.actelion.research.calc.regression.linear.pls
- com.actelion.research.calc.regression.linear.pls.boxcox - package com.actelion.research.calc.regression.linear.pls.boxcox
- com.actelion.research.calc.regression.linear.simple - package com.actelion.research.calc.regression.linear.simple
- com.actelion.research.calc.regression.median - package com.actelion.research.calc.regression.median
- com.actelion.research.calc.regression.neuralnetwork - package com.actelion.research.calc.regression.neuralnetwork
- com.actelion.research.calc.regression.randomforest - package com.actelion.research.calc.regression.randomforest
- com.actelion.research.calc.regression.svm - package com.actelion.research.calc.regression.svm
- com.actelion.research.calc.statistics - package com.actelion.research.calc.statistics
- com.actelion.research.calc.statistics.median - package com.actelion.research.calc.statistics.median
- com.actelion.research.chem - package com.actelion.research.chem
- com.actelion.research.chem.alignment3d - package com.actelion.research.chem.alignment3d
- com.actelion.research.chem.alignment3d.transformation - package com.actelion.research.chem.alignment3d.transformation
- com.actelion.research.chem.chemicalspaces - package com.actelion.research.chem.chemicalspaces
- com.actelion.research.chem.chemicalspaces.synthon - package com.actelion.research.chem.chemicalspaces.synthon
- com.actelion.research.chem.combinatorialspace - package com.actelion.research.chem.combinatorialspace
- com.actelion.research.chem.conf - package com.actelion.research.chem.conf
- com.actelion.research.chem.conf.torsionstrain - package com.actelion.research.chem.conf.torsionstrain
- com.actelion.research.chem.contrib - package com.actelion.research.chem.contrib
- com.actelion.research.chem.coords - package com.actelion.research.chem.coords
- com.actelion.research.chem.descriptor - package com.actelion.research.chem.descriptor
- com.actelion.research.chem.descriptor.flexophore - package com.actelion.research.chem.descriptor.flexophore
- com.actelion.research.chem.descriptor.flexophore.calculator - package com.actelion.research.chem.descriptor.flexophore.calculator
- com.actelion.research.chem.descriptor.flexophore.completegraphmatcher - package com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
- com.actelion.research.chem.descriptor.flexophore.entity - package com.actelion.research.chem.descriptor.flexophore.entity
- com.actelion.research.chem.descriptor.flexophore.example - package com.actelion.research.chem.descriptor.flexophore.example
- com.actelion.research.chem.descriptor.flexophore.generator - package com.actelion.research.chem.descriptor.flexophore.generator
- com.actelion.research.chem.descriptor.flexophore.redgraph - package com.actelion.research.chem.descriptor.flexophore.redgraph
- com.actelion.research.chem.descriptor.pharmacophoregraph - package com.actelion.research.chem.descriptor.pharmacophoregraph
- com.actelion.research.chem.descriptor.pharmacophoretree - package com.actelion.research.chem.descriptor.pharmacophoretree
- com.actelion.research.chem.dnd - package com.actelion.research.chem.dnd
- com.actelion.research.chem.docking - package com.actelion.research.chem.docking
- com.actelion.research.chem.docking.receptorpharmacophore - package com.actelion.research.chem.docking.receptorpharmacophore
- com.actelion.research.chem.docking.scoring - package com.actelion.research.chem.docking.scoring
- com.actelion.research.chem.docking.scoring.chemscore - package com.actelion.research.chem.docking.scoring.chemscore
- com.actelion.research.chem.docking.scoring.idoscore - package com.actelion.research.chem.docking.scoring.idoscore
- com.actelion.research.chem.docking.scoring.plp - package com.actelion.research.chem.docking.scoring.plp
- com.actelion.research.chem.docking.shape - package com.actelion.research.chem.docking.shape
- com.actelion.research.chem.forcefield - package com.actelion.research.chem.forcefield
- com.actelion.research.chem.forcefield.mmff - package com.actelion.research.chem.forcefield.mmff
- com.actelion.research.chem.forcefield.mmff.table - package com.actelion.research.chem.forcefield.mmff.table
- com.actelion.research.chem.forcefield.mmff.type - package com.actelion.research.chem.forcefield.mmff.type
- com.actelion.research.chem.interactionstatistics - package com.actelion.research.chem.interactionstatistics
- com.actelion.research.chem.io - package com.actelion.research.chem.io
- com.actelion.research.chem.io.pdb.converter - package com.actelion.research.chem.io.pdb.converter
- com.actelion.research.chem.io.pdb.parser - package com.actelion.research.chem.io.pdb.parser
- com.actelion.research.chem.mcs - package com.actelion.research.chem.mcs
- com.actelion.research.chem.name - package com.actelion.research.chem.name
- com.actelion.research.chem.optimization - package com.actelion.research.chem.optimization
- com.actelion.research.chem.phesa - package com.actelion.research.chem.phesa
- com.actelion.research.chem.phesa.pharmacophore - package com.actelion.research.chem.phesa.pharmacophore
- com.actelion.research.chem.phesa.pharmacophore.pp - package com.actelion.research.chem.phesa.pharmacophore.pp
- com.actelion.research.chem.phesaflex - package com.actelion.research.chem.phesaflex
- com.actelion.research.chem.potentialenergy - package com.actelion.research.chem.potentialenergy
- com.actelion.research.chem.prediction - package com.actelion.research.chem.prediction
- com.actelion.research.chem.properties.complexity - package com.actelion.research.chem.properties.complexity
- com.actelion.research.chem.properties.fractaldimension - package com.actelion.research.chem.properties.fractaldimension
- com.actelion.research.chem.reaction - package com.actelion.research.chem.reaction
- com.actelion.research.chem.reaction.mapping - package com.actelion.research.chem.reaction.mapping
- com.actelion.research.chem.shredder - package com.actelion.research.chem.shredder
- com.actelion.research.gui - package com.actelion.research.gui
- com.actelion.research.gui.clipboard - package com.actelion.research.gui.clipboard
- com.actelion.research.gui.clipboard.external - package com.actelion.research.gui.clipboard.external
- com.actelion.research.gui.dnd - package com.actelion.research.gui.dnd
- com.actelion.research.gui.dock - package com.actelion.research.gui.dock
- com.actelion.research.gui.editor - package com.actelion.research.gui.editor
- com.actelion.research.gui.generic - package com.actelion.research.gui.generic
- com.actelion.research.gui.hidpi - package com.actelion.research.gui.hidpi
- com.actelion.research.gui.swing - package com.actelion.research.gui.swing
- com.actelion.research.gui.table - package com.actelion.research.gui.table
- com.actelion.research.gui.wmf - package com.actelion.research.gui.wmf
- com.actelion.research.io - package com.actelion.research.io
- com.actelion.research.jfx.dataformat - package com.actelion.research.jfx.dataformat
- com.actelion.research.jfx.gui - package com.actelion.research.jfx.gui
- com.actelion.research.jfx.gui.chem - package com.actelion.research.jfx.gui.chem
- com.actelion.research.jfx.gui.misc - package com.actelion.research.jfx.gui.misc
- com.actelion.research.share.gui - package com.actelion.research.share.gui
- com.actelion.research.share.gui.editor - package com.actelion.research.share.gui.editor
- com.actelion.research.share.gui.editor.actions - package com.actelion.research.share.gui.editor.actions
- com.actelion.research.share.gui.editor.chem - package com.actelion.research.share.gui.editor.chem
- com.actelion.research.share.gui.editor.dialogs - package com.actelion.research.share.gui.editor.dialogs
- com.actelion.research.share.gui.editor.geom - package com.actelion.research.share.gui.editor.geom
- com.actelion.research.share.gui.editor.io - package com.actelion.research.share.gui.editor.io
- com.actelion.research.share.gui.editor.listeners - package com.actelion.research.share.gui.editor.listeners
- com.actelion.research.util - package com.actelion.research.util
- com.actelion.research.util.concurrent - package com.actelion.research.util.concurrent
- com.actelion.research.util.convert - package com.actelion.research.util.convert
- com.actelion.research.util.datamodel - package com.actelion.research.util.datamodel
- com.actelion.research.util.datamodel.table - package com.actelion.research.util.datamodel.table
- com.actelion.research.util.graph.complete - package com.actelion.research.util.graph.complete
- com.actelion.research.util.hash - package com.actelion.research.util.hash
- CombinationGenerator - Class in com.actelion.research.calc.combinatorics
-
CombinationGenerator
- CombinationGenerator() - Constructor for class com.actelion.research.calc.combinatorics.CombinationGenerator
- combineIntsToLong(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- ComboBoxColorItem - Class in com.actelion.research.gui
- ComboBoxColorItem(String, Color) - Constructor for class com.actelion.research.gui.ComboBoxColorItem
- CommandAction - Class in com.actelion.research.share.gui.editor.actions
-
Abstract class for handling of all the actions which handle single type of actions: the action is executed when pressing the button and the current drawing action will remain unchanged
- CommandAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CommandAction
- CommandLineParser - Class in com.actelion.research.util
-
CommandLineParser Simple command line parser.
- CommandLineParser() - Constructor for class com.actelion.research.util.CommandLineParser
- CommandLineParser(String[]) - Constructor for class com.actelion.research.util.CommandLineParser
- CommandLineParser(String, String) - Constructor for class com.actelion.research.util.CommandLineParser
- COMMENT_EXTENSION_LABEL - Static variable in class com.actelion.research.util.AnimatedGIFWriter
- CommonSubGraphHelper - Class in com.actelion.research.chem.reaction
- CommonSubGraphHelper() - Constructor for class com.actelion.research.chem.reaction.CommonSubGraphHelper
- compact() - Method in class com.actelion.research.chem.Molecule3D
- compare(byte[][], byte[][]) - Method in class com.actelion.research.util.ByteArrayArrayComparator
- compare(byte[], byte[]) - Method in class com.actelion.research.util.ByteArrayComparator
- compare(int[], int[]) - Method in class com.actelion.research.util.IntArrayComparator
- compareAndSet(float, float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
- compareArrays(byte[], byte[]) - Static method in class com.actelion.research.util.ByteArray
- compareArrays(byte[], byte[], int) - Static method in class com.actelion.research.util.ByteArray
- compareTo(GaussianProcessRegression) - Method in class com.actelion.research.calc.regression.gaussianprocess.GaussianProcessRegression
- compareTo(NeuralNetworkRegression) - Method in class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkRegression
- compareTo(ParameterRegressionMethod) - Method in class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- compareTo(ParameterRegressionMethod) - Method in class com.actelion.research.calc.regression.knn.ParameterKNN
- compareTo(ParameterRegressionMethod) - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- compareTo(ParameterRegressionMethod) - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- compareTo(ParameterRegressionMethod) - Method in class com.actelion.research.calc.regression.median.ParameterMedian
- compareTo(ParameterRegressionMethod) - Method in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- compareTo(ParameterRegressionMethod) - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- compareTo(ParameterRegressionMethod) - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- compareTo(RandomForestRegression) - Method in class com.actelion.research.calc.regression.randomforest.RandomForestRegression
- compareTo(SVMRegression) - Method in class com.actelion.research.calc.regression.svm.SVMRegression
- compareTo(PheSAAlignmentOptimizer.AlignmentResult) - Method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer.AlignmentResult
- compareTo(CanonizerBaseValue) - Method in class com.actelion.research.chem.CanonizerBaseValue
- compareTo(Conformer) - Method in class com.actelion.research.chem.conf.Conformer
- compareTo(TorsionDescriptor) - Method in class com.actelion.research.chem.conf.TorsionDescriptor
-
Returns 0, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE; Returns -1 if the first non-equivalent torsion angle is smaller for this than for the passed TorsionDescriptor td.
- compareTo(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- compareTo(ClusterNode) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- compareTo(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- compareTo(PPNodeVizTriangle) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- compareTo(DockingEngine.DockingResult) - Method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
- compareTo(SortedPair) - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
-
Compares this object with another.
- compareTo(Molecule3D) - Method in class com.actelion.research.chem.Molecule3D
- compareTo(PheSAAlignment.PheSAResult) - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- compareTo(Fragment3D) - Method in class com.actelion.research.chem.shredder.Fragment3D
- compareTo(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
- compareTo(IdentifiedObject<T>) - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- compareTo(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
- compareTo(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
- compareTo(SolutionCompleteGraph) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- compareTo(RigidFragmentCache.CacheEntry) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache.CacheEntry
- compareTo(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
-
Allows to order TorsionSets in a unique way for quick uniqueness checking against a TreeSet.
- completeAndScoreMapping() - Method in class com.actelion.research.chem.reaction.mapping.ReactionCenterMapper
-
Tries and scores all possible mapping permutations for all of hitherto unmapped atoms.
- CompleteGraphMatcher<T extends ICompleteGraph> - Class in com.actelion.research.util.graph.complete
-
CompleteGraphMatcher
- CompleteGraphMatcher(IObjectiveCompleteGraph<T>) - Constructor for class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- CompleteLinkage - Class in smile.clustering.linkage
-
Complete linkage.
- CompleteLinkage(double[][]) - Constructor for class smile.clustering.linkage.CompleteLinkage
-
Constructor.
- Complex - Class in smile.math
-
Complex number.
- Complex(double, double) - Constructor for class smile.math.Complex
-
Constructor.
- Component() - Constructor for class smile.stat.distribution.Mixture.Component
- Component(double, Distribution) - Constructor for class smile.stat.distribution.Mixture.Component
- CompoundCollectionListener - Interface in com.actelion.research.gui
- CompoundCollectionModel<T> - Interface in com.actelion.research.gui
- CompoundCollectionPane<T> - Class in com.actelion.research.gui
- CompoundCollectionPane(CompoundCollectionModel<T>, boolean) - Constructor for class com.actelion.research.gui.CompoundCollectionPane
-
This is a visual component to display and edit a compound collection maintained by a CompoundCollectionModel.
- CompoundCollectionPane(CompoundCollectionModel<T>, boolean, int, int, int) - Constructor for class com.actelion.research.gui.CompoundCollectionPane
- CompoundFileFilter - Class in com.actelion.research.chem.io
-
A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
- CompoundFileFilter() - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter.
- CompoundFileFilter(String) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter that accepts files with the given extension.
- CompoundFileFilter(String[]) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter from the given string array.
- CompoundFileFilter(String[], String) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter from the given string array and description.
- CompoundFileFilter(String, String) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter that accepts the given file type.
- CompoundFileHelper - Class in com.actelion.research.chem.io
- CompoundFileHelper() - Constructor for class com.actelion.research.chem.io.CompoundFileHelper
- CompoundFileParser - Class in com.actelion.research.chem.io
- CompoundFileParser() - Constructor for class com.actelion.research.chem.io.CompoundFileParser
- CompoundTableConstants - Interface in com.actelion.research.chem.io
- compressMolTable() - Method in class com.actelion.research.chem.Molecule
- compressMolTable() - Method in class com.actelion.research.chem.Molecule3D
- cond() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Two norm condition number
- condition() - Method in class smile.math.matrix.SVD
-
Returns the L2 norm condition number, which is max(S) / min(S).
- CONF_GIVEN_SINGLE_CONFORMATION - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- ConformationRule - Class in org.openmolecules.chem.conf.so
- ConformationRule(int[]) - Constructor for class org.openmolecules.chem.conf.so.ConformationRule
- ConformationSelfOrganizer - Class in org.openmolecules.chem.conf.so
- ConformationSelfOrganizer(StereoMolecule, boolean) - Constructor for class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
Generates a new ConformationSelfOrganizer from the given molecule.
- Conformer - Class in com.actelion.research.chem.conf
- Conformer(Conformer) - Constructor for class com.actelion.research.chem.conf.Conformer
-
Creates a new conformer as an exact copy of the given one.
- Conformer(Conformer, StereoMolecule) - Constructor for class com.actelion.research.chem.conf.Conformer
-
Use at own risk!! Initializes the conformer as a copy of c but replaces the StereoMolecule by the supplied molecule.
- Conformer(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.Conformer
-
Creates a Conformer, i.e.
- ConformerGenerator - Class in org.openmolecules.chem.conf.gen
-
This class generates 3D-conformers of a given molecule using the following strategy: All rotatable, non-ring bonds are determined.
- ConformerGenerator() - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating non-reproducible conformers.
- ConformerGenerator(boolean) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating non-reproducible conformers.
- ConformerGenerator(long, boolean) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating reproducible conformers unless seed is 0L.
- ConformerGenerator(long, RigidFragmentCache, boolean) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating reproducible conformers unless seed is 0L.
- ConformerGenerator(long, RigidFragmentProvider) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating reproducible conformers unless seed is 0L.
- CONFORMERS - Static variable in class com.actelion.research.chem.conf.ConformerSetGenerator
- ConformerSet - Class in com.actelion.research.chem.conf
- ConformerSet() - Constructor for class com.actelion.research.chem.conf.ConformerSet
- ConformerSet(byte[], byte[]) - Constructor for class com.actelion.research.chem.conf.ConformerSet
- ConformerSet(String) - Constructor for class com.actelion.research.chem.conf.ConformerSet
- ConformerSetGenerator - Class in com.actelion.research.chem.conf
- ConformerSetGenerator() - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
- ConformerSetGenerator(boolean) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
- ConformerSetGenerator(boolean, long) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
- ConformerSetGenerator(int) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
-
STRATEGY_LIKELY_RANDOM was evaluated to be the best strategy for reproducing bioactive conformers (J.W.
- ConformerSetGenerator(int, int, boolean, long) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
- conjugate() - Method in class smile.math.Complex
-
Returns the conjugate.
- connected(Molecule3D, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Returns the rotatable bonds (sorted).
- connected(StereoMolecule, int, int, int) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
- connectFragments(Conformer, boolean[], int[]) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
Checks both rigid fragments that are connected by this bond, whether they have been attached to the conformer yet, i.e.
- ConnectionPoint - Static variable in class com.actelion.research.chem.PeriodicTable
- CONNECTOR_OFFSET - Static variable in class com.actelion.research.chem.chemicalspaces.synthon.SynthonReactor
- CONSIDER_DIASTEREOTOPICITY - Static variable in class com.actelion.research.chem.Canonizer
- CONSIDER_ENANTIOTOPICITY - Static variable in class com.actelion.research.chem.Canonizer
- CONSIDER_STEREOHETEROTOPICITY - Static variable in class com.actelion.research.chem.Canonizer
- Constants - Class in com.actelion.research.chem.forcefield.mmff
-
The Constants class holds numerical constants that are reused in multiple classes.
- ConstantsAminoAcidsLabeled - Class in com.actelion.research.chem.io.pdb.converter
-
ConstantsAminoAcidsLabeled
- ConstantsAminoAcidsLabeled() - Constructor for class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
- ConstantsDWAR - Class in com.actelion.research.util
-
ConstantsDWAR
- ConstantsDWAR() - Constructor for class com.actelion.research.util.ConstantsDWAR
- ConstantsFlexophore - Class in com.actelion.research.chem.descriptor.flexophore
- ConstantsFlexophore() - Constructor for class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- ConstantsFlexophoreGenerator - Class in com.actelion.research.chem.descriptor.flexophore.generator
- ConstantsFlexophoreGenerator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- ConstantsFlexophoreHardPPPoints - Class in com.actelion.research.chem.descriptor.flexophore
- ConstantsFlexophoreHardPPPoints() - Constructor for class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ConstantsHistogram - Class in com.actelion.research.calc.histogram
-
ConstantsHistogram
- ConstantsHistogram() - Constructor for class com.actelion.research.calc.histogram.ConstantsHistogram
- ConstantsRegressionMethods - Class in com.actelion.research.calc.regression
-
ConstantsRegressionMethods
- ConstantsRegressionMethods() - Constructor for class com.actelion.research.calc.regression.ConstantsRegressionMethods
- constraints - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- ContainerBitArray - Class in com.actelion.research.chem.properties.complexity
- ContainerBitArray(int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ContainerBitArray
- ContainerBitArray.CapacityReachedError - Exception in com.actelion.research.chem.properties.complexity
- ContainerFragBondsSolutions - Class in com.actelion.research.chem.properties.complexity
- ContainerFragBondsSolutions(int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
-
Fragments are represented as bit arrays.
- ContainerListWithIntVec - Class in com.actelion.research.chem.mcs
- ContainerListWithIntVec(int, int) - Constructor for class com.actelion.research.chem.mcs.ContainerListWithIntVec
- ContainerMemory<S extends AMemorizedObject> - Class in com.actelion.research.util.graph.complete
-
ContainerMemory
- ContainerMemory(int, IFactory<S>) - Constructor for class com.actelion.research.util.graph.complete.ContainerMemory
- contains(double[][], double[]) - Static method in class smile.math.Math
-
Determines if the polygon contains the specified coordinates.
- contains(double[][], double, double) - Static method in class smile.math.Math
-
Determines if the polygon contains the specified coordinates.
- contains(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
-
Checks, whether this drawing object contains the point at x,y
- contains(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- contains(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- contains(double, double) - Method in class com.actelion.research.gui.generic.GenericPolygon
- contains(double, double) - Method in class com.actelion.research.gui.generic.GenericRectangle
- contains(double, double) - Method in interface com.actelion.research.gui.generic.GenericShape
- contains(double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- contains(double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- contains(double, double) - Method in class com.actelion.research.share.gui.Polygon
- contains(int) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- contains(int) - Method in class com.actelion.research.util.hash.HashSetInt
- contains(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- contains(Point2D) - Method in class com.actelion.research.share.gui.Polygon
- contains(String) - Method in class com.actelion.research.chem.SortedStringList
- contains(String) - Method in class com.actelion.research.util.CommandLineParser
- contains(List<int[]>, int[]) - Static method in class com.actelion.research.util.ArrayUtils
- contains(T) - Method in class com.actelion.research.util.SortedList
- contains(T) - Method in class com.actelion.research.util.UniqueList
- containsAtLeastOneAtomicNumbersFromHashSet(ExtendedMolecule, HashSet<Integer>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- containsColumn(String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- containsFragmentOpenRing(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- containsHeteroAtom(ExtendedMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- containsInteractionID(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- containsLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
- containsRow(DoubleVec) - Method in class com.actelion.research.calc.Matrix
- containsSolelyAtomicNumbersFromHashSet(ExtendedMolecule, HashSet<Integer>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- containsUpperCase(String) - Static method in class com.actelion.research.util.StringFunctions
- contentChanged(DrawAreaEvent) - Method in interface com.actelion.research.gui.editor.DrawAreaListener
- convert(Matrix) - Static method in class com.actelion.research.calc.regression.svm.Matrix2SVMNodeConverter
- convert(String) - Static method in class com.actelion.research.util.convert.String2DoubleArray
- convert(ArrayList) - Static method in class com.actelion.research.util.convert.String2DoubleArray
- convert2Binary(Matrix, double) - Static method in class com.actelion.research.calc.MatrixFunctions
- convertDataToPrimitiveTypes(List<Molecule3D>) - Static method in class com.actelion.research.chem.io.AbstractParser
- convertPath(int[][], int[][], int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- convertSingleRow(double[]) - Static method in class com.actelion.research.calc.regression.svm.Matrix2SVMNodeConverter
- convertStereoBondsToSingleBonds(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Converts any stereo bond being attached with the pointed tip to the given potential stereocenter (TH or allene) into a single bond.
- convertToValidFileNameCharacters(String) - Static method in class com.actelion.research.util.StringFunctions
-
Not allowed are: \ / : * ? < > |
- CoordinateInventor - Class in com.actelion.research.chem.coords
- CoordinateInventor() - Constructor for class com.actelion.research.chem.coords.CoordinateInventor
-
Creates an CoordinateInventor, which removes unneeded hydrogen atoms and creates new atom coordinates for all(!) atoms.
- CoordinateInventor(int) - Constructor for class com.actelion.research.chem.coords.CoordinateInventor
-
Creates an CoordinateInventor, which removes unneeded hydrogens, if mode flags include MODE_REMOVE_HYDROGEN.
- coordinates - Variable in class com.actelion.research.util.datamodel.IDCodeCoord
- Coordinates - Class in com.actelion.research.chem
-
Class to encapsulate 3D coordinates
- Coordinates() - Constructor for class com.actelion.research.chem.Coordinates
- Coordinates(double, double, double) - Constructor for class com.actelion.research.chem.Coordinates
- Coordinates(Coordinates) - Constructor for class com.actelion.research.chem.Coordinates
- coordinatesAre3D(byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAre3D(byte[], byte[], int, int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAre3D(String, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAreAbsolute(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAreAbsolute(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAreAbsolute(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- COORDS_ARE_3D - Static variable in class com.actelion.research.chem.Canonizer
- coordVariance(int) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- cOptAvBondLen - Static variable in class com.actelion.research.chem.AbstractDepictor
- copy() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- copy() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- copy() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- copy() - Method in interface smile.math.matrix.DenseMatrix
-
Returns a copy of this matrix.
- copy() - Method in class smile.math.matrix.JMatrix
- copy(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- copy(double[][], double[][]) - Static method in class smile.math.Math
-
Copy x into y.
- copy(double[], double[]) - Static method in class smile.math.Math
-
Copy x into y.
- copy(float[][], float[][]) - Static method in class smile.math.Math
-
Copy x into y.
- copy(float[], float[]) - Static method in class smile.math.Math
-
Copy x into y.
- copy(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- copy(int[][], int[][]) - Static method in class smile.math.Math
-
Copy x into y.
- copy(int[], int[]) - Static method in class smile.math.Math
-
Copy x into y.
- copy(int, Matrix) - Method in class com.actelion.research.calc.Matrix
-
This (target matrix) must have appropriate dimensions.
- copy(Matrix) - Method in class com.actelion.research.calc.Matrix
-
Copies a matrix ma into this, the pointer to ma1 is not changed.
- copy(ParameterPLSBoxCox) - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- copy(ParameterPLS) - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- copy(ParameterRegressionMethod) - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- copy(DistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- copy(MolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- copy(MolDistHistViz) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- copy(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
Copy of node into this.
- copy(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
-
Copy of node into this
- copy(StereoMolecule) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- copy(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
- copy(Object) - Static method in class com.actelion.research.util.ArrayUtils
-
Copy an array
- copy(Object[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- CopyAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/16/13 Time: 3:31 PM
- CopyAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CopyAction
- copyArea(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- copyArea(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- copyAtom(Molecule, int, int, int) - Method in class com.actelion.research.chem.Molecule
-
Creates a new atom in destMol and copies all source atom properties including atom list, custom label, flags, and mapNo to it.
- copyAtom(Molecule, int, int, int) - Method in class com.actelion.research.chem.Molecule3D
- copyAtoms(Molecule3D, Molecule3D, List<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- copyBond(Molecule, int, int, int, int[], boolean) - Method in class com.actelion.research.chem.Molecule
- copyBond(Molecule, int, int, int, int, int, boolean) - Method in class com.actelion.research.chem.Molecule
- copyColumn(Matrix, int, int) - Method in class com.actelion.research.calc.Matrix
- copyFrom(Conformer) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies the conformer's atom coordinates to this Conformer.
- copyFrom(StereoMolecule) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies the molecule's atom coordinates to this Conformer.
- copyImage(Image) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copies an Image to the clipboard
- copyImage(Image) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyImage(Image) - Static method in class com.actelion.research.gui.clipboard.ImageClipboardHandler
- copyIntArray(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- copyIntoThis(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- copyIntoThis(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
-
Deep copy The index is not copied
- copyIntoThis(IBitArray) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- copyIntoThis(AMemorizedObject) - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
-
Has to be a deep copy
- copyIntoThis(AMemorizedObject) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- copyMapNosToReaction(Reaction, int[], int[], int) - Method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
-
Copies the generated mapping numbers from the merged reactant/product molecules into the original reaction.
- copyMetaFile(byte[]) - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copy a windows enhance metafile to the Windows clipboard
- copyMolecule(boolean) - Method in class com.actelion.research.share.gui.editor.actions.CopyAction
- copyMolecule(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- copyMolecule(Molecule) - Method in class com.actelion.research.chem.Molecule
-
Copies this molecule including parity settings, if valid.
- copyMolecule(StereoMolecule) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copies a molecule to the clipboard in various formats: ENHMETAFILE with an embedded sketch MDLSK Sketch MDLCT MDL molfile
- copyMolecule(StereoMolecule) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyMolecule(String) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
- copyMolecule(String) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyMoleculeByAtoms(ExtendedMolecule, boolean[], boolean, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Clears destmol and then copies a part of this Molecule into destMol, being defined by a mask of atoms to be included.
- copyMoleculeByBonds(ExtendedMolecule, boolean[], boolean, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Clears destmol and then copies a part of this Molecule into destMol, being defined by a mask of bonds to be included.
- copyMoleculeProperties(Molecule) - Method in class com.actelion.research.chem.Molecule
-
Copies name,isFragment,chirality and validity of parity & CIP flags.
- copyMoleculeProperties(Molecule) - Method in class com.actelion.research.chem.StereoMolecule
-
Copies name, isFragment, chirality.
- copyMoleculeToClipboard(String, byte[], byte[]) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- copyOf(double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- copyPharmacophorePoint() - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- copyReaction(boolean) - Method in class com.actelion.research.share.gui.editor.actions.CopyAction
- copyReaction(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- copyReaction(Reaction) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copies a reaction to the clipboard in various formats: MDLSK Sketch MDLCT MDL molfile
- copyReaction(Reaction) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyReaction(String) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copies a reaction to the clipboard in various formats: CTAB with an embedded sketch MDLSK Sketch serialized
- copyReaction(String) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyReactionToClipboard(byte[], byte[], byte[]) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- copySign(double, double) - Static method in class smile.math.Math
-
Returns the first floating-point argument with the sign of the second floating-point argument.
- copySign(float, float) - Static method in class smile.math.Math
-
Returns the first floating-point argument with the sign of the second floating-point argument.
- copySizedMoleculeToClipboard(String, byte[], byte[], int, int) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- copyText(String) - Static method in class com.actelion.research.gui.clipboard.TextClipboardHandler
- copyTo(StereoMolecule) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies this conformer's atom coordinates to mol.
- cor(double[][]) - Static method in class smile.math.Math
-
Returns the sample correlation matrix.
- cor(double[][], double[]) - Static method in class smile.math.Math
-
Returns the sample correlation matrix.
- cor(double[], double[]) - Static method in class smile.math.Math
-
Returns the correlation coefficient between two vectors.
- cor(float[], float[]) - Static method in class smile.math.Math
-
Returns the correlation coefficient between two vectors.
- cor(int[], int[]) - Static method in class smile.math.Math
-
Returns the correlation coefficient between two vectors.
- coreToOriginalAtom(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- correlation() - Method in class com.actelion.research.calc.Matrix
-
Generate a correlation matrix, each column contains values of a pulling.
- CorrelationCalculator - Class in com.actelion.research.calc
- CorrelationCalculator() - Constructor for class com.actelion.research.calc.CorrelationCalculator
- corrSquared - Variable in class com.actelion.research.calc.regression.ModelError
- corrSquaredSpearman - Variable in class com.actelion.research.calc.regression.ModelError
- cos() - Method in class com.actelion.research.util.Angle
- cos() - Method in class smile.math.Complex
-
Returns the complex cosine.
- cos(double) - Static method in class smile.math.Math
-
Returns the trigonometric cosine of an angle.
- cosAngle(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- cosAngle(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns the cosine of the angle between this vector and that vector.
- cosh(double) - Static method in class smile.math.Math
-
Returns the hyperbolic cosine of a double value.
- Cosine(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Vectors have to be normed!
- COSINE - Static variable in class com.actelion.research.util.datamodel.ByteVec
- COSINE - Static variable in class com.actelion.research.util.DoubleVec
- countFieldsBiggerThan(Matrix, int, double) - Static method in class com.actelion.research.calc.MatrixFunctions
- countFieldsBiggerThanThreshColWise(Matrix, double) - Static method in class com.actelion.research.calc.MatrixFunctions
- countFieldsBiggerThanThreshColWise(Matrix, int, double) - Static method in class com.actelion.research.calc.MatrixFunctions
- countIntegerInText(String) - Static method in class com.actelion.research.util.StringFunctions
- countOccurence(String, char) - Static method in class com.actelion.research.util.StringFunctions
- countWordInText(String) - Static method in class com.actelion.research.util.StringFunctions
- cov(double[][]) - Static method in class smile.math.Math
-
Returns the sample covariance matrix.
- cov(double[][], double[]) - Static method in class smile.math.Math
-
Returns the sample covariance matrix.
- cov(double[], double[]) - Static method in class smile.math.Math
-
Returns the covariance between two vectors.
- cov(float[], float[]) - Static method in class smile.math.Math
-
Returns the covariance between two vectors.
- cov(int[], int[]) - Static method in class smile.math.Math
-
Returns the covariance between two vectors.
- COVALENT_RADIUS - Static variable in interface com.actelion.research.chem.conf.VDWRadii
-
These covalent single bond radii values were taken from the following source: 'Molecular Double-Bond Covalent Radii for Elements Li–E112', 2009, Pyykkö and Atsumi, doi: 10.1002/chem.200901472
- covariance() - Method in class com.actelion.research.calc.Matrix
-
Generate a covariance matrix, each column contains values of a pulling.
- covrad - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- CovRad - Class in com.actelion.research.chem.forcefield.mmff.table
-
CovRad table, used in the bond stretch empirical calculations of 'kb' and 'r0'.
- CovRad(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.CovRad
- cParentSpecialColumnTypes - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cParity1And - Static variable in class com.actelion.research.chem.Canonizer
- cParity1Or - Static variable in class com.actelion.research.chem.Canonizer
- cParity2And - Static variable in class com.actelion.research.chem.Canonizer
- cParity2Or - Static variable in class com.actelion.research.chem.Canonizer
- cPointedHandCursor - Static variable in class com.actelion.research.util.CursorHelper
- cPointerCursor - Static variable in class com.actelion.research.util.CursorHelper
- cPolarAtomTypeName - Static variable in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- cPropertiesAll - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomAllylic - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomAromatic - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomCharged - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomRingCount - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomRingSize - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomSmallRing - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomStabilized - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesBasicType - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomAromatic - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomNeighbours - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomNeighboursExact - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomSmallRing - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomStabilized - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomType - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomTypeSimple - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnBondOrder - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cPropertiesForCLogP - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesForCLogPCharges - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesForMutator - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesForSolubility - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cPSAUnknown - Static variable in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- cPSAUnknown - Static variable in class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
- cRangeNotAvailable - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cRangeSeparation - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- crd(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the CRD type of an atom given its MMFF type.
- cReactionHiliteModeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionHiliteModeMapping - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionHiliteModeNone - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionHiliteModeReactionCenter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionHiliteModeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionPartDelimiter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionPartProducts - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionPartReactants - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionPartReaction - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- create() - Method in class com.actelion.research.chem.chemicalspaces.ChemicalSpaceCreator
- create() - Static method in class com.actelion.research.gui.hidpi.ScaledEditorKit
- create() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- create() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- create(Conformer, int[], String) - Static method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
- create(Conformer, int, int[], Coordinates, double) - Static method in class com.actelion.research.chem.docking.scoring.chemscore.MetalTerm
- create(Conformer, Conformer, int, int) - Static method in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- create(Conformer, Conformer, int, int, int[], double) - Static method in class com.actelion.research.chem.docking.scoring.chemscore.SimpleMetalTerm
- create(Conformer, Conformer, int, int, int[], int[]) - Static method in class com.actelion.research.chem.docking.scoring.idoscore.InteractionTerm
- create(Conformer, Conformer, int, int, int, boolean, boolean, int[], double) - Static method in class com.actelion.research.chem.docking.scoring.chemscore.HBTerm
- create(Conformer, Conformer, int, int, Map<String, Double>) - Static method in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- create(DescriptorHandler<T, StereoMolecule>, String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- create(IDCodeParser, DescriptorHandlerFlexophore, String) - Static method in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- create(Reaction) - Static method in class com.actelion.research.chem.chemicalspaces.synthon.SynthonCreator
-
only works for reactions with a single product
- create(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- create(StereoMolecule, int) - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
-
Creates a list with ModelExhaustiveStatistics.
- create(StereoMolecule, StereoMolecule, TransformationSequence) - Static method in class com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImageCreator
- create(IDCodeCoord) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- create(String) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandlerFactory
- create(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- create(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
- create(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- create(String) - Method in interface com.actelion.research.chem.descriptor.ISimilarityHandlerFactory
- create(String, String) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- create(List<MultCoordFragIndex>, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- create(List<PPGaussian>, Coordinates) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleCreator
- create(List<double[]>) - Static method in class com.actelion.research.calc.MatrixFunctions
-
List is already used as a constructor for Matrix.
- CREATE_PSEUDO_STEREO_GROUPS - Static variable in class com.actelion.research.chem.Canonizer
- CREATE_SYMMETRY_RANK - Static variable in class com.actelion.research.chem.Canonizer
- createAlignmentSolutions(List<? extends ShapeVolume>, List<? extends ShapeVolume>, double, boolean, boolean, boolean) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
- createArrow(Rectangle2D) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createAtomPropertiesDialog(StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createAtomQueryFeatureDialog(StereoMolecule, int, boolean) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createBarycenter(Coordinates...) - Static method in class com.actelion.research.chem.Coordinates
- createBondFeaturesDialog(StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createBonds(StereoMolecule, boolean, Map<Integer, String>) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
-
Calculates the bonds of a molecule by checking the distance between all atoms.
- createBrushIndirect(int, Color, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- createBrushIndirect(int, Color, int) - Method in class com.actelion.research.gui.wmf.WMF
- createCache(String[], String, int, boolean, int, RigidFragmentProvider) - Static method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
This is a helper method to generate a custom cache and optionally a set of cache files from one or more compound files.
- createCanonicalOrientation(Conformer) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- createCanonicalOrientation(Conformer) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- createCheckBox(String) - Method in interface com.actelion.research.gui.generic.GenericDialog
- createCheckBox(String) - Method in class com.actelion.research.gui.swing.SwingDialog
- createColor(double, double, double, double) - Method in class com.actelion.research.share.gui.DrawConfig
- createColor(long) - Static method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- createColor(Color, float) - Static method in class com.actelion.research.util.ColorHelper
-
Creates a new color with the hue taken from color
c
, but adjusted in brightness to match the desired perceived brightness. - createColor(Color, int) - Static method in class com.actelion.research.gui.hidpi.ColorUtils
- createComboBox() - Method in interface com.actelion.research.gui.generic.GenericDialog
- createComboBox() - Method in class com.actelion.research.gui.swing.SwingDialog
- createCursor(int) - Static method in class com.actelion.research.util.CursorHelper
- createDefaultDocument() - Method in class com.actelion.research.gui.hidpi.ScaledEditorKit
- createDepictor(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- createDepictor(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.Model
- createDepictor(StereoMolecule, boolean, DrawConfig) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- createDescriptor(ConformerSet) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- createDescriptor(Reaction) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
-
This descriptor contains non-hashed counts of predefined overlapping small fragments of organic functional groups.
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
-
This descriptor requires proper up/down bonds, because it encodes stereo parities.
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
-
This descriptor requires proper up/down bonds, because it encodes stereo parities.
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
-
This descriptor requires proper up/down bonds, because it encodes stereo parities.
- createDescriptor(StereoMolecule) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
-
the ShapeDescriptor consists of a whole ensemble of MolecularVolumes (MolecularGaussians), obtained from a conformational search algorithm
- createDescriptor(Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- createDescriptor(U) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- createDescriptor(U) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- createDescriptorSingleConf(ConformerSet) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- createDescriptorSingleConf(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- createDialog(String, DialogEventConsumer) - Method in interface com.actelion.research.gui.generic.GenericDialogHelper
- createDialog(String, DialogEventConsumer) - Method in class com.actelion.research.gui.swing.SwingDialogHelper
- createDisabledIcon(String, int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- createDrawDialog() - Method in class com.actelion.research.gui.JEditableStructureView
- createDrawDialog(String, Reaction) - Method in class com.actelion.research.gui.JEditableChemistryView
- createDrawDialog(String, StereoMolecule[]) - Method in class com.actelion.research.gui.JEditableChemistryView
- createExtendedDepictor() - Method in class com.actelion.research.share.gui.editor.Model
- createFileFilter(int, boolean) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- createFont(int, int, int, int, int, boolean, boolean, boolean, byte, byte, byte, byte, byte, String) - Method in class com.actelion.research.gui.wmf.MetaFile
- createFont(int, int, int, int, int, boolean, boolean, boolean, byte, byte, byte, byte, byte, String) - Method in class com.actelion.research.gui.wmf.WMF
- createFont(Font, int, boolean, boolean) - Method in class com.actelion.research.gui.wmf.MetaFile
- createFont(Font, int, boolean, boolean) - Method in class com.actelion.research.gui.wmf.WMF
- createFragment(StereoMolecule, int[], int) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
- createFromDataFlavor(DataFlavor, Object) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- createFromDataFlavor(DataFlavor, Object) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- createFromDataFlavor(DataFlavor, Object) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- createFromGivenConformation(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- createGenericTautomer() - Method in class com.actelion.research.chem.TautomerHelper
-
If no tautomers can be formed then a copy of the original molecule is returned.
- createHandles() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- createHTMLView(JComponent, String) - Static method in class com.actelion.research.gui.hidpi.ScaledHTML
-
Create an html renderer for the given component and string of html.
- createIcon(String, int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- createIdentifiedObject(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- createImage(String) - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- createImage(String) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
Creates an image from the fileName.
- createImage(String) - Static method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- createIndex(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- createIndexTables() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- createInitialOrientation(Conformer) - Static method in class com.actelion.research.chem.docking.DockingUtils
- createInstance(String) - Static method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- createLabel(String) - Method in interface com.actelion.research.gui.generic.GenericDialog
- createLabel(String) - Method in class com.actelion.research.gui.swing.SwingDialog
- createLaFCompatibleImage(String) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
Creates an image from the fileName.
- createLinearLabelList(double, double) - Static method in class com.actelion.research.util.ScaleLabelCreator
-
Creates a list of scale labels with their relative positions for a linear numerical scale with given numerical value range.
- createLogarithmicLabelList(double, double) - Static method in class com.actelion.research.util.ScaleLabelCreator
-
Creates a list of scale labels with their relative positions for a logarithmical numerical scale with given numerical value range.
- createLongIndex(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- createModel(ModelXYIndex) - Method in class com.actelion.research.calc.regression.gaussianprocess.GaussianProcessRegression
- createModel(ModelXYIndex) - Method in interface com.actelion.research.calc.regression.ICalculateModel
- createModel(ModelXYIndex) - Method in class com.actelion.research.calc.regression.knn.KNNRegression
- createModel(ModelXYIndex) - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- createModel(ModelXYIndex) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- createModel(ModelXYIndex) - Method in class com.actelion.research.calc.regression.median.MedianRegression
- createModel(ModelXYIndex) - Method in class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkRegression
- createModel(ModelXYIndex) - Method in class com.actelion.research.calc.regression.randomforest.RandomForestRegression
- createModel(ModelXYIndex) - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- createModel(ModelXYIndex) - Method in class com.actelion.research.calc.regression.svm.SVMRegression
- createMolecule(int, int) - Method in class com.actelion.research.chem.StereoMolecule
- createMolFromSketchBuffer(StereoMolecule, byte[]) - Static method in class com.actelion.research.util.Sketch
- createMolFromSketchFile(StereoMolecule, String) - Static method in class com.actelion.research.util.Sketch
- createMostCentralRingSystem(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
Modifies mol in-place to represent the most central ring system of the original mol.
- createMultipleConformations(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
-
Conformation generator of Thomas Sander
- createMurckoScaffold(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
Modifies mol in-place to represent the Murcko scaffold from the original mol.
- createNodeIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
This index is used to track the fate of the nodes MvK 17.07.2007
- createObject() - Method in class com.actelion.research.util.graph.complete.FactorySolution
- createObject() - Method in interface com.actelion.research.util.graph.complete.IFactory
- createObject(String) - Static method in class com.actelion.research.chem.DrawingObjectFactory
- createParser(String) - Static method in class com.actelion.research.chem.io.CompoundFileParser
-
Creates the proper parser for the given type of compound file (currently SD or DWAR).
- createPatternBrush(int[], int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- createPatternBrush(int[], int, int) - Method in class com.actelion.research.gui.wmf.WMF
- createPenIndirect(int, int, Color) - Method in class com.actelion.research.gui.wmf.MetaFile
- createPenIndirect(int, int, Color) - Method in class com.actelion.research.gui.wmf.WMF
- createPolygon() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createPopupMenu(DialogEventConsumer) - Method in interface com.actelion.research.gui.generic.GenericDialogHelper
- createPopupMenu(DialogEventConsumer) - Method in class com.actelion.research.gui.swing.SwingDialogHelper
- createPopupMenu(String, boolean) - Method in interface com.actelion.research.gui.dock.PopupProvider
- createPreview(Dockable, Dockable, int, JDockingPanel) - Method in class com.actelion.research.gui.dock.GhostPreview
- createReactantToProductAtomMap(int[], int[]) - Method in class com.actelion.research.chem.reaction.mapping.MappingScorer
- createReactionFromSketchBuffer(Reaction, byte[]) - Static method in class com.actelion.research.util.Sketch
- createReactionFromSketchFile(Reaction, String) - Static method in class com.actelion.research.util.Sketch
- createReactionSmiles(Reaction) - Static method in class com.actelion.research.chem.IsomericSmilesCreator
- createRegressionMethod(ParameterRegressionMethod) - Static method in class com.actelion.research.calc.regression.RegressionMethodContainer
-
Sets the parameter
- createRegressionMethod(String) - Static method in class com.actelion.research.calc.regression.RegressionMethodContainer
- createResidue(Map<String, AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.converter.AminoAcidLabeled
- createSketchFromMol(Molecule) - Static method in class com.actelion.research.util.Sketch
- createSketchFromReaction(Reaction) - Static method in class com.actelion.research.util.Sketch
- createSketchFromReactionOLd(Reaction) - Static method in class com.actelion.research.util.Sketch
- createSmarts(StereoMolecule) - Static method in class com.actelion.research.chem.IsomericSmilesCreator
-
Convenience method to generate a canonical and isomeric SMILES from a given molecule.
- createSmiles(StereoMolecule) - Static method in class com.actelion.research.chem.IsomericSmilesCreator
-
Convenience method to generate a canonical and isomeric SMILES from a given molecule.
- createStateInfo() - Method in class com.actelion.research.gui.dock.TreeRoot
- createTextField(int, int) - Method in interface com.actelion.research.gui.generic.GenericDialog
- createTextField(int, int) - Method in class com.actelion.research.gui.swing.SwingDialog
- createTorsionSet(int[], int[]) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
Creates a new TorsionSet object from a torsion index array.
- createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
Provide the next set of torsion angles using a specific strategy and considering, which angle combinations were already tried, which had failed, and (depending on the strategy) considering the likelyhoods of particular torsions.
- createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyAdaptiveRandom
- createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyLikelySystematic
-
Determine the next likely set of torsion angles and return the TorsionSet containing an array of indexes referring to the torsion value in the RotatableBond and containing the contribution of this conformer to all non colliding ones.
- createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
-
Build a new set of torsion angles by pure or biased random picking.
- createVisualDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
-
This descriptor contains the molecule used for construction.
- createVisualDescriptor(StereoMolecule) - Method in interface com.actelion.research.chem.descriptor.flexophore.IDescriptorHandlerFlexophore
- createVisualDescriptorSingleConf(ConformerSet) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- creatorMolDistHistViz - Variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- CreatorMolDistHistViz - Class in com.actelion.research.chem.descriptor.flexophore.generator
-
CreatorMolDistHistViz
- CreatorMolDistHistViz() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- cRiskNameA - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskNameN - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypeIrritant - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypeMutagenic - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypeReproductiveEffective - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypes - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypeTumorigenic - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- crop(Molecule3D, Coordinates, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- cropLigand(Molecule3D, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- cross(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- cross(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Computes the vector cross product between this vector and that vector.
- CROSSHAIR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- cRoundedMass - Static variable in class com.actelion.research.chem.Molecule
- cSelectRectCursor - Static variable in class com.actelion.research.util.CursorHelper
- cSelectRectPlusCursor - Static variable in class com.actelion.research.util.CursorHelper
- cSolubilityUnknown - Static variable in class com.actelion.research.chem.prediction.SolubilityPredictor
- cStringTypeDouble - Static variable in class com.actelion.research.chem.prediction.ParameterizedStringList
- cStringTypeIDCode - Static variable in class com.actelion.research.chem.prediction.ParameterizedStringList
- cStringTypeText - Static variable in class com.actelion.research.chem.prediction.ParameterizedStringList
- cStructureHiliteModeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cStructureHiliteModeCurrentRow - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cStructureHiliteModeFilter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cStructureHiliteModeNone - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cStructureHiliteModeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeMaximum - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeMean - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeMedian - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeMinimum - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeNormal - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeSum - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSuperposeAlignValueShape - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSuperposeValueReferenceRow - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- Csv - Class in com.actelion.research.chem.forcefield.mmff
-
Basic CSV parser.
- Csv() - Constructor for class com.actelion.research.chem.forcefield.mmff.Csv
- cTemplateTagName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextCursor - Static variable in class com.actelion.research.util.CursorHelper
- cTextExclusionTypeContains - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextExclusionTypeEndsWith - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextExclusionTypeEquals - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextExclusionTypeRegEx - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextExclusionTypeStartsWith - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextMultipleCategories - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cThumbNailExtension - Static variable in class com.actelion.research.gui.JImagePanel
- cTool3Ring - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cTool3Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cTool4Ring - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cTool4Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cTool5Ring - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cTool5Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cTool6Ring - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cTool6Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cTool7Ring - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cTool7Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAromRing - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAromRing - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomBr - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomBr - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomC - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomC - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomCl - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomCl - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomF - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomF - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomH - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomH - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomI - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomI - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomN - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomN - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomO - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomO - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomOther - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomOther - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomP - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomP - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomS - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomS - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolAtomSi - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolAtomSi - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolChain - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolChain - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolDelete - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolDelete - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolDownBond - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolDownBond - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolESR - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolESR - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolESRAbs - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolESRAbs - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolESRAnd - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolESRAnd - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolESROr - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolESROr - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolLassoPointer - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolLassoPointer - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolMapper - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolMapper - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolNegCharge - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolNegCharge - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolPosCharge - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolPosCharge - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolStdBond - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolStdBond - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolText - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolText - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolUnknownParity - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolUnknownParity - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolUpBond - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolUpBond - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cToolZoom - Static variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- cToolZoom - Static variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- cubicDistance(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- cubicDistance(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- cubicDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- cUnknownRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- CursorHelper - Class in com.actelion.research.util
- CursorHelper() - Constructor for class com.actelion.research.util.CursorHelper
- cut(double[], int, int) - Static method in class com.actelion.research.util.ArrayUtils
-
Resize an array of Object
- CUT_LEFT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- CUT_NONE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- CUT_RIGHT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- CutAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/16/13 Time: 3:43 PM
- CutAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CutAction
- CUTOFF_ANGLE - Static variable in class com.actelion.research.chem.alignment3d.transformation.ExponentialMap
- CUTOFF_RADIUS - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- cVersion - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- cViewConfigTagName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cViewNameEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cViewNameStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cZoomCursor - Static variable in class com.actelion.research.util.CursorHelper
D
- d - Variable in class com.actelion.research.util.LittleEndianDataInputStream
- d(int, int) - Method in class smile.clustering.linkage.Linkage
-
Returns the distance/dissimilarity between two clusters/objects, which are indexed by integers.
- d(T, T) - Method in interface smile.math.distance.Distance
-
Returns the distance measure between two objects.
- D - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- da(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'DA' from the table.
- da1 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- da2 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- daeps - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- darad - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- darker(Color, float) - Static method in class com.actelion.research.util.ColorHelper
-
Creates a new
Color
that is a darker version of thisColor
. - data - Variable in class smile.data.Dataset
-
The data objects.
- data() - Method in class smile.data.Dataset
-
Returns the data set.
- data() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the array of storing the matrix.
- data() - Method in class smile.math.matrix.JMatrix
- DATA_FORMATS - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DatabaseReaction - Class in com.actelion.research.chem.reaction
- DatabaseReaction() - Constructor for class com.actelion.research.chem.reaction.DatabaseReaction
- DataProcessor - Class in com.actelion.research.calc
- DataProcessor() - Constructor for class com.actelion.research.calc.DataProcessor
- Dataset<E> - Class in smile.data
-
A set of data objects.
- Dataset() - Constructor for class smile.data.Dataset
-
Constructor.
- Dataset(String) - Constructor for class smile.data.Dataset
-
Constructor.
- Dataset(String, Attribute) - Constructor for class smile.data.Dataset
-
Constructor.
- Dataset(Attribute) - Constructor for class smile.data.Dataset
-
Constructor.
- DATASET_HAS_NO_RESPONSE - Static variable in class smile.data.Dataset
- date(int) - Method in class smile.data.AttributeDataset.Row
-
Returns a date element.
- DATE - smile.data.Attribute.Type
-
Date attribute.
- DATE_FORMAT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- DateAnalysis - Class in com.actelion.research.util
- DateAnalysis() - Constructor for class com.actelion.research.util.DateAnalysis
- DateAttribute - Class in smile.data
-
Data attribute.
- DateAttribute(String) - Constructor for class smile.data.DateAttribute
-
Constructor.
- DateAttribute(String, double) - Constructor for class smile.data.DateAttribute
-
Constructor.
- DateAttribute(String, String, double) - Constructor for class smile.data.DateAttribute
-
Constructor.
- DateAttribute(String, String, double, String) - Constructor for class smile.data.DateAttribute
-
Constructor.
- DateAttribute(String, String, String) - Constructor for class smile.data.DateAttribute
-
Constructor.
- Datum<T> - Class in smile.data
-
An object of generic datum and optional weight.
- Datum(T) - Constructor for class smile.data.Datum
-
Constructor.
- Datum(T, double) - Constructor for class smile.data.Datum
-
Constructor.
- Datum(T, double, double) - Constructor for class smile.data.Datum
-
Constructor.
- debug - Static variable in class com.actelion.research.chem.MolfileParser
- debug - Static variable in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- debug - Static variable in class com.actelion.research.gui.dnd.ReactionDropAdapter
- DEBUG - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- DEBUG - Static variable in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- DEBUG - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a binary fingerprint from a String into an int[].
- decode(byte[]) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- decode(byte[]) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- decode(byte[]) - Static method in class com.actelion.research.util.Base64
-
Low-level access to decoding ASCII characters in the form of a byte array.
- decode(byte[], byte[], byte[], String, byte[], boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
- decode(byte[], int, int, int) - Static method in class com.actelion.research.util.Base64
-
Low-level access to decoding ASCII characters in the form of a byte array.
- decode(String) - Static method in class com.actelion.research.chem.alignment3d.transformation.Rotation
- decode(String) - Static method in class com.actelion.research.chem.alignment3d.transformation.Scaling
- decode(String) - Static method in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- decode(String) - Static method in class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- decode(String) - Static method in class com.actelion.research.chem.alignment3d.transformation.Translation
- decode(String) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- decode(String) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a binary fingerprint from a String into an int[].
- decode(String) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- decode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- decode(String) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- decode(String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- decode(String) - Static method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
- decode(String) - Method in class com.actelion.research.chem.phesa.AtomicGaussian
- decode(String) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- decode(String) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- decode(String) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- decode(String) - Static method in class com.actelion.research.chem.phesa.ShapeVolume
- decode(String) - Static method in class com.actelion.research.util.Base64
-
Decodes data from Base64 notation, automatically detecting gzip-compressed data and decompressing it.
- decode(String) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
- decode(String) - Static method in class com.actelion.research.util.EncoderIntegerNumbers
- decode(String, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
- decode(String, boolean, Reaction) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class and are passed OBJECT_DELIMITER-delimited within one string.
- decode(String, int) - Static method in class com.actelion.research.util.Base64
-
Decodes data from Base64 notation, automatically detecting gzip-compressed data and decompressing it.
- decode(String, int, Reaction) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a Reaction object by interpreting a reaction string encoded by this class.
- decode(String, StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- decode(String, StereoMolecule) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- decode(String, String, String, String, String, boolean, Reaction) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
- DECODE - Static variable in class com.actelion.research.util.Base64
-
Specify decoding in first bit.
- decodeCatalysts(byte[]) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Generates an array of all catalysts of the encoded reaction string as bytes.
- decodeCoordsOnly(String, MolecularVolume) - Static method in class com.actelion.research.chem.phesa.MolecularVolume
- decodeCounts(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a list of fragment/has-value counts from an encoded byte sequence into a byte[].
- decodeCounts(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a list of fragment/has-value counts from an encoded String.
- decodeFileToFile(String, String) - Static method in class com.actelion.research.util.Base64
-
Reads infile and decodes it to outfile.
- decodeFromFile(String) - Static method in class com.actelion.research.util.Base64
-
Convenience method for reading a base64-encoded file and decoding it.
- decodeFull(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.MolecularVolume
- decodeHistograms(String, MolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
- decodeIntArray(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes an int[] without upper limit.
- decodeIntArray(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes an int[] without upper limit.
- decodeLong(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a binary fingerprint from a String into a long[].
- decodeLong(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a binary fingerprint from a String into a long[].
- decodeMolecules(byte[], byte[], byte[], boolean, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Generates an array of all reactants and/or products of the encoded reaction string as bytes.
- decodeMolecules(String, boolean, boolean, boolean, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Generates an array of all reactants and/or products of the encoded reaction string as bytes.
- decodeNodes(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- decodePairs(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes pairs of identifying integer with corresponding count values in the form of an int[n][2], where n is the number of pairs, index=0 refers to the ID value and index=1 refers to the count value.
- decodePairs(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes pairs of identifying integer with corresponding count values in the form of an int[n][2], where n is the number of pairs, index=0 refers to the ID value and index=1 refers to the count value.
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.ARegressionMethod
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.knn.ParameterKNN
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.median.ParameterMedian
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
-
Decodes the properties to the needed variables.
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- decodeProperties2Parameter() - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- decodeToFile(String, String) - Static method in class com.actelion.research.util.Base64
-
Convenience method for decoding data to a file.
- decodeToObject(String) - Static method in class com.actelion.research.util.Base64
-
Attempts to decode Base64 data and deserialize a Java Object within.
- decodeToObject(String, int, ClassLoader) - Static method in class com.actelion.research.util.Base64
-
Attempts to decode Base64 data and deserialize a Java Object within.
- deepCopy(ModelXY) - Method in class com.actelion.research.util.datamodel.ModelXY
- def - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Def - Class in com.actelion.research.chem.forcefield.mmff.table
-
Equivalence table, corresponds to MMFFDEF.PAR parameters table provided in the MMFF literature.
- Def(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Def
- DEFAULT - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- DEFAULT_BG - Static variable in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- DEFAULT_BOND_LENGTH - Static variable in class com.actelion.research.chem.conf.BondLengthSet
- DEFAULT_BOND_STDDEV - Static variable in class com.actelion.research.chem.conf.BondLengthSet
- DEFAULT_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- DEFAULT_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DEFAULT_ELEM_WIDTH - Static variable in class com.actelion.research.chem.SVGDepictor
- DEFAULT_IMAGE_HEIGHT - Static variable in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- DEFAULT_IMAGE_WIDTH - Static variable in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- DEFAULT_MERGE_SPAN - Static variable in class com.actelion.research.chem.conf.TorsionDB
- DEFAULT_MODEL - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- DEFAULT_PITCH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DEFAULT_QUALITY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DEFAULT_SIZE - Static variable in class com.actelion.research.chem.TextDrawingObject
- DEFAULT_STYLE - Static variable in class com.actelion.research.chem.TextDrawingObject
- DEFAULT_VAL - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- DefaultCompoundCollectionModel<T> - Class in com.actelion.research.gui
- DefaultCompoundCollectionModel() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel
- DefaultCompoundCollectionModel.IDCode - Class in com.actelion.research.gui
-
This version of the DefaultCompoundCollectionModel collects molecules as IDCodes.
- DefaultCompoundCollectionModel.IDCodeWithName - Class in com.actelion.research.gui
-
This version of the DefaultCompoundCollectionModel collects molecules as String[2] with idcodes & idcoords (index 0) and molecule name (index 1).
- DefaultCompoundCollectionModel.Molecule - Class in com.actelion.research.gui
-
This version of the DefaultCompoundCollectionModel collects molecules as StereoMolecules.
- DefaultCompoundCollectionModel.Native - Class in com.actelion.research.gui
-
This version of the DefaultCompoundCollectionModel collects IDCodes and StereoMolecules without conversion into their native type.
- DEG2RAD - Static variable in class com.actelion.research.chem.forcefield.mmff.Constants
- degree - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- degree(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns the total number of atoms connected to an atom, including implicit and explicit hydrogens.
- degree(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Charge
- DEGREE_ANALYTICALLY_PARAMETER_CALC - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- Delegator<T> - Class in com.actelion.research.share.gui
- Delegator(T) - Constructor for class com.actelion.research.share.gui.Delegator
- DeleteAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 3/26/13 Time: 4:15 PM
- DeleteAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.DeleteAction
- deleteAtom(int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteAtom(int) - Method in class com.actelion.research.chem.Molecule3D
-
High level function for constructing a molecule.
- deleteAtomOrBond(double, double) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteAtoms(boolean[]) - Method in class com.actelion.research.chem.conf.Conformer
-
Removes atoms Coordinates objects from those atoms that are marked in the given array.
- deleteAtoms(boolean[]) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteAtoms(int[]) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteAtoms(List<Integer>) - Method in class com.actelion.research.chem.Molecule3D
- deleteBond(int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteBond(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- deleteBondAndSurrounding(int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteHandles() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- deleteHydrogens(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- deleteMarkedAtomsAndBonds() - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteMolecule() - Method in class com.actelion.research.chem.Molecule
-
Deprecated.
- deleteMolecule(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.Model
- deleteObject(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- deleteObject(int) - Method in class com.actelion.research.gui.wmf.WMF
- deleteSelectedAtoms() - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- DELIMITER - Static variable in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- DELIMITER_END - Static variable in class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- DELIMITER_START - Static variable in class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- DELTA_BONDS - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- DenseMatrix - Interface in smile.math.matrix
-
An abstract interface of dense matrix.
- DENSITY_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- Depictor - Class in com.actelion.research.chem
-
Deprecated.
- Depictor(StereoMolecule) - Constructor for class com.actelion.research.chem.Depictor
-
Deprecated.
- Depictor(StereoMolecule, int) - Constructor for class com.actelion.research.chem.Depictor
-
Deprecated.
- Depictor2D - Class in com.actelion.research.chem
- Depictor2D(StereoMolecule) - Constructor for class com.actelion.research.chem.Depictor2D
- Depictor2D(StereoMolecule, int) - Constructor for class com.actelion.research.chem.Depictor2D
- DepictorLine() - Constructor for class com.actelion.research.chem.AbstractDepictor.DepictorLine
- DepictorLine(double, double, double, double) - Constructor for class com.actelion.research.chem.AbstractDepictor.DepictorLine
- DepictorTransformation - Class in com.actelion.research.chem
- DepictorTransformation() - Constructor for class com.actelion.research.chem.DepictorTransformation
- DepictorTransformation(double, double, double) - Constructor for class com.actelion.research.chem.DepictorTransformation
- DepictorTransformation(DepictorTransformation) - Constructor for class com.actelion.research.chem.DepictorTransformation
- DepictorTransformation(Rectangle2D.Double, Rectangle2D.Double, double, int) - Constructor for class com.actelion.research.chem.DepictorTransformation
- derivative() - Method in class com.actelion.research.util.FastSpline
-
Returns the derivative of the polynomial spline function as a PolynomialSplineFunction
- derivative() - Method in class com.actelion.research.util.FastSpline.Polynome
- DESCRIBE_ALL - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- DESCRIBE_MAPPED - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Only mapped atoms are described.
- description - Variable in class smile.data.Dataset
-
The optional detailed description of dataset.
- description - Variable in class smile.data.Datum
-
Optional detailed description.
- DESCRIPTOR_BINARY_SKELETONSPHERES - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_CenteredSkeletonFragments - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_END - Static variable in class com.actelion.research.chem.AbstractDrawingObject
- DESCRIPTOR_EXTENDED_LIST - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_FFP512 - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_Flexophore - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_FULL_FRAGMENT_SET - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_HashedCFp - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_IntegerVector - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_LIST - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_MAX_COMMON_SUBSTRUCT - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_OrganicFunctionalGroups - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_PFP512 - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_PhysicoChemicalProperties - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_PTREE - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_ReactionFP - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_ShapeAlign - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_ShapeAlignSingleConf - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_SkeletonSpheres - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_START - Static variable in class com.actelion.research.chem.AbstractDrawingObject
- DESCRIPTOR_SUBSTRUCT_QUERY_IN_BASE - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_TopoPPHistDist - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_TYPE - Static variable in class com.actelion.research.chem.AbstractDrawingObject
- DESCRIPTOR_TYPE_MOLECULE - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_TYPE_REACTION - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_TYPE_UNKNOWN - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DescriptorConstants - Interface in com.actelion.research.chem.descriptor
- DescriptorEncoder - Class in com.actelion.research.chem.descriptor
-
DescriptorEncoder encodes int[] based descriptors into byte arrays that may be used to instantiate Strings
- DescriptorEncoder() - Constructor for class com.actelion.research.chem.descriptor.DescriptorEncoder
- DescriptorHandler<T,U> - Interface in com.actelion.research.chem.descriptor
-
DescriptorHandler is the base Interface for any molecular descriptor handling StereoMolecules or Reactions
- DescriptorHandlerFactory - Interface in com.actelion.research.chem.descriptor
- DescriptorHandlerFFP512 - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerFFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- DescriptorHandlerFlexophore - Class in com.actelion.research.chem.descriptor
-
DescriptorHandlerFlexophore
- DescriptorHandlerFlexophore() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- DescriptorHandlerFlexophore(int, int, double, double, boolean) - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- DescriptorHandlerFlexophore(String) - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- DescriptorHandlerFunctionalGroups - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerFunctionalGroups() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- DescriptorHandlerHashedCFp - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerHashedCFp() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- DescriptorHandlerIntVector<U> - Class in com.actelion.research.chem.descriptor
-
This is a descriptor handler, where the input object is an integer array that typically represents counts of some sort.
- DescriptorHandlerIntVector() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- DescriptorHandlerLongCFP - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerLongCFP() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- DescriptorHandlerLongFFP512 - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerLongFFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- DescriptorHandlerLongPFP512 - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerLongPFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- DescriptorHandlerPFP512 - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerPFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- DescriptorHandlerPTree - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- DescriptorHandlerPTree() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- DescriptorHandlerReactionFP - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerReactionFP() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- DescriptorHandlerShape - Class in com.actelion.research.chem.phesa
- DescriptorHandlerShape() - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(boolean) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(boolean, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(boolean, int, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(int, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShapeOneConf - Class in com.actelion.research.chem.phesa
- DescriptorHandlerShapeOneConf() - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
- DescriptorHandlerShapeOneConf(double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
- DescriptorHandlerShapeOneConf(int, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
- DescriptorHandlerSkeletonSpheres - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerSkeletonSpheres() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- DescriptorHandlerStandard2DFactory - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerStandard2DFactory() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- DescriptorHandlerStandardFactory - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerStandardFactory() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
- DescriptorHelper - Class in com.actelion.research.chem.descriptor
- DescriptorHelper() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHelper
- DescriptorInfo - Class in com.actelion.research.chem.descriptor
- DescriptorInfo(String, String, String, int, boolean, boolean, boolean, boolean) - Constructor for class com.actelion.research.chem.descriptor.DescriptorInfo
- det() - Method in class com.actelion.research.calc.LUDecomposition
-
Determinant
- det() - Method in class com.actelion.research.calc.Matrix
-
Matrix determinant
- det() - Method in class smile.math.matrix.Cholesky
-
Returns the matrix determinant
- det() - Method in class smile.math.matrix.LU
-
Returns the matrix determinant
- detect() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
- detect() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargedGroupDetector
- detect() - Method in class com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector
- determineAromaticity(boolean[], boolean[], int[], boolean) - Method in class com.actelion.research.chem.RingCollection
- devide(double) - Method in class com.actelion.research.calc.Matrix
- devide(Matrix) - Method in class com.actelion.research.calc.Matrix
- devide(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- devide(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- devide(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- devideCols(Matrix) - Method in class com.actelion.research.calc.Matrix
- devideDivisorBigger(Matrix) - Method in class com.actelion.research.calc.Matrix
- devideRow(int, double) - Method in class com.actelion.research.calc.Matrix
- df(double) - Method in interface smile.math.DifferentiableFunction
-
Compute the value of the derivative function at x.
- DF_DOCKABLE_DEF - Static variable in class com.actelion.research.gui.dock.TransferableDockable
- DF_IDCODE - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_IDCODE - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_MDLMOLFILE - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_MDLMOLFILE - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_MDLMOLFILE - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DF_MDLMOLFILEV3 - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_MDLMOLFILEV3 - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_MDLMOLFILEV3 - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DF_REACTION_SMILES - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_SERIALIZED_MOLECULE - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_SERIALIZED_OBJECT - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_SERIALIZED_REACTION - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_SERIALIZEDMOLECULE - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DF_SERIALIZEDREACTANT - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DF_SERIALIZEDSTRUCTURETRANSFERDATA - Static variable in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- DF_SMILES - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_SMILES - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_SMILES - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- dfI2 - Static variable in class com.actelion.research.util.Formatter
- dfI3 - Static variable in class com.actelion.research.util.Formatter
- dfs(Molecule3D, int, Set<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- dfs(Molecule3D, int, Set<Integer>, int, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- dfsb - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Dfsb - Class in com.actelion.research.chem.forcefield.mmff.table
- Dfsb(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Dfsb
- diag() - Method in interface smile.math.matrix.Matrix
-
Returns the diagonal elements.
- diag(double[]) - Static method in interface smile.math.matrix.Matrix
-
Returns a square diagonal matrix with the elements of vector diag on the main diagonal.
- diagonalize() - Method in class com.actelion.research.calc.Matrix
- DialogEvent - Class in com.actelion.research.gui.editor
- DialogEvent(GenericComponent, int, int) - Constructor for class com.actelion.research.gui.editor.DialogEvent
- DialogEvent(GenericComponent, int, String) - Constructor for class com.actelion.research.gui.editor.DialogEvent
- DialogEventConsumer - Interface in com.actelion.research.gui.editor
- dialogEventHappened(DialogEvent) - Method in class com.actelion.research.gui.editor.AtomLabelDialogBuilder
- dialogEventHappened(DialogEvent) - Method in class com.actelion.research.gui.editor.AtomQueryFeatureDialogBuilder
- dialogEventHappened(DialogEvent) - Method in class com.actelion.research.gui.editor.BondQueryFeatureDialogBuilder
- dialogEventHappened(DialogEvent) - Method in interface com.actelion.research.gui.editor.DialogEventConsumer
- dialogEventHappened(DialogEvent) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- dialogEventHappened(DialogEvent) - Method in class com.actelion.research.gui.editor.TextDrawingObjectDialogBuilder
- DialogResult - Enum in com.actelion.research.share.gui
-
Return values from Dialog calls
- DiastereoIDTest - Class in com.actelion.research.chem.contrib
- DiastereoIDTest() - Constructor for class com.actelion.research.chem.contrib.DiastereoIDTest
- DiastereotopicAtomID - Class in com.actelion.research.chem.contrib
- DiastereotopicAtomID() - Constructor for class com.actelion.research.chem.contrib.DiastereotopicAtomID
- DIB_PAL_COLORS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DIB_RGB_COLORS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- difference(double, double) - Static method in class com.actelion.research.util.Angle
-
Determines the normalized difference between a2 and a1, i.e.
- difference(Angle, Angle) - Static method in class com.actelion.research.util.Angle
-
Determines the normalized difference between a2 and a1, i.e.
- DifferentiableFunction - Interface in smile.math
-
A differentiable function is a function whose derivative exists at each point in its domain.
- DifferentiableMultivariateFunction - Interface in smile.math
-
A differentiable function is a function whose derivative exists at each point in its domain.
- DIGITS - Static variable in class smile.math.Math
-
The number of digits (in radix base) in the mantissa.
- disableCollidingTorsionRules(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- disableIfColliding(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.TorsionRule
- disablePlaneRules() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- disableTorsionRules() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- displayURL(String) - Static method in class com.actelion.research.util.BrowserControl
-
Display a file in the system browser.
- DISPOSAL_LEAVE_AS_IS - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- DISPOSAL_RESTORE_TO_BACKGROUND - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- DISPOSAL_RESTORE_TO_PREVIOUS - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- DISPOSAL_TO_BE_DEFINED - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- DISPOSAL_UNSPECIFIED - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- dispose() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- dispose() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- dispose() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- disposeDialog() - Method in interface com.actelion.research.gui.generic.GenericDialog
- disposeDialog() - Method in class com.actelion.research.gui.swing.SwingDialog
- dist() - Method in class com.actelion.research.chem.Coordinates
- dist(InteractionSimilarityTable.InteractionDescriptor) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- DIST_CUTOFF - Static variable in class com.actelion.research.chem.phesa.Gaussian3D
- distance(double[], double[]) - Static method in class smile.math.Math
-
The Euclidean distance.
- distance(float[], float[]) - Static method in class smile.math.Math
-
The Euclidean distance.
- distance(int[], int[]) - Static method in class smile.math.Math
-
The Euclidean distance.
- distance(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- distance(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Computes the euclidean distance between two Vector3s.
- distance(ByteVec, ByteVec, int) - Static method in class com.actelion.research.util.datamodel.ByteVec
- distance(DoubleVec, DoubleVec, int) - Static method in class com.actelion.research.util.DoubleVec
- distance(SparseArray, SparseArray) - Static method in class smile.math.Math
-
The Euclidean distance.
- Distance<T> - Interface in smile.math.distance
-
An interface to calculate a distance measure between two objects.
- DistanceMetrics - Class in com.actelion.research.calc.distance
-
DistanceMetrics
- DistanceMetrics() - Constructor for class com.actelion.research.calc.distance.DistanceMetrics
- DistanceRule - Class in org.openmolecules.chem.conf.so
- DistanceRule() - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
-
Creates a dummy rule to be neglected
- DistanceRule(int[], double, double, int) - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
- DistanceRule(int[], int[], double, double, int) - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
- DistanceRule(int[], int[], double, int) - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
-
Constructor for 2 bonds in between.
- distanceSquared(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- DistHist - Class in com.actelion.research.chem.descriptor.flexophore
- DistHist() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHist
- DistHist(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHist
- DistHist(DistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHist
- DistHistEncoder - Class in com.actelion.research.chem.descriptor.flexophore
- DistHistEncoder() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
- DistHistHelper - Class in com.actelion.research.chem.descriptor.flexophore
-
DistHistHelper
- DistHistHelper() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- DistHistHelper.RangeStatistics - Class in com.actelion.research.chem.descriptor.flexophore
- DISTINGUISH_RACEMIC_OR_GROUPS - Static variable in class com.actelion.research.chem.Canonizer
- distModel - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- distortion() - Method in class smile.clustering.CLARANS
-
Returns the distortion.
- distortion() - Method in class smile.clustering.KMeans
-
Returns the distortion.
- distribution - Variable in class smile.stat.distribution.Mixture.Component
-
The distribution of component.
- Distribution - Interface in smile.stat.distribution
-
Probability distribution of univariate random variable.
- distSq() - Method in class com.actelion.research.chem.Coordinates
- distSquareTo(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- div(double) - Method in interface smile.math.matrix.DenseMatrix
-
In place element-wise division A = A / x
- div(double) - Method in class smile.math.matrix.JMatrix
- div(double, DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
Element-wise addition C = A / x
- div(double, DenseMatrix) - Method in class smile.math.matrix.JMatrix
- div(double, JMatrix) - Method in class smile.math.matrix.JMatrix
- div(int, int, double) - Method in interface smile.math.matrix.DenseMatrix
-
A[i][j] /= x
- div(int, int, double) - Method in class smile.math.matrix.JMatrix
- div(Complex) - Method in class smile.math.Complex
-
Returns a / b.
- div(DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
In place element-wise division A = A / B A = A - B
- div(DenseMatrix) - Method in class smile.math.matrix.JMatrix
- div(DenseMatrix, DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
C = A / B
- div(DenseMatrix, DenseMatrix) - Method in class smile.math.matrix.JMatrix
- div(JMatrix) - Method in class smile.math.matrix.JMatrix
- div(JMatrix, JMatrix) - Method in class smile.math.matrix.JMatrix
- DiversitySelector - Class in com.actelion.research.chem
- DiversitySelector() - Constructor for class com.actelion.research.chem.DiversitySelector
- DiversitySelector.DiversitySelectorRecord - Class in com.actelion.research.chem
- DividerChangeListener - Interface in com.actelion.research.gui.dock
- dividerLocationChanged(TreeFork) - Method in interface com.actelion.research.gui.dock.DividerChangeListener
- DO_BREAK_LINES - Static variable in class com.actelion.research.util.Base64
-
Do break lines when encoding.
- dock(StereoMolecule) - Method in class com.actelion.research.chem.docking.shape.ShapeDocking
- dock(Dockable) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Dock the dockable to the center of the selected view.
- dock(Dockable, int) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Dock the Dockable at the given position to the selected view.
- dock(Dockable, String) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Dock the dockable either as a new root dockable or to the treeElement that contains dockable specified as part dockInfo.
- DOCK_BOTTOM - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- DOCK_CENTER - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- DOCK_LEFT - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- DOCK_RIGHT - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- DOCK_TOP - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- Dockable - Class in com.actelion.research.gui.dock
-
A lightweight component derived from JPanel that features certain subcomponents that make it look similar to a frame or internal frame.
- Dockable(JDockingPanel, JComponent, String, JToolBar) - Constructor for class com.actelion.research.gui.dock.Dockable
-
Constructs a
TitledComponent
with the specified title and content panel. - DOCKABLE_FLAVORS - Static variable in class com.actelion.research.gui.dock.TransferableDockable
- DockableHeader - Class in com.actelion.research.gui.dock
- DockableHeader(Dockable, String, JToolBar) - Constructor for class com.actelion.research.gui.dock.DockableHeader
- DockingEngine - Class in com.actelion.research.chem.docking
- DockingEngine(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.docking.DockingEngine
- DockingEngine(StereoMolecule, StereoMolecule, int, int, DockingEngine.ScoringFunction) - Constructor for class com.actelion.research.chem.docking.DockingEngine
- DockingEngine.DockingResult - Class in com.actelion.research.chem.docking
- DockingEngine.ScoringFunction - Enum in com.actelion.research.chem.docking
-
applies molecular docking to find the binding pose of a ligand molecule into the binding site of the protein nativeLigand: defines the location of the binding site this class is not thread safe! every thread requires it's own instance
- DockingFailedException - Exception in com.actelion.research.chem.docking
- DockingFailedException(String) - Constructor for exception com.actelion.research.chem.docking.DockingFailedException
- DockingResult(StereoMolecule, double, Map<String, Double>) - Constructor for class com.actelion.research.chem.docking.DockingEngine.DockingResult
- DockingUtils - Class in com.actelion.research.chem.docking
- dockMolecule(StereoMolecule) - Method in class com.actelion.research.chem.docking.DockingEngine
- doModal() - Method in interface com.actelion.research.share.gui.editor.dialogs.IDialog
- doModalAt(double, double) - Method in interface com.actelion.research.share.gui.editor.dialogs.IDialog
- DONOR - com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint.Functionality
- DONOR_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- DonorPoint - Class in com.actelion.research.chem.phesa.pharmacophore.pp
- DonorPoint(DonorPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- DonorPoint(StereoMolecule, int, int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- DONT_GUNZIP - Static variable in class com.actelion.research.util.Base64
-
Specify that gzipped data should not be automatically gunzipped.
- dot() - Method in class smile.regression.RegressionTree
-
Returns the graphic representation in Graphviz dot format.
- dot(double[], double[]) - Static method in class smile.math.Math
-
Returns the dot product between two vectors.
- dot(float[], float[]) - Static method in class smile.math.Math
-
Returns the dot product between two vectors.
- dot(int[], int[]) - Static method in class smile.math.Math
-
Returns the dot product between two vectors.
- dot(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- dot(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Computes the vector dot product between this vector and that vector.
- dot(SparseArray, SparseArray) - Static method in class smile.math.Math
-
Returns the dot product between two sparse arrays.
- DoubleArray - Class in com.actelion.research.util.datamodel
-
DoubleArray 26 Jun 2010 MvK: Start implementation
- DoubleArray() - Constructor for class com.actelion.research.util.datamodel.DoubleArray
- DoubleArray(double[]) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
-
Deep constructor
- DoubleArray(int) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
- DoubleArray(int[]) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
- DoubleArray(IntArray) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
- doubleArrayToByteArray(double[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- doubleArrayToString(double[]) - Static method in class com.actelion.research.calc.VectorSOM
- DoubleFormat - Class in com.actelion.research.util
- DoubleFormat() - Constructor for class com.actelion.research.util.DoubleFormat
- doubleToByteArray(double) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- doubleValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- DoubleVec - Class in com.actelion.research.util
- DoubleVec(double[]) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(double[], boolean) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(int) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(int[]) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(DoubleVec) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(DoubleVec, boolean) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(Vector<Double>) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(Vector<Double>, boolean) - Constructor for class com.actelion.research.util.DoubleVec
- DownBondAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:51 PM
- DownBondAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.DownBondAction
- DRAFT_QUALITY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- dragContinued(int) - Method in class com.actelion.research.gui.JMultiPanelView
- dragContinued(int) - Method in interface com.actelion.research.gui.MultiPanelDragListener
- dragDropEnd(DragSourceDropEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragDropEnd(DragSourceDropEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dragDropEnd(DragSourceDropEvent) - Method in class com.actelion.research.gui.JChemistryView
- dragEnter(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragEnter(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dragEnter(DragSourceDragEvent) - Method in class com.actelion.research.gui.JChemistryView
- dragEnter(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- dragEnter(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- dragExit(DragSourceEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragExit(DragSourceEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dragExit(DragSourceEvent) - Method in class com.actelion.research.gui.JChemistryView
- dragExit(DropTargetEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- dragExit(DropTargetEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- dragGestureRecognized(DragGestureEvent) - Method in class com.actelion.research.gui.JChemistryView
- DragGlassPane - Class in com.actelion.research.jfx.gui.chem
-
Project: User: rufenec Date: 2/21/14 Time: 6:14 PM
- DragGlassPane() - Constructor for class com.actelion.research.jfx.gui.chem.DragGlassPane
- dragIsValidAndStarts() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragOver(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragOver(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dragOver(DragSourceDragEvent) - Method in class com.actelion.research.gui.JChemistryView
- dragOver(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- dragOver(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- dragStarted(int, JMultiPanelTitle) - Method in class com.actelion.research.gui.JMultiPanelView
- dragStarted(int, JMultiPanelTitle) - Method in interface com.actelion.research.gui.MultiPanelDragListener
- draw() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- draw(GenericDrawContext, DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDrawingObject
- draw(GenericDrawContext, DepictorTransformation) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- draw(GenericDrawContext, DepictorTransformation) - Method in class com.actelion.research.chem.TextDrawingObject
- draw(IDrawContext) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- draw(IDrawContext, DepictorTransformation) - Method in class com.actelion.research.share.gui.Arrow
- draw(IDrawContext, DepictorTransformation) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- draw(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- DrawAction - Class in com.actelion.research.share.gui.editor.actions
-
Basic class which handles all actions which interact with the drawing surface
- DrawAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.DrawAction
- drawArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- DrawAreaEvent - Class in com.actelion.research.gui.editor
- DrawAreaEvent(Object, int, boolean) - Constructor for class com.actelion.research.gui.editor.DrawAreaEvent
- DrawAreaListener - Interface in com.actelion.research.gui.editor
- drawAtomHighlight(IDrawContext, StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- drawAtomKeyStrokes(IDrawContext, StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.AbstractDepictor
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor2D
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.SVGDepictor
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.gui.generic.GenericDepictor
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- drawBondHighlight(IDrawContext, StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- drawCenteredString(double, double, String) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- drawCenteredString(double, double, String) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- drawCircle(double, double, double) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- drawCircle(double, double, double) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- DrawConfig - Class in com.actelion.research.share.gui
-
User: rufenec Creation Date: 8/24/2016
- DrawConfig() - Constructor for class com.actelion.research.share.gui.DrawConfig
- drawDashedLine(double, double, double, double, int[]) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawDashedLine(double, double, double, double, int[]) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- drawDot(double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- drawDottedLine(double, double, double, double) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- drawDottedLine(double, double, double, double) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.AbstractDepictor
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor2D
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.SVGDepictor
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.gui.generic.GenericDepictor
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- drawDragImage(Transferable, int, int) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- drawDragImage(Transferable, int, int) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- drawGlyphVector(GlyphVector, float, float) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(double, double, Image) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- drawImage(double, double, Image) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- drawImage(BufferedImage, BufferedImageOp, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, AffineTransform, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- DrawingObject - Class in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 5/16/13 Time: 12:31 PM
- DrawingObject() - Constructor for class com.actelion.research.share.gui.editor.chem.DrawingObject
- DrawingObjectFactory - Class in com.actelion.research.chem
- DrawingObjectList - Class in com.actelion.research.chem
- DrawingObjectList() - Constructor for class com.actelion.research.chem.DrawingObjectList
- DrawingObjectList(DrawingObjectList) - Constructor for class com.actelion.research.chem.DrawingObjectList
- DrawingObjectList(String) - Constructor for class com.actelion.research.chem.DrawingObjectList
- drawLine(double, double, double, double) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- drawLine(double, double, double, double) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- drawLine(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawLine(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- drawLine(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawLine(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawPolygon(GenericPolygon) - Method in class com.actelion.research.chem.AbstractDepictor
- drawPolygon(GenericPolygon) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- drawPolygon(GenericPolygon) - Method in class com.actelion.research.chem.Depictor2D
- drawPolygon(GenericPolygon) - Method in class com.actelion.research.chem.SVGDepictor
- drawPolygon(GenericPolygon) - Method in class com.actelion.research.gui.generic.GenericDepictor
- drawPolygon(GenericPolygon) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- drawPolygon(GenericPolygon) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- drawPolygon(GenericPolygon) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- drawPolygon(IPolygon) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawPolygon(IPolygon) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- drawPolyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawPolyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawPressedButton(GenericDrawContext, int) - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- drawPressedButton(Graphics, int) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- drawPreview(Graphics2D) - Method in class com.actelion.research.gui.dock.GhostPreview
- drawRect(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawRect(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- drawRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawRectangle(double, double, double, double) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- drawRectangle(double, double, double, double) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- drawRenderableImage(RenderableImage, AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawRenderedImage(RenderedImage, AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawString(double, double, String) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- drawString(double, double, String) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- drawString(String, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- drawString(String, double, double) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- drawString(String, double, double) - Method in class com.actelion.research.chem.Depictor2D
- drawString(String, double, double) - Method in class com.actelion.research.chem.SVGDepictor
- drawString(String, double, double) - Method in class com.actelion.research.gui.generic.GenericDepictor
- drawString(String, double, double) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- drawString(String, float, float) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawString(String, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawString(String, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawString(AttributedCharacterIterator, float, float) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawString(AttributedCharacterIterator, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawString(AttributedCharacterIterator, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawText(String, double, double, boolean, boolean) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawText(String, double, double, boolean, boolean) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- dRdv(int, double[][]) - Method in class com.actelion.research.chem.alignment3d.transformation.RotationDerivatives
- driver1() - Static method in class com.actelion.research.util.BurtleHasher
- driver3() - Static method in class com.actelion.research.util.BurtleHasher
- drop(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- drop(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- dropActionChanged(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dropActionChanged(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dropActionChanged(DragSourceDragEvent) - Method in class com.actelion.research.gui.JChemistryView
- dropActionChanged(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- dropActionChanged(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- DruglikenessPredictor - Class in com.actelion.research.chem.prediction
- DruglikenessPredictor() - Constructor for class com.actelion.research.chem.prediction.DruglikenessPredictor
- DruglikenessPredictorWithIndex - Class in com.actelion.research.chem.prediction
- DruglikenessPredictorWithIndex() - Constructor for class com.actelion.research.chem.prediction.DruglikenessPredictorWithIndex
- DrugScoreCalculator - Class in com.actelion.research.chem.prediction
-
Created by rufenec on 26/10/15.
- DrugScoreCalculator() - Constructor for class com.actelion.research.chem.prediction.DrugScoreCalculator
- DSTINVERT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DUMMY_INTERACT_ID - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- dump(ChemDrawCDX.CDXNode) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- DW_FRAGMENTS_FILE - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- DWAQ_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- DWAR_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- DWARFileCreator - Class in com.actelion.research.chem.io
- DWARFileCreator(BufferedWriter) - Constructor for class com.actelion.research.chem.io.DWARFileCreator
-
Use a DWARFileCreator for writing native DataWarrior files without a CompoundTableModel.
- DWARFileParser - Class in com.actelion.research.chem.io
- DWARFileParser(File) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a File with coordinate mode MODE_COORDINATES_PREFER_2D.
- DWARFileParser(File, int) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a File with the specified coordinate mode.
- DWARFileParser(Reader) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a Reader with coordinate mode MODE_COORDINATES_PREFER_2D.
- DWARFileParser(Reader, int) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a Reader with the specified coordinate mode.
- DWARFileParser(String) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a file name with coordinate mode MODE_COORDINATES_PREFER_2D.
- DWARFileParser(String, int) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a file name with the specified coordinate mode.
- DWARFileParser.SpecialField - Class in com.actelion.research.chem.io
E
- E - Static variable in class smile.math.Math
-
The base of the natural logarithms.
- edge - Variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- editableProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- eig() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the eigen values in an array of size 2N.
- eig() - Method in class smile.math.matrix.JMatrix
- eig(boolean) - Method in interface smile.math.matrix.DenseMatrix
-
Returns the eigen values in an array of size 2N.
- eigen() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the eigen value decomposition.
- eigen() - Method in class smile.math.matrix.JMatrix
- eigen(boolean) - Method in interface smile.math.matrix.DenseMatrix
-
Returns the eigen value decomposition.
- eigen(int) - Method in interface smile.math.matrix.Matrix
-
Find k largest approximate eigen pairs of a symmetric matrix by the Lanczos algorithm.
- eigen(int, double, int) - Method in interface smile.math.matrix.Matrix
-
Find k largest approximate eigen pairs of a symmetric matrix by the Lanczos algorithm.
- eigen(Matrix, int) - Static method in class smile.math.matrix.Lanczos
-
Find k largest approximate eigen pairs of a symmetric matrix by the Lanczos algorithm.
- eigen(Matrix, int, double, int) - Static method in class smile.math.matrix.Lanczos
-
Find k largest approximate eigen pairs of a symmetric matrix by the Lanczos algorithm.
- Electrostatic - Class in com.actelion.research.chem.forcefield.mmff
-
Nonbonded electrostatic energy term class.
- Electrostatic(MMFFMolecule, int, int, Separation.Relation, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Constructor with default values for distModel and dielConst.
- Electrostatic(MMFFMolecule, int, int, Separation.Relation, double, double, boolean, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Construct a new electrostatic energy term.
- Element - Class in com.actelion.research.chem
- Element() - Constructor for class com.actelion.research.chem.Element
- Element(int, String, String, double, double, double, double) - Constructor for class com.actelion.research.chem.Element
- eliminationRuleString(TorsionSetEliminationRule) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- ellipse(int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- ellipse(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- ELUSIVE - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- EmpiricalLigandStrain - Class in com.actelion.research.chem.potentialenergy
- EmpiricalLigandStrain(Conformer, int[], BondRotationHelper) - Constructor for class com.actelion.research.chem.potentialenergy.EmpiricalLigandStrain
- enableTorsionRules() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- encode() - Method in class com.actelion.research.chem.alignment3d.transformation.Rotation
- encode() - Method in class com.actelion.research.chem.alignment3d.transformation.Scaling
- encode() - Method in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- encode() - Method in class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- encode() - Method in class com.actelion.research.chem.alignment3d.transformation.Translation
- encode() - Method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
- encode() - Method in class com.actelion.research.chem.phesa.AtomicGaussian
- encode() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- encode() - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- encode() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- encode() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- encode() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- encode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- encode(double[], int) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
-
Convenience method to encode a array with a given precision.
- encode(float[], int) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
- encode(int[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- encode(int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes a binary fingerprint stored as int[].
- encode(int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- encode(int[]) - Static method in class com.actelion.research.util.EncoderIntegerNumbers
-
Convenience method to encode a array with a given precision.
- encode(int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- encode(long[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- encode(MolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- encode(PharmacophoreNode) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- encode(PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- encode(PheSAMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- encode(Reaction, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a String containing a unique reaction code by creating idcodes of every reactant and product and concatenating them in lexical order.
- encode(Reaction, boolean, int) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a String containing a reaction code by creating idcodes of every reactant and product and concatenating them in original (if mode includes RETAIN_REACTANT_AND_PRODUCT_ORDER) or in lexical order.
- encode(Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- encode(ByteBuffer, ByteBuffer) - Static method in class com.actelion.research.util.Base64
-
Performs Base64 encoding on the
raw
ByteBuffer, writing it to theencoded
ByteBuffer. - encode(ByteBuffer, CharBuffer) - Static method in class com.actelion.research.util.Base64
-
Performs Base64 encoding on the
raw
ByteBuffer, writing it to theencoded
CharBuffer. - encode(T) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- ENCODE - Static variable in class com.actelion.research.util.Base64
-
Specify encoding in first bit.
- ENCODE_ATOM_CUSTOM_LABELS - Static variable in class com.actelion.research.chem.Canonizer
- ENCODE_ATOM_CUSTOM_LABELS_WITHOUT_RANKING - Static variable in class com.actelion.research.chem.Canonizer
- ENCODE_ATOM_SELECTION - Static variable in class com.actelion.research.chem.Canonizer
- encodeBytes(byte[]) - Static method in class com.actelion.research.util.Base64
-
Encodes a byte array into Base64 notation.
- encodeBytes(byte[], int) - Static method in class com.actelion.research.util.Base64
-
Encodes a byte array into Base64 notation.
- encodeBytes(byte[], int, int) - Static method in class com.actelion.research.util.Base64
-
Encodes a byte array into Base64 notation.
- encodeBytes(byte[], int, int, int) - Static method in class com.actelion.research.util.Base64
-
Encodes a byte array into Base64 notation.
- encodeBytesToBytes(byte[]) - Static method in class com.actelion.research.util.Base64
-
Similar to
Base64.encodeBytes(byte[])
but returns a byte array instead of instantiating a String. - encodeBytesToBytes(byte[], int, int, int) - Static method in class com.actelion.research.util.Base64
-
Similar to
Base64.encodeBytes(byte[], int, int, int)
but returns a byte array instead of instantiating a String. - encodeCoordsOnly() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- encodeCounts(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes a fragment/hash-value count list.
- encodeFileToFile(String, String) - Static method in class com.actelion.research.util.Base64
-
Reads infile and encodes it to outfile.
- encodeFromFile(String) - Static method in class com.actelion.research.util.Base64
-
Convenience method for reading a binary file and base64-encoding it.
- encodeFull() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- EncodeFunctions - Class in com.actelion.research.chem.phesa
-
February 2018 Author: J.
- EncodeFunctions() - Constructor for class com.actelion.research.chem.phesa.EncodeFunctions
- encodeHistograms(DistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
- encodeHTML(String) - Static method in class com.actelion.research.util.StringFunctions
- encodeIntArray(int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes an int[] containing positive values without upper limit.
- encodeLong(long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes a binary fingerprint stored as long[].
- encodeObject(Serializable) - Static method in class com.actelion.research.util.Base64
-
Serializes an object and returns the Base64-encoded version of that serialized object.
- encodeObject(Serializable, int) - Static method in class com.actelion.research.util.Base64
-
Serializes an object and returns the Base64-encoded version of that serialized object.
- encodePairs(int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes pairs of identifying integer with corresponding count values in the form of an int[n][2], where n is the number of pairs, index=0 refers to the ID value and index=1 refers to the count value.
- EncoderFloatingPointNumbers - Class in com.actelion.research.util
- EncoderFloatingPointNumbers(double[], int) - Constructor for class com.actelion.research.util.EncoderFloatingPointNumbers
-
More values can be added after the constructor was called.
- EncoderFloatingPointNumbers(float[], int) - Constructor for class com.actelion.research.util.EncoderFloatingPointNumbers
- EncoderIntegerNumbers - Class in com.actelion.research.util
-
Encodes integer numbers into a string.
- EncoderIntegerNumbers(int[]) - Constructor for class com.actelion.research.util.EncoderIntegerNumbers
-
More values can be added after the constructor was called.
- encodeToFile(byte[], String) - Static method in class com.actelion.research.util.Base64
-
Convenience method for encoding data to a file.
- end() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
- end() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXPage
- end() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXReactionStep
- endBorrowContent() - Method in class com.actelion.research.gui.dock.Dockable
-
Returns the content from temporarily adding it to another copntainer.
- endSubMenu() - Method in interface com.actelion.research.gui.generic.GenericPopupMenu
- endSubMenu() - Method in class com.actelion.research.gui.swing.SwingPopupMenu
- ENERGY_CUTOFF - Static variable in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- EnergyTerm - Interface in com.actelion.research.chem.forcefield.mmff
-
Interface class for energy terms.
- ENOL - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- ensure2DCoordinates() - Method in class com.actelion.research.chem.IDCodeParser
- ensure2DCoordinates() - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- ensureHelperArrays(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
While the Molecule class covers all primary molecule information, its derived class ExtendedMolecule handles secondary, i.e.
- ensureHelperArrays(int) - Method in class com.actelion.research.chem.StereoMolecule
-
ensureHelperArrays() is the essential method when working with molecules.
- ensurePopupMenuCreated() - Method in class com.actelion.research.gui.JScrollableMenu
-
Lazily creates the popup menu.
- entropy() - Method in interface smile.stat.distribution.Distribution
-
Shannon entropy of the distribution.
- entropy() - Method in class smile.stat.distribution.GaussianDistribution
- entropy() - Method in class smile.stat.distribution.Mixture
-
Shannon entropy.
- Entry(int, double) - Constructor for class smile.math.SparseArray.Entry
-
Constructor.
- enumerateExtensionCutFast(int, int[], List<Integer>, Set<Integer>, Set<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
retrieve nodes that are part of extension match ("extension nodes") as well as the nodes that are part of a cut subtree (source nodes) from a cut-string
- enumerateExtensionCutFull(int, int[], List<Integer>, List<Integer>, List<List<Integer>>, List<List<Integer>>, List<Integer>, Set<Integer>, List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
retrieves nodes that are part of extension match ("extension nodes") as well as the different subtrees resulting from the cuts with a list of their edges (in bfs order) as well as the parents of the edges
- eps - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- EPS - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- EPSILON - Static variable in class com.actelion.research.chem.alignment3d.transformation.ExponentialMap
- EPSILON - Static variable in class smile.math.Math
-
The machine precision for the double type, which is the difference between 1 and the smallest value greater than 1 that is representable for the double type.
- EPSILON_SVR - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- equal(byte[], byte[]) - Static method in class com.actelion.research.util.StringFunctions
- equal(Matrix) - Method in class com.actelion.research.calc.Matrix
- equal(Matrix, double) - Method in class com.actelion.research.calc.Matrix
- equal(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
- equal(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
- equal(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
- equalAtoms(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
realize() may be called first.
- equalDimension(Matrix) - Method in class com.actelion.research.calc.Matrix
-
Checks two matrices for equal dimensions.
- equals(double[][], double[][]) - Static method in class smile.math.Math
-
Check if x element-wisely equals y with default epsilon 1E-10.
- equals(double[][], double[][], double) - Static method in class smile.math.Math
-
Check if x element-wisely equals y.
- equals(double[], double[]) - Static method in class smile.math.Math
-
Check if x element-wisely equals y with default epsilon 1E-10.
- equals(double[], double[], double) - Static method in class smile.math.Math
-
Check if x element-wisely equals y.
- equals(double, double) - Static method in class com.actelion.research.calc.MatrixFunctions
- equals(double, double) - Static method in class smile.math.Math
-
Returns true if two double values equals to each other in the system precision.
- equals(float[][], float[][]) - Static method in class smile.math.Math
-
Check if x element-wisely equals y with default epsilon 1E-7.
- equals(float[][], float[][], float) - Static method in class smile.math.Math
-
Check if x element-wisely equals y.
- equals(float[], float[]) - Static method in class smile.math.Math
-
Check if x element-wisely equals y with default epsilon 1E-7.
- equals(float[], float[], float) - Static method in class smile.math.Math
-
Check if x element-wisely equals y.
- equals(int[][], int[][]) - Static method in class smile.math.Math
-
Check if x element-wisely equals y.
- equals(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- equals(int[], int[]) - Static method in class com.actelion.research.util.ArrayUtils
- equals(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntArray
- equals(int[], int[]) - Static method in class smile.math.Math
-
Check if x element-wisely equals y.
- equals(int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Checks if this OutOfPlane's atoms are the same as a given set of 4 atoms, it checks all possible permutations of a1, a2 and a3.
- equals(Conformer) - Method in class com.actelion.research.chem.conf.Conformer
- equals(TorsionDescriptor) - Method in class com.actelion.research.chem.conf.TorsionDescriptor
-
Returns true, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE;
- equals(InventorFragment) - Method in class com.actelion.research.chem.coords.InventorFragment
- equals(Fragment3D) - Method in class com.actelion.research.chem.shredder.Fragment3D
- equals(SortedStringList) - Method in class com.actelion.research.chem.SortedStringList
- equals(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
- equals(SortedList<T>) - Method in class com.actelion.research.util.SortedList
- equals(Object) - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- equals(Object) - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- equals(Object) - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- equals(Object) - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- equals(Object) - Method in class com.actelion.research.chem.Coordinates
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- equals(Object) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- equals(Object) - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
-
Returns true if this SortedPair is equal with another object.
- equals(Object) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Checks for equality between two vectors.
- equals(Object) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- equals(Object) - Method in class com.actelion.research.chem.MolecularFormula
- equals(Object) - Method in class com.actelion.research.chem.Molecule3D
- equals(Object) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- equals(Object) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- equals(Object) - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- equals(Object) - Method in class com.actelion.research.chem.shredder.Fragment
- equals(Object) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondType
- equals(Object) - Method in class com.actelion.research.util.datamodel.ByteVec
- equals(Object) - Method in class com.actelion.research.util.datamodel.IntArray
- equals(Object) - Method in class com.actelion.research.util.datamodel.IntVec
- equals(Object) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- equals(Object) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- equals(Object) - Method in class smile.data.Attribute
- equals(Object) - Method in class smile.math.Complex
- equals(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
-
Returns true, if none of the torsion angles between both conformers are more different than TorsionDescriptor.TORSION_EQUIVALENCE_TOLERANCE; Calling this method requires that calculateDescriptor() has been called earlier.
- equals(T[][], T[][]) - Static method in class smile.math.Math
-
Check if x element-wisely equals y.
- equals(T[], T[]) - Static method in class smile.math.Math
-
Check if x element-wisely equals y.
- erasePrimes(int[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- erf(double) - Static method in class smile.math.special.Erf
-
The Gauss error function.
- Erf - Class in smile.math.special
-
The error function (also called the Gauss error function) is a special function of sigmoid shape which occurs in probability, statistics, materials science, and partial differential equations.
- erfc(double) - Static method in class smile.math.special.Erf
-
The complementary error function.
- erfcc(double) - Static method in class smile.math.special.Erf
-
The complementary error function with fractional error everywhere less than 1.2 × 10-7.
- errMax - Variable in class com.actelion.research.calc.regression.ModelError
- errMin - Variable in class com.actelion.research.calc.regression.ModelError
- error - Variable in class com.actelion.research.calc.regression.ModelError
- error() - Method in class smile.regression.RandomForest
-
Returns the out-of-bag estimation of RMSE.
- ErrorHashMap - Class in com.actelion.research.util
-
ErrorHashMap 2005 MvK: Start implementation
- ErrorHashMap() - Constructor for class com.actelion.research.util.ErrorHashMap
- errorMedian - Variable in class com.actelion.research.calc.regression.ModelError
- errorRelative - Variable in class com.actelion.research.calc.regression.ModelError
- errorRelativeMedian - Variable in class com.actelion.research.calc.regression.ModelError
- errorRelativeWeighted - Variable in class com.actelion.research.calc.regression.ModelError
- errors - Variable in class com.actelion.research.chem.io.AbstractParser
- errSumSquared - Variable in class com.actelion.research.calc.regression.ModelError
- ES - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- escape(int, byte[]) - Method in class com.actelion.research.gui.wmf.MetaFile
- escape(int, byte[]) - Method in class com.actelion.research.gui.wmf.WMF
- escapeDanglingMetaCharacters(String) - Static method in class com.actelion.research.util.StringFunctions
-
Escapes the meta characters in a regular expression pattern with \\.
- esrTypeFromRow(int) - Static method in class com.actelion.research.share.gui.editor.Model
- ESTER - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- ETO_CLIPPED - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- ETO_GRAYED - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- ETO_OPAQUE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- EUCLIDEAN - smile.clustering.ClusteringDistance
-
Squared Euclidean distance for K-Means.
- EUCLIDEAN - Static variable in class com.actelion.research.util.datamodel.ByteVec
- EUCLIDEAN - Static variable in class com.actelion.research.util.DoubleVec
- EUCLIDEAN_FAST - Static variable in class com.actelion.research.util.datamodel.ByteVec
- EUCLIDEAN_FAST - Static variable in class com.actelion.research.util.DoubleVec
- EUCLIDEAN_MISSING_VALUES - smile.clustering.ClusteringDistance
-
Squared Euclidean distance with missing value handling for K-Means.
- euclideanDist(PointDouble, PointDouble) - Static method in class com.actelion.research.util.datamodel.PointDouble
- euclideanDistance(double[], double[]) - Static method in class com.actelion.research.util.DoubleVec
- euclideanDistance(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Euclidean distance
- euclideanDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Euclidean distance
- EuclideanDistanceFast(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Euclidean distance without sqrt
- eulerRodrigues(Coordinates, Coordinates, double) - Static method in class com.actelion.research.chem.chemicalspaces.synthon.SynthonReactor
- EUROPEAN - com.actelion.research.util.Formatter.LocaleFormat
- Evaluable - Interface in com.actelion.research.chem.optimization
- EvaluableFlexibleOverlap - Class in com.actelion.research.chem.phesaflex
- EvaluableFlexibleOverlap(PheSAAlignment, StereoMolecule, StereoMolecule, double, boolean[], double[], Map<String, Object>) - Constructor for class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- EvaluableFlexibleOverlap(EvaluableFlexibleOverlap) - Constructor for class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- EvaluableOverlap - Class in com.actelion.research.chem.phesa
- EvaluableOverlap(EvaluableOverlap) - Constructor for class com.actelion.research.chem.phesa.EvaluableOverlap
- EvaluableOverlap(PheSAAlignment, double[]) - Constructor for class com.actelion.research.chem.phesa.EvaluableOverlap
- EvaluableOverlap(PheSAAlignment, double[], double) - Constructor for class com.actelion.research.chem.phesa.EvaluableOverlap
- evaluate() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- evaluate(double, double) - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- evaluateIntegerBins(double, double) - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- EVD - Class in smile.math.matrix
-
Eigen decomposition of a real matrix.
- EVD(DenseMatrix, double[]) - Constructor for class smile.math.matrix.EVD
-
Private constructor.
- EVD(DenseMatrix, double[], double[]) - Constructor for class smile.math.matrix.EVD
-
Private constructor.
- EX - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- exactly(int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Checks if this OutOfPlane term is exactly equal to a given set of four atoms.
- ExceptionConformationGenerationFailed - Exception in com.actelion.research.chem.descriptor.flexophore
- ExceptionConformationGenerationFailed(String) - Constructor for exception com.actelion.research.chem.descriptor.flexophore.ExceptionConformationGenerationFailed
- EXCLUSION - Static variable in class com.actelion.research.chem.phesa.VolumeGaussian
- execute(String[]) - Static method in class com.actelion.research.util.Platform
-
Start an executable with parameters.
- execute(String, String...) - Static method in class com.actelion.research.util.Platform
-
Start an executable with parameters.
- ExhaustiveFragmentGeneratorAtoms - Class in com.actelion.research.chem.mcs
- ExhaustiveFragmentGeneratorAtoms() - Constructor for class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- ExhaustiveFragmentGeneratorBonds - Class in com.actelion.research.chem.mcs
- ExhaustiveFragmentGeneratorBonds(int, int) - Constructor for class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- ExhaustiveFragmentGeneratorParallizer - Class in com.actelion.research.chem.mcs
- ExhaustiveFragmentGeneratorParallizer(int) - Constructor for class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
- ExhaustiveFragmentsStatistics - Class in com.actelion.research.chem.properties.complexity
- ExhaustiveFragmentsStatistics(int) - Constructor for class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- ExhaustiveFragmentsStatistics(int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- ExhaustiveFragmentsStatistics(int, int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- ExhaustiveMCSGeneratorParallel - Class in com.actelion.research.chem.mcs
- ExhaustiveMCSGeneratorParallel(int) - Constructor for class com.actelion.research.chem.mcs.ExhaustiveMCSGeneratorParallel
- EXIT_VECTOR - com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint.Functionality
- EXIT_VECTOR_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- ExitVectorPoint - Class in com.actelion.research.chem.phesa.pharmacophore.pp
- ExitVectorPoint(ExitVectorPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- ExitVectorPoint(StereoMolecule, int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- exp() - Method in class smile.math.Complex
-
Returns the complex exponential.
- exp(double) - Static method in class smile.math.Math
-
Returns Euler's number e raised to the power of a double value.
- expm1(double) - Static method in class smile.math.Math
-
Returns ex-1.
- ExponentialFamily - Interface in smile.stat.distribution
-
The exponential family is a class of probability distributions sharing a certain form.
- ExponentialMap - Class in com.actelion.research.chem.alignment3d.transformation
-
described in: F.
- ExponentialMap(double, double, double) - Constructor for class com.actelion.research.chem.alignment3d.transformation.ExponentialMap
- ExponentialMap(Quaternion) - Constructor for class com.actelion.research.chem.alignment3d.transformation.ExponentialMap
- ExponentialMap(Coordinates) - Constructor for class com.actelion.research.chem.alignment3d.transformation.ExponentialMap
- EXTENDED - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- EXTENDED_ATOM_FLAG_COUNT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
- ExtendedDepictor - Class in com.actelion.research.chem
- ExtendedDepictor(Reaction, DrawingObjectList, boolean) - Constructor for class com.actelion.research.chem.ExtendedDepictor
- ExtendedDepictor(StereoMolecule[], int, DrawingObjectList) - Constructor for class com.actelion.research.chem.ExtendedDepictor
-
Use this constructor for markush structures.
- ExtendedDepictor(StereoMolecule[], DrawingObjectList) - Constructor for class com.actelion.research.chem.ExtendedDepictor
- ExtendedDepictor(StereoMolecule, DrawingObjectList) - Constructor for class com.actelion.research.chem.ExtendedDepictor
- ExtendedMolecule - Class in com.actelion.research.chem
-
While the Molecule class covers all primary molecule information as atom and bond properties, the atom connectivity and coordinates, its derived class ExtendedMolecule handles secondary, i.e.
- ExtendedMolecule() - Constructor for class com.actelion.research.chem.ExtendedMolecule
- ExtendedMolecule(int, int) - Constructor for class com.actelion.research.chem.ExtendedMolecule
- ExtendedMolecule(Molecule) - Constructor for class com.actelion.research.chem.ExtendedMolecule
- ExtendedMoleculeFunctions - Class in com.actelion.research.chem
-
ExtendedMoleculeFunctions
- ExtendedMoleculeFunctions() - Constructor for class com.actelion.research.chem.ExtendedMoleculeFunctions
- extendedToOriginalAtom(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- EXTENSION_INTRODUCER - Static variable in class com.actelion.research.util.AnimatedGIFWriter
- EXTENSION_MATCH_NODE_NR_LIMIT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- EXTENSION_MATCHES - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- extract(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor
-
Delivers a list of indices that describes sub structures of the given molecule.
- extract(String, String) - Static method in class com.actelion.research.util.StringFunctions
- extractAliphaticRingsAndEndStandingAliphaticGroups(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor
- extractAromaticRing(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- extractCol(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- extractFieldName(String) - Method in class com.actelion.research.chem.io.SDFileParser
- extractForGivenResolution(IntVec, int, int) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Converts the IntVec into an array.
- extractFragment(Molecule3D, T, int[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Extract the Ligand from mol and copy it into res
- extractFragment(Molecule3D, T, List<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- extractFragments(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return all connex components with more than 5 atoms
- extractInverse(String, String) - Static method in class com.actelion.research.util.StringFunctions
- extractLigand(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Extract the Ligand from mol and copy it into res
- extractLigands(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return all ligands with more than 5 atoms
- extractMols() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- extractValue(String) - Static method in class com.actelion.research.calc.SelfOrganizedMap
- extractValue(String) - Static method in class com.actelion.research.chem.io.ODEFileParser
- extractX(List<ScorePoint>) - Static method in class com.actelion.research.util.datamodel.ScorePoint
- EY - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- eye(int) - Static method in interface smile.math.matrix.Matrix
-
Returns an n-by-n identity matrix.
- eye(int, int) - Static method in interface smile.math.matrix.Matrix
-
Returns an m-by-n identity matrix.
F
- f(double) - Method in interface smile.math.Function
-
Compute the value of the function at x.
- f(double) - Method in class smile.math.rbf.GaussianRadialBasis
- f(double[]) - Method in interface smile.math.MultivariateFunction
-
Compute the value of the function at x.
- f(double[], double[]) - Method in interface smile.math.DifferentiableMultivariateFunction
-
Compute the value and gradient of the function at x.
- FACTOR_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- factorial(int) - Static method in class smile.math.Math
-
factorial of n
- factors - Variable in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- FACTORS - Static variable in class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- FACTORS - Static variable in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- FACTORS - Static variable in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- FactorySolution - Class in com.actelion.research.util.graph.complete
-
FactorySolution
- FactorySolution() - Constructor for class com.actelion.research.util.graph.complete.FactorySolution
- failed - Variable in class com.actelion.research.calc.regression.ModelError
- FAILED_BYTES - Static variable in interface com.actelion.research.chem.descriptor.DescriptorHandler
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- FAILED_STRING - Static variable in interface com.actelion.research.chem.descriptor.DescriptorHandler
- FAKE_ATOM_NO - Static variable in class com.actelion.research.share.gui.editor.Model
- FALSE - com.actelion.research.chem.forcefield.mmff.RingBoolean
- falseNegative - Variable in class com.actelion.research.calc.classification.PrecisionAndRecall
- falsePositive - Variable in class com.actelion.research.calc.classification.PrecisionAndRecall
- FastMolecularComplexityCalculator - Class in com.actelion.research.chem.prediction
-
This is a fast version of the MolecularComplexityCalculator in the com.actelion.chem.properties.complexity package.
- FastMolecularComplexityCalculator() - Constructor for class com.actelion.research.chem.prediction.FastMolecularComplexityCalculator
- FastSpline - Class in com.actelion.research.util
-
Represents a polynomial spline function.
- FastSpline(double[], FastSpline.Polynome[]) - Constructor for class com.actelion.research.util.FastSpline
-
Construct a polynomial spline function with the given segment delimiters and interpolating polynomials.
- FastSpline.Polynome - Class in com.actelion.research.util
- FeatureCalculator - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
calculates features for all atoms in a molecule: H-bond acceptors/donors, negatively/positively ionizable, aromatic, lipophilic
- FeatureCalculator(StereoMolecule) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.FeatureCalculator
- FeatureMatch(int[][]) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- FF_DECORATIVE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_DONTCARE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_MODERN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_ROMAN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_SCRIPT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_SWISS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- fget(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
-
Gets a floating point value from a given row and column.
- fieldIndex - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- FILE_SUPPORT_NONE - Static variable in class com.actelion.research.gui.CompoundCollectionPane
- FILE_SUPPORT_OPEN_AND_SAVE_FILES - Static variable in class com.actelion.research.gui.CompoundCollectionPane
- FILE_SUPPORT_OPEN_FILES - Static variable in class com.actelion.research.gui.CompoundCollectionPane
- FILE_SUPPORT_SAVE_FILES - Static variable in class com.actelion.research.gui.CompoundCollectionPane
- fileExists(File) - Static method in class com.actelion.research.gui.FileHelper
-
java.io.File.exists() and java.nio.file.Files.exists() may cause minutes of delay, if a file is/was on a network share which is currently unmounted.
- fileExists(File, long) - Static method in class com.actelion.research.gui.FileHelper
-
java.io.File.exists() and java.nio.file.Files.exists() may cause minutes of delay, if a file is/was on a network share which is currently unmounted.
- FileHelper - Class in com.actelion.research.gui
- FileHelper(Component) - Constructor for class com.actelion.research.gui.FileHelper
- fill(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- FILL - Static variable in interface com.actelion.research.gui.generic.GenericDialog
- fillArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillCircle(double, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- fillCircle(double, double, double) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- fillCircle(double, double, double) - Method in class com.actelion.research.chem.Depictor2D
- fillCircle(double, double, double) - Method in class com.actelion.research.chem.SVGDepictor
- fillCircle(double, double, double) - Method in class com.actelion.research.gui.generic.GenericDepictor
- fillCircle(double, double, double) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- fillCircle(double, double, double) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- fillCircle(double, double, double) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- fillElipse(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- fillElipse(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- fillOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillPolygon(double[], double[], int) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- fillPolygon(double[], double[], int) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- fillPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillPolygon(GenericPolygon) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- fillPolygon(GenericPolygon) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- fillRect(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- fillRect(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- fillRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillRectangle(double, double, double, double) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- fillRectangle(double, double, double, double) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- fillRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillText(String, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- fillText(String, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- filter(byte[]) - Method in class com.actelion.research.calc.filter.SlidingWindow
- filter(byte[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- filter(double[]) - Method in class com.actelion.research.calc.filter.SlidingWindow
- filter(int[]) - Method in class com.actelion.research.calc.filter.SlidingWindow
- filter(int[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- FILTER - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- FILTER07_ - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
-
Filter for sliding window to blurr distance histograms 07.04.2020
- finalize() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- finalize() - Method in class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
- finalize() - Method in class com.actelion.research.io.StringReadChannel
- finalize() - Method in class com.actelion.research.util.BinaryEncoder
-
Writes remaining bits from buffer, if there are any and possibly adds final NL/LF.
- finalizeMolecule(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Remove all atoms without connections.
- finalizeProcessMolecules() - Method in class com.actelion.research.chem.AtomTypeList
- finalizeThreads() - Method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- findAlignment(double[][], TransformationSequence) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- findAlignment(double[][], TransformationSequence, boolean) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- findAlignment(double[][], TransformationSequence, boolean, boolean) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- findAlleneCenterAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
If atom is one of the two ends of an allene then returns allene center atom.
- findAlleneEndAtom(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Crawls along a chain of sp-hybridized atoms starting from atom2 (which may not be sp-hybridized) away from its sp-hybridized neighbour atom1.
- findAtom(double, double) - Method in class com.actelion.research.chem.Molecule
- findAtom(StereoMolecule, Point2D) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- findBestMatchLocation(Object) - Method in class com.actelion.research.calc.SelfOrganizedMap
- findBestMatchLocationQuickly(Object) - Method in class com.actelion.research.calc.SelfOrganizedMap
- findBestMatchLocationSMP(Object) - Method in class com.actelion.research.calc.SelfOrganizedMap
- findBINAPChiralityBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Checks whether atom is one of the two atoms of an axial chirality bond of BINAP type.
- findBond(double, double) - Method in class com.actelion.research.chem.Molecule
- findExactMatchLocation(Object) - Method in class com.actelion.research.calc.SelfOrganizedMap
- findFragmentInMolecule() - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- findFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcher
-
Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms.
- findFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- findFragmentInMolecule(int, int) - Method in class com.actelion.research.chem.SSSearcher
-
Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms.
- findFragmentInMolecule(int, int) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- findFragmentInMolecule(int, int, boolean[]) - Method in class com.actelion.research.chem.SSSearcher
-
Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms that are not flagged to be excluded from matching.
- findFragmentInMolecule(int, int, boolean[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- findFragmentInMoleculeWithoutIndex(int) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- findIdentical(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- findIn(MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.AngleBend
-
Helper function that builds a list of AngleBends for a molecule.
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Finds all bond stretch energy terms in the current molecule.
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Finds all out of plane angles in the current molecule.
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Helper function that builds a list of StretchBends for a molecule.
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Helper function that builds a list of TorsionAngles for a molecule.
- findIn(Tables, MMFFMolecule, Separation) - Static method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Overloaded wrapper function for 'findIn' which sets default values for the nonbonded cutoff, dielectric model and dielectric constant.
- findIn(Tables, MMFFMolecule, Separation, double) - Static method in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
-
Finds all van der Waals energy terms in the current molecule.
- findIn(Tables, MMFFMolecule, Separation, double, boolean, double) - Static method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Finds all Electrostatic energy terms in the current molecule.
- findInitialSplits() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- findLargest(double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- findMostCentralRingSystem(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
This method flags all atoms that are a member of that ring system in mol, which is most central within this molecule graph.
- findMurckoScaffold(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
This method flags all atoms that are a member of the Murcko fragment of mol.
- findPrimeInRow(int[][], int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- findRearAtoms(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
If the atom sequence contains a straight chain of sp-hybridized atoms, then the atom array contain the first two and last two atoms of a sequence of 2n+4 atoms (n: number of conjugated triple bonds).
- findRingSystem(int, boolean, boolean[], boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Starting from startAtom this method locates a system of annelated or bridged ring systems with all members bonds being a ring bond.
- findRotatableBonds(StereoMolecule) - Static method in class com.actelion.research.chem.conf.TorsionDescriptorHelper
-
Calculates an array of all rotatable bonds that can be used multiple times as parameter to calculateDescriptor().
- findRotatableBonds(StereoMolecule, boolean, boolean[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Locates all relevant rotatable bonds, i.e.
- findSmallest(double[][], int[], int[], double) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- findStarInCol(int[][], int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- findUncoveredZero(int[], double[][], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- FingerPrintGenerator - Class in com.actelion.research.chem.descriptor
-
Generator of a path-based Fingerprint Not thread safe!
- FingerPrintGenerator() - Constructor for class com.actelion.research.chem.descriptor.FingerPrintGenerator
- finishWrite(OutputStream) - Method in class com.actelion.research.util.AnimatedGIFWriter
-
This is intended to be called after writing all the frames if we write an animated GIF frame by frame.
- fireDockableSelected(Dockable) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Sends ActionEvent to listeners when the user interactively selected another dockable
- firePruningBarChanged() - Method in class com.actelion.research.gui.JPruningBar
- FISCHER_PROJECTION_LIMIT - Static variable in class com.actelion.research.chem.ExtendedMolecule
-
To interpret a stereo center as fisher projection, all non stereo bonds must be vertical and all stereo bonds must be horizontal.
- FISCHER_PROJECTION_RING_LIMIT - Static variable in class com.actelion.research.chem.ExtendedMolecule
- fit(double[], double[], int, double[], int) - Method in class com.actelion.research.util.NumericalRecipes
- fittingFunction(double, double[], double[], int) - Method in class com.actelion.research.util.FittingFunction
- FittingFunction - Class in com.actelion.research.util
- FittingFunction() - Constructor for class com.actelion.research.util.FittingFunction
- FIXED_PITCH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FLAG_CENTER_ATOM - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- FLAG1 - Static variable in class com.actelion.research.chem.Molecule3D
- flagBackbone(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return a List of int[] representing all the atom-atom pairs having an intermolecular interactions (distance close to sum of VDW)
- FLD_CMNT - Static variable in class com.actelion.research.chem.StructureInfo
- FLD_DENSITY - Static variable in class com.actelion.research.chem.StructureInfo
- FLD_ID - Static variable in class com.actelion.research.chem.StructureInfo
- FLD_NAME - Static variable in class com.actelion.research.chem.StructureInfo
- FLD_PURITY - Static variable in class com.actelion.research.chem.StructureInfo
- flexible - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- FlexibleShapeAlignment - Class in com.actelion.research.chem.phesaflex
-
Performs flexible Alignment of two Molecules that are prealigned.
- FlexibleShapeAlignment(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- FlexibleShapeAlignment(StereoMolecule, StereoMolecule, double) - Constructor for class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- FlexibleShapeAlignment(StereoMolecule, StereoMolecule, MolecularVolume, MolecularVolume, double) - Constructor for class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- FlexophoreCreateFunctions - Class in com.actelion.research.chem.descriptor.flexophore.generator
-
FlexophoreCreateFunctions
- FlexophoreCreateFunctions() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- FlexophorePoint - Class in com.actelion.research.chem.descriptor.flexophore.entity
-
FlexophorePoint
- FlexophorePoint(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- flip(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- flip(double, double, double) - Method in class com.actelion.research.chem.coords.InventorFragment
- flipOneSide(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- floatValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- floor(double) - Static method in class smile.math.Math
-
Returns the largest (closest to positive infinity) double value that is less than or equal to the argument and is equal to a mathematical integer.
- Fluorine - Static variable in class com.actelion.research.chem.PeriodicTable
- flush() - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- flushBase64() - Method in class com.actelion.research.util.Base64.OutputStream
-
Method added by PHIL.
- ForceField - Interface in com.actelion.research.chem.forcefield
- forceFieldAllowsOpenValences() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
-
For using a different forcefield you may override all three forceField...
- ForceFieldChangeListener - Interface in com.actelion.research.chem.forcefield
- forceFieldInitialize() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
-
For using a different forcefield you may override all three forceField...
- forceFieldMinimize(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
-
For using a different forcefield you may override all three forceField...
- ForceFieldMMFF94 - Class in com.actelion.research.chem.forcefield.mmff
- ForceFieldMMFF94(StereoMolecule, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Forcefield constructor.
- ForceFieldMMFF94(StereoMolecule, String, Map<String, Object>) - Constructor for class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Forcefield constructor.
- format(double, DecimalFormat, int) - Static method in class com.actelion.research.calc.Matrix
- format(int) - Static method in class com.actelion.research.calc.Matrix
- format(Object) - Static method in class com.actelion.research.util.Formatter
- format(String) - Static method in class com.actelion.research.util.StringFunctions
-
Keeps the minus.
- format(String, char) - Static method in class com.actelion.research.util.StringFunctions
-
Keeps the minus.
- format0(Double) - Static method in class com.actelion.research.util.Formatter
- format1(Double) - Static method in class com.actelion.research.util.Formatter
- format2(Double) - Static method in class com.actelion.research.util.Formatter
- format2DefinedLengthLeading(String, int) - Static method in class com.actelion.research.util.StringFunctions
- format2DefinedLengthTrailing(String, int) - Static method in class com.actelion.research.util.StringFunctions
- format3(Double) - Static method in class com.actelion.research.util.Formatter
- format4(Double) - Static method in class com.actelion.research.util.Formatter
- format8(Double) - Static method in class com.actelion.research.util.Formatter
- formatDate(Date) - Static method in class com.actelion.research.util.Formatter
- formatDateTime(Date) - Static method in class com.actelion.research.util.Formatter
- formatDateTimeShort(Date) - Static method in class com.actelion.research.util.Formatter
- formatDescription(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- formatE(Double) - Static method in class com.actelion.research.util.Formatter
- formatMax2(Double) - Static method in class com.actelion.research.util.Formatter
- formatMax3(Double) - Static method in class com.actelion.research.util.Formatter
- Formatter - Class in com.actelion.research.util
- Formatter() - Constructor for class com.actelion.research.util.Formatter
- Formatter.LocaleFormat - Enum in com.actelion.research.util
- formatTime(Date) - Static method in class com.actelion.research.util.Formatter
- formatToCharactersAndDigits(String) - Static method in class com.actelion.research.util.StringFunctions
- formatToPrintableCharactersOnly(String) - Static method in class com.actelion.research.util.StringFunctions
-
This function was implemented because in AxoSOMSampleView was a new line in SMILES molConvert from ChemAxon that is not detected by replaceAll("\n", "");
- formatYYYYMMDD() - Static method in class com.actelion.research.util.Formatter
- FormulaParser - Class in com.actelion.research.chem.io.pdb.parser
-
FormulaParser
- FormulaParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.FormulaParser
- FractalDimensionMolecule - Class in com.actelion.research.chem.properties.fractaldimension
-
FractalDimensionMolecule
- FractalDimensionMolecule(int, boolean) - Constructor for class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- FractalDimensionMoleculeMain - Class in com.actelion.research.chem.properties.fractaldimension
-
FractalDimensionMoleculeMain
- FractalDimensionMoleculeMain() - Constructor for class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
- Fragment - Class in com.actelion.research.chem.shredder
-
Fragment Jan 18, 2013 MvK Start implementation
- Fragment(String) - Constructor for class com.actelion.research.chem.shredder.Fragment
- Fragment(String, String) - Constructor for class com.actelion.research.chem.shredder.Fragment
- Fragment3D - Class in com.actelion.research.chem.shredder
- Fragment3D(String, String, TorsionDescriptor, int[]) - Constructor for class com.actelion.research.chem.shredder.Fragment3D
- FragmentAssociation - Class in com.actelion.research.chem.coords
-
Created by thomas on 9/23/16.
- FragmentAssociation(InventorFragment, InventorFragment) - Constructor for class com.actelion.research.chem.coords.FragmentAssociation
-
Uses center of gravity of the fragments as anchor points
- FragmentAssociation(InventorFragment, InventorFragment, int, int) - Constructor for class com.actelion.research.chem.coords.FragmentAssociation
- FragmentDefinedByBondsHasher - Class in com.actelion.research.chem.properties.complexity
- FragmentDefinedByBondsHasher() - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsHasher
- FragmentDefinedByBondsIdCode - Class in com.actelion.research.chem.properties.complexity
- FragmentDefinedByBondsIdCode() - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- FragmentDefinedByBondsIdCode(FragmentDefinedByBondsIdCode) - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- FragmentDefinedByBondsIdCode(IBitArray) - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- Fragmenter3D - Class in com.actelion.research.chem.shredder
- Fragmenter3D(int, int, int, int, int) - Constructor for class com.actelion.research.chem.shredder.Fragmenter3D
- fromString(String) - Static method in class com.actelion.research.chem.phesa.AtomicGaussian
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.PharmacophorePointFactory
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.VolumeGaussian
- full - Variable in class smile.math.matrix.SVD
-
Is this a full decomposition?
- FULL_HOSE_CODE - Static variable in class com.actelion.research.chem.contrib.HoseCodeCreator
- FUNC_GROUP_FLAG_COUNT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
- Function - Interface in smile.math
-
An interface representing a univariate real function.
- FUNCTIONAL_GROUP - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- FUNCTIONAL_GROUP_SHIFT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
- FunctionalGroupClassifier - Class in com.actelion.research.chem.reaction
- FunctionalGroupClassifier(StereoMolecule) - Constructor for class com.actelion.research.chem.reaction.FunctionalGroupClassifier
- FUNCTIONALITY_WEIGHTS - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- FUNCTOL - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- fusion(Molecule3D) - Method in class com.actelion.research.chem.Molecule3D
-
This method will append a Molecule3D to the end.
- FW_BLACK - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FW_BOLD - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FW_DONTCARE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FW_NORMAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FW_THIN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
G
- g_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'G-i' from the table.
- gamma - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- Gaussian3D - Class in com.actelion.research.chem.phesa
- Gaussian3D() - Constructor for class com.actelion.research.chem.phesa.Gaussian3D
- Gaussian3D(int, int, Coordinates, double) - Constructor for class com.actelion.research.chem.phesa.Gaussian3D
- Gaussian3D(Gaussian3D) - Constructor for class com.actelion.research.chem.phesa.Gaussian3D
- GaussianDistribution - Class in smile.stat.distribution
-
The normal distribution or Gaussian distribution is a continuous probability distribution that describes data that clusters around a mean.
- GaussianDistribution(double[]) - Constructor for class smile.stat.distribution.GaussianDistribution
-
Constructor.
- GaussianDistribution(double, double) - Constructor for class smile.stat.distribution.GaussianDistribution
-
Constructor
- GaussianKernel - Class in smile.math.kernel
-
The Gaussian Mercer Kernel.
- GaussianKernel(double) - Constructor for class smile.math.kernel.GaussianKernel
-
Constructor.
- GaussianProcessRegression - Class in com.actelion.research.calc.regression.gaussianprocess
-
GaussianProcessRegression
- GaussianProcessRegression<T> - Class in smile.regression
-
Gaussian Process for Regression.
- GaussianProcessRegression() - Constructor for class com.actelion.research.calc.regression.gaussianprocess.GaussianProcessRegression
- GaussianProcessRegression(ParameterGaussianProcess) - Constructor for class com.actelion.research.calc.regression.gaussianprocess.GaussianProcessRegression
- GaussianProcessRegression(T[], double[], MercerKernel<T>, double) - Constructor for class smile.regression.GaussianProcessRegression
-
Constructor.
- GaussianProcessRegression(T[], double[], T[], MercerKernel<T>, double) - Constructor for class smile.regression.GaussianProcessRegression
-
Constructor.
- GaussianProcessRegression.Trainer<T> - Class in smile.regression
-
Trainer for Gaussian Process for Regression.
- GaussianRadialBasis - Class in smile.math.rbf
-
Gaussian RBF.
- GaussianRadialBasis() - Constructor for class smile.math.rbf.GaussianRadialBasis
-
Constructor.
- GaussianRadialBasis(double) - Constructor for class smile.math.rbf.GaussianRadialBasis
-
Constructor.
- GDIPolyPolygon(Polygon[]) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- generate(StereoMolecule) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- generate(StereoMolecule, Map<Integer, List<Integer>>, List<Set<Integer>>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
-
the parameter rings can be used for fragments/building blocks to submit atoms that will belong to a ring after they react
- generateConformerAndSetCoordinates(ConformerGenerator, int, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
-
08.03.2017 Method set to public for debugging purposes.
- generateConformerFromTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Computes a conformer from a TorsionSet object.
- generateConformerSet(StereoMolecule) - Method in class com.actelion.research.chem.conf.ConformerSetGenerator
-
Generates a set of distinct conformers of the canonical largest fragment of the passed molecule.
- generateDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.pharmacophoregraph.PharmGraphGenerator
- generateFragments() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- generateFragments() - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- generateFragmentsAllBonds() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- generateFragmentsForSingleBond(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- generateMutationList(StereoMolecule, int, boolean) - Method in class com.actelion.research.chem.Mutator
-
Creates a list of possible mutations and their probabilities
- generateOneConformer(long) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
Generates the coordinates for one conformer in the calling thread.
- generateOneConformerInPlace(long) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
This convenience method returns the StereoMolecule that has been passed to the constructor after modifying its atom coordinates to reflect the conformer internally created by generateOneConformer().
- generateRandomArray(double[][], String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- generateSmiles(ExtendedMolecule) - Method in class com.actelion.research.chem.SmilesCreator
-
Deprecated.
- generateSubPharmacophores(MolDistHist, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- generateSubPharmacophores(MolDistHistViz, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
-
Generates a list of sub-fragments.
- generateSubPharmacophores(MolDistHistViz, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- generateSubPharmacophores(List<MolDistHistViz>, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- generateSubPharmacophoresCheckedRange(MolDistHist, int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- GenericCanvas - Interface in com.actelion.research.gui.generic
- GenericCheckBox - Interface in com.actelion.research.gui.generic
- GenericComboBox - Interface in com.actelion.research.gui.generic
- GenericComponent - Interface in com.actelion.research.gui.generic
- GenericDepictor - Class in com.actelion.research.gui.generic
- GenericDepictor(StereoMolecule) - Constructor for class com.actelion.research.gui.generic.GenericDepictor
- GenericDepictor(StereoMolecule, int) - Constructor for class com.actelion.research.gui.generic.GenericDepictor
- GenericDialog - Interface in com.actelion.research.gui.generic
- GenericDialogHelper - Interface in com.actelion.research.gui.generic
- GenericDrawArea - Class in com.actelion.research.gui.editor
- GenericDrawArea(StereoMolecule, int, GenericDialogHelper, GenericCanvas) - Constructor for class com.actelion.research.gui.editor.GenericDrawArea
- GenericDrawContext - Interface in com.actelion.research.gui.generic
- GenericEditorToolbar - Class in com.actelion.research.gui.editor
- GenericEditorToolbar(GenericCanvas, GenericDrawArea) - Constructor for class com.actelion.research.gui.editor.GenericEditorToolbar
- GenericEditorToolbar(GenericCanvas, GenericDrawArea, int) - Constructor for class com.actelion.research.gui.editor.GenericEditorToolbar
- GenericKeyEvent - Class in com.actelion.research.gui.generic
- GenericKeyEvent(int, int, char, boolean) - Constructor for class com.actelion.research.gui.generic.GenericKeyEvent
- GenericKeyListener - Interface in com.actelion.research.gui.generic
- GenericLabel - Interface in com.actelion.research.gui.generic
- GenericMouseEvent - Class in com.actelion.research.gui.generic
- GenericMouseEvent(int, int, int, int, int, boolean, boolean, boolean, boolean) - Constructor for class com.actelion.research.gui.generic.GenericMouseEvent
- GenericMouseListener - Interface in com.actelion.research.gui.generic
- GenericPolygon - Class in com.actelion.research.gui.generic
- GenericPolygon() - Constructor for class com.actelion.research.gui.generic.GenericPolygon
- GenericPolygon(int) - Constructor for class com.actelion.research.gui.generic.GenericPolygon
- GenericPopupMenu - Interface in com.actelion.research.gui.generic
- GenericRectangle - Class in com.actelion.research.gui.generic
- GenericRectangle(double, double, double, double) - Constructor for class com.actelion.research.gui.generic.GenericRectangle
- GenericShape - Interface in com.actelion.research.gui.generic
- GenericTextField - Interface in com.actelion.research.gui.generic
- GeometryCalculator - Class in com.actelion.research.chem.descriptor.flexophore.calculator
-
Utility class to perform 3D geometry calculations on molecules
- GeometryCalculator - Class in com.actelion.research.chem.io.pdb.converter
-
Utility class to perform 3D geometry calculations on molecules
- GeometryCalculator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
- GeometryCalculator() - Constructor for class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
- geomFactory - Variable in class com.actelion.research.share.gui.editor.Model
- GeomFactory - Class in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:15 PM
- GeomFactory(DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.geom.GeomFactory
- get() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- get() - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
- get() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- get() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- get() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- get() - Method in class com.actelion.research.util.datamodel.ByteVec
- get() - Method in class com.actelion.research.util.datamodel.DoubleArray
- get() - Method in class com.actelion.research.util.datamodel.IntArray
- get() - Method in class com.actelion.research.util.datamodel.IntVec
- get() - Method in class com.actelion.research.util.DoubleVec
- get() - Method in class com.actelion.research.util.graph.complete.ContainerMemory
- get() - Static method in class com.actelion.research.util.Prefs
- get(double) - Method in class com.actelion.research.calc.BoxCox
- get(double, double) - Static method in class com.actelion.research.calc.Logarithm
- get(int) - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- get(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
- get(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
-
Returns a bit list.
- get(int) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- get(int) - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
-
Returns list with indices for fragments with
size
atoms. - get(int) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- get(int) - Method in class com.actelion.research.share.gui.Polygon
- get(int) - Method in class com.actelion.research.util.datamodel.ByteVec
- get(int) - Method in class com.actelion.research.util.datamodel.DoubleArray
- get(int) - Method in class com.actelion.research.util.datamodel.IntArray
- get(int) - Method in class com.actelion.research.util.datamodel.IntVec
- get(int) - Method in class com.actelion.research.util.DoubleVec
- get(int) - Method in class com.actelion.research.util.IntQueue
- get(int) - Method in class com.actelion.research.util.SortedList
-
Returns object at given index, or null if index==-1
- get(int) - Method in class com.actelion.research.util.UniqueList
- get(int) - Method in class smile.data.Dataset
-
Returns the element at the specified position in this dataset.
- get(int) - Method in class smile.math.SparseArray
-
Returns the value of i-th entry.
- get(int) - Method in class smile.sort.IntHeapSelect
-
Returns the i-th smallest value seen so far.
- get(int, int) - Method in class com.actelion.research.calc.Matrix
- get(int, int) - Method in interface com.actelion.research.chem.forcefield.mmff.Searchable
-
This should get an integer value given a column and row.
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.Separation
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- get(int, int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- get(int, int) - Method in class smile.math.matrix.JMatrix
- get(int, int) - Method in interface smile.math.matrix.Matrix
-
Returns the entry value at row i and column j.
- get(SortedPair) - Method in class com.actelion.research.chem.forcefield.mmff.Separation
-
Returns the relation of a given pair of atoms.
- get(DoubleArray) - Static method in class com.actelion.research.calc.statistics.StatisticsOverview
- get(Object) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- get(String) - Method in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
- get(String) - Method in class com.actelion.research.util.CommandLineParser
- get_bci_f(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
- get_bci_len() - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
- get_bci_n(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
- getAbs() - Method in class com.actelion.research.calc.Matrix
- getAbsoluteAtomParity(int) - Method in class com.actelion.research.chem.StereoMolecule
-
This returns the absolute(!) atom parity from the canonization procedure.
- getAbsoluteBondParity(int) - Method in class com.actelion.research.chem.StereoMolecule
-
This returns the absolute(!) bond parity from the canonization procedure.
- getAbsoluteBounds(Component) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Calculates bounds of the dockable relative to this JDockingPanel
- getAbsoluteMass(int, int) - Static method in class com.actelion.research.chem.IsotopeHelper
- getAbsoluteWeight() - Method in class com.actelion.research.chem.MolecularFormula
- getAcceptedFormats(Clipboard) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- getAcceptorCount() - Method in class com.actelion.research.chem.PropertyCalculator
- getAcceptorID() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- getActivationFunction() - Method in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- getActivationFunction(String) - Static method in class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkParameterHelper
- getActivationFunctionName(NeuralNetwork.ActivationFunction) - Static method in class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkParameterHelper
- getAdded() - Method in class com.actelion.research.util.Pipeline
- getAdjacencyList(int, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
- getAdjacencyListWithBondOrders(int, List<PharmacophoreTree.BiGramInt>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
- getAlignment() - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- getAlignment() - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getAlkyneAtomCount() - Method in class com.actelion.research.chem.conf.TorsionDetail
- getAllAtoms() - Method in class com.actelion.research.chem.Molecule
- getAllBonds() - Method in class com.actelion.research.chem.Molecule
- getAllCommonSubstructures() - Method in class com.actelion.research.chem.mcs.MCS
-
All molecules which are sub structures of an other molecule in the list are removed.
- getAllCommonSubstructures() - Method in class com.actelion.research.chem.mcs.MCSFast
-
All molecules which are sub structures of an other molecule in the list are removed.
- getAllConnAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getAllConnAtomsPlusMetalBonds(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getAllHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getAllOutOf(int, int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
-
Get all possible index combinations, order independent.
- getAllowedValences(int) - Static method in class com.actelion.research.chem.Molecule
-
For any known atomicNo this returns all allowed atom valences.
- getAllSubStrings(String, int) - Static method in class com.actelion.research.util.StringFunctions
- getAllSubtrees() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getAndSet(float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
- getAngle(double, double, double, double) - Static method in class com.actelion.research.chem.coords.InventorAngle
- getAngle(double, double, double, double) - Static method in class com.actelion.research.chem.Molecule
- getAngle(int, int, int) - Method in class com.actelion.research.chem.conf.BondAngleSet
-
Returns the preferred angle between to three atoms in a row as positive value <= pi.
- getAngle(Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Gets the angle formed between the 2 vectors ([0,PI])
- getAngle(Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
- getAngle(Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
- getAngle(Molecule3D, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Gets the Angle between 3 atoms
- getAngle(Molecule, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
- getAngle(StereoMolecule, int, int, int) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Gets the Angle between 3 atoms
- getAngleDif(double, double) - Static method in class com.actelion.research.chem.Molecule
- getAngleXY(Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Calculates the angle of the line from this location to c projected into the x/y plane.
- getAnisou() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getAppendedSorted(String, String) - Static method in class com.actelion.research.util.StringFunctions
- getAppliedRule() - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRuleEnhancedReactionMapper
- getArea() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getArea(double, double, double) - Static method in class com.actelion.research.calc.geometry.Triangle
- getAreaRightTriangle(double, double) - Static method in class com.actelion.research.calc.geometry.Triangle
- getAromaticRingCount() - Method in class com.actelion.research.chem.ExtendedMolecule
- getArray() - Method in class com.actelion.research.calc.Matrix
- getArrayAsInt() - Method in class com.actelion.research.calc.Matrix
- getArrayCopy() - Method in class com.actelion.research.calc.Matrix
- getArrIndexFrag() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- getArrIndexParentNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- getArrInnerLayerArchitecture() - Method in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- getArrMatchListFrag2Mol() - Method in class com.actelion.research.chem.mcs.MCS
-
delivers the match list indices from getMCSBondArray(...) index is the Fragment atom index, value is the matched atom index in molecule.
- getArrNode() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getArrowBoundingRect(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getAsBoolean(String) - Method in class com.actelion.research.util.CommandLineParser
-
Use contains(...) if only the flag is used.
- getAsDir(String) - Method in class com.actelion.research.util.CommandLineParser
- getAsDouble(String) - Method in class com.actelion.research.util.CommandLineParser
- getAsFile(String) - Method in class com.actelion.research.util.CommandLineParser
- getAsInt(String) - Method in class com.actelion.research.util.CommandLineParser
- getAsList() - Method in class com.actelion.research.util.datamodel.ModelXY
- getAsList(String) - Method in class com.actelion.research.util.CommandLineParser
- getAsListWithIndex() - Method in class com.actelion.research.util.datamodel.ModelXYIndex
- getAsLong(String) - Method in class com.actelion.research.util.CommandLineParser
- getAtom() - Method in class com.actelion.research.chem.CanonizerBaseValue
- getAtomAbnormalValence(int) - Method in class com.actelion.research.chem.Molecule
-
Get an atom's defined maximum valance if different from the default one.
- getAtomAmino(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomAndBondCounts(byte[], int, int[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Determines atom and bond counts of the given idcode
- getAtomAndBondCounts(String, int[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Determines atom and bond counts of the given idcode
- getAtomBfactor(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomChainId(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomCharge(int) - Method in class com.actelion.research.chem.Molecule
- getAtomCIPParity(int) - Method in class com.actelion.research.chem.Molecule
-
The atom Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
- getAtomColor(int) - Method in class com.actelion.research.chem.Molecule
- getAtomCoordinates() - Method in class com.actelion.research.chem.Molecule
- getAtomCount(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getAtomCount(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getAtomCustomLabel(int) - Method in class com.actelion.research.chem.Molecule
-
If a custom atom label is set, a molecule depiction displays the custom label instead of the original one.
- getAtomCustomLabelBytes(int) - Method in class com.actelion.research.chem.Molecule
-
This method is more efficient than getAtomCustomLabel(), because internally atom custom labels are stored as a byte[].
- getAtomDescription(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomESRGroup(int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- getAtomESRType(int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- getAtomFlags(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomFunctionalities() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.FeatureCalculator
- getAtomHashkey(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return a long representing the atom and its neighbours
- getAtomicGaussians() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- getAtomicNo() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getAtomicNo() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getAtomicNo(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getAtomicNo(int) - Method in class com.actelion.research.chem.Molecule
-
In addition to the natural atomic numbers, we support additional pseudo atomic numbers.
- getAtomicNoCodeString(int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getAtomicNoFromInteractionType(int) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getAtomicNoFromLabel(String) - Static method in class com.actelion.research.chem.Molecule
- getAtomicNoRGroup(int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Starts with 1 and goes until 16
- getAtomicNumber(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getAtomId() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getAtomId() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- getAtomIds(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
- getAtomIndex(int, int) - Method in class com.actelion.research.chem.RingCollection
- getAtomIndexConnectionFlexophorePoint() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- getAtomIndexFirstLinkerAtom() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- getAtomIndexLinkerId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getAtomIndices() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- getAtomKeySet() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getAtomKeyStrokeValidity(String) - Method in class com.actelion.research.share.gui.editor.Model
- getAtomLabel(int) - Method in class com.actelion.research.chem.Molecule
- getAtomList() - Method in class org.openmolecules.chem.conf.so.ConformationRule
- getAtomList(int) - Method in class com.actelion.research.chem.Molecule
-
The list of atoms that are allowed at this position during sub-structure search.
- getAtomListString(int) - Method in class com.actelion.research.chem.Molecule
- getAtomMapNo(int) - Method in class com.actelion.research.chem.Molecule
-
Returns an atom mapping number within the context of a reaction.
- getAtomMass(int) - Method in class com.actelion.research.chem.Molecule
- getAtomName() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getAtomName(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomPairsBondsTable(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MDHIndexTables
- getAtomPairSequenceCount() - Method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- getAtomParity(int) - Method in class com.actelion.research.chem.Molecule
-
The atom parity is a calculated property available above/equal helper level cHelperParities.
- getAtomPi(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
This is different from the Hendrickson pi-value, which considers pi-bonds to carbons only.
- getAtomPi(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an atom's pi electron count for the purpose of classifying a connected bond to determine its length.
- getAtomPreferredStereoBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates that single bond which is the preferred one to be converted into up/down bond in order to define the atom chirality.
- getAtomQueryFeatures(int) - Method in class com.actelion.research.chem.Molecule
-
Returns all set query features for this atom.
- getAtomRadical(int) - Method in class com.actelion.research.chem.Molecule
-
Gets an atom's radical state as singulet,dublet,triplet or none
- getAtomRegionNumbers(int[]) - Method in class com.actelion.research.chem.TautomerHelper
-
Identifies connected tautomeric regions and assign region numbers to all atoms.
- getAtomRingBondCount(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getAtomRingCount(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates the number of independent rings of which 'atom' is a member.
- getAtomRingSize(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getAtomRingSize(int) - Method in class com.actelion.research.chem.RingCollection
-
An atom's ring size is the size of the smallest ring the atom is a member of.
- getAtoms() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getAtoms() - Method in class com.actelion.research.chem.ExtendedMolecule
-
A validated molecule (after helper array creation) contains a sorted list of all atoms with the plain (neglegible) hydrogen atoms at the end of the list.
- getAtoms() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getAtoms() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getAtomSequence(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomsMolecule() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getAtomsOnPath(Molecule3D, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Finds on all atoms going on a path from a1 to a2.
- getAtomStrain(int) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- getAtomToGroups(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getAtomToGroups(Molecule3D, List<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
For each molecule in
mol
one group is created. - getAtomType(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
- getAtomType(int) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
-
Get the MMFF atom type of an atom.
- getAtomType(InteractionAtomTypeCalculator.FunctionalGroup, int, boolean, int, boolean) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getAtomType(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getAtomType(StereoMolecule, int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getAtomType(StereoMolecule, int, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getAtomTypeList() - Method in class com.actelion.research.chem.AtomTypeList
- getAtomTypes() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getAtomVolumes(StereoMolecule) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- getAtomX(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- getAtomX(int) - Method in class com.actelion.research.chem.Molecule
- getAtomY(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- getAtomY(int) - Method in class com.actelion.research.chem.Molecule
- getAtomZ(int) - Method in class com.actelion.research.chem.Molecule
- getAttachedHydrogenCount(int) - Method in class com.actelion.research.chem.Molecule3D
- getAuthor() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getAuxiliaryInfo(String) - Method in class com.actelion.research.chem.Molecule3D
- getAuxiliaryInfos() - Method in class com.actelion.research.chem.Molecule3D
- getAvailable() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- getAvailable() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getAverageBondLength() - Method in class com.actelion.research.chem.Molecule
-
Calculates and returns the mean bond length.
- getAverageBondLength() - Method in class com.actelion.research.chem.reaction.Reaction
- getAverageBondLength(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates and returns the mean bond length of all bonds including or not including hydrogen bonds.
- getAverageBondLength(int, int) - Method in class com.actelion.research.chem.Molecule
-
Calculates and returns the mean bond length of all bonds 0...bonds.
- getAverageBondLength(int, int, double) - Method in class com.actelion.research.chem.Molecule
-
Calculates and returns the mean bond length of all bonds 0...bonds.
- getAverageBondLength(int, int, double, Coordinates[]) - Method in class com.actelion.research.chem.Molecule
-
Calculates and returns the mean bond length of all bonds 0...bonds.
- getAverageBondLength(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getAverageTopologicalAtomDistance() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates for every non-H atom the mean value of all shortest routes (bonds in between) to any other atom of the same fragment.
- getB() - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- getB() - Method in class com.actelion.research.calc.regression.linear.pls.RegressionModelCalculatorOptimumFactors
- getBackbone(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getBackboneCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a hash code representing the structure or its largest fragment without stereo information and with all unsaturated bonds converted to single bonds.
- getBackboneHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getBackbones(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getBackbones(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Gets the backbone
- getBackground() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getBackground() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getBackgroundColor() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- getBackgroundColor() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getBackgroundColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getBackgroundColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getBackSpaceKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getBar() - Static method in class com.actelion.research.gui.JMessageBar
- getBase() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getBase() - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getBaseName(File) - Static method in class com.actelion.research.util.IO
- getBaseName(String) - Static method in class com.actelion.research.util.IO
- getBegin() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- getBegin() - Method in class com.actelion.research.util.IntQueue
- getBestCollidingTorsionIndexes() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
If no collision free torsion set can be constructed, this method is called to get the torsion set with the least atom collision strain.
- getBestMatch(MolDistHistViz, MolDistHistViz) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getBestMatch(MolDistHistViz, MolDistHistViz) - Method in interface com.actelion.research.chem.descriptor.flexophore.IDescriptorHandlerFlexophore
- getBestMatchingSolution() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- getBiasFactor(StereoMolecule) - Method in interface com.actelion.research.chem.MutationBiasProvider
- getBiggestFragment(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBiggestFragmentIDCode(String) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBin(int) - Method in class com.actelion.research.calc.histogram.Histogram
- getBindingSiteAtoms(StereoMolecule, Set<Integer>, MoleculeGrid, boolean) - Static method in class com.actelion.research.chem.docking.DockingEngine
- getBinIndex(double) - Method in class com.actelion.research.calc.histogram.Histogram
- getBinomialCoefficient(int, int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
-
Calculate binomial coefficient or n choose k
- getBins() - Method in class com.actelion.research.calc.histogram.Histogram
- getBinsEquallyDistributed(int, int) - Static method in class com.actelion.research.calc.histogram.IntegerHistogram
- getBinsEquallyDistributed(int, int, int) - Static method in class com.actelion.research.calc.histogram.IntegerHistogram
- getBinWidth() - Method in class com.actelion.research.calc.histogram.Histogram
- getBinWithNPercentOfAllCounts(int) - Method in class com.actelion.research.calc.histogram.IntegerHistogram
- getBitArray() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- getBitSetBits(BitSet) - Static method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
- getBitsSet() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- getBitsSet() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- getBitsSet() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- getBitsSet() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- getBitsSet() - Method in class com.actelion.research.util.datamodel.ByteVec
- getBitsSet() - Method in class com.actelion.research.util.datamodel.IntVec
- getBitsSet(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getBitWise() - Method in class com.actelion.research.util.datamodel.IntVec
- getBond() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getBond(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getBond(int, int) - Method in class com.actelion.research.chem.Molecule3D
- getBondAndFragmentCollisionIntensities(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
Calculates for every rotatable bond and for every rigid fragment a collision intensity sum for the given torsion/conformer state from the collision rules already known.
- getBondAngle(int, int) - Method in class com.actelion.research.chem.Molecule
- getBondAtom(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getBondAtom(int, int) - Method in class com.actelion.research.chem.Molecule
- getBondBridgeMaxSize(int) - Method in class com.actelion.research.chem.Molecule
- getBondBridgeMinSize(int) - Method in class com.actelion.research.chem.Molecule
- getBondCIPParity(int) - Method in class com.actelion.research.chem.Molecule
-
The bond Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
- getBondCount(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
- getBondESRGroup(int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- getBondESRType(int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- getBondID(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Constructs a bond classification index from a specific bond in a molecule.
- getBondIDString(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
- getBondIndex(int, boolean, boolean, int, int, int, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Constructs a bond classification ID from individual parameters and returns the ID's index in the sorted list of bond length information.
- getBondIndex(int, int) - Method in class com.actelion.research.chem.RingCollection
- getBondIndex(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Constructs a bond classification ID from a specific bond in a molecule and returns the ID's index in the sorted list of bond length information.
- getBondLength(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an estimate of the bond length based on atom and bond characteristics.
- getBondLength(int) - Method in class com.actelion.research.chem.Molecule
- getBondLengthFromCovalentRadii(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an estimate of the bond length based on atom and bond characteristics.
- getBondNo(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBondOrder(int) - Method in class com.actelion.research.chem.Molecule
-
Returns the formal bond order.
- getBondOrder(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBondParity(int) - Method in class com.actelion.research.chem.Molecule
-
Returns the pre-calculated bond parity, e.g.
- getBondParity(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBondPreferredStereoBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates that single bond which is the preferred one to be converted into up/down bond in order to define the bond chirality.
- getBondQueryFeatures(int) - Method in class com.actelion.research.chem.Molecule
- getBondRingSize(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getBondRingSize(int) - Method in class com.actelion.research.chem.RingCollection
-
A bond's ring size is the size of the smallest ring the bond is a member of.
- getBonds() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getBonds() - Method in class com.actelion.research.chem.ExtendedMolecule
-
The bond list is preprocessed such that all bonds leading to a plain hydrogen atom (natural abundance, no custom labels) are at the end of the list.
- getBonds() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getBondsAtMaxFrag() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getBondsBetweenFragments(int, int) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getBondsFragment() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- getBondsMolecule() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getBondsMolecule() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getBondStdDev(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
- getBondTorsion(int) - Method in class com.actelion.research.chem.conf.Conformer
-
Returns the current bond torsion angle in degrees, it is was set before.
- getBondType() - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- getBondType() - Method in class com.actelion.research.share.gui.editor.actions.DownBondAction
- getBondType() - Method in class com.actelion.research.share.gui.editor.actions.NewBondAction
- getBondType() - Method in class com.actelion.research.share.gui.editor.actions.UpBondAction
- getBondType(int) - Method in class com.actelion.research.chem.Molecule
-
Returns bond type combining bond order and stereo orientation.
- getBondType(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBondTypeSimple(int) - Method in class com.actelion.research.chem.Molecule
-
This is the bond type without stereo information.
- getBorderColor() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getBorderInsets(Component) - Method in class com.actelion.research.gui.dock.ShadowBorder
- getBordersMostFreqOccBin(Matrix, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
-
Gets the upper and lower limit of the most occupied bin.
- getBoundingBox() - Method in class com.actelion.research.share.gui.Polygon
- getBoundingRect() - Method in class com.actelion.research.chem.AbstractDepictor
- getBoundingRect() - Method in class com.actelion.research.share.gui.Arrow
- getBoundingRect() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- getBoundingRect() - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- getBoundingRect(ExtendedMolecule) - Static method in class com.actelion.research.chem.ChemistryHelper
- getBoundingRect(ExtendedMolecule[]) - Static method in class com.actelion.research.chem.ChemistryHelper
- getBoundingRect(Reaction, boolean) - Static method in class com.actelion.research.chem.ChemistryHelper
- getBoundingRect(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getBoundingRect(GenericDrawContext) - Method in class com.actelion.research.chem.AbstractDrawingObject
- getBoundingRect(GenericDrawContext) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- getBoundingRect(GenericDrawContext) - Method in class com.actelion.research.chem.TextDrawingObject
- getBounds() - Method in class com.actelion.research.gui.dock.TreeLeaf
- getBounds() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
- getBounds(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Gets the Bounds of a molecule
- getBounds(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getBounds(StereoMolecule) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Gets the Bounds of a molecule
- getBounds(Rectangle2D.Double) - Method in class com.actelion.research.chem.Molecule
- getBounds(String) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- getBounds(String) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- getBounds(String) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- getBounds(String) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- getBrushFillStyle() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getBufferedReader(String) - Static method in class com.actelion.research.util.IO
-
Do not forget to close BufferedReader
- getBuffWrite(String, boolean) - Static method in class com.actelion.research.util.IO
- getBumpTerm() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getBuriedness(int[]) - Method in class com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage
- getButton() - Method in class com.actelion.research.gui.generic.GenericMouseEvent
- getButtonImage(boolean) - Method in class com.actelion.research.share.gui.editor.ImageProvider
- getButtonLocation(int) - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- getButtonLocation(int) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- getButtonNo(GenericMouseEvent) - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- getButtonNo(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- getByte(int) - Method in class com.actelion.research.util.datamodel.IntVec
- getByte(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getByteVec() - Method in class com.actelion.research.util.datamodel.IntVec
- getByteVec(int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getByteVec(int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getByteWise() - Method in class com.actelion.research.util.datamodel.IntVec
- getCalculatedSimilarityValues() - Method in class com.actelion.research.calc.SimilarityMulticore
- getCalculationsPerSecond() - Method in class com.actelion.research.calc.SimilarityMulticore
- getCandidatePose() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getCanMolecule() - Method in class com.actelion.research.chem.Canonizer
- getCanMolecule(boolean) - Method in class com.actelion.research.chem.Canonizer
- getCanonizer() - Method in class com.actelion.research.chem.StereoMolecule
-
This is a convenience method returning the StereoMolecule's Canonizer object after calling internally ensureHelperArrays(cHelperParities) and, thus, effectively running the canonicalization and validating the Canonizer itself.
- getCapacity() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- getCapacity() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getCapacity() - Method in class com.actelion.research.util.datamodel.IntArray
- getCapacityLimitBreakes() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
-
Is increased by one if more than the the allowed number of fragments was generated.
- getCartCoordinates(int[]) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getCartesianTorsionGradient(int[], Conformer, double[], double, Coordinates[], int[][]) - Static method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
- getCartState() - Method in class com.actelion.research.chem.docking.LigandPose
- getCatalyst(int) - Method in class com.actelion.research.chem.reaction.Reaction
- getCatalystData() - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getCatalysts() - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getCatalysts() - Method in class com.actelion.research.chem.reaction.Reaction
- getcAtomColor2String(int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getCaveat() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getCcMissedMinRange() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- getCcViolatedMaxRange() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- getCcViolatedMinDiffInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- getCenter() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- getCenter() - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- getCenter(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getCentered(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCenteredMatrix() - Method in class com.actelion.research.calc.Matrix
- getCenteredMatrix(Matrix) - Method in class com.actelion.research.calc.Matrix
- getCenterGravity(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMolecule
- getCenterGravity(ExtendedMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMolecule
- getCenterGravity(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Gets the center of Gravity of a molecule
- getCenterGravity(StereoMolecule) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Gets the center of Gravity of a molecule
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- getCenterID() - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- getCentralAtom(int) - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns one of the atoms of the torsion fragment's central rotatable bond.
- getCEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getChainID() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getChainID() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getChainLength() - Method in class com.actelion.research.chem.coords.InventorChain
- getChaos() - Method in class com.actelion.research.calc.SelfOrganizedMap
- getCharge() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getChargeAtom() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getChargedGroups() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargedGroupDetector
- getCharges(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Charge
-
Computes the partial MMFF charges.
- getChargeType(int) - Static method in class com.actelion.research.chem.io.Mol2FileParser
- getCheckerArray() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- getChemDrawBuffer(Reaction) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- getChemDrawBuffer(StereoMolecule) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- getChemistryBounds() - Method in class com.actelion.research.gui.JChemistryView
- getChemistryType() - Method in class com.actelion.research.gui.JChemistryView
- getChild() - Method in class com.actelion.research.gui.dock.TreeRoot
- getChildFieldIndex(String, String) - Method in class com.actelion.research.chem.io.DWARFileParser
- getChirality() - Method in class com.actelion.research.chem.Molecule
-
Gets the overall chirality of the molecule, which is a calculated information considering: Recognition of stereo centers and stereo bonds, defined ESR features, meso detection.
- getChiralText() - Method in class com.actelion.research.chem.ExtendedMolecule
- getChiralText() - Method in class com.actelion.research.chem.StereoMolecule
- getCisPep() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getClassification() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getClassificationResult() - Method in class com.actelion.research.chem.reaction.ReactionClassifier
- getClickCount() - Method in class com.actelion.research.gui.generic.GenericMouseEvent
- getClip() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getClip() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getClipboardData(String) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- getClipboardHandler() - Method in class com.actelion.research.gui.CompoundCollectionPane
- getClipboardHandler() - Method in class com.actelion.research.gui.JStructureView
- getClipBounds() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getClipBounds() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getCLogPIncrements(StereoMolecule, float[]) - Method in class com.actelion.research.chem.prediction.CLogPPredictor
-
Normalizes ambiguous bonds and assigns cLogP increments to every atom based on its enhanced atom type.
- getClosestNeighbour(Coordinates, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Returns the closest neighbour.
- getClusterCenter(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
-
Calculates for nodes cluster the node with the minimum rmsd to the cluster center.
- getClusterCount() - Method in class com.actelion.research.chem.Clusterer
- getClusterLabel() - Method in class smile.clustering.PartitionClustering
-
Returns the cluster labels of data.
- getClusterMember() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- getClusterNo(int) - Method in class com.actelion.research.chem.Clusterer
- getClusterSize() - Method in class smile.clustering.PartitionClustering
-
Returns the size of clusters.
- getCode() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- getCoefficients() - Method in class com.actelion.research.util.FastSpline.Polynome
- getCoefficientVariation() - Method in class com.actelion.research.calc.Matrix
-
Coefficient of variation (CV) is a normalized measure of dispersion of a probability distribution.
- getCol(int) - Method in class com.actelion.research.calc.Matrix
- getColAsDouble(int) - Method in class com.actelion.research.calc.Matrix
- getColAsFloat(int) - Method in class com.actelion.research.calc.Matrix
- getColAsInt(int) - Method in class com.actelion.research.calc.Matrix
- getColAsList(int) - Method in class com.actelion.research.calc.Matrix
- getColDim() - Method in class com.actelion.research.calc.Matrix
- getColIndexContainingMaxVal(int) - Method in class com.actelion.research.calc.Matrix
- getColIndexContainingMaxVal(int, int) - Method in class com.actelion.research.calc.Matrix
- getCollisionIntensity() - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
- getCollisionIntensityMatrix() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getCollisionIntensitySum() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getCollisionList() - Method in class com.actelion.research.chem.coords.InventorFragment
- getCollisionPanalty() - Method in class com.actelion.research.chem.coords.InventorFragment
- getColName(int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- getColor() - Method in class com.actelion.research.gui.ComboBoxColorItem
- getColor() - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- getColor() - Method in class com.actelion.research.gui.swing.SwingDrawContext
- getColor() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getColor() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getColor(Color) - Method in class com.actelion.research.gui.ComboBoxColorItem
- getColorRecord(Molecule, Collection<Integer>, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getColorVal2String(Molecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getColorVectorSubstructure(StereoMolecule, StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Returns the colors vector for the substructure in mol.
- getCols() - Method in class com.actelion.research.util.datamodel.table.TableModelString
- getColumnProperties(String) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
This method, when called after calling setMasterCopy() or after completing defining columns, returns the column properties of the given column.
- getColumnProperties(String) - Method in class com.actelion.research.chem.io.DWARFileParser
-
Returns the original column properties of any source column by column name.
- getColumns(int[]) - Method in class com.actelion.research.calc.Matrix
- getColumns(List<Integer>) - Method in class com.actelion.research.calc.Matrix
- getColumns(Vector<Integer>) - Method in class com.actelion.research.calc.Matrix
-
Deprecated.use getColumns(List
vecIndices) instead - getColumnTitles() - Method in class com.actelion.research.chem.io.DWARFileCreator
-
This method, when called after calling setMasterCopy() or after completing defining columns, returns the list of defined column names in the correct order.
- getCOM() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- getCOM(Conformer) - Static method in class com.actelion.research.chem.docking.DockingUtils
- getCOM(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingUtils
- getCombinations(List<int[]>) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
- getComment() - Method in class com.actelion.research.chem.StructureInfo
- getCompactCopy() - Method in class com.actelion.research.chem.ExtendedMolecule
- getCompactCopy() - Method in class com.actelion.research.chem.StereoMolecule
- getCompactMolecule(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
- getCompactMolecule(byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
- getCompactMolecule(byte[], byte[], int, int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getCompactMolecule(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getCompactMolecule(BufferedReader) - Method in class com.actelion.research.chem.MolfileParser
- getCompactMolecule(File) - Method in class com.actelion.research.chem.MolfileParser
- getCompactMolecule(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
- getCompactMolecule(String) - Method in class com.actelion.research.chem.MolfileParser
- getCompactMolecule(String, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
- getComparatorArea() - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getComparatorAtomsBonds() - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getComparatorBonds() - Static method in class com.actelion.research.chem.mcs.ModelSampleFragments
- getComparatorCoverage() - Static method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- getComparatorDouble() - Static method in class com.actelion.research.util.datamodel.IntegerDouble
- getComparatorError() - Static method in class com.actelion.research.calc.regression.ModelError
- getComparatorId() - Static method in class com.actelion.research.util.datamodel.IdentifiedObject
- getComparatorInt() - Static method in class com.actelion.research.util.datamodel.IntegerDouble
- getComparatorLength() - Static method in class com.actelion.research.util.StringFunctions
- getComparatorNumBonds() - Static method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getComparatorNumIndices() - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- getComparatorOrderNumber() - Static method in class com.actelion.research.chem.Element
- getComparatorScore() - Static method in class com.actelion.research.util.datamodel.ScorePoint
- getComparatorX() - Static method in class com.actelion.research.util.datamodel.ScorePoint
- getComparatorX() - Static method in class com.actelion.research.util.PointUtils
- getComparatorY() - Static method in class com.actelion.research.util.datamodel.ScorePoint
- getComparatorY(int) - Static method in class com.actelion.research.util.datamodel.XY
- getCompatibleFileList(File, int) - Static method in class com.actelion.research.gui.FileHelper
- getComplexityScore() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getComponent() - Method in class com.actelion.research.gui.dock.TreeElement
- getComponent() - Method in class com.actelion.research.gui.swing.SwingComponent
- getComponents() - Method in class smile.stat.distribution.Mixture
-
Returns the list of components in the mixture.
- getComposite() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getCompound() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getCompound(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- getCompound(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- getConformer(int) - Method in class com.actelion.research.chem.phesa.PheSAMolecule
- getConformer(MolecularVolume) - Method in class com.actelion.research.chem.phesa.PheSAMolecule
-
Returns the corresponding conformer of a molecular volume
- getConformerCount() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
- getConformerCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getConformerIndex() - Method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer.AlignmentResult
- getConformerIndexes() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getConformerLikelihood(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getConnAngle(int, int, int) - Method in class com.actelion.research.chem.conf.BondAngleSet
-
Returns the preferred angle between to three atoms in a row as positive value <= pi.
- getConnAtom(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getConnAtom(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getConnAtom(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getConnAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getConnBond(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getConnBond(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getConnBondOrder(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getConnectionID() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- getConnectionPointCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getConnectionTable(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MDHIndexTables
- getConnexComponents(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Returns a List of all Connex Components of the graph (List of List of Integer)
- getContainer() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- getContent() - Method in class com.actelion.research.gui.dock.Dockable
-
Returns the content - null, if none has been set.
- getContent(MouseEvent) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- getContext() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- getContrastColor(Color, Color) - Static method in class com.actelion.research.util.ColorHelper
-
Based on the differences of hue and perceived brightness of foreground color
fg
and background colorbg
, this method checks and possibly adjusts the given foreground colorfg
such that its hue stays unchanged, but its brightness is adapted to make it better perceivable on the background. - getContribution(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
With best current knowledge about colliding torsion combinations and based on the individual frequencies of currently active torsions this method returns the conformers's overall contribution to the total set of non colliding conformers.
- getContributions() - Method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
- getContributions() - Method in class com.actelion.research.chem.docking.LigandPose
- getContributions() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getContributions() - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
- getContributions() - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- getContributions() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- getConverted2CarbonSkeleton(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Replaces all hetero-atoms, except hydrogen, with carbon.
- getCoord() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- getCoordinates() - Method in class com.actelion.research.chem.conf.Conformer
- getCoordinates() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- getCoordinates() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- getCoordinates() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getCoordinates() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Either getIDCode and this method or getMolecule() must be overwritten!!!
- getCoordinates() - Method in class com.actelion.research.chem.io.DWARFileParser
-
This returns encoded atom coordinates according to the defined mode.
- getCoordinates() - Method in class com.actelion.research.chem.io.ODEFileParser
- getCoordinates() - Method in class com.actelion.research.chem.Molecule3D
- getCoordinates() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
- getCoordinates(int) - Method in class com.actelion.research.chem.conf.Conformer
- getCoordinates(int) - Method in class com.actelion.research.chem.Molecule
- getCoordinates(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns the encoded reaction coordinates.
- getCoordinates(Molecule, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
- getCoordinates(StereoMolecule, int) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
- getCoordinates2D() - Method in class com.actelion.research.chem.io.DWARFileParser
- getCoordinates3D() - Method in class com.actelion.research.chem.io.DWARFileParser
- getCoordinatesA() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getCoordinatesB() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getCoordinatesC() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getCopy() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
node deep copy.
- getCopy() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getCoreCoordinates(int, int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getCoreCount() - Method in class com.actelion.research.chem.MarkushStructure
- getCoreSize() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getCoreStructure(int) - Method in class com.actelion.research.chem.MarkushStructure
- getCorrPearson(double[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCorrPearson(Matrix, int, int) - Static method in class com.actelion.research.calc.MatrixFunctions
- getCorrPearson(Matrix, Matrix) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCorrPearson(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getCorrPearson(List<PointDouble>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCorrPearsonStandardized(double[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCorrSpearman(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getCosine(double[], double[]) - Static method in class com.actelion.research.calc.distance.DistanceMetrics
- getCosine(int[], int[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getCosine(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getCosine(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Vectors have to be normed!
- getCount() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
- getCountFromType(long) - Method in class com.actelion.research.chem.AtomTypeList
- getCovalentRadius() - Method in class com.actelion.research.chem.Element
- getCovalentRadius(int) - Static method in interface com.actelion.research.chem.conf.VDWRadii
- getCovariance(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getCovarianceCentered(double[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCovarianceCentered(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getCovarianceMatrix() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getCovarianceMatrix() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- getCreatedSolutions() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- getCreationMode() - Method in class com.actelion.research.calc.SelfOrganizedMap
- getCRingClosureName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getCRingOpeningName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getCRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getCryst1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getCurrentDirectory() - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- getCurrentPositions() - Method in interface com.actelion.research.chem.forcefield.ForceField
- getCurrentPositions() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- getCursor() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.DeleteAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- getCursor(int) - Static method in class com.actelion.research.util.CursorHelper
- getCustomTemplateAtomMask() - Method in class com.actelion.research.chem.coords.CoordinateInventor
- getD() - Method in class smile.math.matrix.EVD
-
Returns the block diagonal eigenvalue matrix whose diagonal are the real part of eigenvalues, lower subdiagonal are positive imaginary parts, and upper subdiagonal are negative imaginary parts.
- getData() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getData() - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- getData() - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
- getData() - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
- getData(String) - Method in class com.actelion.research.chem.StructureInfo
- getDateDeposition() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getDateFloat(String) - Method in class com.actelion.research.util.DateAnalysis
- getDateMillis(String) - Method in class com.actelion.research.util.DateAnalysis
- getDBRef() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getDBRef1DBRef2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getDConstructionName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getDecimalFormat(int) - Static method in class com.actelion.research.util.StringFunctions
- getDeepClone() - Method in interface com.actelion.research.util.datamodel.IModelCloneable
- getDeepClone() - Method in class com.actelion.research.util.datamodel.ModelXY
- getDeepClone() - Method in class com.actelion.research.util.datamodel.ModelXYClassLabel
- getDeepClone() - Method in class com.actelion.research.util.datamodel.ModelXYColTags
- getDeepClone() - Method in class com.actelion.research.util.datamodel.ModelXYIndex
- getDefaultAverageBondLength() - Static method in class com.actelion.research.chem.Molecule
- getDefaultDescriptorHandler(String) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandlerFactory
- getDefaultDescriptorHandler(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- getDefaultDescriptorHandler(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
- getDefaultDescriptorHandler(String) - Method in interface com.actelion.research.chem.descriptor.ISimilarityHandlerFactory
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getDefaultInstance() - Static method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getDefaultInstance() - Static method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getDefaultMaxValenceUncharged(int) - Method in class com.actelion.research.chem.Molecule
-
This is the default maximum valence of the atom neglecting atom charge or radical influences, e.g.
- getDelay() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getDeleteAtomsBondMap(boolean[]) - Method in class com.actelion.research.chem.Molecule
- getDeleteAtomsBondMap(int[]) - Method in class com.actelion.research.chem.Molecule
- getDeleteColsZeroVar(List<Integer>) - Method in class com.actelion.research.calc.Matrix
-
Deletes columns with zero variance.
- getDeleteKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getDeltaNanoBaseBlur() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getDeltaNanoQueryBlur() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getDeltaNanoSimilarity() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getDensity() - Method in class com.actelion.research.chem.StructureInfo
- getDEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getDepictor() - Method in class com.actelion.research.gui.JStructureView
- getDescription() - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Returns the human readable description of this filter.
- getDescription() - Method in class smile.data.Attribute
- getDescription() - Method in class smile.data.Dataset
-
Returns the detailed dataset description.
- getDescriptor() - Method in class com.actelion.research.chem.AbstractDrawingObject
- getDescriptor(int) - Method in class com.actelion.research.chem.StructureSearchSpecification
-
Depending on the mode isLargestFragmentOnly() the descriptor is expected to be represent the whole structure or the largest fragment.
- getDescriptor(int, int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
- getDescriptor(String) - Method in class com.actelion.research.chem.io.CompoundFileParser
-
If the file source contains encoded descriptors, then overwrite this method to save the calculation time.
- getDescriptor(String) - Method in class com.actelion.research.chem.io.DWARFileParser
- getDescriptorColumn(String) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a number to be used in getDescriptor() to address the the descriptor with the given short name.
- getDescriptorDetail() - Method in class com.actelion.research.chem.AbstractDrawingObject
-
Creates a string encoding all properties specific to this drawing object.
- getDescriptorDetail() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- getDescriptorDetail() - Method in class com.actelion.research.chem.TextDrawingObject
- getDescriptorHandlerFactory() - Method in class com.actelion.research.chem.io.CompoundFileParser
- getDescriptorInfo(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getDescriptorShortName() - Method in class com.actelion.research.chem.StructureSearchSpecification
- getDescriptorType(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getDetail() - Method in class com.actelion.research.chem.prediction.DruglikenessPredictor
-
If assessDruglikeness() was called multiple times in multiple threads, then getDetail() won't retrieve the expected detail.
- getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.CLogPPredictor
- getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.SolubilityPredictor
- getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
- getDetail(StereoMolecule, int) - Method in class com.actelion.research.chem.prediction.ToxicityPredictor
- getDetails() - Method in class com.actelion.research.chem.io.DWARFileParser
-
Provided that the mode contains MODE_EXTRACT_DETAILS, then this method returns a map of all embedded detail objects of the DWAR file.
- getDeviceConfiguration() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getDFragmentationName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getDiagonal() - Method in class com.actelion.research.calc.Matrix
-
Matrix diagonal extraction.
- getDiffRect(Rectangle2D, Rectangle2D) - Static method in class com.actelion.research.chem.ChemistryHelper
- getDihedral(Coordinates, Coordinates, Coordinates) - Method in class com.actelion.research.chem.Coordinates
- getDihedral(Coordinates, Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.Coordinates
-
Calculates a signed torsion as an exterior spherical angle from a valid sequence of 4 points in space.
- getDihedral(Molecule3D, int, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Gets the Dihedral Angle between 4 atoms
- getDihedral(StereoMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Gets the Dihedral Angle between 4 atoms
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- getDirectionality() - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- getDirectSim(PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getDiscreteValue(double) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getDisplayMode() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getDisplayMode() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getDisplayMode() - Method in class com.actelion.research.gui.JStructureView
- getDisplayMode() - Method in class com.actelion.research.share.gui.editor.Model
- getDisplayMolecule() - Method in class com.actelion.research.gui.JStructureView
- getDisplaySize() - Method in class com.actelion.research.share.gui.editor.Model
- getDisposalMethod() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getDissimilarity(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
-
D(LigandType_1, LigandType_2) = Sum( d( F(ProteinType_i, LigandType_1), F(ProteinType_i, LigandType_2)), i)
- getDissimilarity(TorsionDescriptor, float[]) - Method in class com.actelion.research.chem.conf.TorsionDescriptor
-
Calculates a similarity value between td and this considering individual torsion values, the importance of the rotatable bond, and the ratio of rotatable/non-rotatable bonds.
- getDissimilarity(Object, Object) - Method in class com.actelion.research.calc.BinarySOM
- getDissimilarity(Object, Object) - Method in class com.actelion.research.calc.SelfOrganizedMap
- getDissimilarity(Object, Object) - Method in class com.actelion.research.calc.VectorSOM
- getDistance(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
- getDistanceArray(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getDistanceHistogram() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getDistanceMatrix(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getDistanceMatrix(List<Point>) - Static method in class com.actelion.research.calc.MatrixFunctions
- getDistanceMatrixTanimotoInv(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
-
Calculates the inverse Tanimoto coefficient from row wise comparison of the two input matrices.
- getDistanceTables() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getDistanceTanimotoInv(Matrix, int, Matrix, int) - Static method in class com.actelion.research.calc.MatrixFunctions
- getDistHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getDistHist(int, int, byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getDistHist(int, int, byte[]) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- getDistHist(MultCoordFragIndex, MultCoordFragIndex) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- getDistHists() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getDistTanimotoInvReduced(Matrix, int, Matrix, int) - Static method in class com.actelion.research.calc.MatrixFunctions
-
Only fields are considered which are not nut 0 in both or in one of the rows we from where the distance is calculated.
- getDistTanimotoInvReduced(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getDividerLocation() - Method in class com.actelion.research.gui.dock.TreeFork
- getDockable() - Method in class com.actelion.research.gui.dock.DockableHeader
- getDockable(int) - Method in class com.actelion.research.gui.dock.TreeLeaf
- getDockable(Component) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Returns the Dockable that contains the given content.
- getDockable(String) - Method in class com.actelion.research.gui.dock.JDockingPanel
- getDockableCount() - Method in class com.actelion.research.gui.dock.JDockingPanel
- getDockableCount() - Method in class com.actelion.research.gui.dock.TreeLeaf
- getDockables() - Method in class com.actelion.research.gui.dock.JDockingPanel
- getDockableTitles() - Method in class com.actelion.research.gui.dock.JDockingPanel
- getDockInfoSequence() - Method in class com.actelion.research.gui.dock.JDockingPanel
-
returns the persistence information necessary to recreate the current docking state.
- getDockingPanel() - Method in class com.actelion.research.gui.dock.Dockable
- getDonorCount() - Method in class com.actelion.research.chem.PropertyCalculator
- getDouble() - Method in class com.actelion.research.util.datamodel.IntegerDouble
- getDoublePivot() - Method in class com.actelion.research.calc.LUDecomposition
-
Return pivot permutation vector as a one-dimensional double array
- getDragable(Point) - Method in class com.actelion.research.gui.dock.TreeLeaf
- getDraggedDockable(DropTargetDragEvent) - Method in class com.actelion.research.gui.dock.JDockingPanel
- getDragHandle() - Method in class com.actelion.research.gui.dock.Dockable
- getDrawArea() - Method in class com.actelion.research.gui.editor.SwingEditorDialog
- getDrawArea() - Method in class com.actelion.research.gui.editor.SwingEditorPanel
- getDrawArea() - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- getDrawArea() - Method in class com.actelion.research.gui.JDrawPanel
-
Deprecated.
- getDrawConfig() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getDrawContext() - Method in class com.actelion.research.gui.editor.SwingEditorArea
- getDrawContext() - Method in class com.actelion.research.gui.editor.SwingEditorToolbar
- getDrawContext() - Method in interface com.actelion.research.gui.generic.GenericCanvas
- getDrawingObjects() - Method in class com.actelion.research.chem.reaction.Reaction
- getDrawingObjects() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getDrawingObjects() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getDrawingObjects() - Method in class com.actelion.research.share.gui.editor.Model
- getDruglikenessString(StereoMolecule) - Method in class com.actelion.research.chem.prediction.DruglikenessPredictor
- getDRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getDummy() - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getEdgeLengths() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getEdges() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getEEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getEFGName(int, int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getEigenValues() - Method in class smile.math.matrix.EVD
-
Returns the eigenvalues, ordered from largest to smallest.
- getEigenvector(Matrix, int, Matrix, Matrix) - Static method in class com.actelion.research.calc.Matrix
-
Householder reduction according num rec 11.2.
- getEigenVectors() - Method in class smile.math.matrix.EVD
-
Returns the eigenvector matrix, ordered by eigen values from largest to smallest.
- getElectronegativity() - Method in class com.actelion.research.chem.Element
- getElectronValenceCorrection(int, int) - Method in class com.actelion.research.chem.Molecule
-
This is the maximum valence correction caused by atom charge or radical status, e.g.
- getElement(int) - Static method in class com.actelion.research.chem.PeriodicTable
- getEliminationRuleList() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getEncodedCoordinates() - Method in class com.actelion.research.chem.Canonizer
-
Encodes the molecule's atom coordinates into a compact String.
- getEncodedCoordinates() - Method in class com.actelion.research.chem.SimpleCanonizer
- getEncodedCoordinates(boolean) - Method in class com.actelion.research.chem.Canonizer
-
Encodes the molecule's atom coordinates into a compact String.
- getEncodedCoordinates(boolean, Coordinates[]) - Method in class com.actelion.research.chem.Canonizer
-
Encodes the molecule's atom coordinates into a compact String.
- getEncodedMapping() - Method in class com.actelion.research.chem.Canonizer
- getEncodedQuery(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Returns the (or one of the) query structures encodes as idcode.
- getEnd() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- getEnd() - Method in class com.actelion.research.util.IntQueue
- getEnergy() - Method in class com.actelion.research.chem.conf.Conformer
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.AngleBend
-
Calculates the angle energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Calculates the bond stretch energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Calculates the electrostatic energy.
- getEnergy(double[]) - Method in interface com.actelion.research.chem.forcefield.mmff.EnergyTerm
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFExternalPositionConstraint
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFPositionConstraint
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Calculates the out of plane energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Calculates the stretch bend energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Calculates the torsional energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
-
Calculates the van der Waals energy.
- getEnterKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getEquivalentTypes(int, double) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
-
Compare similarity values of 2 types (across all lines)
- getERearrangementName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getERegNo() - Method in class com.actelion.research.chem.io.RDFileParser
- getError(List<ModelError>) - Static method in class com.actelion.research.calc.regression.ModelError
- getErrorAverage(List<ModelError>) - Static method in class com.actelion.research.calc.regression.ModelError
- getErrorCount() - Method in class com.actelion.research.chem.io.CompoundFileHelper
- getErrors() - Method in class com.actelion.research.chem.io.AbstractParser
- getERxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getEscapeKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getESRGroupMemberCounts() - Method in class com.actelion.research.chem.StereoMolecule
- getESRImage(boolean) - Method in class com.actelion.research.share.gui.editor.ImageProvider
- getESRImageRows() - Method in class com.actelion.research.share.gui.editor.ImageProvider
- getESRType() - Method in class com.actelion.research.share.gui.editor.Model
- getEuclidDist(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Euclidean distance
- getEuclidDistBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getEuclidDistFast(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Euclidean distance without sqrt
- getEuclideanDistanceFast(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Euclidean distance without sqrt
- getEuclideanDistanceFastRows(int, int) - Method in class com.actelion.research.calc.Matrix
-
Skipping the sqrt.
- getEuclideanDistanceFastRows(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
-
Skipping the sqrt.
- getEventConsumer() - Method in interface com.actelion.research.gui.generic.GenericComponent
- getEventConsumer() - Method in class com.actelion.research.gui.swing.SwingComponent
- getEventConsumer() - Method in class com.actelion.research.gui.swing.SwingDialog
- getExactHash(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns a hash code representing the exact reaction.
- getExcludedNeighbourCount(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
This method returns the count of atom neighbours which are marked as being an exclude group.
- getExhaustiveStatistics() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getExitAtoms() - Method in class com.actelion.research.chem.shredder.Fragment3D
- getExitVectorGaussians() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- getExpdata() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getExplainedVarS() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getExplainedVarX() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getExplainedVarY() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getExplicitHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getExplicitHydrogens(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getExponent(double) - Static method in class smile.math.Math
-
Returns the unbiased exponent used in the representation of a double.
- getExponent(float) - Static method in class smile.math.Math
-
Returns the unbiased exponent used in the representation of a float.
- getExtendedAtomSequence(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
If the atom sequence contains a straight chain of sp-hybridized atoms, then the atom array contain the first two and last two atoms of a sequence of 2n+4 atoms (n: number of conjugated triple bonds).
- getExtendedCoordinates(int, int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getExtendedSize() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getExtension(int) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- getExtension(File) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Return the extension portion of the file's name .
- getExtension(File) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
-
Return the extension portion of the file's name.
- getExtension(File) - Static method in class com.actelion.research.util.IO
- getExtensionCuts(List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
get a list of int[] arrays that define an extension cut: Given a subtree with a designated head-node, an extension cut separates an extension match from the remaining subtrees.
- getExtensionList(int) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- getEZParity(int) - Method in class com.actelion.research.chem.Canonizer
-
Returns the absolute bond parity, which is based on priority ranks.
- getFactorial(int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
- getFactorIsomorphSymmetric() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getFactors() - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- getFactorsMin() - Method in class com.actelion.research.calc.regression.linear.pls.RegressionModelCalculatorOptimumFactors
- getFactory() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- getFactory() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
- getFailureCount() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getFalseNegative() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- getFalsePositive() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- getFcadj(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
-
Returns the formal charge adjustment for a given atom type.
- getFFP() - Method in class com.actelion.research.chem.coords.InventorTemplate
- getFGValue(double) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getFGValue(double[]) - Method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.LigandPose
-
Fuhrmann J, Rurainski A, Lenhof HP, Neumann D.
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.chemscore.HBTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.chemscore.MetalTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.chemscore.SimpleMetalTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.idoscore.InteractionTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- getFGValue(double[]) - Method in interface com.actelion.research.chem.optimization.Evaluable
- getFGValue(double[]) - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- getFGValue(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.AngleConstraint
- getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.BondConstraint
- getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.EmpiricalLigandStrain
- getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.PositionConstraint
- getFGValue(double[]) - Method in interface com.actelion.research.chem.potentialenergy.PotentialEnergyTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.TorsionConstraint
- getFGValuePP(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getFGValueSelfPP(double[], ShapeVolume, boolean) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getFGValueShape(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
-
calculates the gradient of the overlap function with respect to the cartesian coordinates of the atoms
- getFGValueShapeSelf(double[], ShapeVolume, boolean) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getFieldData() - Method in class com.actelion.research.chem.io.RDFileParser
- getFieldData(int) - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Returns the cell content of the current row.
- getFieldData(int) - Method in class com.actelion.research.chem.io.DWARFileParser
- getFieldData(int) - Method in class com.actelion.research.chem.io.ODEFileParser
- getFieldData(int) - Method in class com.actelion.research.chem.io.SDFileParser
- getFieldData(int, int) - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getFieldData(String) - Method in class com.actelion.research.chem.io.RDFileParser
- getFieldData(String) - Method in class com.actelion.research.chem.SDFileMolecule
- getFieldIndex(String) - Method in class com.actelion.research.chem.io.CompoundFileParser
- getFieldNames() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Compiles all column names that contain alpha-numerical information.
- getFieldNames() - Method in class com.actelion.research.chem.io.DWARFileParser
- getFieldNames() - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getFieldNames() - Method in class com.actelion.research.chem.io.ODEFileParser
- getFieldNames() - Method in class com.actelion.research.chem.io.RDFileParser
-
Returns a list of field names.
- getFieldNames() - Method in class com.actelion.research.chem.io.SDFileParser
-
Returns a list of field names.
- getFieldNames(int) - Method in class com.actelion.research.chem.io.SDFileParser
-
Returns a list of field names.
- getFields() - Method in class com.actelion.research.chem.SDFileMolecule
- getFile() - Method in class com.actelion.research.gui.JFileChooserOverwrite
- getFile(Component, String, int) - Static method in class com.actelion.research.gui.FileHelper
-
For compatibility reasons...
- getFileType(String) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- getFinalRank() - Method in class com.actelion.research.chem.Canonizer
- getFingerprint(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
-
Generates a fingerprint of the default size for the given ExtendedMolecule
- getFingerprint(StereoMolecule, int) - Method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
-
Generates the fingerprint of a molecule
- getFirstHittingLongIndexBlockNo() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- getFisherProjectionParity(int, int[], double[], int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
If the atom is a stereo center in fisher projection, then its tetrahedral parity is returned.
- getFitMol() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- getFlatness() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getFlavors() - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- getFlavors() - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- getFlavors() - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- getFlipped() - Method in class com.actelion.research.calc.Matrix
-
Opposite direction to transpose.
- getFont() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getFont() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getFont() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- getFont() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- getFont(AttributeSet) - Method in class com.actelion.research.gui.hidpi.ScaledStyleSheet
- getFontMetrics(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getFontMetrics(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getFontRenderContext() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getFontScaleFactor() - Static method in class com.actelion.research.gui.hidpi.ScaledEditorKit
- getFontSize() - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- getFontSize() - Method in class com.actelion.research.gui.swing.SwingDrawContext
- getFontSize() - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- getForceConstants(MMFFMolecule, int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
-
Gets the force constants associated with a torsion angle.
- getForegroundColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getForegroundColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getFormalCharges(MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Charge
-
Computes the MMFF formal charges for a molecules atoms.
- getFormat() - Method in class smile.data.DateAttribute
-
Returns the date string formatter.
- getFormula() - Method in class com.actelion.research.chem.MolecularFormula
- getFormula(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getFormulaIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getFractalDimension() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getFractionCarbonInteractions() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getFractionMTry() - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- getFragment() - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns the direct surrounding of the previously classified rotatable bond.
- getFragment() - Method in class com.actelion.research.chem.coords.InventorTemplate
- getFragment(int) - Method in class com.actelion.research.chem.coords.FragmentAssociation
- getFragment(int) - Method in class com.actelion.research.chem.prediction.IncrementTable
- getFragment(int) - Method in class com.actelion.research.chem.prediction.IncrementTableWithIndex
- getFragment(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getFragment(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- getFragment(IBitArray, boolean) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- getFragmentAt(Point2D, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- getFragmentAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Returns an array of all atoms for which a path of bonds leads to rootAtom not considering metal ligand bonds.
- getFragmentAtoms(int, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Returns an array of all atoms for which a path of bonds leads to rootAtom.
- getFragmentIdCode(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- getFragmentIdCodeCarbonSkeleton(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- getFragmentList() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
- getFragmentMatches(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find all fragment occurences in mol (only the movable atoms are considered).
- getFragmentNo(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getFragmentNumbers(int[], boolean[], boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates all disconnected fragments in the molecule and assigns fragment numbers (starting from 0) to all atoms.
- getFragmentNumbers(int[], boolean, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates all unconnected fragments in the Molecule and assigns fragment indexes for every atom starting with 0.
- getFragments() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getFragments() - Method in class com.actelion.research.chem.StereoMolecule
-
Separates all disconnected fragments of this Molecule into individual Molecule objects.
- getFragments() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getFragments() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getFragments() - Method in class com.actelion.research.share.gui.editor.Model
- getFragments(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
-
Returns list with indices for fragments with
size
bonds. - getFragments(int[], int) - Method in class com.actelion.research.chem.StereoMolecule
-
Separates all disconnected fragments of this Molecule into individual molecule objects.
- getFragments(StereoMolecule) - Method in class com.actelion.research.chem.shredder.Fragmenter3D
-
Applying the constraints passed to the Fragmenter3D constructor, this method shredders the given 3D-molecule and returns all generated 3D-fragments as an ArrayList.
- getFragmentsForSingleAtom(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- getFrame() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getFrameHeight() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getFrameWidth() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getFreeValence(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The free valence is the number of potential additional single bonded neighbours to reach the atom's maximum valence.
- getFrequencies() - Method in class com.actelion.research.calc.histogram.Histogram
- getFrequency() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- getFrequency() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- getFrequency(int) - Method in class com.actelion.research.calc.histogram.Histogram
- getFrequencyOnePerMol() - Method in class com.actelion.research.chem.shredder.Fragment
- getFrequencySumAll() - Method in class com.actelion.research.chem.shredder.Fragment
- getFromQuadraticMatrix(Matrix, double, double, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getFullyMappedReactions() - Method in class com.actelion.research.chem.reaction.Reactor
-
After instantiating the Reactor with MODE_FULLY_MAP_REACTIONS and after supplying real reactants, this method may be used to construct the fully mapped reaction.
- getFunction(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getFunction(long) - Method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- getFunction(long) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getFunction(String) - Method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- getFunctionalGroupEquivalenceLevel(int, int) - Static method in class com.actelion.research.chem.reaction.FunctionalGroupClassifier
-
Determines the similarity of two functional groups based on their location in the binary functional group similarity tree.
- getFunctionalities() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- getFunctionalityIndex() - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- getFunctionGroupCountMap() - Method in class com.actelion.research.chem.reaction.FunctionalGroupClassifier
-
Applying a predefined dictionary of logically arranged 1024 functional groups this method determines all functional groups present in the molecule, counts how often they occurr in the molecule.
- getGamma() - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- getGaussianProcessRegression() - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getGenericAcceptor() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getGenericDonor() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getGenericDrawArea() - Method in class com.actelion.research.gui.editor.SwingEditorArea
- getGenericNegCharge() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getGenericPosCharge() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getGeomFactory() - Method in class com.actelion.research.share.gui.editor.Model
- getGlobalAtom(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.AngleBend
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in interface com.actelion.research.chem.forcefield.mmff.EnergyTerm
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFExternalPositionConstraint
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFPositionConstraint
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
-
Calculates the gradient and adds it to the gradients array.
- getGradientContribution(Gaussian3D, Gaussian3D, double[], boolean) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getGraphAtoms() - Method in class com.actelion.research.chem.Canonizer
- getGraphIndexes() - Method in class com.actelion.research.chem.Canonizer
- getGraphMapNoCount() - Method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- getGridCoordinates(Coordinates) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getGridSize() - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getGyrationRadius() - Method in class com.actelion.research.chem.docking.LigandPose
- getHalfFitnessWidth(int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getHalignment() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Halignment attribute of the VerticalFlowLayout object
- getHandleHydrogenAtomMap(boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
If ensureHelperArrays() (and with it handleHydrogens()) was not called yet on a fresh molecule and if the molecule contains simple hydrogen atoms within non-hydrogens atoms, then this function returns a map from current atom indexes to those new atom indexes that would result from a call to handleHydrogens.
- getHandleHydrogenBondMap() - Method in class com.actelion.research.chem.ExtendedMolecule
-
If ensureHelperArrays() (and with it handleHydrogens()) was not called yet on a fresh molecule and if the molecule contains simple hydrogen atoms within non-hydrogens atoms, then this function returns a map from current bond indexes to those new bond indexes that would result from a call to handleHydrogens.
- getHandleHydrogenMap() - Method in class com.actelion.research.chem.ExtendedMolecule
-
If ensureHelperArrays() (and with it handleHydrogens()) was not called yet on a fresh molecule and if the molecule contains simple hydrogen atoms within non-hydrogens atoms, then this function returns a map from current atom indexes to those new atom indexes that would result from a call to handleHydrogens.
- getHandleHydrogenMap() - Method in class com.actelion.research.chem.MolfileParser
-
If this MoflileParser was instantiated with MODE_KEEP_HYDROGEN_MAP
- getHarmonicMean(List<PrecisionAndRecall>) - Static method in class com.actelion.research.calc.classification.PrecisionAndRecall
- getHash() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getHash(StereoMolecule, CanonizerUtil.IDCODE_TYPE, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getHashCode(byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- getHashMap(List<IdentifiedObject<T>>) - Static method in class com.actelion.research.util.datamodel.IdentifiedObject
- getHashSetIndexInevitablePPPoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getHConstructionName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHDonorsAcceptors(ExtendedMolecule) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Returns a array of 2 elements [number of donors, number of acceptors]
- getHeader() - Static method in class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- getHeader() - Static method in class com.actelion.research.calc.regression.knn.ParameterKNN
- getHeader() - Static method in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- getHeader() - Static method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- getHeader() - Static method in class com.actelion.research.calc.regression.median.ParameterMedian
- getHeader() - Static method in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- getHeader() - Static method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- getHeader() - Static method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- getHeader() - Static method in class com.actelion.research.calc.regression.svm.ParameterSVM
- getHeader() - Method in class com.actelion.research.gui.dock.Dockable
- getHeaderPaint(boolean, int) - Static method in class com.actelion.research.gui.HeaderPaintHelper
- getHeaderString(int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getHeaderTags() - Static method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getHeadOrTail() - Method in class com.actelion.research.chem.io.DWARFileParser
-
Provided that the mode contains MODE_BUFFER_HEAD_AND_TAIL, then this method returns a list of all header/footer rows of the DWAR file.
- getHeight() - Method in class com.actelion.research.calc.SelfOrganizedMap
- getHeight() - Method in class com.actelion.research.chem.coords.InventorFragment
- getHeight() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getHeight() - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- getHeight() - Method in interface com.actelion.research.gui.generic.GenericCanvas
- getHeight() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getHeight() - Method in class smile.clustering.HierarchicalClustering
-
Returns a set of n-1 non-decreasing real values, which are the clustering height, i.e., the value of the criterion associated with the clustering method for the particular agglomeration.
- getHelix() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getHelperArrayStatus() - Method in class com.actelion.research.chem.ExtendedMolecule
- getHEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHet() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getHetAtomRecords() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getHeteroOnlyNode(PPNode) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getHeteroPosition(int) - Method in class com.actelion.research.chem.RingCollection
-
Returns the position of the electron pair providing hetero atom or carbenium atom in case of 5-membered, respective 7-membered aromatic ring.
- getHexStringFromIndex(int[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getHFragmentationName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHgap() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Hgap attribute of the VerticalFlowLayout object
- getHighestAtomStrain() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- getHighestMapNo() - Method in class com.actelion.research.chem.reaction.Reaction
- getHighLightColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getHighLightColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getHighValue() - Method in class com.actelion.research.gui.JPruningBar
- getHighValue() - Method in class com.actelion.research.gui.PruningBarEvent
- getHiliteAtom() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getHiliteAtom() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getHiliteBond() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getHiliteBond() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getHistogram() - Method in class com.actelion.research.calc.histogram.Histogram
- getHistogram() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getHistogram(double[], Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(float[][], int, Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(float[], Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(Matrix, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(Matrix, Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogramBins(double, double, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistory() - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRuleEnhancedReactionMapper
- getHitCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getHitQuote() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getHMId_Formula() - Method in class com.actelion.research.chem.io.pdb.parser.FormulaParser
- getHmId_Name() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getHMId_Name() - Method in class com.actelion.research.chem.io.pdb.parser.HetNameParser
- getHMId_Site() - Method in class com.actelion.research.chem.io.pdb.parser.SiteParser
- getHMId_Synonyms() - Method in class com.actelion.research.chem.io.pdb.parser.HetSynonymParser
- getHmNo_Remark() - Method in class com.actelion.research.chem.io.pdb.parser.RemarkParser
- getHorizontalFill() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Hfill attribute of the VerticalFlowLayout object
- getHoseCodes(StereoMolecule, int, int) - Static method in class com.actelion.research.chem.contrib.HoseCodeCreator
-
This descriptor requires proper up/down bonds, because it encodes stereo parities.
- getHoseCodesFromDiaID(String, int, int) - Static method in class com.actelion.research.chem.contrib.HoseCodeCreator
- getHRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHRxnGroupDef(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHydrogenMap() - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
- getHydrogens() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getIconScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- getId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getId() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- getId() - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
- getId() - Method in class com.actelion.research.chem.StructureInfo
- getId() - Method in class com.actelion.research.chem.SVGDepictor
- getId() - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- getId() - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
- getID() - Method in class com.actelion.research.calc.Matrix
- getID() - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns the torsion identifier that resulted from the most previous classification.
- getID() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getID() - Method in class com.actelion.research.gui.PruningBarEvent
- getIdcode() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
- getIdCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getIdCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getIdCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- getIdCode() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- getIdCode() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- getIDCode() - Method in class com.actelion.research.chem.Canonizer
- getIDCode() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Either this method and getCoordinates() or getMolecule() must be overwritten!!!
- getIDCode() - Method in class com.actelion.research.chem.io.DWARFileParser
- getIDCode() - Method in class com.actelion.research.chem.io.ODEFileParser
- getIDCode() - Method in class com.actelion.research.chem.shredder.Fragment3D
- getIDCode() - Method in class com.actelion.research.chem.SimpleCanonizer
- getIDCode() - Method in class com.actelion.research.chem.StereoMolecule
-
This is a convenience method that creates the molecule's idcode without explicitly creating a Canonizer object for this purpose.
- getIDCode() - Method in class com.actelion.research.share.gui.editor.Model
- getIDCode(int) - Method in class com.actelion.research.chem.StructureSearchSpecification
-
Returns the (or one of the) query structures encodes as idcode.
- getIDCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns the idcode of the structure or largest fragment.
- getIDCode(StereoMolecule, CanonizerUtil.IDCODE_TYPE, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
-
Generates an IDCODE for a defined and simplified state of a given molecule.
- getIdCodeFromFragment(StereoMolecule, ListWithIntVec) - Static method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- getIDCodeVersion(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getIDCodeVersion(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getIDCoordinates() - Method in class com.actelion.research.chem.shredder.Fragment3D
- getIDCoordinates() - Method in class com.actelion.research.chem.StereoMolecule
-
This is a convenience method that creates the molecule's id-coordinates matching the idcode available with getIDCode().
- getIdentifier() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getIdFlexophorePoint1() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getIdFlexophorePoint2() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getImage() - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Deprecated.Use ImageClipboardHandler.pasteImage for consistency reasons
- getImageData() - Method in interface com.actelion.research.gui.ImageDataSource
- getImagEigenValues() - Method in class smile.math.matrix.EVD
-
Returns the imaginary parts of the eigenvalues, ordered in real part from largest to smallest.
- getImagePath() - Method in class com.actelion.research.gui.JImagePanel
- getImageProvider() - Method in class com.actelion.research.share.gui.editor.Model
- getImplicitHigherValence(int, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
If the explicitly attached neighbors cause an atom valence to exceed the lowest allowed valence for this atomic no, then this method returns the next higher allowed valence, e.g.
- getImplicitHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates and return the number of implicit hydrogens at atom.
- getImplicitHydrogens(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return the number of implicit hydrogens, ie.
- getIncrement(int) - Method in class com.actelion.research.chem.prediction.IncrementTable
- getIncrement(int) - Method in class com.actelion.research.chem.prediction.IncrementTableWithIndex
- getIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- getIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getIndex() - Method in class com.actelion.research.chem.io.DWARFileParser
- getIndex() - Method in class com.actelion.research.chem.io.ODEFileParser
- getIndex() - Method in enum com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint.Functionality
- getIndex() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- getIndex() - Method in class com.actelion.research.chem.properties.complexity.IndexHash
- getIndex() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
- getIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
- getIndex(int) - Method in class com.actelion.research.chem.prediction.IncrementTableWithIndex
- getIndex(int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getIndex(T) - Method in class com.actelion.research.util.SortedList
-
Returns the position index of object in the sorted list.
- getIndex(T) - Method in class com.actelion.research.util.UniqueList
-
When objects were added after the last getIndex() call, then the original-index-map needs to be re-created.
- getIndexAboveEqual(T) - Method in class com.actelion.research.util.SortedList
-
If object is not member of this list, returns potential insert index.
- getIndexBaseFromHeap(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getIndexBelowEqual(T) - Method in class com.actelion.research.util.SortedList
-
If object is not member of this list, returns potential insert index.
- getIndexCenter() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- getIndexCorrespondingBaseNode(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getIndexFromCoord(double, double, double) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getIndexFromHexString(byte[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getIndexFromHexString(String) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.FormulaParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.HetNameParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.HetSynonymParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.ModelParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.RemarkParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.SiteParser
- getIndexMaxNumUniqueFrags(List<Point>) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- getIndexOriginalAtom() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- getIndexOrInsertIndex(T) - Method in class com.actelion.research.util.SortedList
-
Returns the position index of object in the sorted list.
- getIndexPosStartForDistHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getIndexQueryFromHeap(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getIndexSphereVisualization() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getIndicesBitsSet() - Method in class com.actelion.research.util.datamodel.IntVec
- getIndicesUniqueMaxColumnWise(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getIndicesUniqueMaxRowWise(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getInfluence() - Method in class com.actelion.research.calc.SelfOrganizedMap
- getInfo() - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getInfo() - Method in interface com.actelion.research.chem.descriptor.ISimilarityCalculator
- getInfo() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getInfo() - Method in class com.actelion.research.chem.descriptor.SimilarityCalculatorDoubleArray
- getInfo() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getInfo(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getInitialRot() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getInitialTranslate() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getInputVector(int) - Method in interface com.actelion.research.calc.SOMController
-
In VectorSOM the returned Object is changed by the method.
- getInputVectorCount() - Method in interface com.actelion.research.calc.SOMController
- getInsertionCode() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getInsertionCode() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getInstance() - Static method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.MDHIndexTables
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
- getInstance() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getInstance() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
- getInstance() - Static method in class com.actelion.research.chem.name.StructureNameResolver
- getInstance() - Static method in class com.actelion.research.chem.phesa.QuickMathCalculator
- getInstance() - Static method in class com.actelion.research.chem.reaction.ClassificationData
- getInstance() - Static method in class smile.stat.distribution.GaussianDistribution
- getInstance(int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
-
Use this as constructor for serial mode.
- getInt() - Method in class com.actelion.research.util.datamodel.IntegerDouble
- getInt(byte[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getIntegratedAreaWeighted(int[], double[], int) - Static method in class com.actelion.research.chem.properties.complexity.SummaryFragments
-
Takes the natural logarithm for each area fraction.
- getInteractionAtomType(int) - Method in class com.actelion.research.chem.Molecule3D
- getInteractionClass() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- getInteractionClass() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- getInteractionClasses() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getInteractionSimilarity(PPGaussian) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- getInteractionType(int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IPPNode
- getInteractionType(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getInteractionTypeCount() - Method in interface com.actelion.research.chem.descriptor.flexophore.IPPNode
- getInteractionTypeCount() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
realize() may be called first.
- getInteractionTypeFromByteArray(byte, byte, byte) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getIntercept() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getInterMolecularInteractions(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return a List of int[] representing all the atom-atom pairs having an intermolecular interactions (distance close to sum of VDW)
- getInverseTransformation() - Method in class com.actelion.research.chem.DepictorTransformation
- getInvert() - Method in class com.actelion.research.chem.alignment3d.transformation.Rotation
- getIonizableGroups() - Method in class com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector
- getIRegNo() - Method in class com.actelion.research.chem.io.RDFileParser
- getIsotopeList(int) - Static method in class com.actelion.research.chem.IsotopeHelper
- getJaccard(int[], int[]) - Static method in class com.actelion.research.calc.distance.DistanceMetrics
- getJrnl() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getKernelType(int) - Static method in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- getKernelType(String) - Static method in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- getKey(int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getKeyChar() - Method in class com.actelion.research.gui.generic.GenericKeyEvent
- getKeyCode() - Method in class com.actelion.research.gui.generic.GenericKeyEvent
- getKeyFragment(int) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getKeyHandler() - Method in class com.actelion.research.gui.editor.SwingEditorArea
- getKeyStrokeBuffer() - Method in class com.actelion.research.share.gui.editor.Model
- getKeywords() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getKMeanClusters(Matrix, int) - Static method in class com.actelion.research.calc.MatrixFunctions
-
03.10.04 MvK
- getKNN() - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getKoop() - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
- getKoop(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
- getKoop(MMFFMolecule, int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
-
Returns the Koop parameters from the OutOfPlane table.
- getL() - Method in class com.actelion.research.calc.LUDecomposition
-
Return lower triangular factor
- getL() - Method in class smile.math.matrix.Cholesky
-
Returns lower triangular factor.
- getL1() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- getL2() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- getLambda() - Method in class com.actelion.research.calc.BoxCox
- getLambda() - Method in class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- getLambda() - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- getLambda() - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- getLambda() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- getLearningRate() - Method in class smile.regression.NeuralNetwork
-
Returns the learning rate.
- getLeftChild() - Method in class com.actelion.research.gui.dock.TreeFork
- getLeftPosition() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getLength() - Method in class com.actelion.research.chem.Coordinates
- getLength() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- getLength() - Method in interface com.actelion.research.share.gui.editor.chem.IArrow
- getLength(int) - Method in class com.actelion.research.chem.conf.BondLengthSet
- getLengthIntVec() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- getLi() - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
- getLiConnect() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getLigandBounds(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getLigandCenter(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getLigandRMSD(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Gets the root mean square deviation between 2 positions.
- getLigConf() - Method in class com.actelion.research.chem.docking.LigandPose
- getLikelihood() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getLikelyhood() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
-
Tries to estimate the relative likelyhood of this conformer from atom strains considering an unstrained conformer to have a likelyhood of 1.0.
- getLikelyRandomConformerIndex(double, double) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
-
Calculates a random conformer index giving conformers with lower strains a higher chance to be selected.
- getLikelyRandomTorsionIndex(double, double) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
Calculates a random torsion index giving torsions with higher likelyhoods (i.e.
- getLiLiIdCode() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- getLinedCol() - Method in class com.actelion.research.calc.Matrix
- getLineWidth() - Method in class com.actelion.research.chem.AbstractDepictor
- getLineWidth() - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- getLineWidth() - Method in class com.actelion.research.chem.Depictor2D
- getLineWidth() - Method in class com.actelion.research.chem.SVGDepictor
- getLineWidth() - Method in class com.actelion.research.gui.generic.GenericDepictor
- getLineWidth() - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- getLineWidth() - Method in class com.actelion.research.gui.swing.SwingDrawContext
- getLineWidth() - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- getLink() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getLinkerId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- getLinkNodes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getLiNonOverLappingIsomorphSubstruct() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- getList() - Method in class com.actelion.research.calc.Matrix
- getList(int) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class com.actelion.research.gui.table.ChemistryCellRenderer
- getListIndex(String) - Method in class com.actelion.research.chem.SortedStringList
- getListIndex(String) - Method in class com.actelion.research.chem.UniqueStringList
- getListIndexOriginalAtoms() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getLocalAtom(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- getLocaleDateFormat() - Method in enum com.actelion.research.util.Formatter.LocaleFormat
- getLocaleFormat() - Method in class com.actelion.research.util.Formatter
- getLocaleTimeFormat() - Method in enum com.actelion.research.util.Formatter.LocaleFormat
- getLogP() - Method in class com.actelion.research.chem.PropertyCalculator
- getLogPDetail() - Method in class com.actelion.research.chem.PropertyCalculator
- getLogS() - Method in class com.actelion.research.chem.PropertyCalculator
- getLogSDetail() - Method in class com.actelion.research.chem.PropertyCalculator
- getLongestChain(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return the longest molecular chain starting at atm
- getLongIndexFromHexString(byte[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getLongIndexFromHexString(String) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getLowestFreeValence(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The lowest free valence is the number of potential additional single bonded neighbours to reach the atom's lowest valence above or equal its current occupied valence.
- getLowValue() - Method in class com.actelion.research.gui.JPruningBar
- getLowValue() - Method in class com.actelion.research.gui.PruningBarEvent
- getManhattanBlockDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- getManualMapCount() - Method in class com.actelion.research.chem.reaction.mapping.RootAtomPairSource
- getMappableAtomCount() - Method in class com.actelion.research.chem.reaction.mapping.RootAtomPairSource
- getMappedAtomCount() - Method in class com.actelion.research.chem.reaction.mapping.ReactionCenterMapper
- getMapping(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns the encoded reaction mapping.
- getMappingIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getMapToolColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getMapToolColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getMarkushCount() - Method in class com.actelion.research.share.gui.editor.Model
- getMarkushStructure() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getMarkushStructure() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getMarkushStructure() - Method in class com.actelion.research.share.gui.editor.Model
- getMask() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- getMask() - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
- getMaster() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMatch() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- getMatches() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- getMatches() - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- getMatchingTransform(PPTriangle, TransformationSequence, boolean) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getMatchingTransforms(Map<Integer, ArrayList<PPTriangle>>, Map<Integer, ArrayList<PPTriangle>>, int, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher
- getMatchingTransforms(Map<Integer, ArrayList<PPTriangle>>, Map<Integer, ArrayList<PPTriangle>>, int, int, boolean) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher
- getMatchList() - Method in class com.actelion.research.chem.SSSearcher
-
If the match count mode is one of cCountModeFirstMatch, cCountModeOverlapping, cCountModeRigorous then this method returns an arraylist of all counted matches, i.e.
- getMatchList() - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
If the match count mode is one of cCountModeFirstMatch, cCountModeOverlapping, cCountModeRigorous then this method returns an arraylist of all counted matches, i.e.
- getMatchScore() - Method in class com.actelion.research.calc.SelfOrganizedMap
- getMatrix(int[], int[]) - Method in class com.actelion.research.calc.Matrix
-
Get a submatrix.
- getMatrix(int[], int, int) - Method in class com.actelion.research.calc.Matrix
-
Get a submatrix.
- getMatrix(int, int, int[]) - Method in class com.actelion.research.calc.Matrix
-
Get a submatrix.
- getMatrix(int, int, int, int) - Method in class com.actelion.research.calc.Matrix
- getMatrixFromString(String, String) - Static method in class com.actelion.research.util.StringFunctions
- getMax() - Method in class com.actelion.research.calc.Matrix
- getMax(int) - Method in class com.actelion.research.calc.Matrix
-
get max value for that col.
- getMaxAtoms() - Method in class com.actelion.research.chem.Molecule
-
The currently defined maximum of atoms, which increases automatically when using high level construction methods and new atoms exceed the current maximum.
- getMaxBonds() - Method in class com.actelion.research.chem.Molecule
-
The currently defined maximum of bonds, which increases automatically when using high level construction methods and new bonds exceed the current maximum.
- getMaxDistInHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getMaxFreeValence(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getMaximumCapacityBondsInFragment() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- getMaximumCapacityBondsInFragment() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getMaximumCommonSubstructure(List<StereoMolecule>) - Method in class com.actelion.research.chem.mcs.MCSFunctions
- getMaximumDistanceInPPPoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getMaximumNumberBondsInMolecule() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- getMaximumNumberBondsInMolecule() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getMaximumNumberBondsInMolecule() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- getMaximumOverlap(List<String>, int) - Static method in class com.actelion.research.util.StringFunctions
-
Finds the maximum common String in all Strings.
- getMaximumSize() - Method in class com.actelion.research.gui.JPruningBar
- getMaximumSlope() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getMaximumValue() - Method in class com.actelion.research.calc.Matrix
- getMaximumValue() - Method in class com.actelion.research.gui.JPruningBar
- getMaximumVisibleRows() - Method in class com.actelion.research.gui.JScrollablePopupMenu
- getMaximumX() - Method in class com.actelion.research.calc.histogram.Histogram
- getMaximumY() - Method in class com.actelion.research.calc.histogram.Histogram
- getMaxIndex() - Method in class com.actelion.research.calc.Matrix
- getMaxIndexNotZero(byte[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- getMaxMin() - Method in class com.actelion.research.calc.Matrix
-
max and min vals for all cols
- getMaxNeighbor() - Method in class smile.clustering.CLARANS
-
Returns the maximum number of neighbors examined during a search of local minima.
- getMaxNodes() - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- getMaxNumUniqueFrags() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getMaxNumUniqueFrags(List<Point>) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- getMaxOccBin(Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getMaxRow(int) - Method in class com.actelion.research.calc.Matrix
- getMaxRowIndex(int) - Method in class com.actelion.research.calc.Matrix
- getMaxRowIndexRND(int) - Method in class com.actelion.research.calc.Matrix
-
Shuffles the indices before searching the minimum.
- getMaxText(int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getMaxValence(int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getMaxValence(int) - Method in class com.actelion.research.chem.Molecule
-
This is the defined maximum valence (or set abnormal valence) corrected by atom charge or radical influences, e.g.
- getMaxValenceUncharged(int) - Method in class com.actelion.research.chem.Molecule
-
This is the defined maximum valence (or set abnormal valence) neglecting atom charge or radical influences, e.g.
- getMaxX() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getMaxY() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getMCS() - Method in class com.actelion.research.chem.mcs.MCS
- getMCS() - Method in class com.actelion.research.chem.mcs.MCSFast
- getMCS(Reaction, boolean[], SSSearcher) - Static method in class com.actelion.research.chem.reaction.CommonSubGraphHelper
- getMCSBondArray(boolean[], boolean[]) - Method in class com.actelion.research.chem.mcs.MCS
-
Calculates the bond arrays for molecule and fragment for their maximum common substructure.
- getMdltyp() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMean() - Method in class com.actelion.research.calc.Matrix
- getMean() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getMean() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getMean(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getMean(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getMeanAngle(InventorAngle[], int) - Static method in class com.actelion.research.chem.coords.CoordinateInventor
- getMeanCol(int) - Method in class com.actelion.research.calc.Matrix
- getMeanCol(int, int[]) - Method in class com.actelion.research.calc.Matrix
- getMeanCols() - Method in class com.actelion.research.calc.Matrix
- getMeanCols(int[]) - Method in class com.actelion.research.calc.Matrix
- getMeanRow(int) - Method in class com.actelion.research.calc.Matrix
- getMeanRows() - Method in class com.actelion.research.calc.Matrix
- getMeanVector(Object, Object) - Method in class com.actelion.research.calc.BinarySOM
- getMeanVector(Object, Object) - Method in class com.actelion.research.calc.SelfOrganizedMap
- getMeanVector(Object, Object) - Method in class com.actelion.research.calc.VectorSOM
- getMedian() - Method in class com.actelion.research.calc.Matrix
- getMedian() - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getMedian() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getMedian(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getMedian(int) - Method in class com.actelion.research.calc.Matrix
- getMedian(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getMedianBin(byte[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- getMedianCols() - Method in class com.actelion.research.calc.Matrix
- getMedianForDouble(List<Double>) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getMedianForInteger(List<Integer>) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getMedianForLong(List<Long>) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getMedianOverview(DoubleArray) - Static method in class com.actelion.research.calc.statistics.StatisticsOverview
- getMenuComponent(int) - Method in class com.actelion.research.gui.JScrollableMenu
- getMenuComponentCount() - Method in class com.actelion.research.gui.JScrollableMenu
- getMenuComponents() - Method in class com.actelion.research.gui.JScrollableMenu
- getMergedCopy() - Method in class com.actelion.research.chem.reaction.Reaction
-
Merges all reactants into one molecule and all products into another ad creates a new Reaction object from those.
- getMergeRows(Matrix) - Method in class com.actelion.research.calc.Matrix
- getMessage() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getMessage() - Method in class com.actelion.research.gui.editor.DialogEvent
- getMetalBondedConnAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getMin() - Method in class com.actelion.research.calc.Matrix
- getMin(int) - Method in class com.actelion.research.calc.Matrix
- getMinColIndex(int) - Method in class com.actelion.research.calc.Matrix
- getMinDist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getMinimumSize() - Method in class com.actelion.research.gui.JPruningBar
- getMinimumValue() - Method in class com.actelion.research.gui.JPruningBar
- getMinimumX() - Method in class com.actelion.research.calc.histogram.Histogram
- getMinMaxSimilarity(int[], int[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getMinOccBin(Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getMinPos() - Method in class com.actelion.research.calc.Matrix
- getMinRow(int) - Method in class com.actelion.research.calc.Matrix
- getMinRowIndex(int) - Method in class com.actelion.research.calc.Matrix
- getMinRowIndexRND(int) - Method in class com.actelion.research.calc.Matrix
-
03.10.04 MvK Shuffles the indices before searching the minimum.
- getMinRows() - Method in class com.actelion.research.calc.Matrix
- getMinRowsPosCol() - Method in class com.actelion.research.calc.Matrix
- getMinText(int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getMinX() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getMinY() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getMirror(Coordinates, Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.Coordinates
-
Get the mirror image of p through the plane defined by c1, c2, c3
- getMMFFMolecule() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- getMode() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getMode() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getMode() - Method in class com.actelion.research.share.gui.editor.Model
- getModeFlexophore() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getModeFlexophore() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getModel() - Method in class com.actelion.research.gui.CompoundCollectionPane
- getModRes() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMol() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getMol() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getMol() - Method in class com.actelion.research.chem.shredder.Fragment
- getMolDistHist() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getMolecularPathCount(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Returns the number of paths of the given length (gives an idea of the number of branches)
- getMolecule() - Method in class com.actelion.research.chem.conf.Conformer
- getMolecule() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
The atoms of the ff molecule contain the corresponding PPNode indices in the first field of the PPP vector.
- getMolecule() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Either this method or getIDCode() and getCoordinates() must be overwritten!!!
- getMolecule() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getMolecule() - Method in class com.actelion.research.chem.io.SDFileParser
- getMolecule() - Method in class com.actelion.research.chem.phesa.PheSAMolecule
- getMolecule() - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Returns the most recently defined molecule.
- getMolecule() - Method in class com.actelion.research.chem.StructureTransferData
- getMolecule() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getMolecule() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getMolecule() - Method in class com.actelion.research.gui.JStructureView
- getMolecule() - Method in class com.actelion.research.share.gui.editor.Model
- getMolecule() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- getMolecule(int) - Method in class com.actelion.research.chem.ExtendedDepictor
- getMolecule(int) - Method in class com.actelion.research.chem.reaction.Reaction
- getMolecule(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
- getMolecule(int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- getMoleculeAt(Point2D, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- getMoleculeBounds(int) - Method in class com.actelion.research.gui.JChemistryView
-
Returns the bounding rectangle of the indicated molecule, if multiple molecules are shown, e.g.
- getMoleculeColor() - Method in class com.actelion.research.chem.Molecule
-
cMoleculeColorDefault: atom coloring depends on atomic number.
- getMoleculeCount() - Method in class com.actelion.research.chem.ExtendedDepictor
- getMoleculeCount() - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- getMoleculeDepictor(int) - Method in class com.actelion.research.chem.ExtendedDepictor
- getMoleculeDepictor(int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- getMoleculeForDisplay(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- getMoleculeForDisplay(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- getMoleculeName() - Method in class com.actelion.research.chem.io.CompoundFileParser
- getMoleculeName() - Method in class com.actelion.research.chem.io.DWARFileParser
- getMoleculeName() - Method in class com.actelion.research.chem.io.ODEFileParser
- getMoleculeName() - Method in class com.actelion.research.chem.io.SDFileParser
- getMoleculeRegNo(int) - Method in class com.actelion.research.chem.reaction.DatabaseReaction
- getMoleculeRemovedUnrelatedAtoms() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getMolecules() - Method in class com.actelion.research.chem.reaction.Reaction
- getMoleculeTransferable() - Method in class com.actelion.research.gui.JChemistryView
- getMoleculeTransferable(Point) - Method in class com.actelion.research.gui.JStructureView
- getMolfile() - Method in class com.actelion.research.chem.MolfileCreator
-
If a pre-filled StringBuilder was passed to the constructor, then this returns the original content with the appended molfile.
- getMolfile() - Method in class com.actelion.research.chem.MolfileV3Creator
-
If a pre-filled StringBuilder was passed to the constructor, then this returns the original content with the appended molfile.
- getMolFile(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- getMolGauss() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getMolweight() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates a rounded mass of the molecule
- getMomentum() - Method in class smile.regression.NeuralNetwork
-
Returns the momentum factor.
- getMooreNeighborhood(Point, int, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getMooreNeighborhood(Point, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
-
A square-shaped neighborhood that can be used to define a set of cells surrounding a given point.
- getMostCentralRingSystem(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
Creates most central ring system as new StereoMolecule from mol without touching mol.
- getMST() - Method in class com.actelion.research.calc.graph.MinimumSpanningTree
- getmTransformation() - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- getMtrix1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMtrix2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMtrix3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMultivariate(int, int) - Static method in class com.actelion.research.calc.MatrixTests
-
Creates a multivariate test dataset The regression factor factor is the col number, starting with 1.
- getMurckoScaffold(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
Creates Murcko scaffold as new StereoMolecule from mol without touching mol.
- getMutatedSet(StereoMolecule, int, boolean, int) - Method in class com.actelion.research.chem.Mutator
- getName() - Method in class com.actelion.research.calc.regression.ARegressionMethod
- getName() - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- getName() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getName() - Method in class com.actelion.research.chem.conf.Conformer
- getName() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getName() - Method in class com.actelion.research.chem.Element
- getName() - Method in class com.actelion.research.chem.Molecule
-
Allows to set a molecule name or identifier, that is, for instance, written to or read from molfiles.
- getName() - Method in class com.actelion.research.chem.Molecule3D
- getName() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getName() - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRule
- getName() - Method in class com.actelion.research.chem.reaction.Reaction
- getName() - Method in class com.actelion.research.chem.StructureInfo
- getName() - Method in class smile.data.Attribute
- getName() - Method in class smile.data.Dataset
-
Returns the dataset name.
- getName(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getNameIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getNastyFunctionList(StereoMolecule, long[]) - Method in class com.actelion.research.chem.NastyFunctionDetector
- getNastyFunctionString(StereoMolecule, long[]) - Method in class com.actelion.research.chem.NastyFunctionDetector
- getNative() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- getNative() - Method in class com.actelion.research.share.gui.Delegator
- getNative() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- getNative() - Method in interface com.actelion.research.share.gui.editor.geom.StrokeLineCap
- getNaturalPercentage(int, int) - Static method in class com.actelion.research.chem.IsotopeHelper
- getNeededBits(int) - Static method in class com.actelion.research.chem.Canonizer
- getNeededNumberOfBondsInFragment(StereoMolecule) - Static method in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- getNegativeNeighbourCount(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- getNegIonizableAtoms() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
- getNeighbourInfluence(int, int, double) - Method in class com.actelion.research.calc.SelfOrganizedMap
- getNeighbours() - Method in class com.actelion.research.calc.regression.knn.KNNRegression
- getNeighbours() - Method in class com.actelion.research.calc.regression.knn.ParameterKNN
- getNeighbours() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getNeighbours(Coordinates[], double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Gets a Set of all neigbouring atoms.
- getNeighbours(Coordinates, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Gets a Set of all neigbouring atoms.
- getNeighbours(Coordinates, double, boolean) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getNeighbours(Coordinates, double, boolean, int) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Gets a Set of all neigbouring atoms.
- getNeighbours(Molecule, int, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getNeighbours(Molecule, int, double, boolean) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getNeuralNetworkRegression() - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getNew(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128Factory
- getNew(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArrayFactory
- getNewCompleteGraphMatcher() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getNext4NeighboursTorus(int, int) - Method in class com.actelion.research.calc.Matrix
- getNext8NeighboursTorus(int, int) - Method in class com.actelion.research.calc.Matrix
- getNextColor() - Static method in class com.actelion.research.chem.reaction.MCSReactionMapper
- getNextConformer() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
- getNextConformer() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
Picks a new conformer from the conformer pool created by initializeConformers().
- getNextConformer(TorsionSet[]) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Creates the next random, likely or systematic new(!) conformer of the molecule that was passed when calling initializeConformers().
- getNextConformerAsMolecule(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Creates the next random, likely or systematic new(!) conformer of the molecule that was passed when calling initializeConformers().
- getNextEnumeration() - Method in class com.actelion.research.chem.MarkushStructure
-
After calling validate() this method may be called until null is returned to construct one by one a new representation of the Markush structure.
- getNextFieldData() - Method in class com.actelion.research.chem.io.SDFileParser
-
Returns the field data of the current record as one big String as it was read from the input file.
- getNextFileName(String) - Static method in class com.actelion.research.util.IO
-
Has to be the total path of the file or there will be errors.
- getNextMapNo() - Method in class com.actelion.research.share.gui.editor.Model
-
*********************************************************************************************************
- getNextMolecule() - Method in class com.actelion.research.chem.io.RDFileParser
-
RD-files may contains lists of molecules or lists of reactions.
- getNextMolFile() - Method in class com.actelion.research.chem.io.SDFileParser
-
Returns the molfile of the current record as one big String as it was read from the input file.
- getNextReaction() - Method in class com.actelion.research.chem.io.RDFileParser
-
RD-files may contains lists of molecules or lists of reactions.
- getNextResult() - Method in class com.actelion.research.calc.SimilarityMulticore
- getNextTautomer(StereoMolecule) - Method in class com.actelion.research.chem.TautomerHelper
- getNextTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
Creates the next set of torsion indexes to be tried by the ConformerGenerator.
- getNMovables() - Method in class com.actelion.research.chem.Molecule3D
- getNode() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getNode(int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- getNode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
-
!Slow method, it has to iterate through a loop to find the node in the array!
- getNode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNodeA() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getNodeB() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getNodeC() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNodes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getNodes(Collection<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getNodesFromEdges(List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getNodeSize() - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- getNodesQuery() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getNonCachableCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getNonHydrogenNeighbourCount(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
This method returns the non-hydrogen neighbour count of atom.
- getNonPolarAtomTypeCount() - Static method in class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
- getNonPolarAtomTypeCounts(StereoMolecule) - Method in class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
- getNonZeroCols(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getNoOfKeys() - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getNorm() - Method in class com.actelion.research.util.datamodel.ByteVec
- getNorm() - Method in class com.actelion.research.util.datamodel.IntVec
- getNorm() - Method in class com.actelion.research.util.DoubleVec
- getNorm(double[]) - Static method in class com.actelion.research.chem.optimization.OptimizerLBFGS
- getNormalized(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getNormalizedAtomX(int) - Method in class com.actelion.research.chem.coords.InventorTemplate
- getNormalizedAtomY(int) - Method in class com.actelion.research.chem.coords.InventorTemplate
- getNormalizedMatrix() - Method in class com.actelion.research.calc.Matrix
- getNormalizedMatrix(Matrix) - Method in class com.actelion.research.calc.Matrix
- getNormalizedTorsionIndex(String, double) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Normalizes a torsion angle considering the fragments symmetry type by returning the lowest symmetrically equivalent torsion that is >= 0.
- getNormSq(double[]) - Static method in class com.actelion.research.chem.optimization.OptimizerLBFGS
- getNoStereoCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a hash code representing the structure or its largest fragment without any stereo information.
- getNoStereoHash(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns a hash code representing the reaction without any stereo information.
- getNoStereoHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getNoStereoTautomerCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a hash code representing the generic tautomer of the structure or its largest fragment with the stereo information removed before creating the generic tautomer.
- getNoStereoTautomerHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getNu() - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- getNumAcidicOxygen(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumAlcoholicOxygen(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumAliphaticRingAtoms(ExtendedMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumAmide(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumArguments() - Method in class com.actelion.research.util.CommandLineParser
- getNumAromaticAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumArylAmine(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumBasicNitrogen(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumberAbove(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getNumberOfAtomsBetweenBonds(Molecule3D, int, int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Computes a matrix of distances between all the bonds in the graph.
- getNumberOfBondsBetweenAtoms(Molecule3D, int, int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Computes a matrix of distances between all the atoms in the graph.
- getNumberOfBondsBetweenAtoms(StereoMolecule, int, int[][]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
From Joel Freyss developed for the FFMolecule Computes a matrix of distances between all the atoms in the graph.
- getNumberOfHydrogens(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.HydrogenHandler
- getNumberOfTrees() - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- getNumBins() - Method in class com.actelion.research.calc.histogram.Histogram
- getNumBondsAtMaximumFrequency() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getNumBondsAtMaxSlope() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getNumBondsInFragment() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getNumBytesEntry() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getNumBytesEntry() - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getNumCarbonAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumCarboxy(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumCExclusiveNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNumClusters() - Method in class smile.clustering.PartitionClustering
-
Returns the number of clusters.
- getNumCyanoGroups(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Counts cyano and iso-cyano
- getNumData() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getNumElements() - Method in class com.actelion.research.calc.Matrix
- getNumElementsEqual(double) - Method in class com.actelion.research.calc.Matrix
- getNumElementsLarger(double) - Method in class com.actelion.research.calc.Matrix
- getNumHeavyAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumHeteroAromaticAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumHeteroAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumHeteroNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNumIndices() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- getNumInevitablePharmacophorePoints() - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- getNumInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
-
Only for interface compliance needed.
- getNumInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNumIsopropyl(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumLocalMinima() - Method in class smile.clustering.CLARANS
-
Returns the number of local minima to search for.
- getNummdl() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getNumNitroGroupN(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumOverlappingIndices(SubGraphIndices) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- getNumPPNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getNumPPNodes() - Method in interface com.actelion.research.util.graph.complete.ICompleteGraph
- getNumQueryAtoms(ExtendedMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumRegressionPoints() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getNumSubstructure(StereoMolecule, String) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumSulfOxyGroups(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumThioEther(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumWildcards(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getObjectiveCompleteGraph() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getObjectiveCompleteGraph() - Method in interface com.actelion.research.chem.descriptor.flexophore.IDescriptorHandlerFlexophore
- getObjectiveCompleteGraph() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- getObsolete() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getOccupiedValence(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The sum of bond orders of explicitly connected neighbour atoms including explicit hydrogen.
- getOccupiedValence(int) - Method in class com.actelion.research.chem.Molecule
-
The sum of bond orders of explicitly connected neighbour atoms.
- getOccupiedValence(int) - Method in class com.actelion.research.chem.Molecule3D
- getOccurencesArray() - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getOffsetX() - Method in class com.actelion.research.chem.DepictorTransformation
- getOffsetY() - Method in class com.actelion.research.chem.DepictorTransformation
- getOneConformer(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.
- getOneConformerAsMolecule(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.
- getOrderNumber() - Method in class com.actelion.research.chem.Element
- getOrganicFunctionalGroupCounts() - Method in class com.actelion.research.chem.reaction.FunctionalGroupClassifier
- getOrigBB() - Method in class com.actelion.research.chem.combinatorialspace.Synthon
- getOriginalAtomIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getOriginalAtomIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getOrigX1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getOrigX2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getOrigX3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getOverlap(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getOverlap(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getOverlap(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getP() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getP() - Method in class com.actelion.research.chem.alignment3d.transformation.ExponentialMap
- getPaint() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getPairPotentials() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getPanalty() - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRule
- getParameter() - Method in class com.actelion.research.calc.regression.ARegressionMethod
- getParameter() - Method in interface com.actelion.research.calc.regression.ICalculateModel
- getParameter() - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- getParent() - Method in class com.actelion.research.gui.dock.TreeElement
- getParsed(Vector<String>) - Static method in class com.actelion.research.calc.Matrix
-
Parses an vector with Strings and converts it to a Matrix.
- getPartial(int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
-
Gets the partial charge of a bond type and its two atom types.
- getPartialCharge(int) - Method in class com.actelion.research.chem.Molecule3D
- getPassword() - Method in class com.actelion.research.gui.JLoginDialog
- getPath(int[], int, int, int, boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates and returns the shortest path between atoms atom1 and atom2
- getPathBonds(int[], int[], int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Finds bonds of a path that is defined by an atom sequence.
- getPathLength(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates the length of the shortest path between atoms atom1 and atom2
- getPathLength(int, int, int, boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates the length of the shortest path between atoms atom1 and atom2, which is not larger than maxLength and avoids atoms indicated by neglectAtom.
- getPathsFromHeadNode(int, List<Set<Integer>>, Set<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getPbci(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
- getPenStyle() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getPercentageOverlap(DistHist, int, int, DistHist, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.HistogramMatchCalculator
- getPercentile05() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getPercentile95() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getPercentileFromSorted(double[], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getPercentileFromSorted(double[], double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSorted(double[], double, int, int) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSorted(float[], double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSorted(float[], double, int, int) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSorted(int[], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getPercentileFromSorted(List<Double>, double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSortedInt(List<Integer>, double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSortedLong(List<Long>, double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPeripherySimilarity() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getPeripherySimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getPermutationCount() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getPermutations(int[], int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
- getPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- getPharmacophorePoints(StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- getPivot() - Method in class com.actelion.research.calc.LUDecomposition
-
Return pivot permutation vector
- getPlainHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getPLS() - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getPLSBoxCox() - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getPointerErrors() - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getPoints() - Method in class com.actelion.research.gui.generic.GenericPolygon
- getPoints(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getPointsBetween(Point, Point) - Static method in class com.actelion.research.util.PointUtils
- getPolarAtomTypeCount() - Static method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- getPolarAtomTypeCounts(StereoMolecule) - Method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- getPolarSurfaceArea() - Method in class com.actelion.research.chem.PropertyCalculator
- getPolarSurfaceAreaDetail() - Method in class com.actelion.research.chem.PropertyCalculator
- getPolled() - Method in class com.actelion.research.util.Pipeline
- getPopupItems() - Method in interface com.actelion.research.gui.PopupItemProvider
- getPopupMenu() - Method in class com.actelion.research.gui.JScrollableMenu
- getPopupProvider() - Method in class com.actelion.research.gui.dock.Dockable
- getPopupProvider() - Method in class com.actelion.research.gui.dock.DockableHeader
- getPopupProvider() - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- getPose() - Method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
- getPosIonizableAtoms() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
- getPositionInContainer() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- getPositionInContainer() - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
- getPositions(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Sdf
-
Parses a SDF file to extract the positions of each atom.
- getPotentialConformerCount() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Calculates the potential count of conformers by multiplying degrees of freedom (torsions per rotatable bond & rigid fragment multiplicities).
- getPPGaussians() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- getPPP(int) - Method in class com.actelion.research.chem.Molecule3D
- getPPPoints(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getPpWeight() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getPrefactor(int, int) - Method in class com.actelion.research.chem.phesa.QuickMathCalculator
- getPreferredMax(int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getPreferredMin(int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getPreferredSize() - Method in class com.actelion.research.gui.JPruningBar
- getPreProcessTransformations() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getPreviousAlignment() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getPreviousConformerContribution() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
With best current knowledge about colliding torsion combinations and based on the individual frequencies of currently active torsions this method returns the conformers's overall contribution to the total set of non colliding conformers.
- getPreviousPheSAResult() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
-
additional output: element 0: total similarity (identical to getSimilarity(...)) element 1: pharmacophore similarity element 2: contribution to similarity that originates from additional volumes (incl/excl)
- getPriority() - Method in class com.actelion.research.chem.coords.FragmentAssociation
- getProbabilityFromType(long) - Method in class com.actelion.research.chem.AtomTypeList
- getProduct() - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRule
- getProduct() - Method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- getProduct(int) - Method in class com.actelion.research.chem.reaction.Reaction
- getProductData() - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getProductDescriptor(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
- getProductDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getProductIDCodes() - Method in class com.actelion.research.chem.reaction.Reactor
- getProducts() - Method in class com.actelion.research.chem.reaction.Reaction
- getProducts() - Method in class com.actelion.research.chem.reaction.Reactor
- getProducts(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getProductsBoundingRect(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getProgressController() - Method in class com.actelion.research.calc.regression.ARegressionMethod
- getProperties() - Method in class com.actelion.research.calc.regression.ARegressionMethod
- getProperties() - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- getProperties() - Method in class com.actelion.research.gui.JMultiPanelView
- getPropertyCode(int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getPropertyCount() - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getPropertyName(int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getProtAtomRecords() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getPseudoEZGroup(int) - Method in class com.actelion.research.chem.Canonizer
-
If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns this bond's relative stereo feature group number provided this bond is a pseudo stereo bond, i.e.
- getPseudoStereoGroupCount() - Method in class com.actelion.research.chem.Canonizer
-
If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns the number of independent relative stereo feature groups.
- getPseudoTHGroup(int) - Method in class com.actelion.research.chem.Canonizer
-
If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns this atom's relative stereo feature group number provided this atom is a pseudo stereo center, i.e.
- getPurity() - Method in class com.actelion.research.chem.StructureInfo
- getPythag(double, double) - Static method in class com.actelion.research.calc.Matrix
-
pythag computes sqrt(a^2 + b^2) without destructive underflow or overflow.
- getPythag2(double, double) - Static method in class com.actelion.research.calc.Matrix
- getQ() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getQ() - Method in class smile.math.matrix.QR
-
Returns the orthogonal factor.
- getQ0() - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- getQ1() - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- getQ2() - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- getQ3() - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- getQuartile(double) - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getQuery() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getQuery() - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getR() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getR() - Method in class smile.math.matrix.QR
-
Returns the upper triangular factor.
- getRandom() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
- getRandom(int, int) - Static method in class com.actelion.research.util.StringFunctions
- getRandomForestRegression() - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getRandomMatrix(int, int) - Static method in class com.actelion.research.calc.MatrixFunctions
-
generates a matrix with double values between 0 (inclusive) and 1 (exclusive).
- getRandomRotation() - Static method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
-
get a random quaternion, from: https://stackoverflow.com/questions/31600717/how-to-generate-a-random-quaternion-quickly
- getRandomVector() - Method in class com.actelion.research.calc.BinarySOM
- getRandomVector() - Method in class com.actelion.research.calc.SelfOrganizedMap
- getRandomVector() - Method in class com.actelion.research.calc.VectorSOM
- getRangeMax(int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getRangeMin(int) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getRangeStatistics(MolDistHist) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- getRatioCoveredBonds() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getRatioNonSymmetricAtoms() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getRatioSymmetricAtoms(StereoMolecule) - Static method in class com.actelion.research.chem.properties.complexity.SymmetryCalculator
- getRatioUsedBondsUpToMaxFreq() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getReactant() - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRule
- getReactant() - Method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- getReactant(int) - Method in class com.actelion.research.chem.reaction.Reaction
- getReactantAtomSymmetryConstraints() - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRule
- getReactantCount() - Method in class com.actelion.research.share.gui.editor.Model
- getReactantData() - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getReactantDescriptor(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
- getReactantDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getReactants() - Method in class com.actelion.research.chem.reaction.Reaction
- getReactants(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getReactantsBoundingRect(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getReaction() - Method in class com.actelion.research.chem.ExtendedDepictor
- getReaction() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getReaction() - Method in class com.actelion.research.gui.editor.SwingEditorDialog
- getReaction() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getReaction() - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- getReaction() - Method in class com.actelion.research.gui.JEditableChemistryView
- getReaction() - Method in class com.actelion.research.share.gui.editor.Model
- getReaction(int, int) - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getReaction(File) - Method in class com.actelion.research.chem.io.RXNFileParser
- getReaction(File, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- getReaction(String) - Method in class com.actelion.research.chem.io.RXNFileParser
- getReaction(String, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- getReactionAndDrawings() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- getReactionAndDrawings() - Method in class com.actelion.research.gui.editor.SwingEditorDialog
- getReactionAndDrawings() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- getReactionAndDrawings() - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- getReactionCenterAtoms(int, boolean[], boolean[], int[]) - Method in class com.actelion.research.chem.reaction.Reaction
-
Fills an array mapping on the atoms for the given molecule of this reaction.
- getReactionCenterMapNos() - Method in class com.actelion.research.chem.reaction.Reaction
-
This method determines the largest mapping number in use (maxMapNo), creates a boolean array[maxMapNo+1], and within this array flags every mapping number that refers to atoms, which change bonds in the course of the reaction.
- getReactionCenterSimilarity() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getReactionCenterSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getReactionCode(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns the reaction idcode.
- getReactionCount() - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getReactionCount() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Returns the search type as integer including mode flags.
- getReactionDescriptor(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
- getReactionDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getReactionRegNo() - Method in class com.actelion.research.chem.reaction.DatabaseReaction
- getReactions() - Method in class com.actelion.research.chem.combinatorialspace.Synthon
- getReactionTransferable() - Method in class com.actelion.research.gui.JChemistryView
- getReactionType(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getReactionYield() - Method in class com.actelion.research.chem.reaction.DatabaseReaction
- getRealEigenValues() - Method in class smile.math.matrix.EVD
-
Returns the real parts of the eigenvalues, ordered in real part from largest to smallest.
- getRearAtom(int) - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns that neighbor atom of a central atom that lies in the rotatable bond axis.
- getRearAtoms() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getRecentException() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getReceptorAtomTypes(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingEngine
- getReceptorConf() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getRecordCount() - Method in class com.actelion.research.chem.io.CompoundFileHelper
- getRefConformerIndex() - Method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer.AlignmentResult
- getReferenceAtom(int) - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns the reference atom of one part of the torsion fragment.
- getReferenceVector() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- getReferenceVector(int, int) - Method in class com.actelion.research.calc.SelfOrganizedMap
- getRefMol() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- getRefMolGauss() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getRegressionMethod() - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getRegressionMethod(String) - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getRelativeError(double, double) - Static method in class com.actelion.research.calc.regression.ModelError
- getRelativeWeight() - Method in class com.actelion.research.chem.MolecularFormula
- getRelevance() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
- getRelevance(StereoMolecule, boolean[]) - Static method in class com.actelion.research.chem.conf.TorsionRelevanceHelper
-
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
- getRelevance(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionRelevanceHelper
-
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
- getRelMaxDistInHist() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
-
To get the distance in Angstrom the relative distance has to be multiplied with the histogram range
CGMult.RANGE_HISTOGRAM
. - getRelMaxDistInHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
-
To get the distance in Angstrom the relative distance has to be multiplied with the histogram range
CGMult.RANGE_HISTOGRAM
. - getRelMaxDistInHist(int, int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- getRemainingStructure(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCSFunctions
- getRemark(int) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemark0() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemark1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemark2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemark3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemarks() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRenderingHint(RenderingHints.Key) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getRenderingHints() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getREntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRequestCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getResiduals() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getResiduals() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- getResname() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getResName() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getResnum() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getResNum() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getResolution() - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- getResSequence(int) - Method in class com.actelion.research.chem.Molecule3D
- getRetinaScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
Macintosh retina display support for Java 7 and newer.
- getRetronDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getRevdat() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRGroup(int) - Method in class com.actelion.research.chem.MarkushStructure
- getRGroupCount() - Method in class com.actelion.research.chem.MarkushStructure
- getRightChild() - Method in class com.actelion.research.gui.dock.TreeFork
- getRingAtoms() - Method in class com.actelion.research.chem.coords.InventorChain
- getRingAtoms(int) - Method in class com.actelion.research.chem.RingCollection
- getRingBonds() - Method in class com.actelion.research.chem.coords.InventorChain
- getRingBonds(int) - Method in class com.actelion.research.chem.RingCollection
- getRings(Molecule3D, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getRingsAccurate(Molecule3D, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find the smallest covering set of rings for the Molecule.
- getRingSet() - Method in class com.actelion.research.chem.ExtendedMolecule
- getRingSetSimple() - Method in class com.actelion.research.chem.ExtendedMolecule
- getRingsFast(Molecule3D, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find the list of rings for the Molecule.
- getRingSize(int) - Method in class com.actelion.research.chem.RingCollection
- getRingSizeAdjust(int) - Method in class com.actelion.research.chem.AtomTypeList
- getRMS(double[]) - Static method in class com.actelion.research.chem.optimization.OptimizerLBFGS
- getRmsd(Coordinates[], Coordinates[]) - Static method in class com.actelion.research.chem.Coordinates
- getRmsd(Coordinates[], Coordinates[], int) - Static method in class com.actelion.research.chem.Coordinates
- getRMSD() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- getRMSD(ClusterNode, DistHist) - Static method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- getRND(int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getRND(int, int) - Static method in class com.actelion.research.calc.Matrix
- getRole() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- getRoot() - Method in class smile.regression.RegressionTree
-
Returs the root node.
- getRotatableBondCount() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Simple method to calculate rotatable bonds.
- getRotatableBondCount() - Method in class com.actelion.research.chem.PropertyCalculator
- getRotatableBondCount() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
After calling initializeConformers() this method returns the number of rotatable bonds, which are used to separate the molecule into rigid fragments.
- getRotatableBonds() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getRotatableBondWeights(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDescriptor
-
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
- getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- getRotatedDirectionality(double[][], double) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- getRotation() - Method in class com.actelion.research.chem.alignment3d.transformation.Rotation
- getRotationCenters() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getRotationMatrix(double, Coordinates, double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- getRotMatrix() - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
-
from Grassia: q0 corresponds to qw (scalar part)
- getRotMatrix(Coordinates, double, double[][]) - Static method in class com.actelion.research.chem.phesaflex.MathHelper
- getRotMatrixDerivative(Coordinates, double, Coordinates[][]) - Static method in class com.actelion.research.chem.phesaflex.MathHelper
- getRow() - Method in class com.actelion.research.chem.io.DWARFileParser
-
Returns the entire line containing all row data
- getRow(int) - Method in class com.actelion.research.calc.Matrix
-
Flat copy.
- getRowAsFloat(int) - Method in class com.actelion.research.calc.Matrix
- getRowAsList(int) - Method in class com.actelion.research.calc.Matrix
- getRowCopy(int) - Method in class com.actelion.research.calc.Matrix
- getRowCount() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Depending on data source returns the total row count or -1 if unknown
- getRowCount() - Method in class com.actelion.research.chem.io.DWARFileParser
- getRowCount() - Method in class com.actelion.research.chem.io.ODEFileParser
- getRowCount() - Method in class com.actelion.research.chem.io.RDFileParser
-
Only accurate if getFieldNames() or getFieldNames(int) was called earlier and if the number of records of the SD-file is smaller than the number of records that were examined within the the getFieldNames() method.
- getRowCount() - Method in class com.actelion.research.chem.io.SDFileParser
-
Only accurate if getFieldNames() or getFieldNames(int) was called earlier and if the number of records of the SD-file is smaller than the number of records that were examined within the the getFieldNames() method.
- getRowCount() - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
This is the total number of records, whether they qualify for a structure search or not.
- getRowCount() - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
This is the total number of records, whether they qualify for a structure search or not.
- getRowDim() - Method in class com.actelion.research.calc.Matrix
- getRowMinUnique(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getRowName(int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- getRowNumberTable() - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- getRows() - Method in class com.actelion.research.util.datamodel.table.TableModelString
- getRRefuncName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnDef(int, int, int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnFGroups(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnMasks(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnSymmetric(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRuleList() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- getRuleStrain(int) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- getRuleType() - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.ConformationRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.DistanceRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.PlaneRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.StraightLineRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.TorsionRule
- getRXNfile() - Method in class com.actelion.research.chem.io.RXNFileCreator
- getRXNfile() - Method in class com.actelion.research.chem.io.RXNFileV3Creator
- getS() - Method in class smile.math.matrix.SVD
-
Returns the diagonal matrix of singular values
- getScale1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getScale2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getScale3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getScaled(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
-
Centers and divides by standard deviation.
- getScaledByFactor(Matrix, double) - Static method in class com.actelion.research.calc.MatrixFunctions
- getScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIUtil
- getScaleFactor(Graphics2D) - Static method in class com.actelion.research.gui.hidpi.HiDPIUtil
- getScaling() - Method in class com.actelion.research.chem.DepictorTransformation
- getScalingFactor() - Method in class com.actelion.research.chem.alignment3d.transformation.Scaling
- getScalingFactor() - Method in class com.actelion.research.chem.MolfileV3Creator
- getScore() - Method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
- getScore() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getScore() - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
- getScore() - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- getScore() - Method in class com.actelion.research.chem.docking.scoring.ProbeScanning
- getScore() - Method in class com.actelion.research.chem.mcs.MCS
-
Calculates the score by bonds_mcs/Max(bonds_mol, bonds_frag)
- getScore() - Method in class com.actelion.research.chem.mcs.MCSFast
- getScore() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getScore() - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRuleEnhancedReactionMapper
- getScore() - Method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
-
Calculates and returns a score <= 0 for the current mapping.
- getScore() - Method in class com.actelion.research.util.datamodel.ScorePoint
- getScore(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCSFunctions
- getScoreFracBitsCommonQuery(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
(sum bits set common) / (sum bits set in query)
- getScoreFracBitsInCommonBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
(sum bits set common) / (sum bits set in both)
- getScoreQueryInBase(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getScoreQueryInBaseBitWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
-
(sum bits set only in query) / (sum bits set in query)
- getScoreQueryInBaseBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getScoreQueryInBaseByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getScrollBar() - Method in class com.actelion.research.gui.JScrollablePopupMenu
- getSdv() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getSelectedAtom() - Method in class com.actelion.research.share.gui.editor.Model
- getSelectedBond() - Method in class com.actelion.research.share.gui.editor.Model
- getSelectedCopy(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.Model
- getSelectedDockable() - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Returns the currently active Dockable, i.e.
- getSelectedDrawingObject() - Method in class com.actelion.research.share.gui.editor.Model
- getSelectedIndex() - Method in interface com.actelion.research.gui.generic.GenericComboBox
- getSelectedIndex() - Method in class com.actelion.research.gui.swing.SwingComboBox
- getSelectedItem() - Method in interface com.actelion.research.gui.generic.GenericComboBox
- getSelectedItem() - Method in class com.actelion.research.gui.swing.SwingComboBox
- getSelectedItemText() - Method in class com.actelion.research.gui.JComboBoxWithColor
- getSelectedReaction() - Method in class com.actelion.research.share.gui.editor.Model
- getSelectionColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getSelectionColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getSelfAtomOverlap() - Method in class com.actelion.research.chem.phesa.MolecularVolume
-
calculate the self-overlap of the base molecule
- getSelfAtomOverlap() - Method in class com.actelion.research.chem.phesa.ShapeVolume
-
calculate the self-overlap of the base molecule
- getSelfAtomOverlapFit() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getSelfAtomOverlapRef() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getSelfPPOverlap() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- getSelfPPOverlapFit() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getSelfPPOverlapRef() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getSEQADV() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSEQRES() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSerialId() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getSharedRing(int, int) - Method in class com.actelion.research.chem.RingCollection
-
brute force method to check, whether and which ring is shared by two bonds
- getSheet() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getShift() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
- getShiftVector() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- getShortName() - Method in class com.actelion.research.chem.Molecule3D
- getSigma() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- getSim() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- getSim() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- getSim() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- getSimilarities2Calculate() - Method in class com.actelion.research.calc.SimilarityMulticore
- getSimilarity() - Method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer.AlignmentResult
- getSimilarity() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getSimilarity(byte[], byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getSimilarity(double[], double[]) - Method in class com.actelion.research.chem.descriptor.SimilarityCalculatorDoubleArray
- getSimilarity(int[][], int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getSimilarity(int, int) - Method in class com.actelion.research.chem.Clusterer
- getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getSimilarity(DistHist, int, int, DistHist, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.HistogramMatchCalculator
- getSimilarity(IPPNode, IPPNode) - Method in interface com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.IPPNodeSimilarity
- getSimilarity(IPPNode, IPPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarity(PharmacophoreTree, PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- getSimilarity(IPharmacophorePoint) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- getSimilarity(PPGaussian) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- getSimilarity(PPGaussian, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- getSimilarity(PheSAMolecule, PheSAMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
-
calculates the Shape- and/or Pharmacophore similarity of a query molecule with a base molecule
- getSimilarity(StereoMolecule, StereoMolecule, DescriptorHandler) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getSimilarity(SolutionCompleteGraph) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getSimilarity(SolutionCompleteGraph) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getSimilarity(Object, Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getSimilarity(Collection<PharmacophoreNode>, Collection<PharmacophoreNode>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getSimilarity(Collection<Integer>, Collection<Integer>, List<PharmacophoreNode>, List<PharmacophoreNode>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getSimilarity(T, T) - Method in interface com.actelion.research.chem.descriptor.ISimilarityCalculator
- getSimilarityAngleCosine(int[], int[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getSimilarityBytewiseOverlap(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getSimilarityContributions() - Method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer.AlignmentResult
- getSimilarityExtraCarbonConsideration(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityHardMatchAverage(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityHardMatchMultiplicative(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityHardMatchOptimistic(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityHistogram(int, int, int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getSimilarityHistogram(int, int, int, int) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getSimilarityHistogramsForNode(SolutionCompleteGraph, int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getSimilarityList(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityMappingNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getSimilarityMatrix() - Method in class com.actelion.research.calc.SimilarityMulticore
- getSimilarityNode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.ModelSolutionSimilarity
- getSimilarityNodes(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getSimilarityNodes(int, int) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getSimilarityNodes(IPPNode, IPPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getSimilarityNodes(IPPNode, IPPNode) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getSimilaritySimple(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityTanimoto(int[], int[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getSimilarityTanimoto(long[], long[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getSimilarityTanimoto(long[], long[], int, int) - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getSimilarityThreshold() - Method in class com.actelion.research.chem.StructureSearchSpecification
- getSimilars(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.InteractionTypeMap
- getSimpleAtomicNoCodeString(int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getSingularValues() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Return the one-dimensional array of singular values
- getSingularValues() - Method in class smile.math.matrix.SVD
-
Returns the one-dimensional array of singular values, ordered by from largest to smallest.
- getSite(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSiteIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSize() - Method in class com.actelion.research.chem.conf.Conformer
- getSize() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- getSize() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getSize() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getSize() - Method in class com.actelion.research.chem.prediction.IncrementTable
- getSize() - Method in class com.actelion.research.chem.prediction.IncrementTableWithIndex
- getSize() - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
- getSize() - Method in class com.actelion.research.chem.RingCollection
- getSize() - Method in class com.actelion.research.chem.shredder.Fragment
- getSize() - Method in class com.actelion.research.chem.SortedStringList
- getSize() - Method in class com.actelion.research.chem.TextDrawingObject
- getSize() - Method in interface com.actelion.research.gui.CompoundCollectionModel
- getSize() - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- getSize() - Method in class com.actelion.research.gui.generic.GenericPolygon
- getSize() - Method in class com.actelion.research.util.ErrorHashMap
- getSize() - Method in class com.actelion.research.util.IntQueue
- getSize1() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- getSize2() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- getSizeAfterLastBitSet() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- getSizeAfterLastBitSet() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- getSizeArrayLIV() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- getSizeArrayLIV() - Static method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- getSizeBinaryArray() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- getSizeBinaryArray() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getSizeBytes() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getSizeBytes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getSizeForBits(int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getSizeHeap() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getSizes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- getSkinnable() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getSlope() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getSlope() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getSlopeFragments() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getSlopeR2() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getSmallerSideAtomCount() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getSmallerSideAtomLists() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getSmallestRingsOfAtom(RingCollection, int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- getSmartsWarning() - Method in class com.actelion.research.chem.SmilesParser
-
If createSmartsWarning in the constructor was passed as true, then this method returns a list of all SMARTS features, which could not be interpreted in the most recently parsed SMILES/SMARTS pattern.
- getSmiles() - Method in class com.actelion.research.chem.IsomericSmilesCreator
- getSmiles() - Method in class com.actelion.research.chem.properties.fractaldimension.InputObjectFracDimCalc
- getSmiles() - Method in class com.actelion.research.share.gui.editor.Model
- getSmoothing() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- getSolution() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
-
The index is the index of the node in the query molecule.
- getSolventData() - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getSolvents() - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getSorted() - Method in class com.actelion.research.calc.Matrix
-
Sorts the row of the matrix according the compareTo(...) function in DoubleVec
- getSorted(int) - Method in class com.actelion.research.util.UniqueList
- getSortedByY(int) - Method in class com.actelion.research.util.datamodel.ModelXY
- getSortedByY(int) - Method in class com.actelion.research.util.datamodel.ModelXYIndex
- getSortedIndex(T) - Method in class com.actelion.research.util.UniqueList
- getSortedListIndex(String) - Method in class com.actelion.research.chem.UniqueStringList
- getSortedStringAt(int) - Method in class com.actelion.research.chem.UniqueStringList
- getSource() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSource() - Method in class com.actelion.research.gui.editor.DialogEvent
- getSpecialFieldData(int) - Method in class com.actelion.research.chem.io.DWARFileParser
- getSpecialFieldIndex(String) - Method in class com.actelion.research.chem.io.DWARFileParser
- getSpecialFieldMap() - Method in class com.actelion.research.chem.io.DWARFileParser
-
Returns a columnName->SpecialField map of all non-alphanumerical columns.
- getSpline() - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getSplit() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSplittedOverlappingText(List<String>, int, int) - Static method in class com.actelion.research.util.StringFunctions
-
Generates a list with overlap
- getSpread(byte[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- getSprsde() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSQRT() - Method in class com.actelion.research.calc.Matrix
- getSquaredSum() - Method in class com.actelion.research.calc.Matrix
- getSSBond() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getStandardDeviation() - Method in class com.actelion.research.calc.Matrix
- getStandardDeviation(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getStandardDeviationCols() - Method in class com.actelion.research.calc.Matrix
- getStandardized() - Method in class com.actelion.research.calc.Matrix
-
Get the standard scores, also known as z-scores.
- getStandardized(String, String, int) - Static method in class com.actelion.research.chem.MoleculeStandardizer
-
Under normal circumstances, one should never need to standardize a molecule from an idcode, because molecules should be standardized before generating the canonical encoding.
- getState() - Method in class com.actelion.research.chem.docking.LigandPose
- getState() - Method in interface com.actelion.research.chem.optimization.Evaluable
- getState() - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- getState() - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getState(double[]) - Method in class com.actelion.research.chem.docking.LigandPose
- getState(double[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- getState(double[]) - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- getState(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getStbnType(Tables, MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Angle
-
Given three atoms which form an angle, returns the MMFF stretch-bend type of the angle.
- getStdDev(int) - Method in class com.actelion.research.chem.conf.BondLengthSet
- getStdDevFromCovalentRadii(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
- getStereoBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Checks whether at least one of the connected bonds is a stereo bond.
- getStereoCenterCount() - Method in class com.actelion.research.chem.PropertyCalculator
- getStereoCenterCount() - Method in class com.actelion.research.chem.StereoMolecule
- getStereoIsomer(int) - Method in class com.actelion.research.chem.StereoIsomerEnumerator
-
Creates and returns the molecule in a specific atom and bond parity permutation state, i.e.
- getStereoIsomerCount() - Method in class com.actelion.research.chem.StereoIsomerEnumerator
-
This calculates the stereo isomer count that may be requested by the getStereoIsomer() method.
- getStereoProblem(int) - Method in class com.actelion.research.chem.Molecule
-
The stereo problem flag is set by the stereo recognition (available equal/above helper level cHelperParities) if an atom has over- or under-specified stereo bonds attached, i.e.
- getStrain(double[]) - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- getString() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- getString() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getString(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getString(String, String) - Static method in class com.actelion.research.util.Prefs
- getString(String, String, String) - Static method in class com.actelion.research.util.StringFunctions
- getString(String, String, String, int) - Static method in class com.actelion.research.util.StringFunctions
- getStringAt(int) - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
- getStringAt(int) - Method in class com.actelion.research.chem.SortedStringList
- getStringAt(int) - Method in class com.actelion.research.chem.UniqueStringList
- getStringFromRegEx(String, String) - Static method in class com.actelion.research.util.StringFunctions
- getStringTypeAt(int) - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
- getStringWidth(String) - Method in class com.actelion.research.chem.AbstractDepictor
- getStringWidth(String) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- getStringWidth(String) - Method in class com.actelion.research.chem.Depictor2D
- getStringWidth(String) - Method in class com.actelion.research.chem.SVGDepictor
- getStringWidth(String) - Method in class com.actelion.research.gui.generic.GenericDepictor
- getStringWidth(String) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- getStroke() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getStructure() - Method in class com.actelion.research.gui.editor.SwingEditorDialog
- getStructure() - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- getStructureCenter(Molecule3D, int[], int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getStructureCenter(Molecule3D, int, int[], int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
The Structure Center Atom is defined as the atom with the biggest no of rotatables bonds and the closest to the center
- getStructureCoordinates3DColumnName() - Method in class com.actelion.research.chem.io.DWARFileParser
- getStructureCount() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
Returns the search type as integer including mode flags.
- getStructureInfo() - Method in class com.actelion.research.chem.StructureTransferData
- getStructures() - Method in class com.actelion.research.gui.JEditableChemistryView
-
If chemistryType is
- getStyle() - Method in class com.actelion.research.chem.TextDrawingObject
- getStyleSheet() - Method in class com.actelion.research.gui.hidpi.ScaledEditorKit
-
Overriden to return our own slimmed down style sheet.
- getSubElements() - Method in class com.actelion.research.gui.JScrollableMenu
- getSubFragment(MolDistHist, int[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- getSubFragment(MolDistHistViz, int[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- getSubFragmentCheckedRange(MolDistHist, int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- getSubFragments(MolDistHistViz, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
-
Inevitable pharmacophore points are considered (01.11.2012)
- getSubMatrix(int, int, int, int) - Method in class com.actelion.research.calc.Matrix
- getSubMatrix(List<Integer>) - Method in class com.actelion.research.calc.Matrix
- getSubset(int) - Method in class com.actelion.research.chem.conf.ConformerSet
- getSubstituent(int, int, boolean[], ExtendedMolecule, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Determines all atoms of the substituent attached to coreAtom and starting with firstAtom.
- getSubstituent(String) - Static method in class com.actelion.research.chem.NamedSubstituents
- getSubstituentIDCode(String) - Static method in class com.actelion.research.chem.NamedSubstituents
- getSubstituentSize(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Counts the number of atoms of the substituent connected to coreAtom defined by firstAtom and not including the coreAtom.
- getSubTreeSize(List<Integer>, int) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getSum() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- getSum() - Method in class com.actelion.research.calc.Matrix
- getSumCol(int) - Method in class com.actelion.research.calc.Matrix
- getSumCols() - Method in class com.actelion.research.calc.Matrix
- getSumFragsUntilMaximumFrequency() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getSumFromRange(double, double) - Method in class com.actelion.research.calc.histogram.Histogram
-
Parts of the range outside the bins are not considered.
- getSumRow(int) - Method in class com.actelion.research.calc.Matrix
- getSumRows() - Method in class com.actelion.research.calc.Matrix
- getSumSquared() - Method in class com.actelion.research.calc.Matrix
- getSumSquaredDiff(Matrix, int, Matrix, int) - Static method in class com.actelion.research.calc.MatrixFunctions
- getSumUniqueFrags() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getSumUniqueFrags(List<Point>) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- getSumUpperTriangle() - Method in class com.actelion.research.calc.Matrix
-
Matrix has to be quadratic.
- getSumY() - Method in class com.actelion.research.calc.histogram.Histogram
- getSVM() - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- getSvmParameter() - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- getSVMType(int) - Static method in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- getSVMType(String) - Static method in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- getSwingDrawArea() - Method in class com.actelion.research.gui.editor.SwingEditorPanel
- getSymbol() - Method in class com.actelion.research.chem.Element
- getSymmetryRank(int) - Method in class com.actelion.research.chem.Canonizer
-
Returns the symmetry rank before tie breaking.
- getSymmetryRank(int) - Method in class com.actelion.research.chem.StereoMolecule
-
This returns atom symmetry numbers from within the molecule canonicalization procedure.
- getSymmetryRanks() - Method in class com.actelion.research.chem.Canonizer
-
Returns the symmetry ranks before tie breaking.
- getSymmetryType(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
A fragment's symmetry type defines whether one part of a full 360 degree matches symmetrically another range.
- getSynonymIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSynonyms(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSynthon() - Method in class com.actelion.research.chem.combinatorialspace.Synthon
- getSystemProperty(String) - Static method in class com.actelion.research.gui.hidpi.HiDPIUtil
-
Tries to look up the System property for the given key.
- getT() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getT(Matrix) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- getT(Matrix) - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.actelion.research.gui.table.ChemistryCellRenderer
- getTagDescriptorSimilarity(DescriptorInfo) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getTagDescriptorSimilarity(ISimilarityCalculator<?>) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
-
Creates a header tag name from the descriptor short name.
- getTagDescriptorSimilarity(SimilarityCalculatorInfo) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getTagDescriptorSimilarity(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getTanimotoDist(byte[], byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- getTanimotoDist(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoDist(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Calculates the Tanimoto coefficient
- getTanimotoDist(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Calculates the Inverse Tanimoto coefficient
- getTanimotoDistance(double[], double[]) - Static method in class com.actelion.research.util.DoubleVec
- getTanimotoDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Calculates the Inverse Tanimoto coefficient
- getTanimotoDistanceDotProd(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- getTanimotoDistBitWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoDistBitWise(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Calculates the Tanimoto coefficient
- getTanimotoDistBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Calculates the Tanimoto coefficient
- getTanimotoDistInv(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Byte wise inverse Tanimoto distance.
- getTanimotoDistInv(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoDistInvBitWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoDistInvBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Calculates the Inverse Tanimoto coefficient
- getTanimotoDistInvByteWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoDistInvByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoSimilarity(double[], double[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getTanimotoSimilarity(double[], double[]) - Static method in class com.actelion.research.util.DoubleVec
- getTanimotoSimilarity(float[], float[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getTanimotoSimilarity(int[], int[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getTanimotoSimilarity(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Calculates the Tanimoto coefficient according broken link 22.01.2019 http://www.pnylab.com/pny/papers/nmet/nmet/
- getTautomerCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a hash code representing the generic tautomer of the structure or its largest fragment.
- getTautomerCount() - Method in class com.actelion.research.chem.TautomerHelper
- getTautomerHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getText() - Method in class com.actelion.research.chem.TextDrawingObject
- getText() - Method in class com.actelion.research.gui.ComboBoxColorItem
- getText() - Method in interface com.actelion.research.gui.generic.GenericTextField
- getText() - Method in class com.actelion.research.gui.swing.SwingTextField
- getText() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- getTextSize() - Method in class com.actelion.research.chem.AbstractDepictor
- getTextSize() - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- getTextSize() - Method in class com.actelion.research.chem.Depictor2D
- getTextSize() - Method in class com.actelion.research.chem.SVGDepictor
- getTextSize() - Method in class com.actelion.research.gui.generic.GenericDepictor
- getTextSize() - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- getThemeColor(int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- getTHParity(int) - Method in class com.actelion.research.chem.Canonizer
-
Returns the absolute tetrahedral parity, which is based on priority ranks.
- getThreadPoolSize() - Static method in class smile.util.MulticoreExecutor
-
Returns the number of threads in the thread pool.
- getThreadSafeCopy() - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getThreadSafeCopy() - Method in interface com.actelion.research.chem.descriptor.ISimilarityCalculator
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.SimilarityCalculatorDoubleArray
- getThreadSafeCopy() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getThreadSafeCopy() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
- getTimeInfluence(double) - Method in class com.actelion.research.calc.SelfOrganizedMap
- getTitle() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getTitle() - Method in class com.actelion.research.gui.dock.Dockable
-
Returns the title of dockable header.
- getTitle() - Method in class com.actelion.research.gui.dock.DockableHeader
- getTitle(Dockable) - Method in class com.actelion.research.gui.dock.JDockingPanel
- getTokenized(String, String) - Static method in class com.actelion.research.util.StringFunctions
-
Returns the tokenized and trimmed values.
- getTokenizedBySeperatorRegex(String, String) - Static method in class com.actelion.research.util.StringFunctions
- getTokenizedQuoted(String) - Static method in class com.actelion.research.util.StringFunctions
-
Get a list from quoted and comma or otherwise separated phrases.
- getToleratedVDWRadius(int) - Static method in class org.openmolecules.chem.conf.gen.ConformerGenerator
- getTopologicalDistance(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getTopologicalDistanceMatrix(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getTopPosition() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getTorsion(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getTorsionAtoms() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getTorsionBinCounts(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Returns the full circle histogram of torsion angles.
- getTorsionCount() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getTorsionDescriptor() - Method in class com.actelion.research.chem.conf.TorsionDescriptorHelper
-
Creates a TorsionDescriptor from the coordinates of the molecule passed to the constructor using the default method to detect rotatable bonds.
- getTorsionDescriptor(Conformer) - Method in class com.actelion.research.chem.conf.TorsionDescriptorHelper
-
Creates a TorsionDescriptor from the coordinates of the passed conformer assuming that its underlying molecule is the same that waas passed to this TorsionDescriptorHelper's constructor.
- getTorsionFrequencies() - Method in class com.actelion.research.chem.conf.TorsionPrediction
- getTorsionFrequencies(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Returns an array of frequencies in rounded percent.
- getTorsionID(StereoMolecule, int, int[], TorsionDetail) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Determines uniquely an identifying name for the rotatable bond and its vicinity.
- getTorsionIDs() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getTorsionIndexes() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getTorsionLikelyhood(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getTorsionRanges() - Method in class com.actelion.research.chem.conf.TorsionPrediction
- getTorsionRanges(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Returns an array containing left and right limits of the torsion curves, of which the maxima are returned by getTorsions().
- getTorsions() - Method in class com.actelion.research.chem.conf.TorsionPrediction
- getTorsions(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Returns an array of maxima of the smoothened torsion histogram as short values in the range: 0 <= v < 360.
- getTorsionSetCount() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getTorsionStrainClass(String, double) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Checks, whether the torsion angle lies within statistical limits.
- getTorus(int, int) - Method in class com.actelion.research.calc.Matrix
- getTotalAtomOverlap(double[], MolecularVolume) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getTotalAtomOverlap(double[], ShapeVolume) - Method in class com.actelion.research.chem.phesa.ShapeVolume
-
calculate the Overlap of the two molecular volumes as a function a transform vector that is applied to the query molecule overlap Volume of two molecular Volumes formulated as a summed overlap of atomic Gaussians taken from Grant, Gallardo, Pickup, Journal of Computational Chemistry, 17, 1653-1666, 1996 returns a double[2]: the first double is the total overlap, whereas the second value is the specific contribution of additional volume gaussians (inclusion, exclusion)
- getTotalCounts() - Method in class com.actelion.research.calc.histogram.IntegerHistogram
- getTotalEnergy() - Method in interface com.actelion.research.chem.forcefield.ForceField
- getTotalEnergy() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Gets the total energy of the molecule as the sum of the energy terms.
- getTotalEnergy(double[]) - Method in interface com.actelion.research.chem.forcefield.ForceField
- getTotalEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Gets the total energy of the molecule as the sum of the energy terms.Requires the atomic positions to be in the correct order.
- getTotalOccurences() - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getTotalPPOverlap(double[], ShapeVolume) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- getTotalSizeResults() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getTotalStrain() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- getTotalSumSquaredDiffRowWise(Matrix, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- getTrace() - Method in class com.actelion.research.calc.Matrix
-
Matrix trace.
- getTransferable(Point) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- getTransferable(Point) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- getTransferData(DataFlavor) - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dock.TransferableDockable
- getTransferDataFlavors() - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- getTransferDataFlavors() - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- getTransferDataFlavors() - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- getTransferDataFlavors() - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- getTransferDataFlavors() - Method in class com.actelion.research.gui.dock.TransferableDockable
- getTransform() - Method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer.AlignmentResult
- getTransform() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getTransformation() - Method in class com.actelion.research.chem.AbstractDepictor
- getTransformations() - Method in class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- getTransparencyFlag() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getTransparentColor() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getTranspose() - Method in class com.actelion.research.calc.Matrix
- getTree() - Method in class smile.clustering.HierarchicalClustering
-
Returns an n-1 by 2 matrix of which row i describes the merging of clusters at step i of the clustering.
- getTrees() - Method in class smile.regression.RandomForest
-
Returns the regression trees.
- getTrueNegative() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- getTruePositive() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- getType() - Method in class com.actelion.research.gui.editor.DrawAreaEvent
- getType() - Method in class com.actelion.research.gui.PruningBarEvent
- getType() - Method in class smile.data.Attribute
- getType(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns the MMFF type of an atom in a molecule.
- getType(Tables, MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Bond
-
Returns the MMFF bond type of a bond on a molecule.
- getType(Tables, MMFFMolecule, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Bond
-
Returns the MMFF bond type of a bond on a molecule.
- getType(Tables, MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Angle
-
Gets the angle type of an angle bend.
- getType(Tables, MMFFMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Torsion
-
Returns the torsion type of a torsion angle.
- getTypeFromCode(String) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getTypeFromName(String) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getTypeString() - Method in class com.actelion.research.chem.AbstractDrawingObject
- getTypeString() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- getTypeString() - Method in class com.actelion.research.chem.TextDrawingObject
- getTypeString(long, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getU() - Method in class com.actelion.research.calc.LUDecomposition
-
Return upper triangular factor
- getU() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getU() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Return the left singular vectors
- getU() - Method in class smile.math.matrix.SVD
-
Returns the left singular vectors
- getUIScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
For Windows and Linux this method returns the user defined UI scaling factor.
- getUnique() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getUnique(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getUnique(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getUniqueDateDir(File) - Static method in class com.actelion.research.util.IO
- getUniqueDateDir(File, String) - Static method in class com.actelion.research.util.IO
- getUniqueDateDir(String) - Static method in class com.actelion.research.util.IO
- getUniqueDir(File, String) - Static method in class com.actelion.research.util.IO
- getUniqueFileName(File) - Static method in class com.actelion.research.util.IO
- getUniqueFileName(File, File) - Static method in class com.actelion.research.util.IO
- getUniqueFileName(File, File, DecimalFormat) - Static method in class com.actelion.research.util.IO
-
If the file does not exists the input file is returned.
- getUniqueFileName(String) - Static method in class com.actelion.research.util.IO
-
A number is added to the base name of the file
- getUniqueFileName(String, String) - Static method in class com.actelion.research.util.IO
- getUniqueFragments() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- getUniqueFragmentsEstimated() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- getUniqueUserDir() - Static method in class com.actelion.research.util.IO
- getUpperTriangle() - Method in class com.actelion.research.calc.Matrix
-
For a quadratic matrix only.
- getUserData() - Method in class com.actelion.research.chem.Molecule
- getUserID() - Method in class com.actelion.research.gui.JLoginDialog
- getUserInputFlag() - Method in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- getV() - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- getV() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Return the right singular vectors
- getV() - Method in class smile.math.matrix.SVD
-
Returns the right singular vectors
- getValence(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getValidSolutions() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- getValignment() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Valignment attribute of the VerticalFlowLayout object
- getValsAboveHistMax() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getValsBelowHistMin() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- getValuation(double, double, double, double) - Static method in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- getValue() - Method in class com.actelion.research.gui.editor.DialogEvent
- getValue() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- getValue() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getValue() - Method in class com.actelion.research.util.Angle
- getValueAt(int) - Method in interface com.actelion.research.calc.INumericalDataColumn
- getValueAt(int) - Method in class com.actelion.research.util.datamodel.DoubleArray
- getValueAtAbsolutePosition(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getValueCount() - Method in class com.actelion.research.calc.CorrelationCalculator
- getValueCount() - Method in interface com.actelion.research.calc.INumericalDataColumn
- getValueCount() - Method in class com.actelion.research.util.datamodel.DoubleArray
- getValueCountMatrix() - Method in class com.actelion.research.calc.CorrelationCalculator
- getValues() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getValues() - Method in class com.actelion.research.util.hash.HashSetInt
-
Deep copy.
- getValuesAsArray() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getValuesAsArrayX() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getValuesAsArrayY() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getVariableSelectionOnX(IntVec) - Method in class com.actelion.research.util.datamodel.ModelXYIndex
- getVariance() - Method in class com.actelion.research.calc.Matrix
- getVariance(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getVariance(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getVarianceCentered() - Method in class com.actelion.research.calc.Matrix
- getVarianceCol(int) - Method in class com.actelion.research.calc.Matrix
- getVarianceCols() - Method in class com.actelion.research.calc.Matrix
- getVariationCount(int) - Method in class com.actelion.research.chem.io.NativeMDLReactionReader
- getVDWRadius() - Method in class com.actelion.research.chem.Element
- getVDWRadius(int) - Static method in interface com.actelion.research.chem.conf.VDWRadii
- getVectorSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getVectorSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- getVectorSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getVectorSimilarity(IPharmacophorePoint) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- getVectorSimilarity(PPGaussian) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- getVectorSimilarity(PPGaussian, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- getVersion() - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getVersion() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getVersion() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getVgap() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Vgap attribute of the VerticalFlowLayout object
- getView(int) - Method in class com.actelion.research.gui.JMultiPanelView
- getViewCount() - Method in class com.actelion.research.gui.JMultiPanelView
- getViewFactory() - Method in class com.actelion.research.gui.hidpi.ScaledEditorKit
-
Returns the ViewFactory that is used to make sure the Views don't load in the background.
- getViolatedConditionsCount() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- getVolume() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getVolumeGaussians() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getVolumeOverlap(Gaussian3D) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getVolumeOverlap(Gaussian3D, double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getVolumeOverlap(Gaussian3D, Coordinates, double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getVolumes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getVolumes() - Method in class com.actelion.research.chem.phesa.PheSAMolecule
- getWeight() - Method in class com.actelion.research.chem.Element
- getWeight() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getWeight() - Method in class smile.data.Attribute
- getWeight(int) - Static method in class com.actelion.research.chem.PeriodicTable
- getWeight(int) - Method in class smile.regression.NeuralNetwork
-
Returns the weights of a layer.
- getWeightDecay() - Method in class smile.regression.NeuralNetwork
-
Returns the weight decay factor.
- getWeights() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getWhat() - Method in class com.actelion.research.gui.editor.DialogEvent
- getWhat() - Method in class com.actelion.research.gui.generic.GenericKeyEvent
- getWhat() - Method in class com.actelion.research.gui.generic.GenericMouseEvent
- getWidth() - Method in class com.actelion.research.calc.SelfOrganizedMap
- getWidth() - Method in class com.actelion.research.chem.coords.InventorFragment
- getWidth() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getWidth() - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- getWidth() - Method in interface com.actelion.research.gui.generic.GenericCanvas
- getWidth() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getWithCopy(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
- getWithCopy(BitArray128) - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- getWithCopy(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getWithCopy(S) - Method in class com.actelion.research.util.graph.complete.ContainerMemory
- getWordsFormatted(String) - Static method in class com.actelion.research.util.StringFunctions
-
Removes all non characters and digits.
- getWordsFormattedUniqueLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
- getX() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getX() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getX() - Method in class com.actelion.research.gui.generic.GenericMouseEvent
- getX() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- getX(int) - Method in class com.actelion.research.chem.conf.Conformer
- getX(int) - Method in class com.actelion.research.gui.generic.GenericPolygon
- getXMean() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getXMLElement(Document) - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getXMLElement(Document) - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- getXMLElement(Document) - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getXtest() - Method in class com.actelion.research.util.datamodel.ModelXYCrossValidation
-
Deprecated.
- getXtrain() - Method in class com.actelion.research.util.datamodel.ModelXYCrossValidation
-
Deprecated.
- getXvar() - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- getY() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getY() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getY() - Method in class com.actelion.research.gui.generic.GenericMouseEvent
- getY() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- getY(double) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getY(int) - Method in class com.actelion.research.chem.conf.Conformer
- getY(int) - Method in class com.actelion.research.gui.generic.GenericPolygon
- getYHat() - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- getYHat() - Method in class com.actelion.research.calc.regression.linear.pls.RegressionModelCalculatorOptimumFactors
- getYMean() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getYtest() - Method in class com.actelion.research.util.datamodel.ModelXYCrossValidation
-
Deprecated.
- getYtrain() - Method in class com.actelion.research.util.datamodel.ModelXYCrossValidation
-
Deprecated.
- getZ() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getZ() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getZ(int) - Method in class com.actelion.research.chem.conf.Conformer
- getZNeighbour(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Provided that the bond parity of a double bond is available, this method determines, whether connAtom has a counterpart with Z- (cis) configuration at the other end of the double bond.
- gfxConfig - Variable in class com.actelion.research.share.gui.Arrow
- GhostPreview - Class in com.actelion.research.gui.dock
- GhostPreview() - Constructor for class com.actelion.research.gui.dock.GhostPreview
- GIFFrame(BufferedImage) - Constructor for class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- GIFFrame(BufferedImage, int) - Constructor for class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- GIFFrame(BufferedImage, int, int) - Constructor for class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- GIFFrame(BufferedImage, int, int, int, int) - Constructor for class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- GIFFrame(BufferedImage, int, int, int, int, int, int, int) - Constructor for class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- GlobularityCalculator - Class in com.actelion.research.chem.prediction
- GlobularityCalculator() - Constructor for class com.actelion.research.chem.prediction.GlobularityCalculator
- GoodTuring(int[], int[], double[]) - Static method in class smile.math.Math
-
Takes a set of (frequency, frequency-of-frequency) pairs, and applies the "Simple Good-Turing" technique for estimating the probabilities corresponding to the observed frequencies, and P0, the joint probability of all unobserved species.
- grabFocus() - Method in interface com.actelion.research.gui.generic.GenericDialogHelper
- grabFocus() - Method in class com.actelion.research.gui.swing.SwingDialogHelper
- Graph - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- Graph(Map<Integer, List<Integer>>) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.Graph
- Graph.Edge - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- GRAPHIC_CONTROL_LABEL - Static variable in class com.actelion.research.util.AnimatedGIFWriter
- GraphicsContextImpl - Class in com.actelion.research.jfx.gui
-
Project: User: rufenec Date: 11/24/2014 Time: 6:24 PM
- GraphicsContextImpl(GraphicsContext) - Constructor for class com.actelion.research.jfx.gui.GraphicsContextImpl
- GRAY - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- GREEN - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- grid - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- grid - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- GRID_DIMENSION - Static variable in class com.actelion.research.chem.docking.DockingEngine
- GRID_RESOLUTION - Static variable in class com.actelion.research.chem.docking.DockingEngine
- gridSize - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- gridWidth - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- GUANIDINE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- GZIP - Static variable in class com.actelion.research.util.Base64
-
Specify that data should be gzip-compressed in second bit.
H
- HARD_MATCH_OPTIMISTIC_PERCENTILE - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- hasCIPParityDistinctionProblem() - Method in class com.actelion.research.chem.Canonizer
- hascode() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondType
- hasErrors() - Method in class com.actelion.research.util.ErrorHashMap
- hash - Variable in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- hash - Variable in class com.actelion.research.chem.properties.complexity.IndexHash
- hash(String) - Static method in class com.actelion.research.chem.CanonizerUtil.StrongHasher
- hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- hashCode() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- hashCode() - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
-
Returns the hash code of this sorted pair object.
- hashCode() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns the hashcode of this vector.
- hashCode() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- hashCode() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- hashCode() - Method in class com.actelion.research.chem.properties.complexity.IndexHash
- hashCode() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- hashCode() - Method in class com.actelion.research.util.datamodel.ByteVec
-
The hash code has to be calculated before.
- hashCode() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
-
Taken from idcode.
- hashCode() - Method in class com.actelion.research.util.datamodel.IntArray
- hashCode() - Method in class com.actelion.research.util.datamodel.IntegerDouble
- hashCode() - Method in class com.actelion.research.util.datamodel.IntVec
- hashCode() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- hashCode() - Method in class smile.data.Attribute
- hashCode() - Method in class smile.math.Complex
- hasHeteroAtom() - Method in interface com.actelion.research.chem.descriptor.flexophore.IPPNode
- hasHeteroAtom() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- hashlittle(byte[], long) - Static method in class com.actelion.research.util.BurtleHasher
- hashlittle(byte[], long, int) - Static method in class com.actelion.research.util.BurtleHasher
- hashlittle(int[], long) - Static method in class com.actelion.research.util.BurtleHasher
-
MvK 10.02.2010
- hashlittle(int[], long, int) - Static method in class com.actelion.research.util.BurtleHasher
- hashlittle(String, long) - Static method in class com.actelion.research.util.BurtleHasher
- hashmask(int) - Static method in class com.actelion.research.util.BurtleHasher
- HashSetInt - Class in com.actelion.research.util.hash
-
HashSetInt
- HashSetInt() - Constructor for class com.actelion.research.util.hash.HashSetInt
- HashSetInt(int) - Constructor for class com.actelion.research.util.hash.HashSetInt
- HashSetInt(int[]) - Constructor for class com.actelion.research.util.hash.HashSetInt
- HashSetInt(List<Integer>) - Constructor for class com.actelion.research.util.hash.HashSetInt
- hashsize(long) - Static method in class com.actelion.research.util.BurtleHasher
- hashword(String, long) - Static method in class com.actelion.research.util.BurtleHasher
- hasMoreLines() - Method in class com.actelion.research.io.StringReadChannel
- hasMoreResults() - Method in class com.actelion.research.calc.SimilarityMulticore
- hasNeighbours(Coordinates, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- hasNext() - Method in class com.actelion.research.chem.io.RDFileParser
- hasNextPairSequence() - Method in class com.actelion.research.chem.reaction.mapping.RootAtomPairSource
- hasNonCarbonNeighbour(StereoMolecule, int) - Static method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- hasNonCarbonNeighbour(StereoMolecule, int, int) - Static method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- hasOnlyFinite() - Method in class com.actelion.research.calc.Matrix
- hasOxo(StereoMolecule, int) - Static method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- hasOxo(StereoMolecule, int, int) - Static method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- hasSamePosition(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- hasStructureCoordinates() - Method in class com.actelion.research.chem.io.DWARFileParser
- hasStructureCoordinates2D() - Method in class com.actelion.research.chem.io.DWARFileParser
- hasStructureCoordinates3D() - Method in class com.actelion.research.chem.io.DWARFileParser
- hasStructures() - Method in class com.actelion.research.chem.io.DWARFileParser
-
If you don't read any records after calling this method, don't forget to call close() to close the underlying file.
- hasUnbalancedAtomCharge(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- HB_ACCEPTOR - com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage.InteractionProbe
- HB_DONOR - com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage.InteractionProbe
- hblaurie - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- HBOND_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- HBTerm - Class in com.actelion.research.chem.docking.scoring.chemscore
- head(int) - Method in class smile.data.AttributeDataset
-
returns the first few rows.
- head(int) - Method in class smile.data.AttributeVector
-
Shows the first few rows.
- HeaderMouseAdapter - Class in com.actelion.research.gui.dock
- HeaderMouseAdapter(JLabel, Dockable) - Constructor for class com.actelion.research.gui.dock.HeaderMouseAdapter
- HeaderPaintHelper - Class in com.actelion.research.gui
- HeaderPaintHelper() - Constructor for class com.actelion.research.gui.HeaderPaintHelper
- HEIGHT - Static variable in class com.actelion.research.gui.JMultiPanelTitle
- help() - Method in class com.actelion.research.util.CommandLineParser
- HELP - Static variable in class com.actelion.research.util.CommandLineParser
- HerschbachLaurie - Class in com.actelion.research.chem.forcefield.mmff.table
-
Table for Herschbach-Laurie version of Badger's rule.
- HerschbachLaurie(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
- HetNameParser - Class in com.actelion.research.chem.io.pdb.parser
-
HetNameParser
- HetNameParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.HetNameParser
- HetSynonymParser - Class in com.actelion.research.chem.io.pdb.parser
-
HetSynonymParser
- HetSynonymParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.HetSynonymParser
- hex2String(String) - Static method in class com.actelion.research.util.StringFunctions
- hg_step1(int, double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step2(int, double[][], int[][], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step3(int, int[][], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step4(int, double[][], int[][], int[], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step5(int, int[][], int[], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step6(int, double[][], int[], int[], double) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hgAlgorithm(double[][], String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- HiDPIHelper - Class in com.actelion.research.gui.hidpi
- HiDPIHelper() - Constructor for class com.actelion.research.gui.hidpi.HiDPIHelper
- HiDPIIcon - Class in com.actelion.research.gui.hidpi
-
Created by thomas on 07/12/15.
- HiDPIIcon(Image, boolean) - Constructor for class com.actelion.research.gui.hidpi.HiDPIIcon
- HiDPIIconButton - Class in com.actelion.research.gui.hidpi
-
Created by sandert on 04/12/15.
- HiDPIIconButton(String, String, String) - Constructor for class com.actelion.research.gui.hidpi.HiDPIIconButton
-
Creates a button that, if image2 is given, toggles between two states indicated by two different button images.
- HiDPIIconButton(String, String, String, int, String) - Constructor for class com.actelion.research.gui.hidpi.HiDPIIconButton
-
Creates a button that, if image2 is given, toggles between two states indicated by two different button images.
- HiDPIToggleButton - Class in com.actelion.research.gui.hidpi
-
Created by thomas on 07/12/15.
- HiDPIToggleButton(String, String, String, String) - Constructor for class com.actelion.research.gui.hidpi.HiDPIToggleButton
-
Creates a button that, if image2 is given, toggles between two states indicated by two different button images.
- HiDPIUtil - Class in com.actelion.research.gui.hidpi
- HiDPIUtil() - Constructor for class com.actelion.research.gui.hidpi.HiDPIUtil
- HierarchicalClustering - Class in smile.clustering
-
Agglomerative Hierarchical Clustering.
- HierarchicalClustering(Linkage) - Constructor for class smile.clustering.HierarchicalClustering
-
Constructor.
- HIGHLIGHT_ATOM_RADIUS - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- highlightAtom(StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- hilite(GenericDrawContext) - Method in class com.actelion.research.chem.AbstractDrawingObject
- hilite(GenericDrawContext) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- hilite(GenericDrawContext) - Method in class com.actelion.research.chem.TextDrawingObject
- Histogram - Class in com.actelion.research.calc.histogram
-
Histogram
- Histogram(double[], double, double, int) - Constructor for class com.actelion.research.calc.histogram.Histogram
- Histogram(double[], int) - Constructor for class com.actelion.research.calc.histogram.Histogram
- histogram2String(Matrix, int, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- HistogramMatchCalculator - Class in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
-
HistogramMatchCalculator
- HistogramMatchCalculator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.HistogramMatchCalculator
- hit(Rectangle, Shape, boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- HOSE_CODE_CUT_C_SP3_SP3 - Static variable in class com.actelion.research.chem.contrib.HoseCodeCreator
- HoseCodeCreator - Class in com.actelion.research.chem.contrib
- HoseCodeCreator() - Constructor for class com.actelion.research.chem.contrib.HoseCodeCreator
- HS_BDIAGONAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_CROSS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_DIAGCROSS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_FDIAGONAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_HORIZONTAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_VERTICAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HungarianAlgorithm - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- HungarianAlgorithm() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- HYBRID - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- HYBRID_SHIFT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
- Hydrogen - Static variable in class com.actelion.research.chem.PeriodicTable
- HydrogenHandler - Class in com.actelion.research.chem.contrib
- HydrogenHandler() - Constructor for class com.actelion.research.chem.contrib.HydrogenHandler
- hypot(double, double) - Static method in class com.actelion.research.calc.SingularValueDecomposition
- hypot(double, double) - Static method in class smile.math.Math
-
Returns sqrt(x2 +y2) without intermediate overflow or underflow.
I
- i - Variable in class smile.math.SparseArray.Entry
-
The index of entry.
- iAMPAC_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IArrow - Interface in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 11/24/2014 Time: 3:28 PM
- IAtomPropertiesDialog - Interface in com.actelion.research.share.gui.editor.dialogs
-
Project: User: rufenec Date: 11/24/2014 Time: 5:03 PM
- IAtomQueryFeaturesDialog - Interface in com.actelion.research.share.gui.editor.dialogs
-
Project: User: rufenec Date: 11/24/2014 Time: 4:53 PM
- IBitArray - Interface in com.actelion.research.chem.properties.complexity
- IBitArrayFactory<T extends IBitArray> - Interface in com.actelion.research.chem.properties.complexity
- IBondQueryFeaturesDialog - Interface in com.actelion.research.share.gui.editor.dialogs
-
Project: User: rufenec Date: 11/24/2014 Time: 4:57 PM
- ICalculateModel - Interface in com.actelion.research.calc.regression
-
ICalculateModel
- ICalculateYHat - Interface in com.actelion.research.calc.regression
-
ICalculateYHat
- IChangeListener - Interface in com.actelion.research.share.gui.editor.listeners
-
Project: User: rufenec Date: 11/24/2014 Time: 3:25 PM
- IClipboardHandler - Interface in com.actelion.research.gui.clipboard
- IColor - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:21 PM
- ICompleteGraph - Interface in com.actelion.research.util.graph.complete
-
ICompleteGraph
- ICursor - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:21 PM
- id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- id - Variable in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- id(int) - Static method in class com.actelion.research.calc.MatrixFunctions
-
Returns a (n x n) identity matrix.
- ID_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- IDABORT - com.actelion.research.share.gui.DialogResult
- IDCANCEL - com.actelion.research.share.gui.DialogResult
- idcode - Variable in class com.actelion.research.util.datamodel.IDCodeCoord
- IDCode() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
- IDCODE_100 - Static variable in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- IDCODE_101 - Static variable in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- IDCODE_EMPTY - Static variable in class com.actelion.research.util.ConstantsDWAR
- IDCodeCoord - Class in com.actelion.research.util.datamodel
-
IDCodeCoord Apr 12, 2012 MvK: Start implementation
- IDCodeCoord(int, String, String) - Constructor for class com.actelion.research.util.datamodel.IDCodeCoord
- IDCodeCoord(String) - Constructor for class com.actelion.research.util.datamodel.IDCodeCoord
- IDCodeCoord(String, String) - Constructor for class com.actelion.research.util.datamodel.IDCodeCoord
- IDCodeParser - Class in com.actelion.research.chem
- IDCodeParser() - Constructor for class com.actelion.research.chem.IDCodeParser
-
This default constructor creates molecules guaranteed to have 2D-atom-coordinates.
- IDCodeParser(boolean) - Constructor for class com.actelion.research.chem.IDCodeParser
- IDCodeParserWithoutCoordinateInvention - Class in com.actelion.research.chem
-
Typically you should use IDCodeParser instead of this class.
- IDCodeParserWithoutCoordinateInvention() - Constructor for class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- idcodeProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- idcodeProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- IDCodeWithName() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
- idColumn - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- iDEL_RE - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IdentifiedObject<T> - Class in com.actelion.research.util.datamodel
-
IdentifiedObject Nov 2, 2011 MvK: Start implementation
- IdentifiedObject() - Constructor for class com.actelion.research.util.datamodel.IdentifiedObject
- IdentifiedObject(T, long) - Constructor for class com.actelion.research.util.datamodel.IdentifiedObject
- identify(String) - Static method in class com.actelion.research.chem.NamedSubstituents
-
Checks, whether the given nameStart either exactly matches one of the dictionary names or whether exactly one dictionary name starts with the given nameStart.
- identifyHBondFunctionality(StereoMolecule, Set<Integer>, Set<Integer>, Set<Integer>, Set<Integer>, Set<Integer>, Set<Integer>) - Static method in class com.actelion.research.chem.docking.scoring.ChemPLP
- IDepictor<T> - Interface in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 11/24/2014 Time: 3:26 PM
- IDescriptorHandlerFlexophore - Interface in com.actelion.research.chem.descriptor.flexophore
- IDialog - Interface in com.actelion.research.share.gui.editor.dialogs
- iDICT_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IDNO - com.actelion.research.share.gui.DialogResult
- IDOK - com.actelion.research.share.gui.DialogResult
- IdoScore - Class in com.actelion.research.chem.docking.scoring
- IdoScore(StereoMolecule, Set<Integer>, int[], MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.IdoScore
- IDOSCORE - com.actelion.research.chem.docking.DockingEngine.ScoringFunction
- IDrawContext<T> - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:22 PM
- IDrawingObject - Interface in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 11/24/2014 Time: 3:28 PM
- IDRETRY - com.actelion.research.share.gui.DialogResult
- IDYES - com.actelion.research.share.gui.DialogResult
- IEEEremainder(double, double) - Static method in class smile.math.Math
-
Computes the remainder operation on two arguments as prescribed by the IEEE 754 standard.
- IFactory<S extends AMemorizedObject> - Interface in com.actelion.research.util.graph.complete
-
IFactory
- iGAST_HUCK - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- iGASTEIGER - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- iGAUSS80_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- iHUCKEL - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IIdentifiedObject<T> - Interface in com.actelion.research.util.datamodel
-
IIdentifiedObject Nov 4, 2011 MvK: Start implementation
- IKeyCode - Interface in com.actelion.research.share.gui.editor.io
-
Project: User: rufenec Date: 11/24/2014 Time: 4:17 PM
- IKeyEvent - Interface in com.actelion.research.share.gui.editor.io
-
Project: User: rufenec Date: 11/24/2014 Time: 3:20 PM
- im() - Method in class smile.math.Complex
-
Returns the imaginary part.
- IMAGE_SEPARATOR - Static variable in class com.actelion.research.util.AnimatedGIFWriter
- IMAGE_TRAILER - Static variable in class com.actelion.research.util.AnimatedGIFWriter
- ImageClipboardHandler - Class in com.actelion.research.gui.clipboard
- ImageClipboardHandler() - Constructor for class com.actelion.research.gui.clipboard.ImageClipboardHandler
- ImageClipboardHandler.ImageSelection - Class in com.actelion.research.gui.clipboard
- ImageDataSource - Interface in com.actelion.research.gui
-
This is a source for high resolution image data requested by JImagePanel
- ImageProvider<T> - Class in com.actelion.research.share.gui.editor
-
Created by rufenec on 08/05/15.
- ImageProvider() - Constructor for class com.actelion.research.share.gui.editor.ImageProvider
- ImageSelection(Image) - Constructor for class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- imageUpdate(Image, int, int, int, int, int) - Method in class com.actelion.research.gui.JImagePanel
- iMMFF94_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IModelCloneable<T> - Interface in com.actelion.research.util.datamodel
-
IModelClonable
- IMolDistHist - Interface in com.actelion.research.chem.descriptor.flexophore
- IMoleculeView - Interface in com.actelion.research.jfx.gui.chem
- IMouseEvent - Interface in com.actelion.research.share.gui.editor.io
-
Project: User: rufenec Date: 11/24/2014 Time: 3:19 PM
- importance() - Method in class smile.regression.RandomForest
-
Returns the variable importance.
- importance() - Method in class smile.regression.RegressionTree
-
Returns the variable importance.
- IMPORTANT - Static variable in class com.actelion.research.chem.Molecule3D
- iMULLIKEN_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- in - Variable in class com.actelion.research.util.LittleEndianDataInputStream
- INCLUDE_ALL - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_CATALYSTS - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_COORDS - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_DEFAULT - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_DRAWING_OBJECTS - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_MAPPING - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_RXN_CODE_ONLY - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUSION - Static variable in class com.actelion.research.chem.phesa.VolumeGaussian
- increase(int, int, double) - Method in class com.actelion.research.calc.Matrix
- increaseNonCachableCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- INCREMENT - Static variable in class com.actelion.research.chem.prediction.CLogPPredictor
- incrementByte(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- incrementFrequency() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- incrementFrequency() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- incrementFrequencyOnePerMol() - Method in class com.actelion.research.chem.shredder.Fragment
- incrementFrequencySumAll() - Method in class com.actelion.research.chem.shredder.Fragment
- incrementHitCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache.CacheEntry
- IncrementTable - Class in com.actelion.research.chem.prediction
- IncrementTable() - Constructor for class com.actelion.research.chem.prediction.IncrementTable
- IncrementTable(String) - Constructor for class com.actelion.research.chem.prediction.IncrementTable
- IncrementTableWithIndex - Class in com.actelion.research.chem.prediction
- IncrementTableWithIndex() - Constructor for class com.actelion.research.chem.prediction.IncrementTableWithIndex
- IncrementTableWithIndex(String) - Constructor for class com.actelion.research.chem.prediction.IncrementTableWithIndex
- index - Variable in class com.actelion.research.util.datamodel.IDCodeCoord
- index - Variable in class org.machinelearning.svm.libsvm.svm_node
- index(int, int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
-
Returns the index of a row for a given molecule and four connected atoms which form a torsion angle.
- index(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns the index of a row for a given molecule and three connected atoms which form an angle.
- index(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
-
Returns the index that a given set of three atoms have in the Dfsb table.
- index(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
-
Returns the index of a row for a given molecule and three connected atoms which form an angle.
- IndexCoordinates - Class in com.actelion.research.chem.descriptor.flexophore
- IndexCoordinates() - Constructor for class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- IndexCoordinates(int, int, Coordinates) - Constructor for class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- IndexHash - Class in com.actelion.research.chem.properties.complexity
- IndexHash() - Constructor for class com.actelion.research.chem.properties.complexity.IndexHash
- IndexHash(int) - Constructor for class com.actelion.research.chem.properties.complexity.IndexHash
- INDEXLEN - Static variable in class com.actelion.research.chem.reaction.Classification
- indexOf(byte[], byte) - Static method in class com.actelion.research.util.ArrayUtils
- indexOf(byte[], byte, int) - Static method in class com.actelion.research.util.ArrayUtils
- indexOf(int) - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- indexOf(int) - Method in class com.actelion.research.util.IntQueue
- indexOf(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- indexOf(int[], int) - Static method in class com.actelion.research.util.ArrayUtils
- indexOf(int[], int, int) - Static method in class com.actelion.research.util.ArrayUtils
- indexOf(Object[], Object) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- indexOf(Object[], Object) - Static method in class com.actelion.research.util.ArrayUtils
- INFO - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- INFO_AMINO - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_ATOMNAME - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_ATOMSEQUENCE - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_BFACTOR - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_CHAINID - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_DEFAULT - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- INFO_DESCRIPTION - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_INTERACTION_ATOM_TYPE - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_PPP - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_RESSEQUENCE - Static variable in class com.actelion.research.chem.Molecule3D
- informListeners() - Method in class com.actelion.research.gui.JChemistryView
- init() - Method in class com.actelion.research.chem.AbstractDepictor
- init() - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- init() - Method in class com.actelion.research.chem.Depictor2D
- init() - Method in class com.actelion.research.chem.docking.scoring.idoscore.StrainTerm
- init() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- init() - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
- init() - Method in class com.actelion.research.gui.generic.GenericDepictor
- init() - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- init(int) - Method in class com.actelion.research.chem.CanonizerBaseValue
- init(LigandPose, double) - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- init(LigandPose, double) - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
- init(LigandPose, double) - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- init(ProbeScanning.Probe) - Method in class com.actelion.research.chem.docking.scoring.ProbeScanning
- init(StereoMolecule) - Method in class com.actelion.research.chem.mcs.RunBondVector2IdCode
- initHistogramArray(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- initHistogramArray(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- initHistogramArray(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- INITIAL_SPLITS - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- initialCut(int, int, List<Integer>, List<Integer>, List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
a cut divides a edge into a target node and a source node: an edge is defined as a tuple of two nodes (a,b), a left cut results in node a being the source node and b being the target node: a-->--b a right cut results in the right node being the source node: a--<--b returns int array with source node as 0th element and target node as 1st element
- initialize() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- initialize() - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRule
- initialize(double[], double, double, int) - Method in class com.actelion.research.calc.histogram.Histogram
- initialize(int) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Initializes the in memory torsion database by reading torsion list, associated torsion frequencies, torsion peak widths (ranges), and/or normalized 3-degree bins into memory.
- initialize(int) - Method in class com.actelion.research.util.BinaryDecoder
- initialize(int, int) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Initializes the in memory torsion database by reading torsion list, associated torsion frequencies, torsion peak widths (ranges), and/or normalized 3-degree bins into memory.
- initialize(int, int) - Method in class com.actelion.research.util.BinaryEncoder
-
Initializes encoder for writing one binary array
- initialize(StereoMolecule, boolean) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Don't call this method directly.
- initialize(String) - Static method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- initializeConformers(long, int) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
Needs to be called, before getting individual conformers of the same molecule by getNextConformer().
- initializeConformers(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
One of the initializeConformers() methods needs to be called, before getting individual conformers of the same molecule by getNextConformer().
- initializeConformers(StereoMolecule, int, int, boolean) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
One of the initializeConformers() methods needs to be called, before getting individual conformers of the same molecule by getNextConformer().
- initializeExistingSet(int) - Method in class com.actelion.research.chem.DiversitySelector
- initializeNormalization() - Method in class com.actelion.research.calc.BinarySOM
- initializeNormalization() - Method in class com.actelion.research.calc.SelfOrganizedMap
- initializeNormalization() - Method in class com.actelion.research.calc.VectorSOM
- initializeReferenceVectors(int, int, int) - Method in class com.actelion.research.calc.SelfOrganizedMap
- initializeThreadMustDie() - Method in class com.actelion.research.gui.JProgressPanel
-
Resets the progress cancelled flag, which is set by pressing the cancel button.
- initialTransform(int) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
-
.
- initRND(byte, byte) - Method in class com.actelion.research.util.datamodel.ByteVec
- initRND(byte, byte, int, int) - Static method in class com.actelion.research.util.datamodel.ByteVec
- initRND(double[][]) - Method in class com.actelion.research.util.DoubleVec
-
The array contains the maximum and the minimum values for the initialisation of each field in the double vector.
- initRND(double, double) - Method in class com.actelion.research.util.DoubleVec
- injectNewSeed() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- iNO_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- InputObjectFracDimCalc - Class in com.actelion.research.chem.properties.fractaldimension
-
InputObjectFracDimCalc
- InputObjectFracDimCalc(InputObjectFracDimCalc) - Constructor for class com.actelion.research.chem.properties.fractaldimension.InputObjectFracDimCalc
- InputObjectFracDimCalc(StereoMolecule, long, String) - Constructor for class com.actelion.research.chem.properties.fractaldimension.InputObjectFracDimCalc
- InputStream(InputStream) - Constructor for class com.actelion.research.util.Base64.InputStream
-
Constructs a
Base64.InputStream
in DECODE mode. - InputStream(InputStream, int) - Constructor for class com.actelion.research.util.Base64.InputStream
-
Constructs a
Base64.InputStream
in either ENCODE or DECODE mode. - inRingOfSize(MMFFMolecule, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns true if the atom is in any ring of a given size.
- inRingOfSize(MMFFMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Angle
-
Checks if an angle is in a ring of given size.
- inRingOfSize(MMFFMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Torsion
-
Checks and returns the minimum ring size that a torsion is contained in.
- inRings(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns the number of rings that an atom is a member of in a molecule.
- inSameRing(MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns true if two atoms are in the same ring of a given size.
- insert(String, int) - Method in class com.actelion.research.gui.JScrollableMenu
- insert(Action, int) - Method in class com.actelion.research.gui.JScrollableMenu
- insert(JMenuItem, int) - Method in class com.actelion.research.gui.JScrollableMenu
- insertLigand(Molecule3D, Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- insertSeparator(int) - Method in class com.actelion.research.gui.JScrollableMenu
- insideBounds(Coordinates[]) - Method in class com.actelion.research.chem.Coordinates
- INSTANCE - com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
- instantiate(String) - Static method in class com.actelion.research.chem.AbstractDrawingObject
- IntArray - Class in com.actelion.research.util.datamodel
- IntArray() - Constructor for class com.actelion.research.util.datamodel.IntArray
- IntArray(int) - Constructor for class com.actelion.research.util.datamodel.IntArray
- IntArray(int[]) - Constructor for class com.actelion.research.util.datamodel.IntArray
-
Shallow constructor.
- IntArray(IntArray) - Constructor for class com.actelion.research.util.datamodel.IntArray
-
Deep constructor.
- IntArrayComparator - Class in com.actelion.research.util
- IntArrayComparator() - Constructor for class com.actelion.research.util.IntArrayComparator
- intArrayToByteArray(int[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- IntegerDouble - Class in com.actelion.research.util.datamodel
-
IntegerDouble Oct 24, 2011 MvK: Start implementation
- IntegerDouble() - Constructor for class com.actelion.research.util.datamodel.IntegerDouble
- IntegerDouble(int, double) - Constructor for class com.actelion.research.util.datamodel.IntegerDouble
- IntegerDouble(IntegerDouble) - Constructor for class com.actelion.research.util.datamodel.IntegerDouble
- IntegerHistogram - Class in com.actelion.research.calc.histogram
-
IntegerHistogram
- IntegerHistogram(int[][]) - Constructor for class com.actelion.research.calc.histogram.IntegerHistogram
- IntegerHistogram(int[][], boolean) - Constructor for class com.actelion.research.calc.histogram.IntegerHistogram
- INTERACTION_TYPE_NONE - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- InteractionAtomTypeCalculator - Class in com.actelion.research.chem.interactionstatistics
- InteractionAtomTypeCalculator() - Constructor for class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- InteractionAtomTypeCalculator.AtomFlagCount - Enum in com.actelion.research.chem.interactionstatistics
- InteractionAtomTypeCalculator.AtomPropertyMask - Enum in com.actelion.research.chem.interactionstatistics
- InteractionAtomTypeCalculator.AtomPropertyShift - Enum in com.actelion.research.chem.interactionstatistics
- InteractionAtomTypeCalculator.FunctionalGroup - Enum in com.actelion.research.chem.interactionstatistics
- InteractionDescriptor(SplineFunction) - Constructor for class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- InteractionDistanceStatistics - Class in com.actelion.research.chem.interactionstatistics
- InteractionSimilarityTable - Class in com.actelion.research.chem.interactionstatistics
-
distance gives the distance of the point of highest potential.
- InteractionSimilarityTable.InteractionDescriptor - Class in com.actelion.research.chem.interactionstatistics
- InteractionTerm - Class in com.actelion.research.chem.docking.scoring.idoscore
-
ProteinLigandTerm is used to represent the energy between 2 atoms.
- InteractionTypeMap - Class in com.actelion.research.chem.descriptor.flexophore.generator
- InteractionTypeMap(double) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.InteractionTypeMap
- intermediateColor(Color, Color, float) - Static method in class com.actelion.research.util.ColorHelper
-
Creates an intermediate color between color c1 and color c2 in the RGB color space.
- interpolate(double[], double[]) - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- interpreteMonth(String) - Static method in class com.actelion.research.util.DateAnalysis
- interrupt() - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- interrupt() - Method in interface com.actelion.research.chem.forcefield.ForceField
- intersectClipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- intersectClipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- intersects(IRectangle2D) - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- IntHeapSelect - Class in smile.sort
-
This class tracks the smallest values seen thus far in a stream of values.
- IntHeapSelect(int) - Constructor for class smile.sort.IntHeapSelect
-
Constructor.
- IntHeapSelect(int[]) - Constructor for class smile.sort.IntHeapSelect
-
Constructor.
- IntQueue - Class in com.actelion.research.chem.descriptor.flexophore.calculator
-
Implementation for a FIFO of int.
- IntQueue - Class in com.actelion.research.util
-
Implementation for a FIFO of int.
- IntQueue() - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
-
Creeates a new Queue with an initial size of 100
- IntQueue() - Constructor for class com.actelion.research.util.IntQueue
-
Creeates a new Queue with an initial size of 100
- IntQueue(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- IntQueue(int) - Constructor for class com.actelion.research.util.IntQueue
- intToByteArray(int) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- intValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- IntVec - Class in com.actelion.research.util.datamodel
- IntVec() - Constructor for class com.actelion.research.util.datamodel.IntVec
- IntVec(boolean[]) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
Puts an boolean array into an int array.
- IntVec(int) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
Don't forget to calculate the hash code after setting the bits!
- IntVec(int[]) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
Deep copy, hash code is calculated.
- IntVec(int[], boolean) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
If true each int contains only a 0 or a 1.
- IntVec(IntVec) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
Deep copy, hash code is calculated.
- IntVec(List<Integer>) - Constructor for class com.actelion.research.util.datamodel.IntVec
- INumericalDataColumn - Interface in com.actelion.research.calc
- inv(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
-
Returns the inverse of a matrix.
- invalidateCoordinates() - Method in class com.actelion.research.chem.Canonizer
- invalidateHelperArrays(int) - Method in class com.actelion.research.chem.Molecule
-
Clears helperBits from mValidHelperArrays.
- invalidateStrain() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- invent(StereoMolecule) - Method in class com.actelion.research.chem.coords.CoordinateInventor
-
Creates new atom 2D-coordinates for a molecule or a part of a molecule.
- invent(StereoMolecule, long[]) - Method in class com.actelion.research.chem.coords.CoordinateInventor
-
Creates new atom 2D-coordinates for a molecule or a part of a molecule.
- inventCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.IDCodeParser
- inventCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- InventorAngle - Class in com.actelion.research.chem.coords
-
Created by thomas on 9/23/16.
- InventorAngle(double, double) - Constructor for class com.actelion.research.chem.coords.InventorAngle
- InventorAngle(double, double, double, double) - Constructor for class com.actelion.research.chem.coords.InventorAngle
- InventorChain - Class in com.actelion.research.chem.coords
-
Created by thomas on 9/23/16.
- InventorChain(int) - Constructor for class com.actelion.research.chem.coords.InventorChain
- InventorCharge - Class in com.actelion.research.chem.coords
-
Created by thomas on 9/28/16.
- InventorCharge(InventorFragment, int, int) - Constructor for class com.actelion.research.chem.coords.InventorCharge
- InventorDefaultTemplateList - Class in com.actelion.research.chem.coords
- InventorDefaultTemplateList() - Constructor for class com.actelion.research.chem.coords.InventorDefaultTemplateList
- InventorFragment - Class in com.actelion.research.chem.coords
- InventorFragment(InventorFragment) - Constructor for class com.actelion.research.chem.coords.InventorFragment
- InventorFragment(StereoMolecule, int, boolean) - Constructor for class com.actelion.research.chem.coords.InventorFragment
- InventorTemplate - Class in com.actelion.research.chem.coords
- InventorTemplate(StereoMolecule, long[], boolean) - Constructor for class com.actelion.research.chem.coords.InventorTemplate
- inverf(double) - Static method in class smile.math.special.Erf
-
The inverse error function.
- inverfc(double) - Static method in class smile.math.special.Erf
-
The inverse complementary error function.
- inverse() - Method in class smile.math.matrix.Cholesky
-
Returns the matrix inverse.
- inverse() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the inverse matrix.
- inverse() - Method in class smile.math.matrix.LU
-
Returns the matrix inverse.
- inverse(boolean) - Method in interface smile.math.matrix.DenseMatrix
-
Returns the inverse matrix.
- inverse(double) - Method in class com.actelion.research.calc.BoxCox
- inverseTransformSampling() - Method in class smile.stat.distribution.AbstractDistribution
-
Use inverse transform sampling (also known as the inverse probability integral transform or inverse transformation method or Smirnov transform) to draw a sample from the given distribution.
- invLinReg_Yhat(Matrix, Matrix) - Static method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- invLinReg_Yhat(Matrix, Matrix, Matrix, Matrix) - Static method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- IO - Class in com.actelion.research.util
-
IO 2003 MvK: Start implementation
- IO() - Constructor for class com.actelion.research.util.IO
- IObjectiveCompleteGraph<T extends ICompleteGraph> - Interface in com.actelion.research.util.graph.complete
-
IObjectiveCompleteGraph
- Iodine - Static variable in class com.actelion.research.chem.PeriodicTable
- IonizableGroupDetector - Class in com.actelion.research.chem.phesa.pharmacophore
-
derives potentially ionizable Groups, independent of the chosen explicit protonation state
- IonizableGroupDetector(StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector
- IonizableGroupDetector2D - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- IonizableGroupDetector2D(StereoMolecule) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
- IPharmacophorePoint - Interface in com.actelion.research.chem.phesa.pharmacophore.pp
- IPharmacophorePoint.Functionality - Enum in com.actelion.research.chem.phesa.pharmacophore.pp
- IPipeline<T> - Interface in com.actelion.research.util
-
IPipeline Interface to connect several Runable in a pipeline Mar 27, 2012 MvK: Start implementation Oct 9 2012 MvK: wereAllDataFetched() added.
- IPolygon - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 4:45 PM
- IPPNode - Interface in com.actelion.research.chem.descriptor.flexophore
- IPPNodeSimilarity - Interface in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
-
IPPNodeSimilarity
- iPULLMAN - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IReactionArrow - Interface in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 11/24/2014 Time: 5:49 PM
- IReactionMapper - Interface in com.actelion.research.chem.reaction
- IRectangle2D - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:17 PM
- IS_JAVA_10 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_JAVA_11 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_JAVA_8 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_JAVA_8_OR_OLDER - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_JAVA_9 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_VENDOR_APPLE - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- is3D() - Method in class com.actelion.research.chem.Molecule
- is3D(Molecule3D) - Static method in class com.actelion.research.chem.io.AbstractParser
- is64BitJRE() - Static method in class com.actelion.research.util.Platform
- isAcceptable(ArrayList<ConformationRule>) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- isAcceptor(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isAcceptor(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- isAcceptor(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isAcceptor(StereoMolecule, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- isAcidicOxygen(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAcidicOxygenAtPhosphoricAcid(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isActive() - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- isActive() - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- isAdjusting() - Method in class com.actelion.research.gui.PruningBarEvent
- isAlcoholicOxygen(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isAliphatic(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isAliphaticAtom(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isAlkaliMetal(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isAlkaline(int) - Static method in class com.actelion.research.chem.PeriodicTable
- isAlkylAmine(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAllDataIn() - Method in interface com.actelion.research.util.IPipeline
- isAllDataIn() - Method in class com.actelion.research.util.Pipeline
- isAllLetter(String) - Static method in class com.actelion.research.util.StringFunctions
- isAllLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
- isAllUpperCase(String) - Static method in class com.actelion.research.util.StringFunctions
- isAllylicAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isAltDown() - Method in class com.actelion.research.gui.generic.GenericMouseEvent
- isAltDown() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- isAltDown() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- isAmide(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAmideTypeBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Evaluates, whether bond is an amide bond, thio-amide, or amidine bond.
- isAmine(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAnimating() - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
- isAqua() - Static method in class com.actelion.research.gui.LookAndFeelHelper
- isAromatic() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- isAromatic(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isAromatic(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- isAromatic(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- isAromatic(int) - Method in class com.actelion.research.chem.RingCollection
-
Return whether the ring is considered aromatic.
- isAromaticAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isAromaticBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isArylAmine(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAtomColorSupported() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- isAtomColorSupported() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- isAtomColorSupported() - Method in class com.actelion.research.share.gui.editor.Model
- isAtomConfigurationUnknown(int) - Method in class com.actelion.research.chem.Molecule
- isAtomFlag(int, int) - Method in class com.actelion.research.chem.Molecule3D
- isAtomicNoElectronegative(int) - Static method in class com.actelion.research.chem.Molecule
- isAtomicNoElectropositive(int) - Static method in class com.actelion.research.chem.Molecule
- isAtomMarkedForDeletion(int) - Method in class com.actelion.research.chem.Molecule
-
Checks whether this atom was marked to be deleted and not deleted yet.
- isAtomMember(int, int) - Method in class com.actelion.research.chem.RingCollection
- isAtomParityPseudo(int) - Method in class com.actelion.research.chem.Molecule
-
Pseudo paries are parities that indicate a relative configuration.
- isAtomStereoCenter(int) - Method in class com.actelion.research.chem.Molecule
-
Atoms with pseudo parities are not considered stereo centers.
- isAutoMappedAtom(int) - Method in class com.actelion.research.chem.Molecule
- isBackboneSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
A backbone search is a hash code comparison from encoding stereo and unsaturation depleted structures.
- isBasicNitrogen(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isBINAPChiralityBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Checks whether bond is an axial chirality bond of the BINAP type.
- isBinary - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- isBinaryFingerprint(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- isBitSet(int) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- isBitSet(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- isBitSet(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- isBitSet(int) - Method in class com.actelion.research.util.datamodel.IntVec
- isBitSet(int[], int) - Static method in class com.actelion.research.util.BitUtils
- isBitSet(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- isBitSet(int, int) - Static method in class com.actelion.research.util.datamodel.IntVec
- isBondBackgroundHilited(int) - Method in class com.actelion.research.chem.Molecule
-
Used for depiction only.
- isBondBridge(int) - Method in class com.actelion.research.chem.Molecule
- isBondForegroundHilited(int) - Method in class com.actelion.research.chem.Molecule
-
Used for depiction only.
- isBondMarkedForDeletion(int) - Method in class com.actelion.research.chem.Molecule
-
Checks whether this bond was marked to be deleted and not deleted yet.
- isBondMember(int, int) - Method in class com.actelion.research.chem.RingCollection
- isBondParityPseudo(int) - Method in class com.actelion.research.chem.Molecule
- isBondParityUnknownOrNone(int) - Method in class com.actelion.research.chem.Molecule
-
This hint/flag is set by CoordinateInventor for double bonds without given EZ-parity, because the new coordinates may imply a not intended EZ-parity.
- isCancelled() - Method in class com.actelion.research.gui.editor.SwingEditorDialog
- isCancelled() - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- isCanonicalOrientation() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- isCapacityLimitBreakes() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
-
If true not all index combinations were generated.
- isCapacityLimitBreakes() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- isCapacityLimitBreakes() - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
-
If true not all index combinations where generated.
- isCapitalizedWord(String) - Static method in class com.actelion.research.util.StringFunctions
- isCarbonConnected2Hetero(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isCarbonExclusiveNode() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- isCarbonInteraction(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- isCarbonOnlyConnected2Hetero(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isCarbonTwoValencesMinimum(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isCarboxyC(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isCenterData() - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- isCentralAlleneAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isChalcogene(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isChargeNeg(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isChargePos(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isChiralFlagSet() - Method in class com.actelion.research.chem.MolfileParser
- isCluster() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- isCommand() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- isCommand() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- isCommand() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- isConclusive() - Method in class com.actelion.research.util.DateAnalysis
-
Call this only once after calling analyse() once or multiple times.
- isConnected2Hetero(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isConsiderAromaticRings() - Method in class com.actelion.research.chem.mcs.MCS
- isConsiderAromaticRings() - Method in class com.actelion.research.chem.mcs.MCSFast
- isConsiderRings() - Method in class com.actelion.research.chem.mcs.MCS
- isConsiderRings() - Method in class com.actelion.research.chem.mcs.MCSFast
- isControlDown() - Method in class com.actelion.research.gui.generic.GenericMouseEvent
- isControlDown() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- isControlDown() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- isCorrectStereoIsomer(StereoMolecule, int) - Method in class com.actelion.research.chem.StereoIsomerEnumerator
-
Checks, whether the given molecule's atom and bond parities are the expected one's for the given stereo isomer index.
- isCovered(long[], long[]) - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
-
Checks whether mask and data as elimination rule are covered by this rule.
- isCyanoN(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isDarkLookAndFeel() - Static method in class com.actelion.research.gui.LookAndFeelHelper
- isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dock.TransferableDockable
- isDeletable() - Method in class com.actelion.research.chem.AbstractDrawingObject
- isDelocalized(int) - Method in class com.actelion.research.chem.RingCollection
-
Return whether the ring is considered delocalized, which are 6-membered aromatic rings with no preference concerning where the double bonds are located.
- isDelocalizedBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
A bond is considered delocalized, if it has different bond orders in different, but energetically equivalent mesomeric structures.
- isDescriptorShortName(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- isDonor(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isDonor(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- isDonor(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isDonorHeavyAtom(StereoMolecule, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- isDonorHydrogen(StereoMolecule, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- isDragFlavorSupported(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- isDragFlavorSupported(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- isDragFlavorSupported(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- isDropOK(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- isDropOK(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- isEarthAlkaliMetal(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isEditable() - Method in class com.actelion.research.gui.JChemistryView
- isEditable() - Method in class com.actelion.research.gui.JStructureView
- isEditable() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- isElectronegative(int) - Method in class com.actelion.research.chem.Molecule
- isElectropositive(int) - Method in class com.actelion.research.chem.Molecule
- isELUSIVE() - Static method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- isELUSIVE() - Static method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- isELUSIVE() - Static method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- isEmpty() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- isEmpty() - Method in class com.actelion.research.chem.reaction.Reaction
- isEmpty() - Method in class com.actelion.research.util.IntQueue
- isEmpty() - Method in class com.actelion.research.util.Pipeline
- isEmpty() - Method in class smile.math.SparseArray
-
Returns true if the array is empty.
- isEmptyString(String) - Static method in class com.actelion.research.share.gui.editor.actions.ChangeAtomPropertiesAction
- isEnabled() - Method in class org.openmolecules.chem.conf.so.ConformationRule
- isEnd() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- isEndOfRunReached() - Method in class com.actelion.research.chem.mcs.RunBondVector2IdCode
- isEqualCol(Matrix, int, Matrix, int, double) - Static method in class com.actelion.research.calc.MatrixFunctions
- isEtherOxygenAtAromatic(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isExactSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
An exact search is a comparison of idcodes of standardized molecules with full stereo features.
- isExactSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
An exact search is a comparison of idcodes of standardized molecules with full stereo features.
- isExtensionListInDescription() - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Returns whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
- isFailed() - Method in class com.actelion.research.calc.regression.ModelError
- isFinalized() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- isFixedDistance() - Method in class org.openmolecules.chem.conf.so.DistanceRule
- isFlatNitrogen(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Checks whether this nitrogen atom is flat, because it has a double bond, is member of an aromatic ring or is part of amide, an enamine or in resonance with an aromatic ring.
- isFlexible() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- isFragment() - Method in class com.actelion.research.chem.ExtendedDepictor
- isFragment() - Method in class com.actelion.research.chem.Molecule
-
Molecule objects may represent complete molecules or sub-structure fragments, depending on, whether they are flagges as being a fragment or not.
- isFragment() - Method in class com.actelion.research.chem.reaction.Reaction
-
The naming of this method is in analogy to the corresponding method of the Molecule class.
- isFragment() - Method in class com.actelion.research.share.gui.editor.Model
- isFragmentIndexInMoleculeIndex() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- isFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcher
-
Fastest check, whether the molecule contains the fragment.
- isFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- isFragmentInMolecule(int) - Method in class com.actelion.research.chem.SSSearcher
-
Fastest check, whether the molecule contains the fragment.
- isFragmentInMoleculeWithoutIndex() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- isGDIFontDrawing() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- isGDIPenDrawing() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- isGDIPenWidthDrawing() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- isGraphSimilarity - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- isGreaterThan(Angle) - Method in class com.actelion.research.util.Angle
-
Determines whether this angle is on the greater value side of angle a, i.e.
- isHalogene(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isHetero(ExtendedMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- ISimilarityCalculator<T> - Interface in com.actelion.research.chem.descriptor
- ISimilarityHandlerFactory - Interface in com.actelion.research.chem.descriptor
- isInAromaticRingOfSize(MMFFMolecule, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns true if the atom is in an aromatic ring of given size.
- isInevitablePharmacophorePoint(int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- isInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- isInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isInFrontInTabbedPane(String) - Method in class com.actelion.research.gui.dock.JDockingPanel
- isInMesoFragment(int) - Method in class com.actelion.research.chem.CanonizerMesoHelper
- isInverted(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
- isIsMenuShortcut() - Method in class com.actelion.research.gui.generic.GenericKeyEvent
- isIsolatedCarbon(StereoMolecule, int, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isLargestFragmentOnly() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
This setting is relevant for all search types except the substructure search.
- isLayouted() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- isLinear - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- isLinkNode() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- isLinux() - Static method in class com.actelion.research.util.Platform
- isMacintosh() - Static method in class com.actelion.research.util.Platform
- isMarked() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- isMarked(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isMarkedAtom(int) - Method in class com.actelion.research.chem.Molecule
-
Atom marking may be used for any external purpose
- isMaxCapacityMatchListContainerReached() - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
-
The sub structure search algortihm stops if the maximum capacity of the match list container is reached.
- isMaximized() - Method in class com.actelion.research.gui.dock.Dockable
- isMaximized() - Method in class com.actelion.research.gui.dock.JDockingPanel
- isMember(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- isMemberOfNitroGroup(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isMeso() - Method in class com.actelion.research.chem.CanonizerMesoHelper
- isMetalAtom(int) - Method in class com.actelion.research.chem.Molecule
- isMissingParenthesis(String) - Static method in class com.actelion.research.util.StringFunctions
- isModeQuery() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- isMoleculeInOrder() - Method in class com.actelion.research.chem.Molecule3D
- isMoleculeNext() - Method in class com.actelion.research.chem.io.RDFileParser
- isMoreGeneral(long[], long[]) - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
-
Checks whether mask and data constitute a more general rule than this and therefore include this.
- isMovable() - Method in class com.actelion.research.share.gui.Arrow
- isMovable() - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- isNaN() - Method in class com.actelion.research.chem.Coordinates
- isNaturalAbundance(int) - Method in class com.actelion.research.chem.Molecule
- isNewSubstance() - Static method in class com.actelion.research.gui.LookAndFeelHelper
-
This is Substance from version 5
- isNewTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- isNitrogenFamily(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isNitroGroupN(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isNonsingular() - Method in class com.actelion.research.calc.LUDecomposition
-
Is the matrix nonsingular?
- isNoReactionSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- isNoStereoSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
A noStereo search is a hash code comparison from encoding stereo depleted structures.
- isNoStereoSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
A noStereo search is a hash code comparison from encoding stereo depleted structures.
- isNoStereoTautomerSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
A no-stereo-tautomer search is a hash code comparison from encoding stereo depleted generic tautomer structures.
- isNoStructureSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
- isOldSubstance() - Static method in class com.actelion.research.gui.LookAndFeelHelper
-
This is Substance version 3 or 4
- IsomericSmilesCreator - Class in com.actelion.research.chem
- IsomericSmilesCreator(StereoMolecule) - Constructor for class com.actelion.research.chem.IsomericSmilesCreator
-
Creates an IsomericSmilesCreator, which doesn't include atom mapping into generated smiles.
- IsomericSmilesCreator(StereoMolecule, boolean) - Constructor for class com.actelion.research.chem.IsomericSmilesCreator
-
Deprecated.
- IsomericSmilesCreator(StereoMolecule, int) - Constructor for class com.actelion.research.chem.IsomericSmilesCreator
-
Creates an IsomericSmilesCreator with the given mode.
- isOnlyCarbon(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isOnlyOneConformer() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- isOnProductSide(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- isOnProductSide(double, double) - Method in class com.actelion.research.share.gui.editor.Model
- isOnProductSide(float, float) - Method in class com.actelion.research.share.gui.Arrow
- isOnProductSide(float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IArrow
- isOpen() - Method in class com.actelion.research.chem.io.CompoundFileParser
- isOpen() - Method in class smile.data.NominalAttribute
-
Returns true if the string values of the nominal attribute is a open set.
- isOptimize3D() - Method in class com.actelion.research.chem.io.AbstractParser
- isOrganicAtom(int) - Method in class com.actelion.research.chem.Molecule
- IsotopeHelper - Class in com.actelion.research.chem
- IsotopeHelper() - Constructor for class com.actelion.research.chem.IsotopeHelper
- isOverlap(SubGraphIndices) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- isOverlap(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- isOverlap(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- isOverlap(IBitArray) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- isOverlappingBits(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- isPerfectlyMapped() - Method in class com.actelion.research.chem.reaction.Reaction
-
Checks, whether all non-hydrogen atoms are mapped and whether every reactant atom has exactly one assigned product atom.
- isPiConsidered(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
- isPopupMenuVisible() - Method in class com.actelion.research.gui.JScrollableMenu
- isPopupTrigger() - Method in class com.actelion.research.gui.generic.GenericMouseEvent
- isPower2(int) - Static method in class smile.math.Math
-
Returns true if x is a power of 2.
- isPseudoRotatableBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
In a consecutive sequence of sp-hybridized atoms multiple single bonds cause redundant torsions.
- isPurelyOrganic() - Method in class com.actelion.research.chem.Molecule
- isQuaQua() - Static method in class com.actelion.research.gui.LookAndFeelHelper
- isQueryInReaction() - Method in class com.actelion.research.chem.reaction.SRSearcher
-
Performs a reaction substructure search with the SSSearcher.cDefaultMatchMode
- isQueryInReaction(int) - Method in class com.actelion.research.chem.reaction.SRSearcher
- isReaction() - Method in class com.actelion.research.share.gui.editor.Model
- isReactionLayoutRequired() - Method in class com.actelion.research.chem.reaction.Reaction
- isReactionNext() - Method in class com.actelion.research.chem.io.RDFileParser
- isRegexInString(String, String) - Static method in class com.actelion.research.util.StringFunctions
- isRepresentative(int) - Method in class com.actelion.research.chem.Clusterer
- isRetronSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- isRing() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- isRingAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isRingBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isRingExclusively(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isRingInMolecule(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isRotatableBond(int) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- isSelected() - Method in class com.actelion.research.chem.AbstractDrawingObject
- isSelected() - Method in class com.actelion.research.gui.dock.Dockable
-
Answers if the panel is currently selected, i.e.
- isSelected() - Method in class com.actelion.research.gui.dock.TreeElement
- isSelected() - Method in class com.actelion.research.gui.dock.TreeLeaf
- isSelected() - Method in interface com.actelion.research.gui.generic.GenericCheckBox
- isSelected() - Method in class com.actelion.research.gui.swing.SwingCheckBox
- isSelected() - Method in class com.actelion.research.share.gui.Arrow
- isSelected() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- isSelected() - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- isSelectedAtom(int) - Method in class com.actelion.research.chem.Molecule
- isSelectedBond(int) - Method in class com.actelion.research.chem.Molecule
- isSetRingMMFFAromaticity(int) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
-
Returns true if the given ring has had its MMFF aromaticity flag set.
- isShiftDown() - Method in class com.actelion.research.gui.generic.GenericMouseEvent
- isShiftDown() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- isShiftDown() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- isSimilaritySearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- isSimilaritySearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
- isSimpleHydrogen(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Uncharged hydrogen atoms with no isotop information nor with an attached custom label are considered simple and can usually be suppressed, effectively converting them from an explicit to an implicit hydrogen atom.
Note: This method returns true for uncharged, natural abundance hydrogens without custom labels even if they have a non-standard bonding situation (everything being different from having one single bonded non-simple-hydrogen neighbour, e.g. - isSingleConformationModeQuery() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- isSingular() - Method in class smile.math.matrix.LU
-
Returns true if the matrix is singular or false otherwise.
- isSingular() - Method in class smile.math.matrix.QR
-
Returns true if the matrix is singular (not full column rank).
- isSkippingEnantiomers() - Method in class com.actelion.research.chem.StereoIsomerEnumerator
-
Checks and returns, whether skipEnantiomers was chosen in the constructor and whether the complete set of isomers would contain enantiomeric sets, because of the absence of absolute stereo centers and the presence of unknown or relative tetrahedral or atrop stereo configurations.
- isSmallerThan(Angle) - Method in class com.actelion.research.util.Angle
-
Determines whether this angle is on the smaller value side of angle a, i.e.
- isSmallRingAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isSmallRingBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isSquare(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- isStabilizedAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isStereoBond(int) - Method in class com.actelion.research.chem.Molecule
-
Checks whether bond is drawn as up/down single bond
- isStereoBond(int, int) - Method in class com.actelion.research.chem.Molecule
-
Checks whether bond is drawn as up/down single bond and is connected to atom with its pointed tip
- isSubreactionSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- isSubstance() - Static method in class com.actelion.research.gui.LookAndFeelHelper
- isSubstructureSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
- isSulfoxyGroup(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isSupportedSearchType(ReactionSearchSpecification) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns true if idcodes and/or hash codes for this particular search specification are directly available by the source, i.e.
- isSupportedSearchType(StructureSearchSpecification) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns true if idcodes and/or hash codes for this particular search specification are directly available by the source, i.e.
- isSurroundedBy(GenericShape) - Method in class com.actelion.research.chem.AbstractDrawingObject
- isSymmetric() - Method in class smile.math.matrix.JMatrix
- isSymmetric() - Method in interface smile.math.matrix.Matrix
-
Returns true if the matrix is symmetric.
- isSymmetric(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- isTautomerSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
A tautomer search is a hash code comparison from encoding generic tautomer structures.
- isTerminal() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- isTerminalC() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- isThioEther(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isTransparent() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- IStructureNameResolver - Interface in com.actelion.research.chem.name
-
Created by thomas on 7/13/17.
- isUnix() - Static method in class com.actelion.research.util.Platform
- isUpperAndLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
- isUsed() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- isUsed() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- isUserChange() - Method in class com.actelion.research.gui.editor.DrawAreaEvent
- isV3000() - Method in class com.actelion.research.chem.MolfileParser
- isValid() - Method in class com.actelion.research.chem.conf.TorsionDetail
- isValidBitIndex(int) - Method in class com.actelion.research.util.datamodel.IntVec
- isValidBitIndex(int[], int) - Static method in class com.actelion.research.util.BitUtils
- isValidSolution(SolutionCompleteGraph) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
-
If a single histogram is not matching the solution is invalid.
- isValidSolution(SolutionCompleteGraph) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- isValidSubstituentNameStart(String) - Static method in class com.actelion.research.chem.NamedSubstituents
- isValidType(int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- isVector - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- isVertical() - Method in class com.actelion.research.gui.dock.TreeFork
- isVisibleDockable() - Method in class com.actelion.research.gui.dock.Dockable
-
Answers if the panel is currently visible, i.e.
- isVisibleInSplitPane(String, boolean) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Checks, whether a dockable with the given title exists, and whether it is visible (selected if in a JTabbedPane) and whether it is in the left or right branch (depending on parameter left) of a JSplitPane.
- isVoidTransformation() - Method in class com.actelion.research.chem.DepictorTransformation
- isWildcard(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isWindows() - Static method in class com.actelion.research.util.Platform
- isWorseThan(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
-
Checks whether the total strain of this Conformer is larger than that of conformer, assuming that the calculated strain values are up-to-date.
- isZero(double) - Static method in class smile.math.Math
-
Tests if a floating number is zero.
- isZero(double, double) - Static method in class smile.math.Math
-
Tests if a floating number is zero with given epsilon.
- isZero(float) - Static method in class smile.math.Math
-
Tests if a floating number is zero.
- isZero(float, float) - Static method in class smile.math.Math
-
Tests if a floating number is zero with given epsilon.
- itemStateChanged(ItemEvent) - Method in class com.actelion.research.gui.JAtomQueryFeatureDialog
-
Deprecated.
- itemStateChanged(ItemEvent) - Method in class com.actelion.research.gui.swing.SwingComboBox
- iterator() - Method in class smile.data.Dataset
-
Returns an iterator over the elements in this dataset in proper sequence.
- iterator() - Method in class smile.math.SparseArray
-
Returns an iterator of nonzero entries.
- iUSER_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IValidationListener - Interface in com.actelion.research.share.gui.editor.listeners
-
Project: User: rufenec Date: 11/24/2014 Time: 3:27 PM
J
- JAtomLabelDialog - Class in com.actelion.research.gui
-
Deprecated.
- JAtomLabelDialog(Frame, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.JAtomLabelDialog
-
Deprecated.
- JAtomQueryFeatureDialog - Class in com.actelion.research.gui
-
Deprecated.
- JAtomQueryFeatureDialog(Dialog, ExtendedMolecule, int, boolean) - Constructor for class com.actelion.research.gui.JAtomQueryFeatureDialog
-
Deprecated.
- JAtomQueryFeatureDialog(Frame, ExtendedMolecule, int, boolean) - Constructor for class com.actelion.research.gui.JAtomQueryFeatureDialog
-
Deprecated.
- JBondQueryFeatureDialog - Class in com.actelion.research.gui
-
Deprecated.
- JBondQueryFeatureDialog(Dialog, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.JBondQueryFeatureDialog
-
Deprecated.
- JBondQueryFeatureDialog(Frame, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.JBondQueryFeatureDialog
-
Deprecated.
- JBrowseButtons - Class in com.actelion.research.gui.hidpi
- JBrowseButtons(boolean, int, int, ActionListener) - Constructor for class com.actelion.research.gui.hidpi.JBrowseButtons
- JBrowseButtons(boolean, ActionListener) - Constructor for class com.actelion.research.gui.hidpi.JBrowseButtons
- JChemistryView - Class in com.actelion.research.gui
- JChemistryView(int) - Constructor for class com.actelion.research.gui.JChemistryView
-
Creates a new JChemistryView for showing a reaction or molecules.
- JChemistryView(int, int, int) - Constructor for class com.actelion.research.gui.JChemistryView
-
Creates a new JChemistryView for showing a reaction or molecules.
- JComboBoxWithColor - Class in com.actelion.research.gui
- JComboBoxWithColor() - Constructor for class com.actelion.research.gui.JComboBoxWithColor
- JDockingPanel - Class in com.actelion.research.gui.dock
- JDockingPanel() - Constructor for class com.actelion.research.gui.dock.JDockingPanel
-
Creates a docking panel to which any Dockables may be added by the respective dock methods.
- JDrawArea - Class in com.actelion.research.gui
-
Deprecated.
- JDrawArea(StereoMolecule, int) - Constructor for class com.actelion.research.gui.JDrawArea
-
Deprecated.
- JDrawDialog - Class in com.actelion.research.gui
-
Deprecated.
- JDrawDialog(Dialog, Reaction, String, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Dialog, StereoMolecule) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Dialog, StereoMolecule[], String, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Dialog, StereoMolecule, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Dialog, StereoMolecule, String) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Dialog, StereoMolecule, String, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, boolean) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, boolean, String) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, Reaction) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, Reaction, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, Reaction, String) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, Reaction, String, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, StereoMolecule) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, StereoMolecule[]) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, StereoMolecule[], Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, StereoMolecule[], String) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, StereoMolecule[], String, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, StereoMolecule, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, StereoMolecule, String) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawDialog(Frame, StereoMolecule, String, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- JDrawPanel - Class in com.actelion.research.gui
-
Deprecated.
- JDrawPanel(StereoMolecule) - Constructor for class com.actelion.research.gui.JDrawPanel
-
Deprecated.
- JDrawPanel(StereoMolecule, boolean) - Constructor for class com.actelion.research.gui.JDrawPanel
-
Deprecated.
- JDrawPanel(StereoMolecule, int) - Constructor for class com.actelion.research.gui.JDrawPanel
-
Deprecated.
- JDrawToolbar - Class in com.actelion.research.gui
-
Deprecated.
- JDrawToolbar(JDrawArea) - Constructor for class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- JDrawToolbar(JDrawArea, int) - Constructor for class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- JEditableChemistryView - Class in com.actelion.research.gui
- JEditableChemistryView(int) - Constructor for class com.actelion.research.gui.JEditableChemistryView
-
Creates a new JEditableChemistryView for showing & editing a reaction or molecule(s).
- JEditableStructureView - Class in com.actelion.research.gui
- JEditableStructureView() - Constructor for class com.actelion.research.gui.JEditableStructureView
- JEditableStructureView(int, int) - Constructor for class com.actelion.research.gui.JEditableStructureView
- JEditableStructureView(StereoMolecule) - Constructor for class com.actelion.research.gui.JEditableStructureView
- JEditableStructureView(StereoMolecule, int, int) - Constructor for class com.actelion.research.gui.JEditableStructureView
- JENSEN_SHANNON_DIVERGENCE - smile.clustering.ClusteringDistance
-
Jensen-Shannon divergence for SIB.
- JensenShannonDivergence(double[], double[]) - Static method in class smile.math.Math
-
Jensen-Shannon divergence JS(P||Q) = (KL(P||M) + KL(Q||M)) / 2, where M = (P+Q)/2.
- JensenShannonDivergence(double[], SparseArray) - Static method in class smile.math.Math
-
Jensen-Shannon divergence JS(P||Q) = (KL(P||M) + KL(Q||M)) / 2, where M = (P+Q)/2.
- JensenShannonDivergence(SparseArray, double[]) - Static method in class smile.math.Math
-
Jensen-Shannon divergence JS(P||Q) = (KL(P||M) + KL(Q||M)) / 2, where M = (P+Q)/2.
- JensenShannonDivergence(SparseArray, SparseArray) - Static method in class smile.math.Math
-
Jensen-Shannon divergence JS(P||Q) = (KL(P||M) + KL(Q||M)) / 2, where M = (P+Q)/2.
- JFileChooserOverwrite - Class in com.actelion.research.gui
- JFileChooserOverwrite() - Constructor for class com.actelion.research.gui.JFileChooserOverwrite
- JFXCanvasDepictor - Class in com.actelion.research.jfx.gui.chem
-
Project: User: rufenec Date: 10/12/11 Time: 6:00 PM
- JFXCanvasDepictor(StereoMolecule) - Constructor for class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- JFXCanvasDepictor(StereoMolecule, int) - Constructor for class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- JImagePanel - Class in com.actelion.research.gui
- JImagePanel() - Constructor for class com.actelion.research.gui.JImagePanel
- JImagePanel(String) - Constructor for class com.actelion.research.gui.JImagePanel
- JImagePanel(String, boolean) - Constructor for class com.actelion.research.gui.JImagePanel
- JImagePanelFixedSize - Class in com.actelion.research.gui
- JImagePanelFixedSize() - Constructor for class com.actelion.research.gui.JImagePanelFixedSize
- JImagePanelFixedSize(String) - Constructor for class com.actelion.research.gui.JImagePanelFixedSize
- JLoginDialog - Class in com.actelion.research.gui
- JLoginDialog(Frame, ActionListener) - Constructor for class com.actelion.research.gui.JLoginDialog
- JMatrix - Class in smile.math.matrix
-
A pure Java implementation of DenseMatrix whose data is stored in a single 1D array of doubles in column major order.
- JMatrix(double[]) - Constructor for class smile.math.matrix.JMatrix
-
Constructor of a column vector/matrix with given array as the internal storage.
- JMatrix(double[][]) - Constructor for class smile.math.matrix.JMatrix
-
Constructor.
- JMatrix(int, int) - Constructor for class smile.math.matrix.JMatrix
-
Constructor of all-zero matrix.
- JMatrix(int, int, double) - Constructor for class smile.math.matrix.JMatrix
-
Constructor.
- JMatrix(int, int, double[]) - Constructor for class smile.math.matrix.JMatrix
-
Constructor.
- JMessageBar - Class in com.actelion.research.gui
- JMultiPanelTitle - Class in com.actelion.research.gui
- JMultiPanelTitle(MultiPanelDragListener, String) - Constructor for class com.actelion.research.gui.JMultiPanelTitle
- JMultiPanelView - Class in com.actelion.research.gui
- JMultiPanelView() - Constructor for class com.actelion.research.gui.JMultiPanelView
- JPopupButton - Class in com.actelion.research.gui
- JPopupButton(ActionListener) - Constructor for class com.actelion.research.gui.JPopupButton
- JProgressDialog - Class in com.actelion.research.gui
- JProgressDialog(Frame) - Constructor for class com.actelion.research.gui.JProgressDialog
-
Creates a JProgressDialog and schedule it with invokeLater() to be set visible without blocking the calling thread.
- JProgressDialog(Frame, boolean) - Constructor for class com.actelion.research.gui.JProgressDialog
-
Creates a JProgressDialog.
- JProgressPanel - Class in com.actelion.research.gui
- JProgressPanel(boolean) - Constructor for class com.actelion.research.gui.JProgressPanel
- JPruningBar - Class in com.actelion.research.gui
-
Lightweight Slider for maintaining two values within given limits
- JPruningBar() - Constructor for class com.actelion.research.gui.JPruningBar
- JPruningBar(boolean) - Constructor for class com.actelion.research.gui.JPruningBar
- JPruningBar(boolean, int) - Constructor for class com.actelion.research.gui.JPruningBar
- JPruningBar(float, float, boolean, int) - Constructor for class com.actelion.research.gui.JPruningBar
- JPruningBar(float, float, boolean, int, boolean) - Constructor for class com.actelion.research.gui.JPruningBar
- JScrollableMenu - Class in com.actelion.research.gui
- JScrollableMenu() - Constructor for class com.actelion.research.gui.JScrollableMenu
-
Constructs a new
JMenu
with no text. - JScrollableMenu(String) - Constructor for class com.actelion.research.gui.JScrollableMenu
-
Constructs a new
JMenu
with the supplied string as its text. - JScrollableMenu(Action) - Constructor for class com.actelion.research.gui.JScrollableMenu
-
Constructs a menu whose properties are taken from the
Action
supplied. - JScrollablePopupMenu - Class in com.actelion.research.gui
- JScrollablePopupMenu() - Constructor for class com.actelion.research.gui.JScrollablePopupMenu
- JScrollablePopupMenu(String) - Constructor for class com.actelion.research.gui.JScrollablePopupMenu
- JScrollablePopupMenu.ScrollPopupMenuLayout - Class in com.actelion.research.gui
- JStructureView - Class in com.actelion.research.gui
- JStructureView() - Constructor for class com.actelion.research.gui.JStructureView
- JStructureView(int, int) - Constructor for class com.actelion.research.gui.JStructureView
- JStructureView(StereoMolecule) - Constructor for class com.actelion.research.gui.JStructureView
-
This creates a standard structure view where the displayed molecule is used for D&D and clipboard transfer after removing atom colors and bond highlights.
- JStructureView(StereoMolecule, int, int) - Constructor for class com.actelion.research.gui.JStructureView
-
This creates a standard structure view where the displayed molecule is used for D&D and clipboard transfer after removing atom colors and bond highlights.
- JStructureView(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.gui.JStructureView
-
This creates a structure view that distinguishes between displayed molecule and the one being used for D&D and clipboard transfer.
- JStructureView(StereoMolecule, StereoMolecule, int, int) - Constructor for class com.actelion.research.gui.JStructureView
-
This creates a structure view that distinguishes between displayed molecule and the one being used for D&D and clipboard transfer.
- JTableWithRowNumbers - Class in com.actelion.research.gui.table
- JTableWithRowNumbers() - Constructor for class com.actelion.research.gui.table.JTableWithRowNumbers
- JTableWithRowNumbers(int, int) - Constructor for class com.actelion.research.gui.table.JTableWithRowNumbers
- JTableWithRowNumbers(Object[][], Object[]) - Constructor for class com.actelion.research.gui.table.JTableWithRowNumbers
- JTableWithRowNumbers(Vector, Vector) - Constructor for class com.actelion.research.gui.table.JTableWithRowNumbers
- JTableWithRowNumbers(TableModel) - Constructor for class com.actelion.research.gui.table.JTableWithRowNumbers
- JTableWithRowNumbers(TableModel, TableColumnModel) - Constructor for class com.actelion.research.gui.table.JTableWithRowNumbers
- JTableWithRowNumbers(TableModel, TableColumnModel, ListSelectionModel) - Constructor for class com.actelion.research.gui.table.JTableWithRowNumbers
- JTextDrawingObjectDialog - Class in com.actelion.research.gui
-
Deprecated.
- JTextDrawingObjectDialog(Dialog, TextDrawingObject) - Constructor for class com.actelion.research.gui.JTextDrawingObjectDialog
-
Deprecated.
- JTextDrawingObjectDialog(Frame, TextDrawingObject) - Constructor for class com.actelion.research.gui.JTextDrawingObjectDialog
-
Deprecated.
K
- k - Variable in class smile.clustering.PartitionClustering
-
The number of clusters.
- k(double[], double[]) - Method in class smile.math.kernel.GaussianKernel
- k(T, T) - Method in interface smile.math.kernel.MercerKernel
-
Kernel function.
- ka - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- ka(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns 'ka' the force constant for a given index in the table.
- ka(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns 'ka' given a molecule and three connected atoms which form an angle.
- KabschAlignment - Class in com.actelion.research.chem.alignment3d
-
described in: DOI 10.1002/jcc.20110 "Using Quaternions to Calculate RMSD"
- KabschAlignment(Conformer, Conformer) - Constructor for class com.actelion.research.chem.alignment3d.KabschAlignment
-
first conformer is the reference, second conformer is rotated and translated to minimize the RMSD
- KabschAlignment(Coordinates[], Coordinates[], int[][]) - Constructor for class com.actelion.research.chem.alignment3d.KabschAlignment
- kb - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
- kb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
-
Returns 'kb' the force constant at a given index in the Bndk table.
- kb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
-
Returns the 'kb' value at the given index from the Bond table.
- kb(MMFFMolecule, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
-
Returns 'kb' given a molecule and two atoms in that molecule that form a bond.
- kb(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
-
Returns the equivalent 'kb' value for a given set of three atoms.
- Kb() - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- Kb(double, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- Kb(int) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- kba(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
-
Returns 'kba' for a given index in the table.
- kba_ijk - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- kba_kji - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- kCDXObj_Bond - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- kCDXObj_Fragment - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- kCDXObj_Group - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- kCDXObj_Node - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- kCDXObj_Page - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- KEEP_INITIAL_COORDINATES - Static variable in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- keepAbsoluteOrientation() - Method in class com.actelion.research.chem.coords.InventorTemplate
- kendall(double[], double[]) - Static method in class smile.math.Math
-
The Kendall Tau Rank Correlation Coefficient is used to measure the degree of correspondence between sets of rankings where the measures are not equidistant.
- kendall(float[], float[]) - Static method in class smile.math.Math
-
The Kendall Tau Rank Correlation Coefficient is used to measure the degree of correspondence between sets of rankings where the measures are not equidistant.
- kendall(int[], int[]) - Static method in class smile.math.Math
-
The Kendall Tau Rank Correlation Coefficient is used to measure the degree of correspondence between sets of rankings where the measures are not equidistant.
- kernel_type - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- KERNEL_TYPE_LINEAR - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- KERNEL_TYPE_POLY - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- KERNEL_TYPE_PRECOMPUTED - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- KERNEL_TYPE_RBF - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- KERNEL_TYPE_SIGMOID - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- KEY_IS_ATOM_LABEL - Static variable in class com.actelion.research.share.gui.editor.Model
- KEY_IS_INVALID - Static variable in class com.actelion.research.share.gui.editor.Model
- KEY_IS_SUBSTITUENT - Static variable in class com.actelion.research.share.gui.editor.Model
- KEY_IS_VALID_START - Static variable in class com.actelion.research.share.gui.editor.Model
- KEY_PRESSED - Static variable in class com.actelion.research.gui.generic.GenericKeyEvent
- KEY_RELEASED - Static variable in class com.actelion.research.gui.generic.GenericKeyEvent
- KEY_TYPED - Static variable in class com.actelion.research.gui.generic.GenericKeyEvent
- keyActionHappened(GenericKeyEvent) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- keyActionHappened(GenericKeyEvent) - Method in interface com.actelion.research.gui.generic.GenericKeyListener
- keyPressed(KeyEvent) - Method in class com.actelion.research.gui.hidpi.JBrowseButtons
- keyPressed(KeyEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- keyPressed(KeyEvent) - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- keyPressed(KeyEvent) - Method in class com.actelion.research.gui.JImagePanel
- keyPressed(KeyEvent) - Method in class com.actelion.research.gui.swing.SwingKeyHandler
- keyReleased(KeyEvent) - Method in class com.actelion.research.gui.hidpi.JBrowseButtons
- keyReleased(KeyEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- keyReleased(KeyEvent) - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- keyReleased(KeyEvent) - Method in class com.actelion.research.gui.JImagePanel
- keyReleased(KeyEvent) - Method in class com.actelion.research.gui.swing.SwingKeyHandler
- KEYSTROKEFONTSIZE - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- keyTyped(KeyEvent) - Method in class com.actelion.research.gui.hidpi.JBrowseButtons
- keyTyped(KeyEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- keyTyped(KeyEvent) - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- keyTyped(KeyEvent) - Method in class com.actelion.research.gui.JImagePanel
- keyTyped(KeyEvent) - Method in class com.actelion.research.gui.swing.SwingKeyHandler
- KMeans - Class in smile.clustering
-
K-Means clustering.
- KMeans(double[][], int) - Constructor for class smile.clustering.KMeans
-
Constructor.
- KMeans(double[][], int, int) - Constructor for class smile.clustering.KMeans
-
Constructor.
- KMeans(double[][], int, int, int) - Constructor for class smile.clustering.KMeans
-
Clustering data into k clusters.
- KNNRegression - Class in com.actelion.research.calc.regression.knn
-
KNNRegression kNN regression seems to be very inappropriate for regression problems.
- KNNRegression() - Constructor for class com.actelion.research.calc.regression.knn.KNNRegression
- KullbackLeiblerDivergence(double[], double[]) - Static method in class smile.math.Math
-
Kullback-Leibler divergence.
- KullbackLeiblerDivergence(double[], SparseArray) - Static method in class smile.math.Math
-
Kullback-Leibler divergence.
- KullbackLeiblerDivergence(SparseArray, double[]) - Static method in class smile.math.Math
-
Kullback-Leibler divergence.
- KullbackLeiblerDivergence(SparseArray, SparseArray) - Static method in class smile.math.Math
-
Kullback-Leibler divergence.
L
- l - Variable in class org.machinelearning.svm.libsvm.svm_model
- l - Variable in class org.machinelearning.svm.libsvm.svm_problem
- L - Variable in class smile.math.matrix.Cholesky
-
Array for internal storage of decomposition.
- label - Variable in class com.actelion.research.util.ScaleLabel
- label - Variable in class org.machinelearning.svm.libsvm.svm_model
- label() - Method in class smile.data.AttributeDataset.Row
-
Returns the class label in string format.
- labels() - Method in class smile.data.Dataset
-
Returns the class labels.
- LAMBDA - Static variable in class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- LAMBDA - Static variable in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- LAMBDA - Static variable in class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- Lanczos - Class in smile.math.matrix
-
The Lanczos algorithm is a direct algorithm devised by Cornelius Lanczos that is an adaptation of power methods to find the most useful eigenvalues and eigenvectors of an nth order linear system with a limited number of operations, m, where m is much smaller than n.
- Lanczos() - Constructor for class smile.math.matrix.Lanczos
- lassoColor() - Static method in class com.actelion.research.gui.editor.GenericDrawArea
- lassoColor() - Static method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- lastHightlightPoint - Variable in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- lastIndexOf(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- lastIndexOfNot(byte[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- layoutChildren() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- layoutContainer(Container) - Method in class com.actelion.research.gui.JScrollablePopupMenu.ScrollPopupMenuLayout
- layoutContainer(Container) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- ld() - Method in interface smile.math.matrix.DenseMatrix
-
The LDA (and LDB, LDC, etc.) parameter in BLAS is effectively the stride of the matrix as it is laid out in linear memory.
- ld() - Method in class smile.math.matrix.JMatrix
- learn(double[][], double[]) - Method in class smile.regression.NeuralNetwork
-
Trains the neural network with the given dataset for one epoch by stochastic gradient descent.
- learn(double[], double) - Method in class smile.regression.NeuralNetwork
- learn(double[], double, double) - Method in class smile.regression.NeuralNetwork
-
Update the neural network with given instance and associated target value.
- learn(T, double) - Method in interface smile.regression.OnlineRegression
-
Online update the regression model with a new training instance.
- learnGaussianRadialBasis(double[][], double[][]) - Static method in class smile.util.SmileUtils
-
Learns Gaussian RBF function and centers from data.
- learnGaussianRadialBasis(double[][], double[][], double) - Static method in class smile.util.SmileUtils
-
Learns Gaussian RBF function and centers from data.
- learnGaussianRadialBasis(double[][], double[][], int) - Static method in class smile.util.SmileUtils
-
Learns Gaussian RBF function and centers from data.
- learnGaussianRadialBasis(T[], T[], Metric<T>) - Static method in class smile.util.SmileUtils
-
Learns Gaussian RBF function and centers from data.
- learnGaussianRadialBasis(T[], T[], Metric<T>, double) - Static method in class smile.util.SmileUtils
-
Learns Gaussian RBF function and centers from data.
- learnGaussianRadialBasis(T[], T[], Metric<T>, int) - Static method in class smile.util.SmileUtils
-
Learns Gaussian RBF function and centers from data.
- LEFT - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- LEN_INTEGER_BYTES - Static variable in class com.actelion.research.util.datamodel.IntVec
- length() - Method in interface com.actelion.research.chem.forcefield.mmff.Searchable
-
This function should return the total number of rows in a searchable table.
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- length() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns the length (or magnitude) of this vector.
- length() - Method in class com.actelion.research.util.datamodel.IntArray
- LIBSVM_VERSION - Static variable in class com.actelion.research.calc.regression.svm.svm
- LIBSVM_VERSION - Static variable in class org.machinelearning.svm.libsvm.svm
- liClassLabel - Variable in class com.actelion.research.util.datamodel.ModelXYClassLabel
- LIGAND - Static variable in class com.actelion.research.chem.Molecule3D
- LIGAND_GROUP - Static variable in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- LigandPose - Class in com.actelion.research.chem.docking
- LigandPose(Conformer, AbstractScoringEngine, double) - Constructor for class com.actelion.research.chem.docking.LigandPose
- liIndex - Variable in class com.actelion.research.util.datamodel.ModelXYIndex
- likelihood(double[]) - Method in class smile.stat.distribution.AbstractDistribution
-
The likelihood given a sample set following the distribution.
- likelihood(double[]) - Method in interface smile.stat.distribution.Distribution
-
The likelihood of the sample set following this distribution.
- LIMIT_NEIGHBOURS_SINCE_LAST_ADDED - Static variable in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- LIMIT_ROWS_ANALYTICAL - Static variable in class com.actelion.research.calc.regression.svm.SVMRegression
- linear(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the linear bool of an atom given its MMFF type.
- LINEAR - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- LinearRegression - Class in com.actelion.research.calc.regression.linear.simple
-
LinearRegression 2009 MvK: Start implementation
- LinearRegression() - Constructor for class com.actelion.research.calc.regression.linear.simple.LinearRegression
- lineTo(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- lineTo(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- LINK_NODE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- Linkage - Class in smile.clustering.linkage
-
A measure of dissimilarity between clusters (i.e.
- Linkage() - Constructor for class smile.clustering.linkage.Linkage
- Linker - Class in com.actelion.research.chem.descriptor.flexophore.entity
-
Linker
- Linker(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- LIPO_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- listeners - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- ListInteger<T> - Class in com.actelion.research.chem.io.pdb.parser
-
ListInteger
- ListInteger(List<T>, int) - Constructor for class com.actelion.research.chem.io.pdb.parser.ListInteger
- ListWithIntVec - Class in com.actelion.research.chem.mcs
- ListWithIntVec() - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
- ListWithIntVec(int) - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
- ListWithIntVec(int, int) - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
- ListWithIntVec(ListWithIntVec) - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
- ListWithIntVecIdCode - Class in com.actelion.research.chem.properties.complexity
- ListWithIntVecIdCode(int) - Constructor for class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- ListWithIntVecIdCode(ListWithIntVec) - Constructor for class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
-
Flat constructor.
- ListWithIntVecIdCode(ListWithIntVecIdCode) - Constructor for class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
-
Deep constructor.
- liTagX - Variable in class com.actelion.research.util.datamodel.ModelXYColTags
- liTagY - Variable in class com.actelion.research.util.datamodel.ModelXYColTags
- LittleEndianDataInputStream - Class in com.actelion.research.util
- LittleEndianDataInputStream(InputStream) - Constructor for class com.actelion.research.util.LittleEndianDataInputStream
- LittleEndianDataOutputStream - Class in com.actelion.research.util
- LittleEndianDataOutputStream(OutputStream) - Constructor for class com.actelion.research.util.LittleEndianDataOutputStream
- lloyd(double[][], int) - Static method in class smile.clustering.KMeans
-
The implementation of Lloyd algorithm as a benchmark.
- lloyd(double[][], int, int) - Static method in class smile.clustering.KMeans
-
The implementation of Lloyd algorithm as a benchmark.
- lloyd(double[][], int, int, int) - Static method in class smile.clustering.KMeans
-
The implementation of Lloyd algorithm as a benchmark.
- load(File) - Method in class com.actelion.research.chem.io.AbstractParser
- load(String) - Method in class com.actelion.research.chem.io.AbstractParser
- load(String, Reader) - Method in class com.actelion.research.chem.io.AbstractParser
- loadCache(String) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
Loads pre-calculated rigid fragment coordinates from a cache file, which is either a text file created by the createCacheFiles() method, or a zip archive of the text file.
- loadDefaultCache() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
This loads the default cache file
- loadGroup(String) - Method in class com.actelion.research.chem.io.AbstractParser
- loadGroup(String, Reader) - Method in class com.actelion.research.chem.io.AbstractParser
- loadGroup(String, Reader, int, int) - Method in class com.actelion.research.chem.io.AbstractParser
- loadGroup(String, Reader, int, int) - Method in class com.actelion.research.chem.io.Mol2FileParser
- loadTable(String, Tables) - Static method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Loads and registers a tables object with the ForceField class so it can be used by new ForceField instances.
- locateBonds() - Method in class com.actelion.research.chem.coords.InventorFragment
- locateDelocalizedDoubleBonds(boolean[]) - Method in class com.actelion.research.chem.AromaticityResolver
-
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.
- locateDelocalizedDoubleBonds(boolean[], boolean, boolean) - Method in class com.actelion.research.chem.AromaticityResolver
-
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.
- log() - Method in class com.actelion.research.calc.Matrix
-
Log function from the class Math .
- log(double) - Static method in class smile.math.Math
-
Returns the natural logarithm (base e) of a double value.
- log10(double) - Static method in class smile.math.Math
-
Returns the base 10 logarithm of a double value.
- log1p(double) - Static method in class smile.math.Math
-
Returns the natural logarithm of the sum of the argument and 1.
- log2(double) - Static method in class smile.math.Math
-
Log of base 2.
- log2(int) - Static method in class com.actelion.research.calc.Logarithm
- Logarithm - Class in com.actelion.research.calc
-
Logarithm Mar 14, 2013 MvK Start implementation
- Logarithm() - Constructor for class com.actelion.research.calc.Logarithm
- logChoose(int, int) - Static method in class smile.math.Math
-
log of n choose k
- logFactorial(int) - Static method in class smile.math.Math
-
log of factorial of n
- logistic(double) - Static method in class smile.math.Math
-
Logistic sigmoid function.
- LOGISTIC_SIGMOID - smile.regression.NeuralNetwork.ActivationFunction
-
Logistic sigmoid activation function (default): sigma(v)=1/(1+exp(-v))
- logLikelihood(double[]) - Method in class smile.stat.distribution.AbstractDistribution
-
The likelihood given a sample set following the distribution.
- logLikelihood(double[]) - Method in interface smile.stat.distribution.Distribution
-
The log likelihood of the sample set following this distribution.
- logp(double) - Method in interface smile.stat.distribution.Distribution
-
The density at x in log scale, which may prevents the underflow problem.
- logp(double) - Method in class smile.stat.distribution.GaussianDistribution
- logp(double) - Method in class smile.stat.distribution.Mixture
- longValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- LookAndFeelHelper - Class in com.actelion.research.gui
- LookAndFeelHelper() - Constructor for class com.actelion.research.gui.LookAndFeelHelper
- lookupBondLength(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an estimate of the bond length based on atom and bond characteristics.
- lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- lu - Variable in class smile.math.matrix.LU
-
Array for internal storage of decomposition.
- lu() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the LU decomposition.
- lu() - Method in class smile.math.matrix.JMatrix
-
LU decomposition is computed by a "left-looking", dot-product, Crout/Doolittle algorithm.
- lu(boolean) - Method in interface smile.math.matrix.DenseMatrix
-
Returns the LU decomposition.
- LU - Class in smile.math.matrix
-
For an m-by-n matrix A with m ≥ n, the LU decomposition is an m-by-n unit lower triangular matrix L, an n-by-n upper triangular matrix U, and a permutation vector piv of length m so that A(piv,:) = L*U.
- LU(DenseMatrix, int[], boolean) - Constructor for class smile.math.matrix.LU
-
Constructor.
- LU(DenseMatrix, int[], int, boolean) - Constructor for class smile.math.matrix.LU
-
Constructor.
- LUDecomposition - Class in com.actelion.research.calc
-
LU Decomposition.
- LUDecomposition(Matrix) - Constructor for class com.actelion.research.calc.LUDecomposition
-
LU Decomposition Structure to access L, U and piv.
M
- m - Variable in class smile.math.matrix.SVD
-
The number of rows.
- M(double[], double[]) - Method in interface smile.stat.distribution.ExponentialFamily
-
The M step in the EM algorithm, which depends the specific distribution.
- M(double[], double[]) - Method in class smile.stat.distribution.GaussianDistribution
- MACHEP - Static variable in class smile.math.Math
-
The largest negative integer such that 1.0 + RADIXMACHEP ≠ 1.0, except that machep is bounded below by -(DIGITS+3)
- mad(double[]) - Static method in class smile.math.Math
-
Returns the median absolute deviation (MAD).
- mad(float[]) - Static method in class smile.math.Math
-
Returns the median absolute deviation (MAD).
- mad(int[]) - Static method in class smile.math.Math
-
Returns the median absolute deviation (MAD).
- main(String[]) - Static method in class com.actelion.research.calc.BoxCox
- main(String[]) - Static method in class com.actelion.research.calc.classification.PrecisionAndRecall
- main(String[]) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
- main(String[]) - Static method in class com.actelion.research.calc.filter.SlidingWindow
- main(String[]) - Static method in class com.actelion.research.calc.histogram.Histogram
- main(String[]) - Static method in class com.actelion.research.calc.histogram.IntegerHistogram
- main(String[]) - Static method in class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- main(String[]) - Static method in class com.actelion.research.calc.regression.knn.ParameterKNN
- main(String[]) - Static method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- main(String[]) - Static method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- main(String[]) - Static method in class com.actelion.research.calc.regression.ModelError
- main(String[]) - Static method in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- main(String[]) - Static method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- main(String[]) - Static method in class com.actelion.research.chem.alignment3d.transformation.ExponentialMap
- main(String[]) - Static method in class com.actelion.research.chem.contrib.DiastereoIDTest
- main(String[]) - Static method in class com.actelion.research.chem.contrib.HoseCodeCreator
- main(String[]) - Static method in class com.actelion.research.chem.contrib.testChiralDia
- main(String[]) - Static method in class com.actelion.research.chem.contrib.testDiaID
- main(String[]) - Static method in class com.actelion.research.chem.contrib.testHoses
- main(String[]) - Static method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
- main(String[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- main(String[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- main(String[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
- main(String[]) - Static method in exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
- main(String[]) - Static method in class com.actelion.research.chem.io.Mol2FileParser
- main(String[]) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
- main(String[]) - Static method in class com.actelion.research.chem.SmilesParser
- main(String[]) - Static method in class com.actelion.research.gui.clipboard.ImageClipboardHandler
- main(String[]) - Static method in class com.actelion.research.util.BrowserControl
-
Simple example.
- main(String[]) - Static method in class com.actelion.research.util.BurtleHasher
- main(String[]) - Static method in class com.actelion.research.util.CommandLineParser
- main(String[]) - Static method in class com.actelion.research.util.convert.String2DoubleArray
- main(String[]) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
- main(String[]) - Static method in class com.actelion.research.util.EncoderIntegerNumbers
- main(String[]) - Static method in class com.actelion.research.util.ErrorHashMap
- main(String[]) - Static method in class com.actelion.research.util.Formatter
- main(String[]) - Static method in class com.actelion.research.util.SizeOf
- main(String[]) - Static method in class com.actelion.research.util.StringFunctions
- main(String[]) - Static method in class org.openmolecules.chem.conf.so.StraightLineRule
-
Test code...
- makeColor(int, int, int) - Static method in class com.actelion.research.chem.SVGDepictor
- makeProteinFlexible(Molecule3D, Coordinates, double, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- makeProteinRigid(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- makeSkeleton(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- mAllAtoms - Variable in class com.actelion.research.chem.Molecule
- mAllBonds - Variable in class com.actelion.research.chem.Molecule
- mAllowedDragAction - Variable in class com.actelion.research.gui.JStructureView
- mAllowedDropAction - Variable in class com.actelion.research.gui.JStructureView
- manhattanBlockDistance(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- manhattanBlockDistance(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- map(Reaction) - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRuleEnhancedReactionMapper
- map(Reaction) - Method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
-
Entirely maps the given reaction by setting all reactant's and product's mapping numbers.
- map(StereoMolecule, StereoMolecule, int[], int[]) - Method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
-
Entirely maps the given reaction by setting all reactant's and product's mapping numbers.
- MappingScorer - Class in com.actelion.research.chem.reaction.mapping
- MappingScorer(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.reaction.mapping.MappingScorer
-
Instantiates a mapping scorer that judges the quality of a mapping by adding penalties for every bond being broken, created, or changed.
- mapReaction(int, Point2D, Point2D) - Method in class com.actelion.research.share.gui.editor.Model
- mapReaction(Reaction, SSSearcher) - Method in interface com.actelion.research.chem.reaction.IReactionMapper
- mapReaction(Reaction, SSSearcher) - Method in class com.actelion.research.chem.reaction.mapping.ChemicalRuleEnhancedReactionMapper
- mapReaction(Reaction, SSSearcher) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
- mapToolColor() - Static method in class com.actelion.research.gui.editor.GenericDrawArea
- mapToolColor() - Static method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- mArea - Variable in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- mArea - Variable in class com.actelion.research.gui.JDrawPanel
-
Deprecated.
- markAtomForDeletion(int) - Method in class com.actelion.research.chem.Molecule
-
Marks this atom to be deleted in a later call to deleteMarkedAtomsAndBonds().
- markBondForDeletion(int) - Method in class com.actelion.research.chem.Molecule
-
Marks this bond to be deleted in a later call to deleteMarkedAtomsAndBonds().
- markDiastereotopicAtoms(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
-
In order to debug we could number the group of diastereotopic atoms
- markLigand(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find the most likely ligand (in term of size, rings, polar atoms) and mark it
- markLigand(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Marks a numbered ligand
- markLigands(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find the most likely ligands (in term of size)
- MarkushStructure - Class in com.actelion.research.chem
- MarkushStructure() - Constructor for class com.actelion.research.chem.MarkushStructure
- MarkushStructure(StereoMolecule[], int) - Constructor for class com.actelion.research.chem.MarkushStructure
- MASK_FIRST_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_FIRST_SHORT - Static variable in class com.actelion.research.util.BitUtils
- MASK_FOURTH_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_FOURTH_SHORT - Static variable in class com.actelion.research.util.BitUtils
- MASK_INVERSE_FIRST_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_INVERSE_FOURTH_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_INVERSE_SEC_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_INVERSE_THIRD_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_SEC_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_SEC_SHORT - Static variable in class com.actelion.research.util.BitUtils
- MASK_THIRD_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_THIRD_SHORT - Static variable in class com.actelion.research.util.BitUtils
- maskByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- match(String, String) - Static method in class com.actelion.research.util.StringFunctions
- match(T) - Method in interface com.actelion.research.jfx.gui.misc.Selector
- MATCH_BALANCE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- MATCH_NODE_NR_LIMIT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- MATCH_SIZE_LIMIT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- matches(TorsionSetEliminationRule, double) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- matchesReactionRole(Reaction, SSSearcherWithIndex[], int, StereoMolecule, long[]) - Static method in class com.actelion.research.chem.chemicalspaces.ChemicalSpaceCreator
- matchFirst(String, String) - Static method in class com.actelion.research.util.StringFunctions
- MatchFlexophoreNodesMain - Class in com.actelion.research.chem.descriptor.flexophore.example
- MatchFlexophoreNodesMain() - Constructor for class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- matchReaction(Reaction) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
- matchSearch() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
-
finds a set of balanced, high-scoring initial splits that are then used as an input for the extension match algorithm
- Math - Class in smile.math
-
A collection of useful mathematical functions.
- MathHelper - Class in com.actelion.research.chem.phesaflex
- mAtom - Variable in class com.actelion.research.chem.coords.InventorChain
- mAtom - Variable in class org.openmolecules.chem.conf.so.ConformationRule
- mAtomCharge - Variable in class com.actelion.research.chem.Molecule
- mAtomCustomLabel - Variable in class com.actelion.research.chem.Molecule
- mAtomFlags - Variable in class com.actelion.research.chem.Molecule
- mAtomicNo - Variable in class com.actelion.research.chem.Molecule
- mAtomList - Variable in class com.actelion.research.chem.Molecule
- mAtomList - Variable in class com.actelion.research.chem.Mutation
- mAtomMapNo - Variable in class com.actelion.research.chem.Molecule
- mAtomMass - Variable in class com.actelion.research.chem.Molecule
- mAtomQueryFeatures - Variable in class com.actelion.research.chem.Molecule
- mAtomX - Variable in class com.actelion.research.chem.coords.InventorFragment
- mAtomY - Variable in class com.actelion.research.chem.coords.InventorFragment
- Matrix - Class in com.actelion.research.calc
- Matrix - Interface in smile.math.matrix
-
An abstract interface of matrix.
- Matrix() - Constructor for class com.actelion.research.calc.Matrix
- Matrix(boolean, byte[]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(boolean, double[]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(boolean, int[]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(boolean, List<Double>) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(byte[][]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(double[][]) - Constructor for class com.actelion.research.calc.Matrix
-
Deep copy
- Matrix(double[][], boolean) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(float[][]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(int[][]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(int, int) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(Matrix) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(List<DoubleVec>) - Constructor for class com.actelion.research.calc.Matrix
- Matrix2SVMNodeConverter - Class in com.actelion.research.calc.regression.svm
-
Matrix2SVMNodeConverter
- Matrix2SVMNodeConverter() - Constructor for class com.actelion.research.calc.regression.svm.Matrix2SVMNodeConverter
- MatrixBasedHistogram - Class in com.actelion.research.calc.histogram
-
MatrixBasedHistogram
- MatrixBasedHistogram() - Constructor for class com.actelion.research.calc.histogram.MatrixBasedHistogram
- MatrixFunctions - Class in com.actelion.research.calc
-
Title: MatrixFunctions
- MatrixFunctions() - Constructor for class com.actelion.research.calc.MatrixFunctions
- MatrixMultiplication<A,B> - Interface in smile.math.matrix
-
Matrix multiplication interface.
- MatrixTests - Class in com.actelion.research.calc
-
MatrixData
- MatrixTests() - Constructor for class com.actelion.research.calc.MatrixTests
- max - Variable in class com.actelion.research.calc.statistics.ModelStatisticsOverview
- max - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- max() - Method in class com.actelion.research.util.datamodel.DoubleArray
- max() - Method in class com.actelion.research.util.datamodel.IntArray
- max(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(double[]) - Static method in class com.actelion.research.util.ArrayUtils
- max(double[]) - Static method in class smile.math.Math
-
Returns the maximum value of an array.
- max(double[][]) - Static method in class smile.math.Math
-
Returns the maximum of a matrix.
- max(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(double, double) - Static method in class smile.math.Math
-
Returns the greater of two double values.
- max(double, double, double) - Static method in class smile.math.Math
-
maximum of 3 doubles
- max(float[]) - Static method in class com.actelion.research.util.ArrayUtils
- max(float[]) - Static method in class smile.math.Math
-
Returns the maximum value of an array.
- max(float[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(float, float) - Static method in class smile.math.Math
-
Returns the greater of two float values.
- max(float, float, float) - Static method in class smile.math.Math
-
maximum of 3 floats
- max(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- max(int[]) - Static method in class smile.math.Math
-
Returns the maximum value of an array.
- max(int[][]) - Static method in class smile.math.Math
-
Returns the maximum of a matrix.
- max(int, int) - Static method in class smile.math.Math
-
Returns the greater of two int values.
- max(int, int, int) - Static method in class smile.math.Math
-
maximum of 3 integers
- max(long, long) - Static method in class smile.math.Math
-
Returns the greater of two long values.
- max(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- max(Coordinates[]) - Static method in class com.actelion.research.chem.Coordinates
- max(String, String) - Static method in class com.actelion.research.util.StringFunctions
- MAX - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- MAX - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- MAX_ALLOWED_COLLISION_INTENSITY - Static variable in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- MAX_ATOM_BITS - Static variable in class com.actelion.research.chem.SimpleCanonizer
- MAX_CONNATOMS - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- MAX_CONNATOMS - Static variable in class com.actelion.research.share.gui.editor.Model
- MAX_COUNT_VALUE - Static variable in class com.actelion.research.chem.descriptor.DescriptorEncoder
- MAX_DEFAULT_CURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- MAX_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- MAX_NODES - Static variable in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- MAX_NUM_BITS - Static variable in class com.actelion.research.chem.properties.complexity.BitArray128
- MAX_NUM_BONDS - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- MAX_NUM_HEAVY_ATOMS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- MAX_NUM_NODES - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- MAX_NUM_NODES_FLEXOPHORE - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- MAX_NUM_SOLUTIONS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- MAX_NUM_SOLUTIONS - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- MAX_RING_SIZE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- MAX_SMALL_RING_SIZE - Static variable in class com.actelion.research.chem.RingCollection
- MAX_UNDO_SIZE - Static variable in class com.actelion.research.share.gui.editor.Model
- MAX_VAL_INTERACTION_TYPE - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- maxConfs - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- maxDepth() - Method in class smile.regression.RegressionTree
-
Returns the maximum depth" of the tree -- the number of nodes along the longest path from the root node down to the farthest leaf node.
- maxDouble(List<Double>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- MAXENDUR - Static variable in class com.actelion.research.chem.reaction.Classification
- MAXFLASH - Static variable in class com.actelion.research.chem.reaction.Classification
- maximize(String, JToolBar) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Toggle the maximization state of the dockable in the docking panel.
- maximumVisibleRows - Variable in class com.actelion.research.gui.JScrollablePopupMenu
- MAXINDICES - Static variable in class com.actelion.research.chem.reaction.Classification
- maxInt(List<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- MAXMOLS - Static variable in class com.actelion.research.util.Sketch
- maxRange - Variable in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper.RangeStatistics
- MAXSTEP - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- MAXUNITS - Static variable in class com.actelion.research.chem.reaction.Classification
- mBond - Variable in class com.actelion.research.chem.coords.InventorChain
- mBondAtom - Variable in class com.actelion.research.chem.Molecule
- mBondFlags - Variable in class com.actelion.research.chem.Molecule
- mBondQueryFeatures - Variable in class com.actelion.research.chem.Molecule
- mBondType - Variable in class com.actelion.research.chem.Molecule
- mChirality - Variable in class com.actelion.research.chem.Molecule
- mChngGrps - Variable in class com.actelion.research.chem.reaction.Classification
- mClassName - Variable in class com.actelion.research.chem.reaction.Classification
- mClassResult - Variable in class com.actelion.research.chem.reaction.Classification
- mComponent - Variable in class com.actelion.research.gui.dock.TreeElement
- mContext - Variable in class com.actelion.research.chem.AbstractDepictor
- mController - Variable in class com.actelion.research.calc.SelfOrganizedMap
- mCoordinates - Variable in class com.actelion.research.chem.Molecule
- MCS - Class in com.actelion.research.chem.mcs
- MCS() - Constructor for class com.actelion.research.chem.mcs.MCS
- MCS(int) - Constructor for class com.actelion.research.chem.mcs.MCS
- MCS(int, SSSearcher) - Constructor for class com.actelion.research.chem.mcs.MCS
- MCS_EXHAUSTIVENESS - Static variable in class com.actelion.research.chem.docking.DockingEngine
- MCSFast - Class in com.actelion.research.chem.mcs
- MCSFast() - Constructor for class com.actelion.research.chem.mcs.MCSFast
- MCSFast(int) - Constructor for class com.actelion.research.chem.mcs.MCSFast
- MCSFunctions - Class in com.actelion.research.chem.mcs
- MCSFunctions() - Constructor for class com.actelion.research.chem.mcs.MCSFunctions
- MCSReactionMapper - Class in com.actelion.research.chem.reaction
- MCSReactionMapper() - Constructor for class com.actelion.research.chem.reaction.MCSReactionMapper
- mCurrentTool - Variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- mCurrentTool - Variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mDepictor - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- MDHIndexTables - Class in com.actelion.research.chem.descriptor.flexophore
- mDiagnosticCollisionAtoms - Variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- mDiagnosticCollisionString - Variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- mDiagnosticTorsionString - Variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- mDim - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mDisplayMode - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mDoLayoutMolecules - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mDotProduct - Variable in class com.actelion.research.chem.DiversitySelector.DiversitySelectorRecord
- mDrawingObjectList - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mDropAdapter - Variable in class com.actelion.research.gui.JStructureView
- MDYNE_A_TO_KCAL_MOL - Static variable in class com.actelion.research.chem.forcefield.mmff.Constants
- mean() - Method in interface smile.stat.distribution.Distribution
-
The mean of distribution.
- mean() - Method in class smile.stat.distribution.GaussianDistribution
- mean() - Method in class smile.stat.distribution.Mixture
- mean(double[]) - Static method in class smile.math.Math
-
Returns the mean of an array.
- mean(float[]) - Static method in class smile.math.Math
-
Returns the mean of an array.
- mean(int[]) - Static method in class smile.math.Math
-
Returns the mean of an array.
- mean(Angle, Angle) - Static method in class com.actelion.research.util.Angle
-
Determines the mean angle between a1 and a2 on that side of the circle where a1 and a2 have the shorter connection.
- meanClust() - Static method in class com.actelion.research.util.datamodel.ByteVec
- measure(double[], double[]) - Method in interface smile.validation.RegressionMeasure
-
Returns an index to measure the quality of regression.
- measure(double[], double[]) - Method in class smile.validation.RMSE
- median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- median - Variable in class com.actelion.research.calc.statistics.ModelStatisticsOverviewMedian
- median() - Method in class com.actelion.research.util.datamodel.DoubleArray
- median(double[]) - Static method in class smile.math.Math
-
Find the median of an array of type double.
- median(double[]) - Static method in class smile.sort.QuickSelect
-
Find the median of an array of type double.
- median(float[]) - Static method in class smile.math.Math
-
Find the median of an array of type float.
- median(float[]) - Static method in class smile.sort.QuickSelect
-
Find the median of an array of type float.
- median(int[]) - Static method in class smile.math.Math
-
Find the median of an array of type int.
- median(int[]) - Static method in class smile.sort.QuickSelect
-
Find the median of an array of type integer.
- median(T[]) - Static method in class smile.math.Math
-
Find the median of an array of type double.
- median(T[]) - Static method in class smile.sort.QuickSelect
-
Find the median of an array of type double.
- medianRange - Variable in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper.RangeStatistics
- MedianRegression - Class in com.actelion.research.calc.regression.median
-
MedianRegression
- MedianRegression() - Constructor for class com.actelion.research.calc.regression.median.MedianRegression
- MedianStatisticFunctions - Class in com.actelion.research.calc.statistics.median
-
MedianStatisticFunctions Aug 5, 2011 MvK: Start implementation
- MedianStatisticFunctions() - Constructor for class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- medoids() - Method in class smile.clustering.CLARANS
-
Returns the medoids.
- mEFlashAtom - Variable in class com.actelion.research.chem.reaction.Classification
- mEFlashMol - Variable in class com.actelion.research.chem.reaction.Classification
- mEnduringFG - Variable in class com.actelion.research.chem.reaction.Classification
- mEnduringFGs - Variable in class com.actelion.research.chem.reaction.Classification
- MercerKernel<T> - Interface in smile.math.kernel
-
A Mercer Kernel is a kernel that is positive semi-definite.
- merge(int, int) - Method in class smile.clustering.linkage.CompleteLinkage
- merge(int, int) - Method in class smile.clustering.linkage.Linkage
-
Merge two clusters into one and update the proximity matrix.
- merge(int, int) - Method in class smile.clustering.linkage.SingleLinkage
- merge(int, int) - Method in class smile.clustering.linkage.UPGMALinkage
- merge(int, int) - Method in class smile.clustering.linkage.UPGMCLinkage
- merge(int, int) - Method in class smile.clustering.linkage.WardLinkage
- merge(int, int) - Method in class smile.clustering.linkage.WPGMALinkage
- merge(int, int) - Method in class smile.clustering.linkage.WPGMCLinkage
- merge(MolDistHistViz, MolDistHist) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Deprecated.
- merge(SubGraphIndices) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- merge(List<SubGraphIndices>) - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
-
Merges fragments containing a common atom index.
- merge(RandomForest) - Method in class smile.regression.RandomForest
-
Merges together two random forests and returns a new forest consisting of trees from both input forests.
- mergeOverlapping(List<SubGraphIndices>, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
-
Merges overlapping fragments.
- MERGEPAINT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- mergeReactantsAndProducts(Reaction) - Method in class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
-
Copies all reactant/product molecules into one StereoMolecule for easier processing Use getReactant() and getProduct() from outside to access these.
- MersenneTwister - Class in smile.math.random
- MersenneTwister() - Constructor for class smile.math.random.MersenneTwister
-
Constructor.
- MersenneTwister(int) - Constructor for class smile.math.random.MersenneTwister
-
Constructor.
- MersenneTwister(long) - Constructor for class smile.math.random.MersenneTwister
-
Constructor.
- mESRHilited - Variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- mESRHilited - Variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mESRMenuVisible - Variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- mESRMenuVisible - Variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mESRSelected - Variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- mESRSelected - Variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- META_ALDUS_APM - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ANIMATEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ARC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_BITBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CHORD - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEBITMAP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEBITMAPINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEBRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEBRUSHINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEFONTINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEPATTERNBRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEPENINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DELETEOBJECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DIBBITBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DIBCREATEPATTERNBRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DIBSTRETCHBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DRAWTEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ELLIPSE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ESCAPE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_EXCLUDECLIPRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_EXTFLOODFILL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_EXTTEXTOUT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_FILLREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_FLOODFILL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_FRAMEREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_INTERSECTCLIPRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_INVERTREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_LINETO - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_MOVETO - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_ANSI_FIXED_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_ANSI_VAR_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_BLACK_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_BLACK_PEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_DEFAULT_PALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_DEVICE_DEFAULT_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_DKGRAY_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_GRAY_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_HOLLOW_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_LTGRAY_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_NULL_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_NULL_PEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_OEM_FIXED_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_SYSTEM_FIXED_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_SYSTEM_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_WHITE_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_WHITE_PEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OFFSETCLIPRGN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OFFSETVIEWPORTORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OFFSETWINDOWORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_PAINTREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_PATBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_PIE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_POLYBEZIER16 - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_POLYGON - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_POLYLINE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_POLYPOLYGON - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_REALIZEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_RECTANGLE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_RESIZEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_RESTOREDC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ROUNDRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SAVEDC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SCALEVIEWPORTEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SCALEWINDOWEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SELECTCLIPREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SELECTOBJECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SELECTPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETBKCOLOR - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETBKMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETDIBTODEV - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETMAPMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETMAPPERFLAGS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETPALENTRIES - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETPIXEL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETPOLYFILLMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETRELABS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETROP2 - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETSTRETCHBLTMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETTEXTALIGN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETTEXTCHAREXTRA - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETTEXTCOLOR - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETTEXTJUSTIFICATION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETVIEWPORTEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETVIEWPORTORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETWINDOWEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETWINDOWORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_STRETCHBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_STRETCHDIB - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_TEXTOUT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MetaFile - Class in com.actelion.research.gui.wmf
- MetaFile() - Constructor for class com.actelion.research.gui.wmf.MetaFile
- METAL_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- MetalTerm - Class in com.actelion.research.chem.docking.scoring.chemscore
- Metric<T> - Interface in smile.math.distance
-
A metric function defines a distance between elements of a set.
- MetropolisMonteCarloHelper - Class in com.actelion.research.chem.phesaflex
- MetropolisMonteCarloHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
- MFCOMMENT - Static variable in class com.actelion.research.gui.wmf.WMF
- MFCOMMENT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- mFixedAtoms - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mFlashAtom - Variable in class com.actelion.research.chem.reaction.Classification
- mFlashMol - Variable in class com.actelion.research.chem.reaction.Classification
- mFragment - Variable in class com.actelion.research.chem.SSSearcher
- mFragmentNoColor - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mGlobalAtom - Variable in class com.actelion.research.chem.coords.InventorFragment
- mGlobalBond - Variable in class com.actelion.research.chem.coords.InventorFragment
- mGlobalToLocalAtom - Variable in class com.actelion.research.chem.coords.InventorFragment
- mGrad - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mHeight - Variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- min - Variable in class com.actelion.research.calc.statistics.ModelStatisticsOverview
- min - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- min() - Method in class com.actelion.research.util.datamodel.DoubleArray
- min(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- min(double[]) - Static method in class com.actelion.research.util.ArrayUtils
- min(double[]) - Static method in class smile.math.Math
-
Returns the minimum value of an array.
- min(double[][]) - Static method in class smile.math.Math
-
Returns the minimum of a matrix.
- min(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- min(double, double) - Static method in class smile.math.Math
-
Returns the smaller of two double values.
- min(double, double, double) - Static method in class smile.math.Math
-
minimum of 3 doubles
- min(float[]) - Static method in class smile.math.Math
-
Returns the minimum value of an array.
- min(float[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- min(float, float) - Static method in class smile.math.Math
-
Returns the smaller of two float values.
- min(float, float, float) - Static method in class smile.math.Math
-
minimum of 3 floats
- min(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- min(int[]) - Static method in class smile.math.Math
-
Returns the minimum value of an array.
- min(int[][]) - Static method in class smile.math.Math
-
Returns the minimum of a matrix.
- min(int, int) - Static method in class smile.math.Math
-
Returns the smaller of two int values.
- min(int, int, int) - Static method in class smile.math.Math
-
minimum of 3 integers
- min(long, long) - Static method in class smile.math.Math
-
Returns the smaller of two long values.
- min(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- min(Coordinates[]) - Static method in class com.actelion.research.chem.Coordinates
- min(String, String) - Static method in class com.actelion.research.util.StringFunctions
- min(DifferentiableMultivariateFunction, double[], double) - Static method in class smile.math.Math
-
This method solves the unconstrained minimization problem
- min(DifferentiableMultivariateFunction, double[], double, int) - Static method in class smile.math.Math
-
This method solves the unconstrained minimization problem
- min(DifferentiableMultivariateFunction, int, double[], double) - Static method in class smile.math.Math
-
This method solves the unconstrained minimization problem
- min(DifferentiableMultivariateFunction, int, double[], double, int) - Static method in class smile.math.Math
-
This method solves the unconstrained minimization problem
- MIN_BOND_LENGTH_SQUARE - Static variable in class com.actelion.research.share.gui.editor.Model
- MIN_NUM_ATOMS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- MIN_NUM_NODES_SIM - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- MIN_NUM_VAR_SPLIT - Static variable in class com.actelion.research.calc.regression.randomforest.RandomForestRegression
- mIndex - Variable in class com.actelion.research.chem.reaction.Classification
- mInfluence - Variable in class com.actelion.research.calc.SelfOrganizedMap
- MINI_CUTOFF - Static variable in class com.actelion.research.chem.docking.DockingEngine
- minimise() - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- minimise() - Method in interface com.actelion.research.chem.forcefield.ForceField
- minimise(int, double, double) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
-
Minimise the current molecule.
- minimumLayoutSize(Container) - Method in class com.actelion.research.gui.JScrollablePopupMenu.ScrollPopupMenuLayout
- minimumLayoutSize(Container) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- MinimumSpanningTree - Class in com.actelion.research.calc.graph
-
MinimumSpanningTree Kruskal's algorithm
- MinimumSpanningTree(Matrix) - Constructor for class com.actelion.research.calc.graph.MinimumSpanningTree
- MINLEN_FRAG - Static variable in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- minus(double[], double[]) - Static method in class smile.math.Math
-
Element-wise subtraction of two arrays y = y - x.
- minus(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- minus(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- minus(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- minus(Complex) - Method in class smile.math.Complex
-
Returns this - b.
- mIsEnabled - Variable in class org.openmolecules.chem.conf.so.ConformationRule
- mIsFragment - Variable in class com.actelion.research.chem.Molecule
- mIsInterrupted - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mIsMarkushStructure - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mIsRacemate - Variable in class com.actelion.research.chem.Molecule
- mIsSelected - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mix64(BurtleHasherABC) - Static method in class com.actelion.research.util.BurtleHasher
- Mixture - Class in smile.stat.distribution
-
A finite mixture model is a probabilistic model for density estimation using a mixture distribution.
- Mixture(List<Mixture.Component>) - Constructor for class smile.stat.distribution.Mixture
-
Constructor.
- Mixture.Component - Class in smile.stat.distribution
-
A component in the mixture distribution is defined by a distribution and its weight in the mixture.
- mkdirs(File) - Static method in class com.actelion.research.util.IO
- mkdirs(String) - Static method in class com.actelion.research.util.IO
- mKeepMarkedAtoms - Variable in class com.actelion.research.chem.coords.InventorFragment
- mltb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the MLTB type of an atom given its MMFF type.
- MM_ANISOTROPIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_ANISOTROPIC - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
- MM_HIENGLISH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_HIMETRIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_HITWIPS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_ISOTROPIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_LOENGLISH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_LOMETRIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_TEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- mMainClass - Variable in class com.actelion.research.chem.reaction.Classification
- mMaxAtoms - Variable in class com.actelion.research.chem.Molecule
- mMaxBonds - Variable in class com.actelion.research.chem.Molecule
- MMFF94 - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- MMFF94S - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- MMFF94SPLUS - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- MMFFExternalPositionConstraint - Class in com.actelion.research.chem.forcefield.mmff
- MMFFExternalPositionConstraint(int, double[], double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.MMFFExternalPositionConstraint
- MMFFMolecule - Class in com.actelion.research.chem.forcefield.mmff
-
MMFF molecule is a wrapper class for the ExtendedMolecule.
- MMFFMolecule(StereoMolecule) - Constructor for class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
- MMFFPositionConstraint - Class in com.actelion.research.chem.forcefield.mmff
- MMFFPositionConstraint(StereoMolecule, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.MMFFPositionConstraint
- mMode - Variable in class com.actelion.research.calc.SelfOrganizedMap
- mMode - Variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- mMode - Variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mMol - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mMol - Variable in class com.actelion.research.gui.dnd.MoleculeTransferable
- mMolecule - Variable in class com.actelion.research.chem.SSSearcher
- mMolecule - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mMutationType - Variable in class com.actelion.research.chem.Mutation
- mNewpos - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mNX - Variable in class com.actelion.research.calc.SelfOrganizedMap
- mNY - Variable in class com.actelion.research.calc.SelfOrganizedMap
- MODE_ADD_NA_AND_CL - Static variable in class com.actelion.research.chem.MoleculeStandardizer
- MODE_ALLOW_CHARGE_CORRECTIONS - Static variable in class com.actelion.research.chem.reaction.Reactor
- MODE_ANGLES - Static variable in class com.actelion.research.chem.conf.TorsionDB
- MODE_BINS - Static variable in class com.actelion.research.chem.conf.TorsionDB
- MODE_BUFFER_HEAD_AND_TAIL - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_CONSIDER_MARKED_ATOMS - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_COORDINATES_PREFER_2D - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_COORDINATES_PREFER_3D - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_COORDINATES_REQUIRE_2D - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_COORDINATES_REQUIRE_3D - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_CREATE_SMARTS - Static variable in class com.actelion.research.chem.IsomericSmilesCreator
- MODE_DEFAULT - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_DRAWING_OBJECTS - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- MODE_DRAWING_OBJECTS - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- MODE_DRAWING_OBJECTS - Static variable in class com.actelion.research.share.gui.editor.Model
- MODE_EXTRACT_DETAILS - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_FULLY_MAP_REACTIONS - Static variable in class com.actelion.research.chem.reaction.Reactor
- MODE_GET_PARENT - Static variable in class com.actelion.research.chem.MoleculeStandardizer
- MODE_HARD_PPPOINTS - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- MODE_INCLUDE_MAPPING - Static variable in class com.actelion.research.chem.IsomericSmilesCreator
- MODE_INCLUDE_TAUTOMERIC_BONDS - Static variable in class com.actelion.research.chem.RingCollection
- MODE_KEEP_HYDROGEN_MAP - Static variable in class com.actelion.research.chem.MolfileParser
- MODE_KEEP_MARKED_ATOM_COORDS - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_KEKULIZED_OUTPUT - Static variable in class com.actelion.research.chem.IsomericSmilesCreator
- MODE_LARGEST_FRAGMENT_ONLY - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- MODE_MAKE_HYDROGEN_EXPLICIT - Static variable in class com.actelion.research.chem.SmilesParser
- MODE_MARKUSH_STRUCTURE - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- MODE_MARKUSH_STRUCTURE - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- MODE_MARKUSH_STRUCTURE - Static variable in class com.actelion.research.share.gui.editor.Model
- MODE_MULTIPLE_FRAGMENTS - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- MODE_MULTIPLE_FRAGMENTS - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- MODE_MULTIPLE_FRAGMENTS - Static variable in class com.actelion.research.share.gui.editor.Model
- MODE_PPNODE_SIMILARITY_COMPARISON - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- MODE_PREFER_MARKED_ATOM_COORDS - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_REACTION - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- MODE_REACTION - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- MODE_REACTION - Static variable in class com.actelion.research.share.gui.editor.Model
- MODE_REMOVE_DUPLICATE_PRODUCTS - Static variable in class com.actelion.research.chem.reaction.Reactor
- MODE_REMOVE_HYDROGEN - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_RETAIN_COORDINATES - Static variable in class com.actelion.research.chem.reaction.Reactor
- MODE_SKIP_COORDINATE_TEMPLATES - Static variable in class com.actelion.research.chem.SmilesParser
- MODE_SKIP_DEFAULT_TEMPLATES - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_SMALL_AND_LARGE_RINGS - Static variable in class com.actelion.research.chem.RingCollection
- MODE_SMALL_AND_LARGE_RINGS_AND_AROMATICITY - Static variable in class com.actelion.research.chem.RingCollection
- MODE_SMALL_RINGS_AND_AROMATICITY - Static variable in class com.actelion.research.chem.RingCollection
- MODE_SMALL_RINGS_ONLY - Static variable in class com.actelion.research.chem.RingCollection
- MODE_SOFT_PPPOINTS - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- model - Variable in class com.actelion.research.share.gui.editor.actions.CommandAction
- model - Variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- Model - Class in com.actelion.research.share.gui.editor
-
Project: User: rufenec Date: 1/24/13 Time: 5:02 PM
- Model(GeomFactory, int) - Constructor for class com.actelion.research.share.gui.editor.Model
- MODEL_GAUSSIAN_PROCESS - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- MODEL_KNN - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- MODEL_MEDIAN - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- MODEL_NEURAL_NETWORK - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- MODEL_PLS - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- MODEL_PLS_POWER - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- MODEL_RND_FOREST - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- MODEL_SVM - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- Model.AtomHighlightCallback - Interface in com.actelion.research.share.gui.editor
- Model.BondHighlightCallback - Interface in com.actelion.research.share.gui.editor
- ModelError - Class in com.actelion.research.calc.regression
-
ModelError This class is a data model for the error.
- ModelError() - Constructor for class com.actelion.research.calc.regression.ModelError
- ModelExhaustiveStatistics - Class in com.actelion.research.chem.properties.complexity
- ModelExhaustiveStatistics(int, int, int, double) - Constructor for class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- ModelMedianDouble - Class in com.actelion.research.calc.statistics.median
- ModelMedianDouble() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianDouble
- ModelMedianDouble(double, double, double, int, int) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianDouble
- ModelMedianDouble(ModelMedianDouble) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianDouble
- ModelMedianFloat - Class in com.actelion.research.calc.statistics.median
- ModelMedianFloat() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianFloat
- ModelMedianFloat(float, float, float, int, int) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianFloat
- ModelMedianFloat(ModelMedianFloat) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianFloat
- ModelMedianInteger - Class in com.actelion.research.calc.statistics.median
-
ModelMedianInteger Feb 9, 2012 MvK: Start implementation
- ModelMedianInteger() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianInteger
- ModelMedianLong - Class in com.actelion.research.calc.statistics.median
-
ModelMedianInteger Feb 14, 2017 MvK: Start implementation
- ModelMedianLong() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianLong
- ModelParser - Class in com.actelion.research.chem.io.pdb.parser
-
ModelParser
- ModelParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.ModelParser
- ModelSampleFragments - Class in com.actelion.research.chem.mcs
- ModelSampleFragments(int) - Constructor for class com.actelion.research.chem.mcs.ModelSampleFragments
- ModelSampleFragments(int, int, int) - Constructor for class com.actelion.research.chem.mcs.ModelSampleFragments
- ModelSolutionSimilarity - Class in com.actelion.research.chem.descriptor.flexophore
- ModelSolutionSimilarity(SolutionCompleteGraph, float[]) - Constructor for class com.actelion.research.chem.descriptor.flexophore.ModelSolutionSimilarity
- ModelStatisticsOverview - Class in com.actelion.research.calc.statistics
-
ModelStatisticsOverview
- ModelStatisticsOverview() - Constructor for class com.actelion.research.calc.statistics.ModelStatisticsOverview
- ModelStatisticsOverview(double, double, double, double) - Constructor for class com.actelion.research.calc.statistics.ModelStatisticsOverview
- ModelStatisticsOverviewMedian - Class in com.actelion.research.calc.statistics
-
ModelStatisticsOverviewMedian
- ModelStatisticsOverviewMedian() - Constructor for class com.actelion.research.calc.statistics.ModelStatisticsOverviewMedian
- ModelStatisticsOverviewMedian(double, double, double, double, double) - Constructor for class com.actelion.research.calc.statistics.ModelStatisticsOverviewMedian
- ModelXY - Class in com.actelion.research.util.datamodel
-
ModelDataXY X and Y are assumed to have the same row dim.
- ModelXY() - Constructor for class com.actelion.research.util.datamodel.ModelXY
- ModelXY(int, int, int) - Constructor for class com.actelion.research.util.datamodel.ModelXY
- ModelXY(Matrix, Matrix) - Constructor for class com.actelion.research.util.datamodel.ModelXY
- ModelXY(ModelXY) - Constructor for class com.actelion.research.util.datamodel.ModelXY
-
Deep copy constructor
- ModelXY(List<XY>) - Constructor for class com.actelion.research.util.datamodel.ModelXY
- ModelXYClassLabel - Class in com.actelion.research.util.datamodel
-
ModelXYClassLabel
- ModelXYClassLabel() - Constructor for class com.actelion.research.util.datamodel.ModelXYClassLabel
- ModelXYClassLabel(ModelXYClassLabel) - Constructor for class com.actelion.research.util.datamodel.ModelXYClassLabel
-
Deep copy constructor
- ModelXYColTags - Class in com.actelion.research.util.datamodel
-
ModelXYColTags
- ModelXYColTags() - Constructor for class com.actelion.research.util.datamodel.ModelXYColTags
- ModelXYColTags(ModelXYColTags) - Constructor for class com.actelion.research.util.datamodel.ModelXYColTags
- ModelXYCrossValidation - Class in com.actelion.research.util.datamodel
-
Deprecated.
- ModelXYCrossValidation(ModelXY) - Constructor for class com.actelion.research.util.datamodel.ModelXYCrossValidation
-
Deprecated.
- ModelXYIndex - Class in com.actelion.research.util.datamodel
-
ModelDataXY
- ModelXYIndex() - Constructor for class com.actelion.research.util.datamodel.ModelXYIndex
- ModelXYIndex(int, int, int) - Constructor for class com.actelion.research.util.datamodel.ModelXYIndex
- ModelXYIndex(Matrix, Matrix) - Constructor for class com.actelion.research.util.datamodel.ModelXYIndex
- ModelXYIndex(ModelXY) - Constructor for class com.actelion.research.util.datamodel.ModelXYIndex
- ModelXYIndex(ModelXYIndex) - Constructor for class com.actelion.research.util.datamodel.ModelXYIndex
-
Deep copy constructor
- mol - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- mol - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- mol - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- mol_ - Variable in class com.actelion.research.chem.AtomComparator
- Mol2FileParser - Class in com.actelion.research.chem.io
- Mol2FileParser() - Constructor for class com.actelion.research.chem.io.Mol2FileParser
- MolDistHist - Class in com.actelion.research.chem.descriptor.flexophore
- MolDistHist() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- MolDistHist(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- MolDistHist(MolDistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- MolDistHistEncoder - Class in com.actelion.research.chem.descriptor.flexophore
- MolDistHistEncoder() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- MolDistHistViz - Class in com.actelion.research.chem.descriptor.flexophore
-
Class for Flexophore visualization and atom tracking.
- MolDistHistViz() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistViz(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistViz(int, Molecule3D) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistViz(MolDistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistViz(MolDistHistViz) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistVizEncoder - Class in com.actelion.research.chem.descriptor.flexophore
- MolDistHistVizEncoder() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
- MolDistHistVizFrag - Class in com.actelion.research.chem.descriptor.flexophore
- MolDistHistVizFrag() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MolDistHistVizFrag(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MolDistHistVizFrag(int, Molecule3D) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MolDistHistVizFrag(MolDistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MolDistHistVizFrag(MolDistHistVizFrag) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MOLECULAR_PROPERTY_ACIDIC_OXYGENS - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_AROMRINGCOUNT - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_BASIC_NITROGENS - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_CLOGP - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_CLOGS - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_COMPLEXITY - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_FLEXIBILITY - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_HACCEPTORS - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_HDONORS - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_MOLWEIGHT - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_ROTATABLEBONDS - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_SHAPE - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_SMALLRINGCOUNT - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_STEREOCENTERS - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MOLECULAR_PROPERTY_TPSA - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MolecularComplexityCalculator - Class in com.actelion.research.chem.properties.complexity
- MolecularComplexityCalculator() - Constructor for class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
- MolecularFlexibilityCalculator - Class in com.actelion.research.chem.conf
- MolecularFlexibilityCalculator() - Constructor for class com.actelion.research.chem.conf.MolecularFlexibilityCalculator
- MolecularFormula - Class in com.actelion.research.chem
- MolecularFormula(ExtendedMolecule) - Constructor for class com.actelion.research.chem.MolecularFormula
- MolecularPropertyHelper - Class in com.actelion.research.chem.prediction
- MolecularPropertyHelper() - Constructor for class com.actelion.research.chem.prediction.MolecularPropertyHelper
- MolecularShapeCalculator - Class in com.actelion.research.chem.prediction
- MolecularShapeCalculator() - Constructor for class com.actelion.research.chem.prediction.MolecularShapeCalculator
- MolecularVolume - Class in com.actelion.research.chem.phesa
- MolecularVolume(MolecularVolume) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
-
calculate the Overlap of the two molecular volumes as a function a transform vector that is applied to the query molecule overlap Volume of two molecular Volumes formulated as a summed overlap of atomic Gaussians taken from Grant, Gallardo, Pickup, Journal of Computational Chemistry, 17, 1653-1666, 1996 returns a double[2]: the first double is the total overlap, whereas the second value is the specific contribution of additional volume gaussians (inclusion, exclusion)
- MolecularVolume(MolecularVolume, Conformer) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
- MolecularVolume(StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
- MolecularVolume(List<AtomicGaussian>, List<PPGaussian>, List<VolumeGaussian>, List<Coordinates>) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
- Molecule - Class in com.actelion.research.chem
- Molecule() - Constructor for class com.actelion.research.chem.Molecule
- Molecule() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
- Molecule(int, int) - Constructor for class com.actelion.research.chem.Molecule
- MOLECULE_DELIMITER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- MOLECULE_DELIMITER_STRING - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- MOLECULE_FLAVORS - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- molecule3D - Variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- Molecule3D - Class in com.actelion.research.chem
- Molecule3D() - Constructor for class com.actelion.research.chem.Molecule3D
- Molecule3D(int, int) - Constructor for class com.actelion.research.chem.Molecule3D
- Molecule3D(Molecule3D) - Constructor for class com.actelion.research.chem.Molecule3D
- Molecule3D(StereoMolecule) - Constructor for class com.actelion.research.chem.Molecule3D
- Molecule3DFunctions - Class in com.actelion.research.chem
- Molecule3DFunctions() - Constructor for class com.actelion.research.chem.Molecule3DFunctions
- MoleculeAutoMapper - Class in com.actelion.research.chem.reaction
- MoleculeAutoMapper(StereoMolecule) - Constructor for class com.actelion.research.chem.reaction.MoleculeAutoMapper
- moleculeChanged() - Method in class com.actelion.research.gui.editor.GenericDrawArea
-
Use this to inform the JDrawArea after changing its molecule from outside.
- moleculeChanged() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.Use this to inform the JDrawArea after changing its molecule from outside.
- moleculeChanged(boolean) - Method in class com.actelion.research.gui.editor.GenericDrawArea
-
Ideally don't use this from outside JDrawArea.
- moleculeChanged(boolean) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.Ideally don't use this from outside JDrawArea.
- MoleculeDataFormats - Class in com.actelion.research.jfx.dataformat
-
Deprecated.
- MoleculeDataFormats() - Constructor for class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- MoleculeDragAdapter - Class in com.actelion.research.gui.dnd
- MoleculeDragAdapter(Component) - Constructor for class com.actelion.research.gui.dnd.MoleculeDragAdapter
- MoleculeDropAdapter - Class in com.actelion.research.gui.dnd
- MoleculeDropAdapter() - Constructor for class com.actelion.research.gui.dnd.MoleculeDropAdapter
- MoleculeFilter - Interface in com.actelion.research.chem
- MoleculeGrid - Class in com.actelion.research.chem.io.pdb.converter
-
Class used to speed up the calculation of neighbours by creating a grid.
- MoleculeGrid(StereoMolecule) - Constructor for class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- MoleculeGrid(StereoMolecule, double, Coordinates) - Constructor for class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Creates the Grid: Complexity O(nAtoms)
- MoleculeNeutralizer - Class in com.actelion.research.chem
- MoleculeNeutralizer() - Constructor for class com.actelion.research.chem.MoleculeNeutralizer
- moleculeQualifies(StereoMolecule) - Method in interface com.actelion.research.chem.MoleculeFilter
- moleculeQualifies(StereoMolecule) - Method in class com.actelion.research.chem.SubstructureFilter
- MoleculeStandardizer - Class in com.actelion.research.chem
-
MoleculeStandardizer
- MoleculeStandardizer() - Constructor for class com.actelion.research.chem.MoleculeStandardizer
- MoleculeTransferable - Class in com.actelion.research.gui.dnd
- MoleculeTransferable(StereoMolecule) - Constructor for class com.actelion.research.gui.dnd.MoleculeTransferable
- MoleculeView - Class in com.actelion.research.jfx.gui.chem
-
Project: User: rufenec Date: 10/12/11 Time: 4:03 PM
- MoleculeView() - Constructor for class com.actelion.research.jfx.gui.chem.MoleculeView
- MoleculeView(StereoMolecule) - Constructor for class com.actelion.research.jfx.gui.chem.MoleculeView
- MoleculeViewSkin - Class in com.actelion.research.jfx.gui.chem
-
Project: User: rufenec Date: 10/12/11 Time: 4:10 PM
- MoleculeViewSkin(MoleculeView) - Constructor for class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- MolfileCreator - Class in com.actelion.research.chem
- MolfileCreator(ExtendedMolecule) - Constructor for class com.actelion.research.chem.MolfileCreator
-
This creates a new molfile version 2 from the given molecule.
- MolfileCreator(ExtendedMolecule, boolean) - Constructor for class com.actelion.research.chem.MolfileCreator
-
This creates a new molfile version 2 from the given molecule.
- MolfileCreator(ExtendedMolecule, boolean, double, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileCreator
-
This creates a new molfile version 2 from the given molecule.
- MolfileCreator(ExtendedMolecule, boolean, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileCreator
-
This creates a new molfile version 2 from the given molecule.
- MolfileParser - Class in com.actelion.research.chem
- MolfileParser() - Constructor for class com.actelion.research.chem.MolfileParser
-
Constructor of a MolFileParser, which will mirror Y,Z coordinates
- MolfileParser(int) - Constructor for class com.actelion.research.chem.MolfileParser
- MolfileV3Creator - Class in com.actelion.research.chem
-
This class generates an MDL molfile version 3.0 from a StereoMolecule as described by MDL in 'CTFile Formats June 2005'.
- MolfileV3Creator(StereoMolecule) - Constructor for class com.actelion.research.chem.MolfileV3Creator
-
This creates a new molfile version 3 from the given molecule.
- MolfileV3Creator(StereoMolecule, boolean) - Constructor for class com.actelion.research.chem.MolfileV3Creator
-
This creates a new molfile version 3 from the given molecule.
- MolfileV3Creator(StereoMolecule, boolean, double, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileV3Creator
-
This creates a new molfile version 3 from the given molecule.
- MolfileV3Creator(StereoMolecule, boolean, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileV3Creator
-
This creates a new molfile version 3 from the given molecule.
- moreRecordsAvailable() - Method in class com.actelion.research.chem.io.ODEFileParser
- MOUSE_CLICKED - Static variable in class com.actelion.research.gui.generic.GenericMouseEvent
- MOUSE_DRAGGED - Static variable in class com.actelion.research.gui.generic.GenericMouseEvent
- MOUSE_ENTERED - Static variable in class com.actelion.research.gui.generic.GenericMouseEvent
- MOUSE_EXITED - Static variable in class com.actelion.research.gui.generic.GenericMouseEvent
- MOUSE_MOVED - Static variable in class com.actelion.research.gui.generic.GenericMouseEvent
- MOUSE_PRESSED - Static variable in class com.actelion.research.gui.generic.GenericMouseEvent
- MOUSE_RELEASED - Static variable in class com.actelion.research.gui.generic.GenericMouseEvent
- mouseActionHappened(GenericMouseEvent) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- mouseActionHappened(GenericMouseEvent) - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- mouseActionHappened(GenericMouseEvent) - Method in interface com.actelion.research.gui.generic.GenericMouseListener
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JEditableChemistryView
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JEditableStructureView
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JImagePanel
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JMultiPanelTitle
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JPruningBar
-
If this pruning bar allows changes via double click and text input, then such an action will cause a PruningBarEvent with type=TYPE_TYPED.
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.swing.SwingMouseHandler
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JImagePanel
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JMultiPanelTitle
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JPruningBar
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.swing.SwingMouseHandler
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JImagePanel
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JMultiPanelTitle
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JPruningBar
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.swing.SwingMouseHandler
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JImagePanel
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JMultiPanelTitle
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JPruningBar
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.swing.SwingMouseHandler
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JImagePanel
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JMultiPanelTitle
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JPruningBar
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.swing.SwingMouseHandler
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JImagePanel
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JMultiPanelTitle
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JPruningBar
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.swing.SwingMouseHandler
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JImagePanel
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JMultiPanelTitle
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JPruningBar
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.swing.SwingMouseHandler
- mouseWheelMoved(MouseWheelEvent) - Method in class com.actelion.research.gui.JImagePanel
- move(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- move(double, double) - Method in class com.actelion.research.chem.DepictorTransformation
- move(float, float) - Method in class com.actelion.research.share.gui.Arrow
- move(float, float) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- move(float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- moveAtomWithUnboundedNeighbors(Conformer, int, double, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- moveFieldToStart(String) - Method in class com.actelion.research.chem.SDFileMolecule
- moveGroup(Conformer, int, int[], double, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
-
Move one atom and all non-ring-bond substituents, provided attachment atom is not part of the notList.
- moveSubstituent(Conformer, int, int, double, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
-
Moves all atoms of the substituent connected to rootAtom starting with firstAtom.
- moveTo(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- moveTo(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- MOVETOL - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mParent - Variable in class com.actelion.research.gui.dock.TreeElement
- mPoint - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mPos - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mPressedButton - Variable in class com.actelion.research.gui.editor.GenericEditorToolbar
- mPressedButton - Variable in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- mPriority - Variable in class com.actelion.research.chem.coords.InventorFragment
- mProbability - Variable in class com.actelion.research.chem.Mutation
- mProtectedFromDeletion - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mProtectHydrogen - Variable in class com.actelion.research.chem.Molecule
- mReactantOrCoreCount - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mReaction - Variable in class com.actelion.research.gui.dnd.ReactionTransferable
- mReader - Variable in class com.actelion.research.chem.io.CompoundFileParser
- mRearStrandLen - Variable in class com.actelion.research.chem.reaction.Classification
- mReferenceVector - Variable in class com.actelion.research.calc.SelfOrganizedMap
- mRigidFragment - Variable in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- mRotatableBond - Variable in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- mrqmin(double[], double[], double[], int, double[], int[], int, double[][], double[][], FittingFunction) - Method in class com.actelion.research.util.NumericalRecipes
- MSDIFF_OFFSET - Static variable in class com.actelion.research.util.Sketch
- mSmiles - Variable in class com.actelion.research.chem.SmilesCreator
-
Deprecated.
- mSpecifier1 - Variable in class com.actelion.research.chem.Mutation
- mSpecifier2 - Variable in class com.actelion.research.chem.Mutation
- mStereoInfo - Variable in class com.actelion.research.chem.reaction.Classification
- mTables - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- mTimeInterval - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mToolBar - Variable in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- mToolBar - Variable in class com.actelion.research.gui.JDrawPanel
-
Deprecated.
- mTotalEnergy - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mTransformation - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mTransformationReferenceX - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mTransformationReferenceY - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mTransformationValue1 - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mTransformationValue2 - Variable in class com.actelion.research.chem.AbstractDrawingObject
- MTRY - Static variable in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- mul(double) - Method in interface smile.math.matrix.DenseMatrix
-
In place element-wise multiplication A = A * x
- mul(double) - Method in class smile.math.matrix.JMatrix
- mul(double, DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
Element-wise addition C = A * x
- mul(double, DenseMatrix) - Method in class smile.math.matrix.JMatrix
- mul(double, JMatrix) - Method in class smile.math.matrix.JMatrix
- mul(int, int, double) - Method in interface smile.math.matrix.DenseMatrix
-
A[i][j] *= x
- mul(int, int, double) - Method in class smile.math.matrix.JMatrix
- mul(DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
In place element-wise multiplication A = A * B
- mul(DenseMatrix) - Method in class smile.math.matrix.JMatrix
- mul(DenseMatrix, DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
C = A * B
- mul(DenseMatrix, DenseMatrix) - Method in class smile.math.matrix.JMatrix
- mul(JMatrix) - Method in class smile.math.matrix.JMatrix
- mul(JMatrix, JMatrix) - Method in class smile.math.matrix.JMatrix
- mult(byte[], byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- mult(double) - Method in class com.actelion.research.util.datamodel.ByteVec
- mult(double) - Method in class com.actelion.research.util.datamodel.IntVec
- mult(double) - Method in class com.actelion.research.util.DoubleVec
- mult(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- mult(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- mult(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- mult(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- MULT_FREQ - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- multByteWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- multByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- multCols(Matrix) - Method in class com.actelion.research.calc.Matrix
- MultCoordFragIndex - Class in com.actelion.research.chem.descriptor.flexophore.generator
- MultCoordFragIndex(int[]) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- multEl(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Elementwise multiplication
- multEl(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Elementwise multiplication
- multEl(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Elementwise multiplication
- MulticoreExecutor - Class in smile.util
-
Utility class to run tasks in a thread pool on multi-core systems.
- MultiPanelDragListener - Interface in com.actelion.research.gui
- MultipleNonOverlapSolution - Class in com.actelion.research.chem.properties.complexity
- MultipleNonOverlapSolution(int, FragmentDefinedByBondsIdCode, int) - Constructor for class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- MultipleNonOverlapSolution(MultipleNonOverlapSolution) - Constructor for class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- multiply(boolean, boolean, Matrix) - Method in class com.actelion.research.calc.Matrix
-
Multiplication of two matrices.
- multiply(double) - Method in class com.actelion.research.calc.Matrix
- multiply(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
- multiply(Matrix) - Method in class com.actelion.research.calc.Matrix
- multiply(Quaternion) - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
-
convert Quaternion to a rotation matrix
- multiplyInverseMatrix(double[][], double[][], double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- multiplyMatrix(double[][], double[][], double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- multiplyValByVal(Matrix) - Method in class com.actelion.research.calc.Matrix
-
Value by value multiplication Matrices must have the same dimensions.
- MultivariateFunction - Interface in smile.math
-
An interface representing a multivariate real function.
- mUnitName - Variable in class com.actelion.research.chem.reaction.Classification
- mUnitRxns - Variable in class com.actelion.research.chem.reaction.Classification
- mUseGraphics2D - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mutate(StereoMolecule) - Method in class com.actelion.research.chem.Mutator
-
Does an in-place mutation of the molecule allowing any kind of mutation at any of the molecules non-selected atoms aiming for 4-24 non-H atoms with an optimum of 9 atoms.
- mutate(StereoMolecule, int, boolean) - Method in class com.actelion.research.chem.Mutator
-
Does an in-place mutation of the molecule allowing the defined mutation kinds at any of the molecules unselected atoms.
- mutate(StereoMolecule, ArrayList<Mutation>) - Method in class com.actelion.research.chem.Mutator
-
Selects a likely mutation from the list, performs the mutation and removes it from the list.
- Mutation - Class in com.actelion.research.chem
- Mutation() - Constructor for class com.actelion.research.chem.Mutation
- Mutation(int, int, int, int, int[], double) - Constructor for class com.actelion.research.chem.Mutation
- Mutation(int, int, int, int, int, double) - Constructor for class com.actelion.research.chem.Mutation
- MUTATION_ADD_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_ANY - Static variable in class com.actelion.research.chem.Mutator
- MUTATION_CHANGE_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CHANGE_BOND - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CHANGE_RING - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CLOSE_RING - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CLOSE_RING_AND_AROMATIZE - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CUTOUT_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CUTOUT_SFRAGMENT - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_DELETE_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_DELETE_BOND - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_DELETE_SUBSTITUENT - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_GROW - Static variable in class com.actelion.research.chem.Mutator
- MUTATION_INSERT_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_INVERT_PARITY - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_KEEP_SIZE - Static variable in class com.actelion.research.chem.Mutator
- MUTATION_MIGRATE - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_SHRINK - Static variable in class com.actelion.research.chem.Mutator
- MUTATION_SWAP_SUBSTITUENT - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_TOGGLE_AMID_SULFONAMID - Static variable in class com.actelion.research.chem.Mutation
- MutationBiasProvider - Interface in com.actelion.research.chem
- Mutator - Class in com.actelion.research.chem
- Mutator(AtomTypeList) - Constructor for class com.actelion.research.chem.Mutator
-
Creates a new Mutator that calculates probabilities of individual mutations from a given atom type list.
- Mutator(String) - Constructor for class com.actelion.research.chem.Mutator
-
Creates a new Mutator that calculates probabilities of individual mutations from a given atom type file.
- mValidHelperArrays - Variable in class com.actelion.research.chem.Molecule
- mValue - Variable in class com.actelion.research.chem.CanonizerBaseValue
- mWhere1 - Variable in class com.actelion.research.chem.Mutation
- mWhere2 - Variable in class com.actelion.research.chem.Mutation
- mWidth - Variable in class com.actelion.research.gui.editor.GenericEditorToolbar
N
- n - Variable in class smile.math.matrix.SVD
-
The number of columns.
- N - Variable in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- n_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'N-i' from the table.
- N_SP2_TAUT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- name - Variable in class com.actelion.research.chem.descriptor.SimilarityCalculatorInfo
- name - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- name - Variable in class smile.data.Dataset
-
The name of dataset.
- name - Variable in class smile.data.Datum
-
Name of datum.
- name(int) - Static method in class com.actelion.research.chem.PeriodicTable
- NAME - Static variable in class com.actelion.research.chem.descriptor.SimilarityCalculatorDoubleArray
- NAME_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- NamedSubstituents - Class in com.actelion.research.chem
- NamedSubstituents() - Constructor for class com.actelion.research.chem.NamedSubstituents
- names() - Method in class smile.data.AttributeVector
-
Returns the name vector.
- nameToShortName(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- NastyFunctionDetector - Class in com.actelion.research.chem
- NastyFunctionDetector() - Constructor for class com.actelion.research.chem.NastyFunctionDetector
- Native() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
- NativeClipboardAccessor - Class in com.actelion.research.gui.clipboard
- NativeClipboardAccessor() - Constructor for class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NativeMDLReactionReader - Class in com.actelion.research.chem.io
- NativeMDLReactionReader(String) - Constructor for class com.actelion.research.chem.io.NativeMDLReactionReader
- NC_ALDUSMETAFILE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_BITMAP - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_CHEMDRAWINTERCHANGE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_CTAB - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_DIB - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_EMBEDDEDSKETCH - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_IDCODE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_METAFILE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_MOLFILE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_SERIALIZEMOLECULE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_SERIALIZEREACTION - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_SKETCH - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- ncols() - Method in class smile.math.matrix.JMatrix
- ncols() - Method in interface smile.math.matrix.Matrix
-
Returns the number of columns.
- needsCoordinates - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- needsLayout() - Method in class com.actelion.research.share.gui.editor.Model
- needsLayout(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- NEG - Static variable in enum com.actelion.research.calc.classification.ClassificationAttr
- NEG_CHARGE - com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage.InteractionProbe
- NEG_CHARGE - com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint.Functionality
- negate() - Method in class com.actelion.research.chem.Coordinates
- negate() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns this vector negated (signs swapped).
- NEGATIVE - com.actelion.research.calc.classification.ClassificationAttr
- NegativeReceptorImage - Class in com.actelion.research.chem.docking.receptorpharmacophore
- NegativeReceptorImage(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage
- NegativeReceptorImage(StereoMolecule, StereoMolecule, double, Coordinates) - Constructor for class com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage
- NegativeReceptorImage.InteractionProbe - Enum in com.actelion.research.chem.docking.receptorpharmacophore
- NegativeReceptorImageCreator - Class in com.actelion.research.chem.docking.receptorpharmacophore
- NegativeReceptorImageCreator() - Constructor for class com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImageCreator
- NEGEP - Static variable in class smile.math.Math
-
The largest negative integer such that 1.0 - RADIXNEGEP ≠ 1.0, except that negeps is bounded below by -(DIGITS+3)
- neglectSpaceDelimitedCoordinates() - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
IDCodeParsers allow passing idcode and coordinates as one String with a space as separator in between.
- NEIGHBOURS - Static variable in class com.actelion.research.calc.regression.knn.KNNRegression
- NEIGHBOURS_SHIFT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
- NeuralNetwork - Class in smile.regression
-
Multilayer perceptron neural network for regression.
- NeuralNetwork(int...) - Constructor for class smile.regression.NeuralNetwork
-
Constructor.
- NeuralNetwork(NeuralNetwork.ActivationFunction, double, double, int...) - Constructor for class smile.regression.NeuralNetwork
-
Constructor.
- NeuralNetwork(NeuralNetwork.ActivationFunction, int...) - Constructor for class smile.regression.NeuralNetwork
-
Constructor.
- NeuralNetwork.ActivationFunction - Enum in smile.regression
- NeuralNetwork.Trainer - Class in smile.regression
-
Trainer for neural networks.
- NeuralNetworkParameterHelper - Class in com.actelion.research.calc.regression.neuralnetwork
-
NeuralNetworkParameterHelper
- NeuralNetworkParameterHelper() - Constructor for class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkParameterHelper
- NeuralNetworkRegression - Class in com.actelion.research.calc.regression.neuralnetwork
-
NeuralNetworkRegression
- NeuralNetworkRegression() - Constructor for class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkRegression
- NeuralNetworkRegression(ParameterNeuralNetwork) - Constructor for class com.actelion.research.calc.regression.neuralnetwork.NeuralNetworkRegression
- neutralizeChargedMolecule(StereoMolecule) - Method in class com.actelion.research.chem.MoleculeNeutralizer
-
Tries to neutralize all charged atoms of the molecule unless a charged atom has a neighbour atom with opposite charge.
- NewBondAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:28 PM
- NewBondAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.NewBondAction
- NewChainAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 3/26/13 Time: 3:42 PM
- NewChainAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.NewChainAction
- newInstance(double[]) - Static method in interface smile.math.matrix.Matrix
-
Returns a column vector/matrix initialized by given one-dimensional array.
- newInstance(double[][]) - Static method in interface smile.math.matrix.Matrix
-
Returns an matrix initialized by given two-dimensional array.
- newInstance(int, int, double) - Static method in interface smile.math.matrix.Matrix
-
Creates a matrix filled with given value.
- NEWLINE - Static variable in class com.actelion.research.chem.io.AbstractParser
- NEWLINE_REGEX - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- NEWLINE_STRING - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- newMMFF94(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Tables
-
Returns a new MMFF94 table.
- next() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Advances the row counter to the next row
- next() - Method in class com.actelion.research.util.datamodel.ModelXYCrossValidation
-
Deprecated.
- next(int) - Method in class smile.math.random.MersenneTwister
- next(int) - Method in interface smile.math.random.RandomNumberGenerator
-
Returns up to 32 random bits.
- next(int) - Method in class smile.math.random.UniversalGenerator
- next(String) - Static method in class com.actelion.research.util.IO
- next(String, DecimalFormat) - Static method in class com.actelion.research.util.IO
- nextAfter(double, double) - Static method in class smile.math.Math
-
Returns the floating-point number adjacent to the first argument in the direction of the second argument.
- nextAfter(float, double) - Static method in class smile.math.Math
-
Returns the floating-point number adjacent to the first argument in the direction of the second argument.
- nextClosing(String, int, char, char) - Static method in class com.actelion.research.util.StringFunctions
-
finds the next corresponding closing bracket char to the first open char
- nextClosingBracket(String, int) - Static method in class com.actelion.research.util.StringFunctions
-
finds the next balanced closing bracket "]" to the first open bracket "[" in the string.
- nextDouble() - Method in class smile.math.random.MersenneTwister
- nextDouble() - Method in class smile.math.Random
-
Generator a random number uniformly distributed in [0, 1).
- nextDouble() - Method in interface smile.math.random.RandomNumberGenerator
-
Returns the next pseudorandom, uniformly distributed double value between 0.0 and 1.0 from this random number generator's sequence.
- nextDouble() - Method in class smile.math.random.UniversalGenerator
- nextDouble(double, double) - Method in class smile.math.Random
-
Generate a uniform random number in the range [lo, hi)
- nextDoubles(double[]) - Method in class smile.math.random.MersenneTwister
- nextDoubles(double[]) - Method in class smile.math.Random
-
Generate n uniform random numbers in the range [0, 1)
- nextDoubles(double[]) - Method in interface smile.math.random.RandomNumberGenerator
-
Returns a vector of pseudorandom, uniformly distributed double values between 0.0 and 1.0 from this random number generator's sequence.
- nextDoubles(double[]) - Method in class smile.math.random.UniversalGenerator
- nextDoubles(double[], double, double) - Method in class smile.math.Random
-
Generate n uniform random numbers in the range [lo, hi)
- nextInt() - Method in class smile.math.random.MersenneTwister
- nextInt() - Method in class smile.math.Random
-
Returns a random integer.
- nextInt() - Method in interface smile.math.random.RandomNumberGenerator
-
Returns the next pseudorandom, uniformly distributed int value from this random number generator's sequence.
- nextInt() - Method in class smile.math.random.UniversalGenerator
- nextInt(int) - Method in class smile.math.random.MersenneTwister
- nextInt(int) - Method in class smile.math.Random
-
Returns a random integer in [0, n).
- nextInt(int) - Method in interface smile.math.random.RandomNumberGenerator
-
Returns a pseudorandom, uniformly distributed int value between 0 (inclusive) and the specified value (exclusive), drawn from this random number generator's sequence.
- nextInt(int) - Method in class smile.math.random.UniversalGenerator
- nextLong() - Method in class smile.math.random.MersenneTwister
- nextLong() - Method in class smile.math.Random
- nextLong() - Method in interface smile.math.random.RandomNumberGenerator
-
Returns the next pseudorandom, uniformly distributed long value from this random number generator's sequence.
- nextLong() - Method in class smile.math.random.UniversalGenerator
- nextPair() - Method in class com.actelion.research.chem.reaction.mapping.RootAtomPairSource
-
This creates and returns the next reactant/product atom pair to serve as starting point for building equivalent atom graphs that logically match reactant subgraphs to product subgraphs.
- nextUp(double) - Static method in class smile.math.Math
-
Returns the floating-point value adjacent to d in the direction of positive infinity.
- nextUp(float) - Static method in class smile.math.Math
-
Returns the floating-point value adjacent to f in the direction of positive infinity.
- NF - Static variable in class com.actelion.research.calc.regression.linear.pls.SimPLSLMOValidation
-
Deprecated.
- NITRO - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- Nitrogen - Static variable in class com.actelion.research.chem.PeriodicTable
- nNotFiniteRelError - Variable in class com.actelion.research.calc.regression.ModelError
- NO - Static variable in enum com.actelion.research.calc.classification.ClassificationAttr
- NO_OPTIONS - Static variable in class com.actelion.research.util.Base64
-
No options specified.
- NODE_SIZE - Static variable in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- NOMINAL - smile.data.Attribute.Type
-
Nominal attribute.
- NominalAttribute - Class in smile.data
-
Nominal attribute.
- NominalAttribute(String) - Constructor for class smile.data.NominalAttribute
-
Constructor.
- NominalAttribute(String, double) - Constructor for class smile.data.NominalAttribute
-
Constructor.
- NominalAttribute(String, double, String[]) - Constructor for class smile.data.NominalAttribute
-
Constructor.
- NominalAttribute(String, String) - Constructor for class smile.data.NominalAttribute
-
Constructor.
- NominalAttribute(String, String[]) - Constructor for class smile.data.NominalAttribute
-
Constructor.
- NominalAttribute(String, String, double) - Constructor for class smile.data.NominalAttribute
-
Constructor.
- NominalAttribute(String, String, double, String[]) - Constructor for class smile.data.NominalAttribute
-
Constructor.
- NominalAttribute(String, String, String[]) - Constructor for class smile.data.NominalAttribute
-
Constructor.
- NONE - com.actelion.research.calc.classification.ClassificationAttr
- NONHNEIGHBOURS - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- NONPOLAR_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- nonZero() - Method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Checks that at least one of the constants is non-zero.
- norm() - Method in interface smile.math.matrix.DenseMatrix
-
L2 matrix norm.
- norm() - Method in class smile.math.matrix.SVD
-
Returns the L2 matrix norm.
- norm(double[]) - Static method in class smile.math.Math
-
L2 vector norm.
- norm1() - Method in interface smile.math.matrix.DenseMatrix
-
L1 matrix norm.
- norm1(double[]) - Static method in class smile.math.Math
-
L1 vector norm.
- norm2() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Two norm
- norm2() - Method in interface smile.math.matrix.DenseMatrix
-
L2 matrix norm.
- norm2(double[]) - Static method in class smile.math.Math
-
L2 vector norm.
- norm2One() - Method in class com.actelion.research.util.datamodel.ByteVec
- norm2One() - Method in class com.actelion.research.util.datamodel.IntVec
- norm2One() - Method in class com.actelion.research.util.DoubleVec
- NORMAL - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- normalise() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Normalises a vector.
- normalize() - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- normalize() - Method in class com.actelion.research.util.Angle
- normalize(double[][]) - Static method in class smile.math.Math
-
Unitizes each column of a matrix to unit length (L_2 norm).
- normalize(double[][], boolean) - Static method in class smile.math.Math
-
Unitizes each column of a matrix to unit length (L_2 norm).
- normalizeAmbiguousBonds() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Normalizes different forms of functional groups (e.g.
- normalizeCoordinates() - Method in class com.actelion.research.chem.coords.InventorTemplate
- normalizeEnantiomer() - Method in class com.actelion.research.chem.Canonizer
-
This normalizes all absolute tetrahedral-, allene- and atrop-parities within the molecule.
- normalizeESRGroups() - Method in class com.actelion.research.chem.CanonizerMesoHelper
-
If a meso fragment contains stereo atoms belonging to ESR groups then there may be an alternative way of specifying the same meso fragment because of the symmetry of the fragment.
- normalizeESRGroupSwappingAndRemoval(int[]) - Method in class com.actelion.research.chem.CanonizerMesoHelper
- normalizeID(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
- normalizeValue(double) - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- normalizeValue(double) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- normalizeVector(Object) - Method in class com.actelion.research.calc.BinarySOM
- normalizeVector(Object) - Method in class com.actelion.research.calc.SelfOrganizedMap
- normalizeVector(Object) - Method in class com.actelion.research.calc.VectorSOM
- normFro() - Method in interface smile.math.matrix.DenseMatrix
-
Frobenius matrix norm.
- normInf() - Method in interface smile.math.matrix.DenseMatrix
-
Infinity matrix norm.
- normInf(double[]) - Static method in class smile.math.Math
-
L-infinity vector norm.
- normSquared() - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- NOSTEREO - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- NOSTEREO_TAUTOMER - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- NOT_SET - com.actelion.research.chem.forcefield.mmff.RingBoolean
- notifyVisibility(boolean) - Method in class com.actelion.research.gui.dock.Dockable
-
Method used by the JDockingPanel to inform the dockable when its visibility changes.
- NOTSRCCOPY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- NOTSRCERASE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- npara() - Method in interface smile.stat.distribution.Distribution
-
The number of parameters of the distribution.
- npara() - Method in class smile.stat.distribution.GaussianDistribution
- npara() - Method in class smile.stat.distribution.Mixture
- nr_class - Variable in class org.machinelearning.svm.libsvm.svm_model
- nr_weight - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- nrows() - Method in class smile.math.matrix.JMatrix
- nrows() - Method in interface smile.math.matrix.Matrix
-
Returns the number of rows.
- nSV - Variable in class org.machinelearning.svm.libsvm.svm_model
- nu - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- NU - Static variable in class com.actelion.research.calc.regression.svm.SVMRegression
- NU_SVC - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- NU_SVR - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- NULL_MATCH_SCALING - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- nullity() - Method in class smile.math.matrix.SVD
-
Returns the dimension of null space.
- nullspace() - Method in class smile.math.matrix.SVD
-
Returns a matrix of which columns give an orthonormal basis for the null space.
- NUM_BONDS_START_REGRESSION_SMALL_MOLECULE - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- NUM_BYTES_INTERACTION_TYPE - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- NUM_CONFORMATIONS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- NUM_TREES - Static variable in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- number(String) - Static method in class com.actelion.research.chem.PeriodicTable
- NUMBER_ELEMENTS - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
- NUMERIC - smile.data.Attribute.Type
-
Numeric attribute.
- NumericalRecipes - Class in com.actelion.research.util
- NumericalRecipes() - Constructor for class com.actelion.research.util.NumericalRecipes
- NumericAttribute - Class in smile.data
-
Numeric attribute.
- NumericAttribute(String) - Constructor for class smile.data.NumericAttribute
-
Constructor.
- NumericAttribute(String, double) - Constructor for class smile.data.NumericAttribute
-
Constructor.
- NumericAttribute(String, String) - Constructor for class smile.data.NumericAttribute
-
Constructor.
- NumericAttribute(String, String, double) - Constructor for class smile.data.NumericAttribute
-
Constructor.
O
- OBJECT_DELIMITER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- OBJECT_DELIMITER_STRING - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- ObjectiveBlurFlexophoreHardMatchUncovered - Class in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
-
ObjectiveBlurFlexophoreHardMatchUncovered The weighting of the coverage is hard.
- ObjectiveBlurFlexophoreHardMatchUncovered() - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- ObjectiveBlurFlexophoreHardMatchUncovered(int, int, double, double) - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- ObjectiveExhaustiveStatistics - Class in com.actelion.research.chem.properties.complexity
- ObjectiveExhaustiveStatistics() - Constructor for class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- OCCURENCE_CUTOFF - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- OCCURENCE_CUTOFF - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- ODE_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- ODEFileParser - Class in com.actelion.research.chem.io
- ODEFileParser(File) - Constructor for class com.actelion.research.chem.io.ODEFileParser
- ODEFileParser(Reader) - Constructor for class com.actelion.research.chem.io.ODEFileParser
- ODEFileParser(String) - Constructor for class com.actelion.research.chem.io.ODEFileParser
- OEM_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- onActionEnter() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- onActionLeave() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onActionLeave() - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onActionLeave() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onActionLeave() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onAddBond(int, int) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- onChange() - Method in interface com.actelion.research.share.gui.editor.listeners.IChangeListener
- onChangeBond(int) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- onChangeBond(int) - Method in class com.actelion.research.share.gui.editor.actions.DownBondAction
- onChangeBond(int) - Method in class com.actelion.research.share.gui.editor.actions.UpBondAction
- onCommand() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.CleanAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.ClearAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.CopyAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.CutAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.UndoAction
- onDoubleClick(IMouseEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onDoubleClick(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onDoubleClick(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onDoubleClick(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onDrag(Point2D) - Method in class com.actelion.research.share.gui.editor.actions.AddRingAction
- onDrag(Point2D) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- onDrag(Point2D) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- onDragBegin(DragGestureEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- onDragBegin(DragGestureEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- onDragEnter() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- onDragEnter() - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- onDragEnter() - Method in class com.actelion.research.gui.JChemistryView
- onDragEnter() - Method in class com.actelion.research.gui.JStructureView
- onDragExit() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- onDragExit() - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- onDragExit() - Method in class com.actelion.research.gui.JChemistryView
- onDragExit() - Method in class com.actelion.research.gui.JStructureView
- onDragOver() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- onDragOver() - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- onDragOver() - Method in class com.actelion.research.gui.JChemistryView
- onDragOver() - Method in class com.actelion.research.gui.JStructureView
- onDrawAtom(int, String, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- onDrawAtom(int, String, double, double) - Method in class com.actelion.research.chem.SVGDepictor
- onDrawBond(int, double, double, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- onDrawBond(int, double, double, double, double) - Method in class com.actelion.research.chem.SVGDepictor
- onDrop() - Method in class com.actelion.research.gui.JChemistryView
- onDrop() - Method in class com.actelion.research.gui.JStructureView
- onDropMolecule(StereoMolecule, Point) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- onDropReaction(Reaction, Point) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- ONE_CLASS - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- ONE_FOUR - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- ONE_ONE - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- ONE_THREE - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- ONE_TWO - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- ONE_X - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- ones(int, int) - Static method in interface smile.math.matrix.Matrix
-
Return an all-one matrix.
- onHighlight(int, boolean) - Method in interface com.actelion.research.share.gui.editor.Model.AtomHighlightCallback
- onHighlight(int, boolean) - Method in interface com.actelion.research.share.gui.editor.Model.BondHighlightCallback
- onKeyPressed(IKeyEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onKeyReleased(IKeyEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onKeyReleased(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onKeyReleased(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onKeyReleased(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- OnlineRegression<T> - Interface in smile.regression
-
Regression model with online learning capability.
- onMouseDown(IMouseEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
-
Handles Mouse down events
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AddRingAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- onMouseMove(IMouseEvent, boolean) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- onMouseUp(IMouseEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
-
Handles the MouseUp event
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AddRingAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ChangeAtomAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ChangeAtomPropertiesAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ChangeChargeAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.DeleteAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.UnknownParityAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- oop - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- OPAQUE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- openChemistryFile(boolean) - Method in interface com.actelion.research.gui.generic.GenericDialogHelper
- openChemistryFile(boolean) - Method in class com.actelion.research.gui.swing.SwingDialogHelper
- openDocument(String) - Static method in class com.actelion.research.util.Platform
-
Given a filename, open this file with the default application
- openReader(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
- optimalDist - Variable in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- optimalStrength - Variable in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- optimize(Evaluable) - Method in class com.actelion.research.chem.optimization.OptimizerLBFGS
-
Optimization routine using the limited Broyden-Fletcher-Goldfarb-Shanno algorithm
- optimize(SelfOrganizedConformer, int, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- OPTIMIZE_RIGID_FRAGS - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- optimize3D - Variable in class com.actelion.research.chem.io.AbstractParser
- optimizeAtomCoordinates(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- OptimizerLBFGS - Class in com.actelion.research.chem.optimization
-
taken from DD_chem3d, small changes necessary because a different output structure is needed it returns not only a value (the objective function), but the transformation array for achieving the best alignment
- OptimizerLBFGS(int, double) - Constructor for class com.actelion.research.chem.optimization.OptimizerLBFGS
- OR(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Makes an logical OR and calculates the hash code.
- OR(List<IntVec>) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Makes an logical OR and calculates the hash code.
- order - Variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- ORDERED - Static variable in class com.actelion.research.util.Base64
-
Encode using the special "ordered" dialect of Base64 described here: http://www.faqs.org/qa/rfcc-1940.html.
- org.machinelearning.svm.libsvm - package org.machinelearning.svm.libsvm
- org.openmolecules.chem.conf.gen - package org.openmolecules.chem.conf.gen
- org.openmolecules.chem.conf.so - package org.openmolecules.chem.conf.so
- organize() - Method in class com.actelion.research.calc.SelfOrganizedMap
- originalToExtendedAtom(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- OUT_CHARACTER_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_DEFAULT_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_DEVICE_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_RASTER_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_SEPARATOR_COL - Static variable in class com.actelion.research.calc.Matrix
- OUT_SEPARATOR_ROW - Static variable in class com.actelion.research.calc.Matrix
- OUT_STRING_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_STROKE_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_TT_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUTLIER - Static variable in interface smile.clustering.Clustering
-
Cluster label for outliers or noises.
- OutOfPlane - Class in com.actelion.research.chem.forcefield.mmff
-
Out of plane energy term class.
- OutOfPlane - Class in com.actelion.research.chem.forcefield.mmff.table
- OutOfPlane(Tables, MMFFMolecule, int, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Construct a new out of plane energy term.
- OutOfPlane(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
- OutputStream(OutputStream) - Constructor for class com.actelion.research.util.Base64.OutputStream
-
Constructs a
Base64.OutputStream
in ENCODE mode. - OutputStream(OutputStream, int) - Constructor for class com.actelion.research.util.Base64.OutputStream
-
Constructs a
Base64.OutputStream
in either ENCODE or DECODE mode. - overlapDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- Oxygen - Static variable in class com.actelion.research.chem.PeriodicTable
P
- p - Static variable in class com.actelion.research.chem.phesa.MolecularVolume
- p - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- p(double) - Method in interface smile.stat.distribution.Distribution
-
The probability density function for continuous distribution or probability mass function for discrete distribution at x.
- p(double) - Method in class smile.stat.distribution.GaussianDistribution
- p(double) - Method in class smile.stat.distribution.Mixture
- P - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- PACKAGE_DATAWARRIOR_IDORSIA - Static variable in class com.actelion.research.util.ConstantsDWAR
- paint(GenericDrawContext) - Method in class com.actelion.research.chem.ExtendedDepictor
- paint(IDrawContext) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- paint(IDrawContext<T>) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- paint(Graphics) - Method in class com.actelion.research.gui.dock.JDockingPanel
- paint(Object) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- paint(T) - Method in class com.actelion.research.chem.AbstractDepictor
- paint(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- paintBorder(Component, Graphics, int, int, int, int) - Method in class com.actelion.research.gui.dock.ShadowBorder
- paintChildren(Graphics) - Method in class com.actelion.research.gui.JScrollablePopupMenu
- paintComponent(Graphics) - Method in class com.actelion.research.gui.dock.DockableHeader
- paintComponent(Graphics) - Method in class com.actelion.research.gui.editor.SwingEditorArea
- paintComponent(Graphics) - Method in class com.actelion.research.gui.editor.SwingEditorToolbar
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JChemistryView
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JEditableChemistryView
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JEditableStructureView
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JImagePanel
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JImagePanelFixedSize
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JMultiPanelTitle
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JPruningBar
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JStructureView
- paintComponent(Graphics) - Method in class com.actelion.research.gui.table.ChemistryRenderPanel
- paintComponent(Graphics) - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- paintContent(GenericDrawContext) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- paintContent(GenericDrawContext) - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- paintDrawingObjects(GenericDrawContext) - Method in class com.actelion.research.chem.ExtendedDepictor
- paintDrawingObjects(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- paintFragmentNumbers(GenericDrawContext) - Method in class com.actelion.research.chem.ExtendedDepictor
- paintFragmentNumbers(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- paintIcon(Component, Graphics, int, int) - Method in class com.actelion.research.gui.hidpi.HiDPIIcon
- paintStructures(GenericDrawContext) - Method in class com.actelion.research.chem.ExtendedDepictor
- paintStructures(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- pairMatch(String, String) - Static method in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- PAR_CLEAVE_RINGS - Static variable in class com.actelion.research.chem.mcs.MCS
- PAR_CLEAVE_RINGS - Static variable in class com.actelion.research.chem.mcs.MCSFast
- PAR_KEEP_AROMATIC_RINGS - Static variable in class com.actelion.research.chem.mcs.MCS
- PAR_KEEP_AROMATIC_RINGS - Static variable in class com.actelion.research.chem.mcs.MCSFast
- PAR_KEEP_RINGS - Static variable in class com.actelion.research.chem.mcs.MCS
- PAR_KEEP_RINGS - Static variable in class com.actelion.research.chem.mcs.MCSFast
- PARA_TAG_HISTOGRAM_SIMILARITY_THRESH - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- PARA_TAG_MODE_MATCH - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- PARA_TAG_MODE_SINGLE_CONFORMATION_QUERY - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- PARA_TAG_PPNODE_SIMILARITY_THRESH - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- param - Variable in class org.machinelearning.svm.libsvm.svm_model
- ParameterGaussianProcess - Class in com.actelion.research.calc.regression.gaussianprocess
-
ParameterGaussianProcess
- ParameterGaussianProcess() - Constructor for class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- ParameterizedStringList - Class in com.actelion.research.chem.prediction
- ParameterizedStringList() - Constructor for class com.actelion.research.chem.prediction.ParameterizedStringList
- ParameterKNN - Class in com.actelion.research.calc.regression.knn
-
ParameterKNN
- ParameterKNN() - Constructor for class com.actelion.research.calc.regression.knn.ParameterKNN
- ParameterKNN(int) - Constructor for class com.actelion.research.calc.regression.knn.ParameterKNN
- ParameterMedian - Class in com.actelion.research.calc.regression.median
-
ParameterMedian
- ParameterMedian() - Constructor for class com.actelion.research.calc.regression.median.ParameterMedian
- ParameterNeuralNetwork - Class in com.actelion.research.calc.regression.neuralnetwork
-
ParameterNeuralNetwork
- ParameterNeuralNetwork() - Constructor for class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- ParameterPLS - Class in com.actelion.research.calc.regression.linear.pls
-
ParameterPLS
- ParameterPLS() - Constructor for class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- ParameterPLS(int) - Constructor for class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- ParameterPLS(ParameterPLS) - Constructor for class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- ParameterPLS(String, int) - Constructor for class com.actelion.research.calc.regression.linear.pls.ParameterPLS
-
For inheritance of BxCox power transformation.
- ParameterPLSBoxCox - Class in com.actelion.research.calc.regression.linear.pls.boxcox
-
ParameterPLSBoxCox
- ParameterPLSBoxCox() - Constructor for class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- ParameterPLSBoxCox(int) - Constructor for class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- ParameterPLSBoxCox(ParameterPLSBoxCox) - Constructor for class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- ParameterRandomForest - Class in com.actelion.research.calc.regression.randomforest
-
ParameterRandomForest
- ParameterRandomForest() - Constructor for class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- parameterRegressionMethod - Variable in class com.actelion.research.calc.regression.ARegressionMethod
- ParameterRegressionMethod - Class in com.actelion.research.calc.regression
-
ParameterRegressionMethod
- ParameterRegressionMethod() - Constructor for class com.actelion.research.calc.regression.ParameterRegressionMethod
- ParameterRegressionMethod(ParameterRegressionMethod) - Constructor for class com.actelion.research.calc.regression.ParameterRegressionMethod
- ParameterRegressionMethod(String) - Constructor for class com.actelion.research.calc.regression.ParameterRegressionMethod
- ParameterSVM - Class in com.actelion.research.calc.regression.svm
-
ParameterSVM
- ParameterSVM() - Constructor for class com.actelion.research.calc.regression.svm.ParameterSVM
- ParameterSVM(double) - Constructor for class com.actelion.research.calc.regression.svm.ParameterSVM
- ParameterSVM(ParameterSVM) - Constructor for class com.actelion.research.calc.regression.svm.ParameterSVM
- ParameterSVM(String) - Constructor for class com.actelion.research.calc.regression.svm.ParameterSVM
- ParameterSVM(svm_parameter) - Constructor for class com.actelion.research.calc.regression.svm.ParameterSVM
- parent - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- parse(Reaction, BufferedReader) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, BufferedReader, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, File) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, File, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, String) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, String, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(StereoMolecule, byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, byte[]) - Method in class com.actelion.research.chem.SmilesParser
- parse(StereoMolecule, byte[], boolean, boolean) - Method in class com.actelion.research.chem.SmilesParser
- parse(StereoMolecule, byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, byte[], byte[], int, int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, byte[], int, int) - Method in class com.actelion.research.chem.SmilesParser
- parse(StereoMolecule, byte[], int, int, boolean, boolean) - Method in class com.actelion.research.chem.SmilesParser
- parse(StereoMolecule, BufferedReader) - Method in class com.actelion.research.chem.MolfileParser
- parse(StereoMolecule, File) - Method in class com.actelion.research.chem.MolfileParser
- parse(StereoMolecule, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, String) - Method in class com.actelion.research.chem.MolfileParser
- parse(StereoMolecule, String) - Method in class com.actelion.research.chem.SmilesParser
-
Parses the given smiles into the molecule, creates proper atom coordinates to reflect correct double bond geometries and translates tetrahedral and allene parities into up/down-bonds.
- parse(StereoMolecule, StringBuffer) - Method in class com.actelion.research.chem.MolfileParser
- parse(StereoMolecule, String, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(BufferedInputStream) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- parse(BufferedReader) - Method in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- parse(File) - Method in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- parse(String[]) - Method in class com.actelion.research.util.CommandLineParser
- parse(List<String>, int, List<AtomRecord>, List<AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.parser.ModelParser
- parse2Double(String, String) - Static method in class com.actelion.research.util.StringFunctions
- parse2PrecisionAndRecall(String) - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- parseCoordinates(byte[], int, StereoMolecule, Coordinates[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
This method parses an id-coordinate string (new format only) and writes the coordinates into a Coordinates array.
- parseDate(String) - Static method in class com.actelion.research.util.Formatter
- parseDateTime(String) - Static method in class com.actelion.research.util.Formatter
- parseInteger(InputStream) - Static method in class com.actelion.research.util.datamodel.IntArray
- parseInteger(String, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- parseLong(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.BitArray128
- parseMapping(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- parseMapping(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- parseMolecule(byte[]) - Method in class com.actelion.research.chem.SmilesParser
-
Convenience method to quickly obtain a StereoMolecule from a SMILES string.
- parseMolecule(String) - Method in class com.actelion.research.chem.SmilesParser
- parseReaction(byte[]) - Method in class com.actelion.research.chem.SmilesParser
- parseReaction(String) - Method in class com.actelion.research.chem.SmilesParser
- parseString(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- parseString(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- partition(double) - Method in class smile.clustering.HierarchicalClustering
-
Cuts a tree into several groups by specifying the cut height.
- partition(int) - Method in class smile.clustering.HierarchicalClustering
-
Cuts a tree into several groups by specifying the desired number.
- PartitionClustering<T> - Class in smile.clustering
-
Abstract class of partition clustering.
- PartitionClustering() - Constructor for class smile.clustering.PartitionClustering
- paste() - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- PASTE_AND_DROP_OPTION_ALLOW_FRAGMENT_STATE_CHANGE - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_KEEP_ATOM_COLORS - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_KEEP_BOND_HIGHLIGHTING - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_LAYOUT_REACTION - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_REMOVE_CATALYSTS - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_REMOVE_DRAWING_OBJECTS - Static variable in class com.actelion.research.gui.JChemistryView
- PasteAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/16/13 Time: 3:39 PM
- PasteAction(Model, Dimension) - Constructor for class com.actelion.research.share.gui.editor.actions.PasteAction
- pasteImage() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
- pasteImage() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- pasteImage() - Static method in class com.actelion.research.gui.clipboard.ImageClipboardHandler
- pasteMolecule() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Get one Molecule from the Clipboard.
- pasteMolecule() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- pasteMolecule() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
- pasteMolecule(boolean, int) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
- pasteMolecule(boolean, int) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- pasteMolecule(double, double) - Method in class com.actelion.research.share.gui.editor.Model
- pasteMolecules() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Get one or more Molecule(s) from the Clipboard.
- pasteMolecules() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- pasteReaction() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Get a Reaction from the Clipboard
- pasteReaction() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- pasteReaction() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
- pasteReaction(double, double) - Method in class com.actelion.research.share.gui.editor.Model
- pasteReactionWindowsNative() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
- pasteText() - Static method in class com.actelion.research.gui.clipboard.TextClipboardHandler
- PAT_NOT_ALPHANUMERIC - Static variable in class com.actelion.research.util.StringFunctions
- PAT_WHITESPACE - Static variable in class com.actelion.research.util.StringFunctions
- PATCOPY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PATINVERT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PATPAINT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PATTERN_NF_DWAR - Static variable in class com.actelion.research.util.ConstantsDWAR
- PATTERN_NF_DWAR4 - Static variable in class com.actelion.research.util.ConstantsDWAR
- PDBCoordEntryFile - Class in com.actelion.research.chem.io.pdb.parser
-
PDBCoordEntryFile
- PDBCoordEntryFile() - Constructor for class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- PDBFileParser - Class in com.actelion.research.chem.io.pdb.parser
-
PDBFileParser
- PDBFileParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- pdist(double[][]) - Static method in class smile.math.Math
-
Pairwise distance between pairs of objects.
- pdist(double[][], double[][], boolean, boolean) - Static method in class smile.math.Math
-
Pairwise distance between pairs of objects.
- peek() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
-
Peek the first element of the Queue (do not increment the queue index)
- peek() - Method in class com.actelion.research.util.IntQueue
-
Peek the first element of the Queue (do not increment the queue index)
- peek() - Method in class smile.sort.IntHeapSelect
-
Returns the k-th smallest value seen so far.
- perceivedBrightness(Color) - Static method in class com.actelion.research.util.ColorHelper
-
This is a color's perceived brightness by the human eye
- percentile05 - Variable in class com.actelion.research.calc.statistics.ModelStatisticsOverviewMedian
- percentile25 - Variable in class com.actelion.research.calc.statistics.ModelStatisticsOverviewMedian
- percentile75 - Variable in class com.actelion.research.calc.statistics.ModelStatisticsOverviewMedian
- percentile95 - Variable in class com.actelion.research.calc.statistics.ModelStatisticsOverviewMedian
- performMutation(StereoMolecule, Mutation) - Method in class com.actelion.research.chem.Mutator
-
Performs the given mutation on the molecule, updates atom coordinates, and updates stereo bonds to reflect lost or new stereo centers.
- PeriodicTable - Class in com.actelion.research.chem.forcefield.mmff
- PeriodicTable - Class in com.actelion.research.chem
- PERIPHERY_WEIGHT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- permutate(double[]) - Static method in class smile.math.Math
-
Generates a permutation of given array.
- permutate(double[]) - Method in class smile.math.Random
-
Generates a permutation of given array.
- permutate(float[]) - Static method in class smile.math.Math
-
Generates a permutation of given array.
- permutate(float[]) - Method in class smile.math.Random
-
Generates a permutation of given array.
- permutate(int) - Static method in class smile.math.Math
-
Generates a permutation of 0, 1, 2, ..., n-1, which is useful for sampling without replacement.
- permutate(int) - Method in class smile.math.Random
-
Generates a permutation of 0, 1, 2, ..., n-1, which is useful for sampling without replacement.
- permutate(int[]) - Static method in class smile.math.Math
-
Generates a permutation of given array.
- permutate(int[]) - Method in class smile.math.Random
-
Generates a permutation of given array.
- permutate(Object[]) - Static method in class smile.math.Math
-
Generates a permutation of given array.
- permutate(Object[]) - Method in class smile.math.Random
-
Generates a permutation of given array.
- PharmacophoreCalculator - Class in com.actelion.research.chem.phesa.pharmacophore
- PharmacophoreNode - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
A PharmacophoreNode represents a node in a PharmacophoreTree.
- PharmacophoreNode(List<Integer>, int[][], double[], boolean, boolean) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- PharmacophoreNode(List<Integer>, int[][], double[], int, boolean, boolean) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- PharmacophoreNode(List<Integer>, int[], List<Double>, List<Double>, int) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- PharmacophorePointFactory - Class in com.actelion.research.chem.phesa.pharmacophore.pp
- PharmacophorePointFactory() - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.PharmacophorePointFactory
- PharmacophoreTree - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
A PharmacophoreTree closely follows the concepts of FeatureTrees as described by Rarey and Dixon (DOI:10.1023/a:1008068904628).
- PharmacophoreTree(List<PharmacophoreNode>, List<int[]>) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- PharmacophoreTree.BiGramInt - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
container of an undirected edge
- PharmacophoreTreeGenerator - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
Generates a PharmacophoreTree from a StereoMolecule.
- PharmGraphGenerator - Class in com.actelion.research.chem.descriptor.pharmacophoregraph
- PharmGraphGenerator() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoregraph.PharmGraphGenerator
- phase() - Method in class smile.math.Complex
-
Returns angle/phase/argument between -pi and pi.
- PheSAAlignment - Class in com.actelion.research.chem.phesa
- PheSAAlignment(MolecularVolume, MolecularVolume) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
- PheSAAlignment(ShapeVolume, ShapeVolume, double) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
- PheSAAlignment(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
- PheSAAlignment(StereoMolecule, StereoMolecule, double) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
- PheSAAlignment.axis - Enum in com.actelion.research.chem.phesa
- PheSAAlignment.PheSAResult - Class in com.actelion.research.chem.phesa
- PheSAAlignmentOptimizer - Class in com.actelion.research.chem.alignment3d
- PheSAAlignmentOptimizer.AlignmentResult - Class in com.actelion.research.chem.alignment3d
- PheSAMolecule - Class in com.actelion.research.chem.phesa
- PheSAMolecule() - Constructor for class com.actelion.research.chem.phesa.PheSAMolecule
- PheSAMolecule(StereoMolecule, MolecularVolume) - Constructor for class com.actelion.research.chem.phesa.PheSAMolecule
- PheSAMolecule(StereoMolecule, ArrayList<MolecularVolume>) - Constructor for class com.actelion.research.chem.phesa.PheSAMolecule
- PheSAResult(StereoMolecule, StereoMolecule, double) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- PHOSPHONATE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- Phosphorus - Static variable in class com.actelion.research.chem.PeriodicTable
- PI - Static variable in class com.actelion.research.util.Sketch
- PI - Static variable in class smile.math.Math
-
The ratio of the circumference of a circle to its diameter.
- pie(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- pie(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- pilp(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the PILP type of an atom given its MMFF type.
- Pipeline<T> - Class in com.actelion.research.util
-
Pipeline Enables concurrent access to a queue.
- Pipeline() - Constructor for class com.actelion.research.util.Pipeline
- Pipeline(List<T>) - Constructor for class com.actelion.research.util.Pipeline
-
The 'all data in' flag is set true.
- Pipeline2FileWriter<T> - Class in com.actelion.research.util
-
Modest v.
- Pipeline2FileWriter(Pipeline<T>, File) - Constructor for class com.actelion.research.util.Pipeline2FileWriter
- piv - Variable in class smile.math.matrix.LU
-
Internal storage of pivot vector.
- pivsign - Variable in class smile.math.matrix.LU
-
pivot sign.
- PlaneRule - Class in org.openmolecules.chem.conf.so
- PlaneRule(int[], StereoMolecule) - Constructor for class org.openmolecules.chem.conf.so.PlaneRule
- Platform - Class in com.actelion.research.util
-
Requires JRE 1.6
- Platform() - Constructor for class com.actelion.research.util.Platform
- PLATFORM_NAME_DATAWARRIOR - Static variable in class com.actelion.research.util.ConstantsDWAR
- PLPTerm - Class in com.actelion.research.chem.docking.scoring.plp
-
piecewise linear potential (PLP) as described in doi:10.1021/ci800298z parameters from model 3 (M3)
- pls(Matrix, Matrix, String, int, boolean, String) - Static method in class com.actelion.research.calc.MatrixTests
- PLSBoxCoxY - Class in com.actelion.research.calc.regression.linear.pls.boxcox
-
PLSBoxCoxY
- PLSBoxCoxY() - Constructor for class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- PLSBoxCoxY(ParameterPLSBoxCox) - Constructor for class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- PLSRegressionModelCalculator - Class in com.actelion.research.calc.regression.linear.pls
-
PLSRegressionModelCalculator
- PLSRegressionModelCalculator() - Constructor for class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- PLSRegressionModelCalculator(ParameterPLS) - Constructor for class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- plus(double[], double[]) - Static method in class smile.math.Math
-
Element-wise sum of two arrays y = x + y.
- plus(Matrix) - Method in class com.actelion.research.calc.Matrix
- plus(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- plus(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- plus(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- plus(Complex) - Method in class smile.math.Complex
-
Returns this + b.
- PointDouble - Class in com.actelion.research.util.datamodel
- PointDouble() - Constructor for class com.actelion.research.util.datamodel.PointDouble
- PointDouble(double, double) - Constructor for class com.actelion.research.util.datamodel.PointDouble
- PointDouble(Point) - Constructor for class com.actelion.research.util.datamodel.PointDouble
- PointUtils - Class in com.actelion.research.util
- PointUtils() - Constructor for class com.actelion.research.util.PointUtils
- PolarSurfaceAreaPredictor - Class in com.actelion.research.chem.prediction
-
This class predicts the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.
- PolarSurfaceAreaPredictor() - Constructor for class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- pollAll() - Method in class com.actelion.research.util.Pipeline
- pollAllWithWait() - Method in class com.actelion.research.util.Pipeline
-
all data in flag has to be set.
- pollData() - Method in class com.actelion.research.util.Pipeline
- POLY - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- polygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.MetaFile
- polygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMF
- Polygon - Class in com.actelion.research.share.gui
- Polygon() - Constructor for class com.actelion.research.share.gui.Polygon
- polyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.MetaFile
- polyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMF
- Polynome(double[]) - Constructor for class com.actelion.research.util.FastSpline.Polynome
- polypolygon(Polygon[]) - Method in class com.actelion.research.gui.wmf.MetaFile
- polypolygon(Polygon[]) - Method in class com.actelion.research.gui.wmf.WMF
- pop() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
-
Pop the first element of the Queue
- pop() - Method in class com.actelion.research.util.IntQueue
-
Pop the first element of the Queue
- popUndo() - Method in class com.actelion.research.share.gui.editor.Model
- PopupItemProvider - Interface in com.actelion.research.gui
- PopupProvider - Interface in com.actelion.research.gui.dock
- POS - Static variable in enum com.actelion.research.calc.classification.ClassificationAttr
- POS_CHARGE - com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage.InteractionProbe
- POS_CHARGE - com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint.Functionality
- position - Variable in class com.actelion.research.util.ScaleLabel
- PositionConstraint - Class in com.actelion.research.chem.potentialenergy
- PositionConstraint(Conformer, int, double, double) - Constructor for class com.actelion.research.chem.potentialenergy.PositionConstraint
- POSITIVE - com.actelion.research.calc.classification.ClassificationAttr
- PotentialEnergyTerm - Interface in com.actelion.research.chem.potentialenergy
- pow(double) - Method in class com.actelion.research.calc.Matrix
- pow(double[], double) - Static method in class smile.math.Math
-
Raise each element of an array to a scalar power.
- pow(double, double) - Static method in class smile.math.Math
-
Returns the value of the first argument raised to the power of the second argument.
- power - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- PPGaussian - Class in com.actelion.research.chem.phesa.pharmacophore.pp
- PPGaussian(int, IPharmacophorePoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- PPGaussian(PPGaussian) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- ppGaussians - Variable in class com.actelion.research.chem.phesa.ShapeVolume
- PPNode - Class in com.actelion.research.chem.descriptor.flexophore
- PPNode() - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNode
- PPNode(PPNode) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNode
- PPNodeRGroup - Class in com.actelion.research.chem.descriptor.flexophore.entity
-
PPNodeStructure
- PPNodeRGroup() - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- PPNodeRGroup(PPNode, String) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- PPNodeSimilarity - Class in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
-
PPNodeSimilarity
- PPNodeSimilarity(int, int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
-
This constructor is used for parallel mode.
- PPNodeViz - Class in com.actelion.research.chem.descriptor.flexophore
-
Pharmacophore node with information about corresponding atoms in the molecule used for construction.
- PPNodeViz() - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- PPNodeViz(PPNode) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- PPNodeViz(PPNodeViz) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- PPNodeVizTriangle - Class in com.actelion.research.chem.descriptor.flexophore
- PPNodeVizTriangle(PPNodeViz, PPNodeViz, PPNodeViz) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- PPTriangle - Class in com.actelion.research.chem.phesa.pharmacophore
- PPTriangle(IPharmacophorePoint, IPharmacophorePoint, IPharmacophorePoint, double, double, double, Coordinates) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- PPTriangleCreator - Class in com.actelion.research.chem.phesa.pharmacophore
- PPTriangleMatcher - Class in com.actelion.research.chem.phesa.pharmacophore
- ppWeight - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- precisionAndRecall - Variable in class com.actelion.research.calc.regression.ModelError
- PrecisionAndRecall - Class in com.actelion.research.calc.classification
-
PrecisionAndRecall
- PrecisionAndRecall() - Constructor for class com.actelion.research.calc.classification.PrecisionAndRecall
- PrecisionAndRecall(int, int, int, int) - Constructor for class com.actelion.research.calc.classification.PrecisionAndRecall
- PRECOMPUTED - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- predict(double[]) - Method in class smile.clustering.KMeans
-
Cluster a new instance.
- predict(double[]) - Method in class smile.regression.NeuralNetwork
- predict(double[]) - Method in class smile.regression.RandomForest
- predict(double[]) - Method in class smile.regression.RegressionTree
- predict(int[]) - Method in class smile.regression.RegressionTree
-
Predicts the dependent variable of an instance with sparse binary features.
- predict(T) - Method in class smile.clustering.CLARANS
-
Cluster a new instance.
- predict(T) - Method in interface smile.clustering.Clustering
-
Cluster a new instance.
- predict(T) - Method in class smile.regression.GaussianProcessRegression
- predict(T) - Method in interface smile.regression.Regression
-
Predicts the dependent variable of an instance.
- predict(T[]) - Method in interface smile.regression.Regression
-
Predicts the dependent variables of an array of instances.
- predictAtomSequence(StereoMolecule, int, int[], int[]) - Static method in class com.actelion.research.chem.conf.BondRotationHelper
- PREFERENCES_KEY_USERID - Static variable in class com.actelion.research.gui.JLoginDialog
- PREFERRED - Static variable in interface com.actelion.research.gui.generic.GenericDialog
- preferredLayoutSize(Container) - Method in class com.actelion.research.gui.JScrollablePopupMenu.ScrollPopupMenuLayout
- preferredLayoutSize(Container) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- PREFIX_OUTPUT - Static variable in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
- Prefs - Class in com.actelion.research.util
- Prefs() - Constructor for class com.actelion.research.util.Prefs
- PREOPTIMIZED - Static variable in class com.actelion.research.chem.Molecule3D
- prepareForWrite(OutputStream, int, int) - Method in class com.actelion.research.util.AnimatedGIFWriter
-
This is intended to be called first when writing an animated GIF frame by frame.
- preProcess(Conformer) - Method in class com.actelion.research.chem.phesa.ShapeVolume
-
Move COM of the molecular volume to the origin of the lab-frame and orient molecules so that their principal moments of inertia coincide with the 3 axis of the coordinate system
- print(String) - Method in interface org.machinelearning.svm.libsvm.svm_print_interface
- PRINT_DEBUG_INDEXES - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- PRINT_ELIMINATION_RULES_WITH_STRUCTURES - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- PRINT_EXIT_REASON - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- PRINT_TORSION_AND_FRAGMENT_LIKELYHOODS - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- printAtomType(long) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- printAtomType(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- printContent(byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- printMutationList(ArrayList<Mutation>, boolean) - Method in class com.actelion.research.chem.Mutator
- printStatus() - Method in class com.actelion.research.gui.dock.TreeElement
- printStatus() - Method in class com.actelion.research.gui.dock.TreeFork
- printStatus() - Method in class com.actelion.research.gui.dock.TreeLeaf
- printStatus() - Method in class com.actelion.research.gui.dock.TreeRoot
- printTime(double) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- priori - Variable in class smile.stat.distribution.Mixture.Component
-
The priori probability of component.
- probA - Variable in class org.machinelearning.svm.libsvm.svm_model
- probability - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- probB - Variable in class org.machinelearning.svm.libsvm.svm_model
- Probe(Coordinates, IPharmacophorePoint.Functionality) - Constructor for class com.actelion.research.chem.docking.scoring.ProbeScanning.Probe
- ProbeScanning - Class in com.actelion.research.chem.docking.scoring
-
scans a receptor binding site for interaction points using a probe atom
- ProbeScanning(StereoMolecule, Set<Integer>, MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.ProbeScanning
- ProbeScanning.Probe - Class in com.actelion.research.chem.docking.scoring
- process(InputObjectFracDimCalc) - Method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- process(Pipeline<StereoMolecule>, int, boolean, boolean) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
- process(List<StereoMolecule>, File) - Method in class com.actelion.research.chem.mcs.ExhaustiveMCSGeneratorParallel
- processMolecule(StereoMolecule, TreeSet<String>) - Method in class com.actelion.research.chem.AtomTypeList
- PRODUCT_IDENTIFIER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- ProgressController - Interface in com.actelion.research.calc
- ProgressListener - Interface in com.actelion.research.calc
- PROOF_QUALITY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- properties - Variable in class com.actelion.research.calc.regression.ParameterRegressionMethod
- PropertyCalculator - Class in com.actelion.research.chem
- PropertyCalculator(StereoMolecule) - Constructor for class com.actelion.research.chem.PropertyCalculator
- PROTEIN_GROUP - Static variable in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- ProteinSynthesizer - Class in com.actelion.research.chem.io.pdb.parser
- ProteinSynthesizer() - Constructor for class com.actelion.research.chem.io.pdb.parser.ProteinSynthesizer
- pruningBarChanged(PruningBarEvent) - Method in interface com.actelion.research.gui.PruningBarListener
- PruningBarEvent - Class in com.actelion.research.gui
- PruningBarEvent(Object, float, float, boolean, int) - Constructor for class com.actelion.research.gui.PruningBarEvent
- PruningBarEvent(Object, float, float, boolean, int, int) - Constructor for class com.actelion.research.gui.PruningBarEvent
- PruningBarListener - Interface in com.actelion.research.gui
- PS_DASH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_DASHDOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_DASHDOTDOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_DOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_INSIDEFRAME - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_NULL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_SOLID - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PURITY_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- push(int) - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
-
Push an element on top of the queue
- push(int) - Method in class com.actelion.research.util.IntQueue
-
Push an element on top of the queue
- pushUndo() - Method in class com.actelion.research.share.gui.editor.Model
- putContent(Clipboard) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- putImage(Image) - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Deprecated.You may use ImageClipboardHandler.copyImage for consistency reasons
Q
- Q - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- q1(double[]) - Static method in class smile.math.Math
-
Find the first quantile (p = 1/4) of an array of type double.
- q1(double[]) - Static method in class smile.sort.QuickSelect
-
Find the first quantile (p = 1/4) of an array of type double.
- q1(float[]) - Static method in class smile.math.Math
-
Find the first quantile (p = 1/4) of an array of type float.
- q1(float[]) - Static method in class smile.sort.QuickSelect
-
Find the first quantile (p = 1/4) of an array of type float.
- q1(int[]) - Static method in class smile.math.Math
-
Find the first quantile (p = 1/4) of an array of type int.
- q1(int[]) - Static method in class smile.sort.QuickSelect
-
Find the first quantile (p = 1/4) of an array of type integer.
- q1(T[]) - Static method in class smile.math.Math
-
Find the first quantile (p = 1/4) of an array of type double.
- q1(T[]) - Static method in class smile.sort.QuickSelect
-
Find the first quantile (p = 1/4) of an array of type double.
- q3(double[]) - Static method in class smile.math.Math
-
Find the third quantile (p = 3/4) of an array of type double.
- q3(double[]) - Static method in class smile.sort.QuickSelect
-
Find the third quantile (p = 3/4) of an array of type double.
- q3(float[]) - Static method in class smile.math.Math
-
Find the third quantile (p = 3/4) of an array of type float.
- q3(float[]) - Static method in class smile.sort.QuickSelect
-
Find the third quantile (p = 3/4) of an array of type float.
- q3(int[]) - Static method in class smile.math.Math
-
Find the third quantile (p = 3/4) of an array of type int.
- q3(int[]) - Static method in class smile.sort.QuickSelect
-
Find the third quantile (p = 3/4) of an array of type integer.
- q3(T[]) - Static method in class smile.math.Math
-
Find the third quantile (p = 3/4) of an array of type double.
- q3(T[]) - Static method in class smile.sort.QuickSelect
-
Find the third quantile (p = 3/4) of an array of type double.
- qr - Variable in class smile.math.matrix.QR
-
Array for internal storage of decomposition.
- qr() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the QR decomposition.
- qr() - Method in class smile.math.matrix.JMatrix
-
QR Decomposition is computed by Householder reflections.
- qr(boolean) - Method in interface smile.math.matrix.DenseMatrix
-
Returns the QR decomposition.
- QR - Class in smile.math.matrix
-
For an m-by-n matrix A with m ≥ n, the QR decomposition is an m-by-n orthogonal matrix Q and an n-by-n upper triangular matrix R such that A = Q*R.
- QR(DenseMatrix, double[], boolean) - Constructor for class smile.math.matrix.QR
-
Constructor.
- qualifiesAsAmideTypeBond(int) - Method in class com.actelion.research.chem.RingCollection
-
Checks, whether this bond may contribute pi-electrons from an amide-resonance to an aromatic ring.
- qualifiesAsAromatic(int) - Static method in class com.actelion.research.chem.RingCollection
- quantile(double) - Method in interface smile.stat.distribution.Distribution
-
The quantile, the probability to the left of quantile is p.
- quantile(double) - Method in class smile.stat.distribution.GaussianDistribution
-
The quantile, the probability to the left of quantile(p) is p.
- quantile(double) - Method in class smile.stat.distribution.Mixture
- quantile(double, double, double) - Method in class smile.stat.distribution.AbstractDistribution
-
Inversion of CDF by bisection numeric root finding of "cdf(x) = p" for continuous distribution.
- quantile(double, double, double, double) - Method in class smile.stat.distribution.AbstractDistribution
-
Inversion of CDF by bisection numeric root finding of "cdf(x) = p" for continuous distribution.
- Quaternion - Class in com.actelion.research.chem.alignment3d.transformation
- Quaternion(double, double, double, double) - Constructor for class com.actelion.research.chem.alignment3d.transformation.Quaternion
- Quaternion(Coordinates, double) - Constructor for class com.actelion.research.chem.alignment3d.transformation.Quaternion
- quickExp(double) - Method in class com.actelion.research.chem.phesa.QuickMathCalculator
- QuickMathCalculator - Class in com.actelion.research.chem.phesa
- QuickSelect - Class in smile.sort
-
Selection is asking for the k th smallest element out of n elements.
- QuickSort - Class in smile.sort
-
Quicksort is a well-known sorting algorithm that, on average, makes O(n log n) comparisons to sort n items.
R
- R - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- r_star(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'R*' which is derived from the table.
- r0 - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
- r0(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
-
Returns 'r0' the ideal bond length at a given index in the Bndk table.
- r0(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
-
Returns the 'r0' value at the given index from the Bond table.
- r0(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
-
Returns the 'r0' (or covRad) parameter from the table given an index.
- r0(MMFFMolecule, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
-
Returns 'r0' given a molecule and two atoms in that molecule that form a bond.
- r0i - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- r0k - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- R2_BLACK - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_COPYPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MASKNOTPENNOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MASKPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MASKPENNOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MERGENOTPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MERGEPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MERGEPENNOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOTCOPYPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOTMASKPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOTMERGEPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOTXORPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_WHITE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_XORPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- RAD2DEG - Static variable in class com.actelion.research.chem.forcefield.mmff.Constants
- RadialBasisFunction - Interface in smile.math.rbf
-
A radial basis function (RBF) is a real-valued function whose value depends only on the distance from the origin, so that φ(x)=φ(||x||); or alternatively on the distance from some other point c, called a center, so that φ(x,c)=φ(||x-c||).
- RADIX - Static variable in class smile.math.Math
-
The base of the exponent of the double type.
- rand - Static variable in class com.actelion.research.calc.regression.svm.svm
- rand - Static variable in class org.machinelearning.svm.libsvm.svm
- rand() - Method in interface smile.stat.distribution.Distribution
-
Generates a random number following this distribution.
- rand() - Method in class smile.stat.distribution.GaussianDistribution
-
Uses the Box-Muller algorithm to transform Random.random()'s into Gaussian deviates.
- rand() - Method in class smile.stat.distribution.Mixture
- randInverseCDF() - Method in class smile.stat.distribution.GaussianDistribution
-
Uses Inverse CDF method to generate a Gaussian deviate.
- randn(int, int) - Static method in interface smile.math.matrix.Matrix
-
Returns a random matrix of standard normal distributed values with given mean and standard dev.
- randn(int, int, double, double) - Static method in interface smile.math.matrix.Matrix
-
Returns a random matrix of normal distributed values with given mean and standard dev.
- random() - Static method in class com.actelion.research.chem.Coordinates
- random() - Static method in class smile.math.Math
-
Generate a random number in [0, 1).
- random(double[]) - Static method in class smile.math.Math
-
Given a set of n probabilities, generate a random number in [0, n).
- random(double[], int) - Static method in class smile.math.Math
-
Given a set of m probabilities, draw with replacement a set of n random number in [0, m).
- random(double, double) - Static method in class smile.math.Math
-
Generate a uniform random number in the range [lo, hi).
- random(double, double, int) - Static method in class smile.math.Math
-
Generate n uniform random numbers in the range [lo, hi).
- random(int) - Static method in class smile.math.Math
-
Generate n random numbers in [0, 1).
- Random - Class in smile.math
-
This is a high quality random number generator as a replacement of the standard Random class of Java system.
- Random() - Constructor for class smile.math.Random
-
Initialize with default random number generator engine.
- Random(long) - Constructor for class smile.math.Random
-
Initialize with given seed for default random number generator engine.
- RANDOM - Static variable in class com.actelion.research.util.datamodel.ByteVec
- RandomForest - Class in smile.regression
-
Random forest for regression.
- RandomForest(double[][], double[], int) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(double[][], double[], int, int, int, int) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(Attribute[], double[][], double[], int) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(Attribute[], double[][], double[], int, int) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(Attribute[], double[][], double[], int, int, int) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(Attribute[], double[][], double[], int, int, int, int) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(Attribute[], double[][], double[], int, int, int, int, double) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(Attribute[], double[][], double[], int, int, int, int, double, double[]) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(AttributeDataset, int) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(AttributeDataset, int, int) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(AttributeDataset, int, int, int) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest(AttributeDataset, int, int, int, int, double, double[]) - Constructor for class smile.regression.RandomForest
-
Constructor.
- RandomForest.Trainer - Class in smile.regression
-
Trainer for random forest.
- RandomForestRegression - Class in com.actelion.research.calc.regression.randomforest
-
RandomForestRegression
- RandomForestRegression() - Constructor for class com.actelion.research.calc.regression.randomforest.RandomForestRegression
- RandomForestRegression(ParameterRandomForest) - Constructor for class com.actelion.research.calc.regression.randomforest.RandomForestRegression
- randomInt(int) - Static method in class smile.math.Math
-
Returns a random integer in [0, n).
- randomInt(int, int) - Static method in class smile.math.Math
-
Returns a random integer in [lo, hi).
- RandomNumberGenerator - Interface in smile.math.random
-
Random number generator interface.
- randomPerturbation(Random) - Method in class com.actelion.research.chem.docking.LigandPose
- randomVectorInSphere(Random) - Static method in class com.actelion.research.chem.docking.DockingUtils
- range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianLong
- range() - Method in class smile.math.matrix.SVD
-
Returns a matrix of which columns give an orthonormal basis for the range space.
- range(int, int) - Method in class smile.data.AttributeDataset
-
Returns the rows in the given range [from, to).
- RANGE_HISTOGRAM - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
-
Range histogram in Angstrom.
- RangeStatistics() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHistHelper.RangeStatistics
- rank() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Effective numerical matrix rank
- rank() - Method in class smile.math.matrix.SVD
-
Returns the effective numerical matrix rank.
- RBF - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- rbind(double[]...) - Static method in class smile.math.Math
-
Take a sequence of vector arguments and combine by rows.
- rbind(float[]...) - Static method in class smile.math.Math
-
Take a sequence of vector arguments and combine by rows.
- rbind(int[]...) - Static method in class smile.math.Math
-
Take a sequence of vector arguments and combine by rows.
- rbind(String[]...) - Static method in class smile.math.Math
-
Take a sequence of vector arguments and combine by rows.
- RDFileParser - Class in com.actelion.research.chem.io
-
Quick and dirty RD-File parser that reads non-hierarchical RD-Files.
- RDFileParser(File) - Constructor for class com.actelion.research.chem.io.RDFileParser
- RDFileParser(Reader) - Constructor for class com.actelion.research.chem.io.RDFileParser
- RDFileParser(String) - Constructor for class com.actelion.research.chem.io.RDFileParser
- re() - Method in class smile.math.Complex
-
Returns the real part.
- react(List<StereoMolecule>) - Static method in class com.actelion.research.chem.chemicalspaces.synthon.SynthonReactor
- Reaction - Class in com.actelion.research.chem.reaction
- Reaction() - Constructor for class com.actelion.research.chem.reaction.Reaction
- Reaction(Reaction) - Constructor for class com.actelion.research.chem.reaction.Reaction
- Reaction(StereoMolecule[], int) - Constructor for class com.actelion.research.chem.reaction.Reaction
- Reaction(String) - Constructor for class com.actelion.research.chem.reaction.Reaction
- REACTION_CENTER_LONG_COUNT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- REACTION_CENTER_WEIGHT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- REACTION_FLAVORS - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- REACTION_TYPE_NOMOLS - Static variable in class com.actelion.research.chem.ChemistryHelper
- REACTION_TYPE_NOPRODUCTS - Static variable in class com.actelion.research.chem.ChemistryHelper
- REACTION_TYPE_NORMAL - Static variable in class com.actelion.research.chem.ChemistryHelper
- REACTION_TYPE_REACTANTS - Static variable in class com.actelion.research.chem.ChemistryHelper
- ReactionArrow - Class in com.actelion.research.chem.reaction
- ReactionArrow() - Constructor for class com.actelion.research.chem.reaction.ReactionArrow
- ReactionArrow(String) - Constructor for class com.actelion.research.chem.reaction.ReactionArrow
- ReactionCenterMapper - Class in com.actelion.research.chem.reaction.mapping
-
This is a helper class for the RuleEnhancedMapper, which expects most of a reaction's atoms to be already mapped using an MCS or similarity guided graph-matching approach.
- ReactionCenterMapper(StereoMolecule, StereoMolecule, int[], int[], int) - Constructor for class com.actelion.research.chem.reaction.mapping.ReactionCenterMapper
- ReactionClassifier - Class in com.actelion.research.chem.reaction
- ReactionClassifier() - Constructor for class com.actelion.research.chem.reaction.ReactionClassifier
- ReactionDragAdapter - Class in com.actelion.research.gui.dnd
- ReactionDragAdapter(Component) - Constructor for class com.actelion.research.gui.dnd.ReactionDragAdapter
- ReactionDropAdapter - Class in com.actelion.research.gui.dnd
- ReactionDropAdapter() - Constructor for class com.actelion.research.gui.dnd.ReactionDropAdapter
- ReactionEncoder - Class in com.actelion.research.chem.reaction
- ReactionSearch - Class in com.actelion.research.chem.reaction
- ReactionSearch(ReactionSearchSpecification, ReactionSearchDataSource, StructureSearchController, ProgressController) - Constructor for class com.actelion.research.chem.reaction.ReactionSearch
-
This contructs a new structure search, which upon calling start() runs a multithreaded structure search on the structure rows provided by dataSource.
- ReactionSearchDataSource - Interface in com.actelion.research.chem.reaction
- ReactionSearchSpecification - Class in com.actelion.research.chem.reaction
- ReactionSearchSpecification(int, String[], long[][], long[][], long[][]) - Constructor for class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Creates a complete specification for a reaction substructure search with one or more query generic reactions.
- ReactionSearchSpecification(int, String[], long[][], long[][], long[][], float, float) - Constructor for class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Creates a complete specification for a reaction similarity search with one or more query reactions.
- ReactionSearchSpecification(String[], long[][]) - Constructor for class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Creates a complete specification for a retron search with one or more query retron substructures.
- ReactionTransferable - Class in com.actelion.research.gui.dnd
- ReactionTransferable(Reaction) - Constructor for class com.actelion.research.gui.dnd.ReactionTransferable
- Reactor - Class in com.actelion.research.chem.reaction
- Reactor(Reaction) - Constructor for class com.actelion.research.chem.reaction.Reactor
-
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
- Reactor(Reaction, boolean) - Constructor for class com.actelion.research.chem.reaction.Reactor
-
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
- Reactor(Reaction, boolean, boolean, int, boolean) - Constructor for class com.actelion.research.chem.reaction.Reactor
-
Deprecated.
- Reactor(Reaction, int, int) - Constructor for class com.actelion.research.chem.reaction.Reactor
-
Constructs a Reactor that is able to build products from a generic reaction (transformation) and a list of real world reactants.
- read() - Method in class com.actelion.research.util.Base64.InputStream
-
Reads enough of the input stream to convert to/from Base64 and returns the next byte.
- read() - Method in class com.actelion.research.util.BinaryDecoder
- read(byte[], int, int) - Method in class com.actelion.research.util.Base64.InputStream
-
Calls
Base64.InputStream.read()
repeatedly until the end of stream is reached or len bytes are read. - read(byte[], int, int) - Method in class com.actelion.research.util.LittleEndianDataInputStream
- read(BufferedReader) - Method in class com.actelion.research.calc.BinarySOM
- read(BufferedReader) - Method in class com.actelion.research.calc.SelfOrganizedMap
- read(BufferedReader) - Method in class com.actelion.research.calc.VectorSOM
- read(File) - Static method in class com.actelion.research.calc.MatrixFunctions
- read(File) - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- read(File) - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- read(File) - Static method in class com.actelion.research.util.datamodel.IntVec
- read(File) - Static method in class com.actelion.research.util.datamodel.ScorePoint
- read(File) - Static method in class com.actelion.research.util.IO
- read(File, boolean) - Static method in class com.actelion.research.calc.MatrixFunctions
- read(InputStream) - Static method in class com.actelion.research.calc.MatrixFunctions
- read(InputStream) - Static method in class com.actelion.research.chem.mcs.ListWithIntVec
- read(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.BitArray128
- read(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- read(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- read(InputStream) - Static method in class com.actelion.research.util.datamodel.IntArray
- read(InputStream) - Static method in class com.actelion.research.util.datamodel.IntVec
- read(InputStream) - Static method in class com.actelion.research.util.IO
- read(InputStream, boolean) - Static method in class com.actelion.research.calc.MatrixFunctions
- read(String) - Static method in class com.actelion.research.calc.MatrixFunctions
- read(String) - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- read(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- read(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- read(String) - Static method in class com.actelion.research.util.datamodel.IntArray
- read(String) - Method in class com.actelion.research.util.datamodel.IntVec
- readAsLineBase64Encoded(String) - Static method in class com.actelion.research.calc.MatrixFunctions
- readBetweenTags(String, String, String, Vector<String>) - Static method in class com.actelion.research.util.IO
- readBitStringDense(File) - Static method in class com.actelion.research.util.datamodel.IntVec
- readBitStringDense(String) - Static method in class com.actelion.research.util.datamodel.IntVec
- readBoolean() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readByte() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readChar() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readContent(Clipboard) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- readCSV(File) - Static method in class com.actelion.research.calc.MatrixFunctions
- readDouble() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readDoubleArray(String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- readDoubleArray(String, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- readEncoded(String, String) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
- readFile(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Csv
-
Read a file at location 'path' and parse it as a CSV file.
- readFloat() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readFromFile() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- readFromTag(String, String, Vector<String>) - Static method in class com.actelion.research.util.IO
-
Reads all lines after a given tag and stores the lines as Strings in a vector object.
- readFully(byte[]) - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readFully(byte[], int, int) - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readIDCodesFromFile() - Method in class com.actelion.research.chem.io.CompoundFileHelper
- readIDCodesFromFile(File) - Method in class com.actelion.research.chem.io.CompoundFileHelper
-
Reads all compounds as idcode list from the given file.
- readIDCodesWithNamesFromFile(File, boolean) - Method in class com.actelion.research.chem.io.CompoundFileHelper
-
Reads all compounds as idcode list with identifiers from the given file.
- readInput(String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- readInt() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readIntArray(String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Separator is ','.
- readIntArray(String, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- readIntsFile(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Csv
-
A helper function that casts and returns a CSV file consisting entirely of ints on all rows and columns.
- readLine() - Method in class com.actelion.research.io.StringReadChannel
- readLine() - Method in class com.actelion.research.util.LittleEndianDataInputStream
-
Deprecated.
- readLine(InputStream) - Static method in class com.actelion.research.util.IO
- readLine(Reader) - Static method in class com.actelion.research.util.IO
- readLine(FileChannel) - Static method in class com.actelion.research.util.IO
- readLines2DoubleArray(File) - Static method in class com.actelion.research.util.IO
- readLines2IntArray(File) - Static method in class com.actelion.research.util.IO
-
Reads a file that contains one int per line.
- readLines2List(File) - Static method in class com.actelion.research.util.IO
- readLines2List(InputStream) - Static method in class com.actelion.research.util.IO
-
The stream is not closed.
- readLines2List(List<File>) - Static method in class com.actelion.research.util.IO
- readListIntger(File) - Static method in class com.actelion.research.util.IO
- readLong() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readNodes(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
-
reads a MolDistHist from the toString() method.
- readSerialized(File) - Static method in class com.actelion.research.calc.Matrix
- readShort() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readStructuresFromFile(boolean) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- readStructuresFromFile(File, boolean) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- readUnsignedByte() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readUnsignedShort() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readUTF() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readUTF(DataInput) - Static method in class com.actelion.research.util.LittleEndianDataInputStream
- readXMLElement(Element) - Static method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- readXMLElement(Element) - Static method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- readXMLElement(Element) - Static method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- realize() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
-
Resizes the node array to the needed length.
- realize() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Canonizes the
MolDistHistViz
Must be called after changes in the nodes or distance histograms. - realize() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
May be called after finishing adding new interaction types.
- recalculateCoordPPPoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Recalculates the coordinates off the pharmacophore nodes.
- recentException - Variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- receptorConf - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- receycle(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- reciprocal() - Method in class smile.math.Complex
-
Returns the reciprocal.
- rect - Variable in class com.actelion.research.share.gui.Arrow
- rectangle(int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- rectangle(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- RED - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- redistribute() - Method in class com.actelion.research.gui.dock.JDockingPanel
- reduce(List<Integer>) - Method in class com.actelion.research.util.datamodel.IntVec
-
Removes all values with no corresponding index in the list.
- reduce(Vector<Integer>) - Method in class com.actelion.research.util.datamodel.ByteVec
- reduce(Vector<Integer>) - Method in class com.actelion.research.util.DoubleVec
- referenceVectorToString(int, int) - Method in class com.actelion.research.calc.BinarySOM
- referenceVectorToString(int, int) - Method in class com.actelion.research.calc.SelfOrganizedMap
- referenceVectorToString(int, int) - Method in class com.actelion.research.calc.VectorSOM
- refineNativePose(double, double[]) - Method in class com.actelion.research.chem.docking.DockingEngine
-
the parameter d defines how much the atoms are allowed to move from their original position
- regenerateClusterNos() - Method in class com.actelion.research.chem.Clusterer
-
Renumber cluster numbers starting at 1 to eliminate unused numbers.
- REGEX_FILE_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- REGEX_META_CHARACTERS - Static variable in class com.actelion.research.util.StringFunctions
- registerAtomHighlightCallback(Model.AtomHighlightCallback) - Method in class com.actelion.research.share.gui.editor.Model
- registerBondHighlightCallback(Model.BondHighlightCallback) - Method in class com.actelion.research.share.gui.editor.Model
- registerDragEvent() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- regress() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- Regression<T> - Interface in smile.regression
-
Regression analysis includes any techniques for modeling and analyzing the relationship between a dependent variable and one or more independent variables.
- regressionEpsilonSVR() - Static method in class com.actelion.research.calc.regression.svm.SVMParameterHelper
-
Regression epsilon-SVR Degree set to trigger analytical parameter determination in createModel(....)
- RegressionMeasure - Interface in smile.validation
-
An abstract interface to measure the regression performance.
- RegressionMethodContainer - Class in com.actelion.research.calc.regression
-
RegressionMethodContainer
- RegressionMethodContainer() - Constructor for class com.actelion.research.calc.regression.RegressionMethodContainer
- RegressionModelCalculatorOptimumFactors - Class in com.actelion.research.calc.regression.linear.pls
-
RegressionModelCalculatorOptimumFactors
- RegressionModelCalculatorOptimumFactors() - Constructor for class com.actelion.research.calc.regression.linear.pls.RegressionModelCalculatorOptimumFactors
- regressionNuSVR(double) - Static method in class com.actelion.research.calc.regression.svm.SVMParameterHelper
-
Regression nu-SVR
- RegressionTrainer<T> - Class in smile.regression
-
Abstract regression model trainer.
- RegressionTrainer() - Constructor for class smile.regression.RegressionTrainer
-
Constructor.
- RegressionTrainer(Attribute[]) - Constructor for class smile.regression.RegressionTrainer
-
Constructor.
- RegressionTree - Class in smile.regression
-
Decision tree for regression.
- RegressionTree(double[][], double[], int) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(double[][], double[], int, int) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(int, int[][], double[], int) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(int, int[][], double[], int, int) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(int, int[][], double[], int, int, int[], RegressionTree.NodeOutput) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(Attribute[], double[][], double[], int) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(Attribute[], double[][], double[], int, int) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(Attribute[], double[][], double[], int, int, int, int[][], int[], RegressionTree.NodeOutput) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(Attribute[], double[][], double[], int, int, int, int[][], int[], RegressionTree.NodeOutput, double[]) - Constructor for class smile.regression.RegressionTree
- RegressionTree(AttributeDataset, int) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(AttributeDataset, int, int) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(AttributeDataset, int, int, int, int[][], int[], RegressionTree.NodeOutput) - Constructor for class smile.regression.RegressionTree
-
Constructor.
- RegressionTree(AttributeDataset, int, int, int, int[][], int[], RegressionTree.NodeOutput, double[]) - Constructor for class smile.regression.RegressionTree
- RegressionTree.NodeOutput - Interface in smile.regression
-
An interface to calculate node output.
- RegressionTree.Trainer - Class in smile.regression
-
Trainer for regression tree.
- rejection(double, double, double) - Method in class smile.stat.distribution.AbstractDistribution
-
Use the rejection technique to draw a sample from the given distribution.
- rel - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- relocateView(String, String, int, float) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
May be overriden to catch user initiated drag&drop
- RemarkParser - Class in com.actelion.research.chem.io.pdb.parser
-
RemarkParser
- RemarkParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.RemarkParser
- remove(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- remove(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- remove(int) - Method in class com.actelion.research.gui.JScrollableMenu
- remove(int) - Method in class com.actelion.research.gui.JScrollablePopupMenu
- remove(int) - Method in class com.actelion.research.util.hash.HashSetInt
- remove(int) - Method in class com.actelion.research.util.SortedList
- remove(int) - Method in class smile.data.Dataset
-
Removes the element at the specified position in this dataset.
- remove(int) - Method in class smile.math.SparseArray
-
Removes an entry.
- remove(Component) - Method in class com.actelion.research.gui.JScrollableMenu
- remove(Point2D) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- remove(Point2D) - Method in class com.actelion.research.share.gui.Polygon
- remove(String...) - Method in class smile.data.AttributeDataset
-
Returns a new dataset without given columns.
- remove(JComponent) - Method in class com.actelion.research.gui.JMultiPanelView
- remove(JMenuItem) - Method in class com.actelion.research.gui.JScrollableMenu
- removeAll() - Method in class com.actelion.research.gui.JScrollableMenu
- removeAll() - Method in class com.actelion.research.util.SortedList
- removeAllAtomsWithoutNeighbours(Molecule3D) - Static method in class com.actelion.research.chem.Molecule3DFunctions
- removeAllItems() - Method in interface com.actelion.research.gui.generic.GenericComboBox
- removeAllItems() - Method in class com.actelion.research.gui.swing.SwingComboBox
- removeAllStrings() - Method in class com.actelion.research.chem.SortedStringList
- removeAtomColors() - Method in class com.actelion.research.chem.Molecule
- removeAtomCustomLabels() - Method in class com.actelion.research.chem.Molecule
-
This removes all custom labels from the atoms.
- removeAtomMapping(boolean) - Method in class com.actelion.research.chem.Molecule
- removeAtomMapping(boolean) - Method in class com.actelion.research.chem.reaction.Reaction
- removeAtomMarkers() - Method in class com.actelion.research.chem.Molecule
- removeAtomSelection() - Method in class com.actelion.research.chem.Molecule
- removeBondHiliting() - Method in class com.actelion.research.chem.Molecule
- removeCatalysts() - Method in class com.actelion.research.chem.reaction.Reaction
- removeChangeListener(IChangeListener) - Method in class com.actelion.research.share.gui.editor.Model
- removeCharacter(StringBuilder, char) - Static method in class com.actelion.research.util.StringFunctions
- removeCharacter(String, char) - Static method in class com.actelion.research.util.StringFunctions
- removeCol(int) - Method in class com.actelion.research.calc.Matrix
- removeCompoundCollectionListener(CompoundCollectionListener) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- removeCompoundCollectionListener(CompoundCollectionListener) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- removeConstraints() - Method in class com.actelion.research.chem.docking.LigandPose
- removeConstraints() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- removeContent(Dockable, boolean) - Method in class com.actelion.research.gui.dock.TreeLeaf
-
undockes and removes a Dockable from the docking tree and from the component tree
- removeDescriptors() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- removeDescriptors() - Method in class com.actelion.research.chem.StructureSearchSpecification
- removeDividerChangeLister(DividerChangeListener) - Method in class com.actelion.research.gui.dock.JDockingPanel
- removeDoubletsInt(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- removeDoubletsIntOrderIndepend(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Removes arrays which contains identical integer.
- removeDrawingObjects() - Method in class com.actelion.research.chem.reaction.Reaction
- removeExplicitHydrogens() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Removes all plain explicit hydrogens atoms from the molecule, converting them effectively to implicit ones.
- removeExplicitHydrogens(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Removes all plain explicit hydrogens atoms from the molecule, converting them effectively to implicit ones.
- removeExtension(String) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
-
Provided that filePath has a recognized extension, then the extension is removed.
- removeInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- removeLast() - Method in class com.actelion.research.util.datamodel.IntArray
- removeLastPoint() - Method in class com.actelion.research.gui.generic.GenericPolygon
- removeLayoutComponent(Component) - Method in class com.actelion.research.gui.JScrollablePopupMenu.ScrollPopupMenuLayout
- removeLayoutComponent(Component) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- removeLigand(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeListener(GenericKeyListener) - Method in class com.actelion.research.gui.swing.SwingKeyHandler
- removeListener(GenericMouseListener) - Method in class com.actelion.research.gui.swing.SwingMouseHandler
- removeLonePairs(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeMapping(Reaction) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
- removeMappingNo(int) - Method in class com.actelion.research.chem.Molecule
- removeNode(PharmacophoreNode) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- removePathAndExtension(String) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
-
Provided that fileName has a leading file path, then path and separator are removed.
- removeProgressListener(ProgressListener) - Method in class com.actelion.research.calc.DataProcessor
- removePruningBarListener(PruningBarListener) - Method in class com.actelion.research.gui.JPruningBar
- removeQueryFeatures() - Method in class com.actelion.research.chem.Molecule
-
Removes any query features from the molecule
- removeRings() - Method in class com.actelion.research.chem.phesa.ShapeVolume
- removeStructureListener(StructureListener) - Method in class com.actelion.research.gui.JChemistryView
- removeStructureListener(StructureListener) - Method in class com.actelion.research.gui.JStructureView
- removeSubstructureFromMolecule(StereoMolecule, StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- removeSubStructures(List<StereoMolecule>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Removes all molecules that are a substructure of one of the molecules in the input list.
- removeSubstructuresFromMolecule(StereoMolecule, List<StereoMolecule>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Deletes the substructures, if found, in the molecule.
- removeValidationListener(IValidationListener) - Method in class com.actelion.research.share.gui.editor.Model
- removeValue(int) - Method in class com.actelion.research.util.datamodel.IntArray
-
Computational expensive operation!
- removeWater(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeWater(Molecule3D, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeWaterSalts(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeWildcards(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- removeWithLeaf(TreeLeaf) - Method in class com.actelion.research.gui.dock.TreeContainer
- removeWithLeaf(TreeLeaf) - Method in class com.actelion.research.gui.dock.TreeFork
- removeWithLeaf(TreeLeaf) - Method in class com.actelion.research.gui.dock.TreeRoot
- renumberESRGroups(int) - Method in class com.actelion.research.chem.Molecule
-
For the given ESR type (AND or OR) renumbers all group indexes starting from 0.
- reorderAtoms() - Method in class com.actelion.research.chem.Molecule3D
-
Reorganizes atom indexes, so that moveable atoms are first
- repaint() - Method in interface com.actelion.research.gui.generic.GenericCanvas
- repairMolecule3D(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingUtils
- replaceAtoms(ExtendedMolecule[], int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- replaceAtoms(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- replaceChildElement(TreeElement, TreeElement) - Method in class com.actelion.research.gui.dock.TreeContainer
- replaceChildElement(TreeElement, TreeElement) - Method in class com.actelion.research.gui.dock.TreeFork
- replaceChildElement(TreeElement, TreeElement) - Method in class com.actelion.research.gui.dock.TreeRoot
- replaceLigand(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- replaceLigand(Molecule3D, Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Replaces the preoptimized ligand in mol
- replaceNaN(double) - Method in interface smile.math.matrix.DenseMatrix
-
Replaces NaN's with given value.
- replaceNaN(double) - Method in class smile.math.matrix.JMatrix
- REPTerm - Class in com.actelion.research.chem.docking.scoring.plp
-
repulsive term, see PLPTerm for reference
- reset() - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
- reset() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- reset() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- reset() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- reset() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- reset() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- reset() - Method in class com.actelion.research.gui.JPruningBar
-
Sets high and low values to max and min, respectively.
- reset() - Method in class com.actelion.research.util.datamodel.IntArray
- reset() - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
- reset() - Method in class com.actelion.research.util.graph.complete.ContainerMemory
- reset() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- reset() - Method in class com.actelion.research.util.Pipeline
-
Sets all to 0 and allDataIn to false..
- reset(int) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
-
Clears the hash map with the records that contain the given number of bits set.
- resetAllCounters() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- resetFragments(Reaction) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
- resetInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- resetInfoColor() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- resetInfoColor() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- Residue - Class in com.actelion.research.chem.io.pdb.parser
-
ModelGroupAtoms handles a group of atoms, e.g.
- Residue(List<AtomRecord>) - Constructor for class com.actelion.research.chem.io.pdb.parser.Residue
- resize(boolean[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(boolean[][], int, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(boolean[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(byte[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(double[][], int, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(double[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(int) - Method in class com.actelion.research.util.datamodel.IntVec
- resize(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(int[], int) - Static method in class com.actelion.research.util.datamodel.IntArray
- resize(int, int) - Method in class com.actelion.research.calc.Matrix
-
Resizes the matrix, the old data are written to the new matrix, if possible.
- resize(Object, int) - Static method in class com.actelion.research.util.ArrayUtils
-
Resize an array
- resize(String[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Resize an array of Object
- resolve(String) - Static method in class com.actelion.research.chem.name.StructureNameResolver
- resolveLocal(String) - Method in interface com.actelion.research.chem.name.IStructureNameResolver
-
Local and typically quick name resolution
- resolveLocal(String) - Static method in class com.actelion.research.chem.name.StructureNameResolver
-
If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name, i.e.
- resolveRemote(String) - Method in interface com.actelion.research.chem.name.IStructureNameResolver
-
Typically remote server based name resolution that requires a network round trip
- resolveRemote(String) - Static method in class com.actelion.research.chem.name.StructureNameResolver
-
If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name, i.e.
- resolveRemote(String[]) - Method in interface com.actelion.research.chem.name.IStructureNameResolver
-
Remote server based name resolution of multiple names packed into one network round trip
- resolveRemote(String[]) - Static method in class com.actelion.research.chem.name.StructureNameResolver
-
If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name list, i.e.
- RESOURCE_AAS_LABELED - Static variable in class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
- response - Variable in class smile.data.Dataset
-
The attribute property of response variable.
- response() - Method in class smile.data.Dataset
-
Returns the response attribute vector.
- RESPONSE_NOT_NOMINAL - Static variable in class smile.data.Dataset
- RESPONSE_NOT_NUMERIC - Static variable in class smile.data.Dataset
- responseAttribute() - Method in class smile.data.Dataset
-
Returns the attribute of the response variable.
- restore() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- restore() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- restoreState() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- restoreState() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- restrainedRelaxation(StereoMolecule, double) - Method in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- RESULT_EVALUATOR_BALANCED_R2_TRAIN_TEST - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- RESULT_EVALUATOR_MAXIMUM_R2_TEST - Static variable in class com.actelion.research.calc.regression.ConstantsRegressionMethods
- ResultFracDimCalc - Class in com.actelion.research.chem.properties.fractaldimension
-
ResultFracDimCalc
- ResultFracDimCalc(InputObjectFracDimCalc) - Constructor for class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- ResultFragmentsStatistic - Class in com.actelion.research.chem.properties.complexity
- ResultFragmentsStatistic(StereoMolecule, List<ModelExhaustiveStatistics>) - Constructor for class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- ResultObjective - Class in com.actelion.research.chem.properties.complexity
- ResultObjective() - Constructor for class com.actelion.research.chem.properties.complexity.ResultObjective
- resumeEncoding() - Method in class com.actelion.research.util.Base64.OutputStream
-
Resumes encoding of the stream.
- RETAIN_REACTANT_AND_PRODUCT_ORDER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- reTransform(Matrix, BoxCox) - Static method in class com.actelion.research.calc.BoxCox
- retrieveHighestValuesFrom2DArray(double[][], double[], int[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
- retrieveProtein() - Method in class com.actelion.research.chem.io.pdb.parser.ProteinSynthesizer
- reverse(byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- reverse(double[]) - Static method in class smile.math.Math
-
Reverses the order of the elements in the specified array.
- reverse(float[]) - Static method in class smile.math.Math
-
Reverses the order of the elements in the specified array.
- reverse(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- reverse(int[]) - Static method in class smile.math.Math
-
Reverses the order of the elements in the specified array.
- reverse(Object[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- reverse(T[]) - Static method in class smile.math.Math
-
Reverses the order of the elements in the specified array.
- RGROUPS - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- rho - Variable in class org.machinelearning.svm.libsvm.svm_model
- RIGHT - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- RIGID - Static variable in class com.actelion.research.chem.Molecule3D
- RigidFragment - Class in org.openmolecules.chem.conf.gen
- RigidFragment(int, int[], int[], int[], int[], Conformer[], double[]) - Constructor for class org.openmolecules.chem.conf.gen.RigidFragment
- RigidFragmentCache - Class in org.openmolecules.chem.conf.gen
-
This class implements a thread-save, concurrent cache of rigid fragments' 3D-atom-coordinates.
- RigidFragmentCache.CacheEntry - Class in org.openmolecules.chem.conf.gen
- RigidFragmentProvider - Class in org.openmolecules.chem.conf.gen
-
An instance of this class is used by any ConformerGenerator to hand out one or multiple 3D-coordinate sets for rigid fragments within a molecules.
- RigidFragmentProvider(long, RigidFragmentCache, boolean) - Constructor for class org.openmolecules.chem.conf.gen.RigidFragmentProvider
- rik2 - Variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
- RingBoolean - Enum in com.actelion.research.chem.forcefield.mmff
- RingCollection - Class in com.actelion.research.chem
- RingCollection(ExtendedMolecule, int) - Constructor for class com.actelion.research.chem.RingCollection
-
Generates the complete set of small rings, which don't contain metal atoms and have up to 7 members.
If mode includes LARGE_RINGS, then it determines for every atom and bond the size of the smallest ring, which they are a member of.
If mode includes AROMATICITY then every small ring is checked, whether it is aromatic. - RingCollection(ExtendedMolecule, int, int) - Constructor for class com.actelion.research.chem.RingCollection
-
Generates the complete set of small rings, which don't contain metal atoms and have up to 7 members.
If mode includes LARGE_RINGS, then it determines for every atom and bond the size of the smallest ring, which they are a member of.
If mode includes AROMATICITY then every small ring is checked, whether it is aromatic. - ringIsMMFFAromatic(int) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
-
Determine if a ring is aromatic according to MMFF criteria.
- ringIsMMFFAromatic(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Determine if a ring is aromatic according to MMFF criteria.
- rint(double) - Static method in class smile.math.Math
-
Returns the double value that is closest in value to the argument and is equal to a mathematical integer.
- RISK_NAME - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- RMSE - Class in smile.validation
-
Root mean squared error.
- RMSE() - Constructor for class smile.validation.RMSE
- rnorm(int, double, double) - Static method in class com.actelion.research.calc.MatrixFunctions
- root(DifferentiableFunction, double, double, double) - Static method in class smile.math.Math
-
Returns the root of a function whose derivative is available known to lie between x1 and x2 by Newton-Raphson method.
- root(DifferentiableFunction, double, double, double, int) - Static method in class smile.math.Math
-
Returns the root of a function whose derivative is available known to lie between x1 and x2 by Newton-Raphson method.
- root(Function, double, double, double) - Static method in class smile.math.Math
-
Returns the root of a function known to lie between x1 and x2 by Brent's method.
- root(Function, double, double, double, int) - Static method in class smile.math.Math
-
Returns the root of a function known to lie between x1 and x2 by Brent's method.
- RootAtomPairSource - Class in com.actelion.research.chem.reaction.mapping
- RootAtomPairSource(StereoMolecule, StereoMolecule, int[], int[]) - Constructor for class com.actelion.research.chem.reaction.mapping.RootAtomPairSource
- rot(long, long) - Static method in class com.actelion.research.util.BurtleHasher
- RotatableBond - Class in org.openmolecules.chem.conf.gen
-
A RotatableBond knows the two rigid fragments within a molecule that are connected by this bond.
- RotatableBond(StereoMolecule, int, int[], int[], int, RigidFragment[], Random) - Constructor for class org.openmolecules.chem.conf.gen.RotatableBond
- RotatableBond(StereoMolecule, int, int[], int[], int, RigidFragment[], Random, boolean) - Constructor for class org.openmolecules.chem.conf.gen.RotatableBond
- rotate(double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- rotate(double[][]) - Method in class com.actelion.research.chem.Coordinates
- rotate(double, double, double) - Method in class com.actelion.research.chem.coords.InventorFragment
- rotate(double, double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- rotate(Coordinates, double) - Method in class com.actelion.research.chem.Coordinates
- rotate180DegreeAroundAxis(PheSAAlignment.axis) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- rotate180DegreeAroundAxis(PheSAAlignment.axis) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- rotateAroundBond(int, double, Conformer, boolean) - Method in class com.actelion.research.chem.conf.BondRotationHelper
-
rotate torsion angle of a conformer
- rotateAtom(Conformer, int, int, Coordinates, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- rotateBond(Molecule3D, int, int, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Make sure the parity of mol match the one from ref, otherwise fix it.
- rotateC(double[][]) - Method in class com.actelion.research.chem.Coordinates
- rotateCoordsAroundAxis180(Coordinates, PheSAAlignment.axis) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateGaussian(List<? extends Gaussian3D>, double[][]) - Static method in class com.actelion.research.chem.phesa.ShapeVolume
- rotateGaussians180DegreeAroundAxis(List<? extends Gaussian3D>, PheSAAlignment.axis) - Static method in class com.actelion.research.chem.phesa.ShapeVolume
- rotateLigand(Molecule3D, double, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- rotateMol(Conformer, double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMol(Conformer, Quaternion, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMol(StereoMolecule, double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMol(StereoMolecule, Quaternion, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMolAroundAxis180(Conformer, PheSAAlignment.axis) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateShift(Matrix) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- rotateSmallerSide(int, double) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- rotateTo(Conformer, short) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
Rotate the smaller side of the molecule around this bond to reach the defined torsion angle.
- rotateToIndex(Conformer, int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
Rotate the smaller side of the molecule around this bond to reach the torsion angle defined by torsionIndex.
- Rotation - Class in com.actelion.research.chem.alignment3d.transformation
- Rotation() - Constructor for class com.actelion.research.chem.alignment3d.transformation.Rotation
- Rotation(double[][]) - Constructor for class com.actelion.research.chem.alignment3d.transformation.Rotation
- ROTATION - Static variable in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- RotationDerivatives - Class in com.actelion.research.chem.alignment3d.transformation
-
Rotation derivatives for rotations expressed by means of the exponential map http://www.cs.cmu.edu/~spiff/exp-map/ Grassi,98 --> we take the transpose because of different convention!
- RotationDerivatives(double[]) - Constructor for class com.actelion.research.chem.alignment3d.transformation.RotationDerivatives
- round(double) - Static method in class smile.math.Math
-
Returns the closest long to the argument.
- round(double, int) - Static method in class smile.math.Math
-
Round a double vale to given digits such as 10^n, where n is a positive or negative integer.
- round(float) - Static method in class smile.math.Math
-
Returns the closest int to the argument.
- ROUND_STYLE - Static variable in class smile.math.Math
-
Rounding style.
- roundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- roundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- row(int) - Static method in class com.actelion.research.chem.forcefield.mmff.PeriodicTable
-
Returns which row in the periodic table an atom with given atomic number is in.
- Row(double[]) - Constructor for class smile.data.AttributeDataset.Row
-
Constructor.
- Row(double[], double) - Constructor for class smile.data.AttributeDataset.Row
-
Constructor.
- Row(double[], double, double) - Constructor for class smile.data.AttributeDataset.Row
-
Constructor.
- row2Matrix(int, int) - Method in class com.actelion.research.calc.Matrix
- rowFromESRType(int) - Static method in class com.actelion.research.share.gui.editor.Model
- rowMax(double[][]) - Static method in class smile.math.Math
-
Returns the row maximum for a matrix.
- rowMeans() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the mean of each row for a matrix.
- rowMeans(double[][]) - Static method in class smile.math.Math
-
Returns the row means for a matrix.
- rowMin(double[][]) - Static method in class smile.math.Math
-
Returns the row minimum for a matrix.
- rowNumberClicked(int) - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- rowQualifies(int) - Method in interface com.actelion.research.chem.StructureSearchController
-
If the structure search specification is part of a broader criteria list, then this method determines, whether all other, i.e.
- rows() - Method in class com.actelion.research.calc.Matrix
- rowSds(double[][]) - Static method in class smile.math.Math
-
Returns the row standard deviations for a matrix.
- rowSums() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the sum of each row for a matrix.
- rowSums(double[][]) - Static method in class smile.math.Math
-
Returns the row sums for a matrix.
- rowtm(int) - Static method in class com.actelion.research.chem.forcefield.mmff.PeriodicTable
-
Returns which row in the periodic table an atom is in with transition metals having their row number multiplied by 10.
- rstar_ij - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- RULE_NAME - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_BINAP - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_DISTANCE - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_LINE - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_PLANE - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_STEREO - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_TORSION - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- run() - Method in class com.actelion.research.chem.mcs.RunBondVector2IdCode
- run() - Method in class com.actelion.research.gui.JProgressDialog
- run(IdentifiedObject<T>, List<IdentifiedObject<T>>) - Method in class com.actelion.research.calc.SimilarityMulticore
- run(Collection<? extends Callable<T>>) - Static method in class smile.util.MulticoreExecutor
-
Executes the given tasks serially or parallel depending on the number of cores of the system.
- run(List<IdentifiedObject<T>>) - Method in class com.actelion.research.calc.SimilarityMulticore
- run(List<IdentifiedObject<T>>, List<IdentifiedObject<T>>) - Method in class com.actelion.research.calc.SimilarityMulticore
- run_minimiser(int, double, double) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- RunBondVector2IdCode - Class in com.actelion.research.chem.mcs
- RunBondVector2IdCode(int, Pipeline<IBitArray>, Pipeline<FragmentDefinedByBondsIdCode>) - Constructor for class com.actelion.research.chem.mcs.RunBondVector2IdCode
- RXN_CODE_TAG - Static variable in class com.actelion.research.chem.io.RXNFileCreator
- RXN_CODE_TAG - Static variable in class com.actelion.research.chem.io.RXNFileV3Creator
- RXNFileCreator - Class in com.actelion.research.chem.io
- RXNFileCreator(Reaction) - Constructor for class com.actelion.research.chem.io.RXNFileCreator
- RXNFileCreator(Reaction, String) - Constructor for class com.actelion.research.chem.io.RXNFileCreator
- RXNFileParser - Class in com.actelion.research.chem.io
- RXNFileParser() - Constructor for class com.actelion.research.chem.io.RXNFileParser
- RXNFileV3Creator - Class in com.actelion.research.chem.io
- RXNFileV3Creator(Reaction) - Constructor for class com.actelion.research.chem.io.RXNFileV3Creator
- RXNFileV3Creator(Reaction, String) - Constructor for class com.actelion.research.chem.io.RXNFileV3Creator
S
- s - Variable in class smile.math.matrix.SVD
-
Array for internal storage of singular values.
- s(T, T) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
-
Function used in swapping variables in one line.
- s(T, T) - Static method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
- save() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- save() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- save(Molecule3D, Writer) - Method in class com.actelion.research.chem.io.AbstractParser
- save(Molecule3D, Writer) - Method in class com.actelion.research.chem.io.Mol2FileParser
- save(Molecule3D, String) - Method in class com.actelion.research.chem.io.AbstractParser
- save(List<Molecule3D>, int, Writer) - Method in class com.actelion.research.chem.io.Mol2FileParser
-
Writes also the partial charges
- save(List<Molecule3D>, Writer) - Method in class com.actelion.research.chem.io.AbstractParser
-
If not subclassed, save the files separately
- save(List<Molecule3D>, Writer) - Method in class com.actelion.research.chem.io.Mol2FileParser
- save(List<Molecule3D>, String) - Method in class com.actelion.research.chem.io.AbstractParser
- saveRXNFile(Reaction) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- sbmb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the SBMB type of an atom given its MMFF type.
- ScaffoldHelper - Class in com.actelion.research.chem
- ScaffoldHelper() - Constructor for class com.actelion.research.chem.ScaffoldHelper
- scalb(double, int) - Static method in class smile.math.Math
-
Returns d x 2scaleFactor rounded as if performed by a single correctly rounded floating-point multiply to a member of the double value set.
- scalb(float, int) - Static method in class smile.math.Math
-
Returns f x 2scaleFactor rounded as if performed by a single correctly rounded floating-point multiply to a member of the float value set.
- scale(double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- scale(double) - Method in class com.actelion.research.chem.Coordinates
- scale(double) - Method in class com.actelion.research.chem.TextDrawingObject
- scale(double[][]) - Static method in class smile.math.Math
-
Scales each column of a matrix to range [0, 1].
- scale(double[][], double, double) - Static method in class smile.math.Math
-
Scales each column of a matrix to range [lo, hi].
- scale(double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- scale(double, double[]) - Static method in class smile.math.Math
-
Scale each element of an array by a constant x = a * x.
- scale(double, double[], double[]) - Static method in class smile.math.Math
-
Scale each element of an array by a constant y = a * x.
- scale(float) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
This is a convenience method that scales the passed int value with getUIScaleFactor() and returns the rounded result.
- scale(float) - Method in class com.actelion.research.share.gui.Arrow
- scale(float) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- scale(float) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- scale(float, float) - Method in class com.actelion.research.share.gui.editor.Model
- scale(BufferedImage) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- SCALE - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- scaleC(double) - Method in class com.actelion.research.chem.Coordinates
- scaleCoords(double) - Method in class com.actelion.research.chem.Molecule
- ScaledEditorKit - Class in com.actelion.research.gui.hidpi
- ScaledEditorKit() - Constructor for class com.actelion.research.gui.hidpi.ScaledEditorKit
- ScaledHTML - Class in com.actelion.research.gui.hidpi
- ScaledHTML() - Constructor for class com.actelion.research.gui.hidpi.ScaledHTML
- ScaledStyleSheet - Class in com.actelion.research.gui.hidpi
- ScaledStyleSheet() - Constructor for class com.actelion.research.gui.hidpi.ScaledStyleSheet
- scaleInto(Reaction, double, double, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- scaleIntoF(Reaction, double, double, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- scaleIntoOld(Reaction, double, double, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- ScaleLabel - Class in com.actelion.research.util
-
Contains shown label, the relative position on the scale and the numerical value
- ScaleLabel(String, double, double) - Constructor for class com.actelion.research.util.ScaleLabel
-
Create an ScaleLabel object consisting of visible label, its relative position on the scale and the numerical value behind.
- ScaleLabelCreator - Class in com.actelion.research.util
- ScaleLabelCreator() - Constructor for class com.actelion.research.util.ScaleLabelCreator
- scaleRetinaAndUI(float) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
This is a convenience method that scales the passed int value with getUIScaleFactor() and with getRetinaScaleFactor() and returns the rounded result.
- Scaling - Class in com.actelion.research.chem.alignment3d.transformation
- Scaling(double) - Constructor for class com.actelion.research.chem.alignment3d.transformation.Scaling
- SCALING - Static variable in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- scoreMapping(int[]) - Method in class com.actelion.research.chem.reaction.mapping.MappingScorer
- ScorePoint - Class in com.actelion.research.util.datamodel
- ScorePoint() - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScorePoint(int, int) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScorePoint(int, int, double) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScorePoint(Point) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScorePoint(Point, double) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScoringTask - Class in com.actelion.research.chem.docking
- ScoringTask() - Constructor for class com.actelion.research.chem.docking.ScoringTask
- ScrollPaneAutoScrollerWhenDragging - Class in com.actelion.research.gui
- ScrollPaneAutoScrollerWhenDragging(JScrollPane, boolean) - Constructor for class com.actelion.research.gui.ScrollPaneAutoScrollerWhenDragging
- ScrollPopupMenuLayout() - Constructor for class com.actelion.research.gui.JScrollablePopupMenu.ScrollPopupMenuLayout
- sd() - Method in interface smile.stat.distribution.Distribution
-
The standard deviation of distribution.
- sd() - Method in class smile.stat.distribution.GaussianDistribution
- sd() - Method in class smile.stat.distribution.Mixture
- sd(double[]) - Static method in class smile.math.Math
-
Returns the standard deviation of an array.
- sd(float[]) - Static method in class smile.math.Math
-
Returns the standard deviation of an array.
- sd(int[]) - Static method in class smile.math.Math
-
Returns the standard deviation of an array.
- Sdf - Class in com.actelion.research.chem.forcefield.mmff
-
The Sdf class provides helper functions for dealing with the SDF file format.
- Sdf() - Constructor for class com.actelion.research.chem.forcefield.mmff.Sdf
- SDF_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- Sdf.OnMolecule - Interface in com.actelion.research.chem.forcefield.mmff
- SDFileMolecule - Class in com.actelion.research.chem
- SDFileMolecule() - Constructor for class com.actelion.research.chem.SDFileMolecule
- SDFileMolecule(Molecule) - Constructor for class com.actelion.research.chem.SDFileMolecule
- SDFileMolecule(SDFileMolecule) - Constructor for class com.actelion.research.chem.SDFileMolecule
- SDFileMoleculeDropAdapter - Class in com.actelion.research.gui.dnd
- SDFileMoleculeDropAdapter() - Constructor for class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- SDFileMoleculeTransferable - Class in com.actelion.research.gui.dnd
- SDFileMoleculeTransferable(StereoMolecule, StructureInfo) - Constructor for class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- SDFileParser - Class in com.actelion.research.chem.io
- SDFileParser(File) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(File, String[]) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(Reader) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(Reader, String[]) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(String) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(String, String[]) - Constructor for class com.actelion.research.chem.io.SDFileParser
- sdv - Variable in class com.actelion.research.calc.statistics.ModelStatisticsOverview
- SE_RESIZE - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- Search - Class in com.actelion.research.chem.forcefield.mmff
-
The search class provides binary searching on arrays.
- Search() - Constructor for class com.actelion.research.chem.forcefield.mmff.Search
- SEARCH_TYPE_NOT_SUPPORTED - Static variable in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
- SEARCH_TYPE_NOT_SUPPORTED - Static variable in interface com.actelion.research.chem.StructureSearchDataSource
- Searchable - Interface in com.actelion.research.chem.forcefield.mmff
-
Interface that must be implemented for array objects that can be searched by the binary search function.
- seed(double[][], int, ClusteringDistance) - Static method in class smile.clustering.PartitionClustering
-
Initialize cluster membership of input objects with KMeans++ algorithm.
- seed(Distance<T>, T[], T[], int[], double[]) - Static method in class smile.clustering.PartitionClustering
-
Initialize cluster membership of input objects with KMeans++ algorithm.
- SEED - Static variable in class com.actelion.research.chem.docking.LigandPose
- select(double[], int) - Static method in class smile.sort.QuickSelect
-
Given k in [0, n-1], returns an array value from arr such that k array values are less than or equal to the one returned.
- select(float[], int) - Static method in class smile.sort.QuickSelect
-
Given k in [0, n-1], returns an array value from arr such that k array values are less than or equal to the one returned.
- select(int[], int) - Static method in class smile.sort.QuickSelect
-
Given k in [0, n-1], returns an array value from arr such that k array values are less than or equal to the one returned.
- select(long[][], int) - Method in class com.actelion.research.chem.DiversitySelector
- select(T[], int) - Static method in class smile.sort.QuickSelect
-
Given k in [0, n-1], returns an array value from arr such that k array values are less than or equal to the one returned.
- selectDockable(Dockable) - Method in class com.actelion.research.gui.dock.JDockingPanel
- selectFileToOpen(String, int) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- selectFileToOpen(String, int) - Method in class com.actelion.research.gui.FileHelper
- selectFileToOpen(String, int, String) - Method in class com.actelion.research.gui.FileHelper
-
Shows a file-open-dialog, lets the user choose and returns the selected file.
- selectFileToSave(String, int, String) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- selectFileToSave(String, int, String) - Method in class com.actelion.research.gui.FileHelper
-
Shows a file-save-dialog, lets the user choose and return the file's path and name.
- selectFragmentByAtom(int) - Method in class com.actelion.research.share.gui.editor.Model
- SELECTION_COLOR - Static variable in class com.actelion.research.chem.AbstractDrawingObject
- SelectionAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/24/13 Time: 5:57 PM
- SelectionAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.SelectionAction
- selectionColor() - Static method in class com.actelion.research.gui.editor.GenericDrawArea
- selectionColor() - Static method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- selectObject(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- selectObject(int) - Method in class com.actelion.research.gui.wmf.WMF
- selectOption(String, String, String[]) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- selectOption(String, String, String[]) - Method in class com.actelion.research.gui.FileHelper
- Selector<T> - Interface in com.actelion.research.jfx.gui.misc
-
Created with IntelliJ IDEA.
- SelfOrganizedConformer - Class in org.openmolecules.chem.conf.so
- SelfOrganizedConformer(StereoMolecule) - Constructor for class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- SelfOrganizedMap - Class in com.actelion.research.calc
- SelfOrganizedMap() - Constructor for class com.actelion.research.calc.SelfOrganizedMap
-
Constructor to be used if SOM interna are read from a SOM file with read()
- SelfOrganizedMap(int, int, int) - Constructor for class com.actelion.research.calc.SelfOrganizedMap
- SEP - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
- SEP - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- SEP - Static variable in class com.actelion.research.util.IO
- SEP - Static variable in class com.actelion.research.util.StringFunctions
- SEP_LINE - Static variable in class com.actelion.research.util.ConstantsDWAR
- SEP_PARAMETER - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- SEP_TAG - Static variable in class com.actelion.research.util.CommandLineParser
- SEP_VALUE - Static variable in class com.actelion.research.util.ConstantsDWAR
- Separation - Class in com.actelion.research.chem.forcefield.mmff
-
The Separation class is an efficient storage of an adjacency matrix representing how many degrees of separation there are between any two atoms.
- Separation(MMFFMolecule) - Constructor for class com.actelion.research.chem.forcefield.mmff.Separation
-
Constructs a new separation table for a molecule.
- Separation.Relation - Enum in com.actelion.research.chem.forcefield.mmff
-
Relation class shows the relationship between two atoms A1 and A2.
- SEPARATOR_ATOMS - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- serializeCache(String, int) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
Writes for every distinct fragment: one idcode, multiple encoded coordinate sets, multiple conformer likelihoods
- serialVersionUID - Static variable in exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
- serialVersionUID - Static variable in class com.actelion.research.gui.editor.AtomLabelDialogBuilder
- serialVersionUID - Static variable in class com.actelion.research.gui.JAtomLabelDialog
-
Deprecated.
- set(boolean[], boolean) - Static method in class com.actelion.research.util.ArrayUtils
- set(byte) - Method in class com.actelion.research.util.datamodel.ByteVec
- set(byte[], byte) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
Flat copy from node into this.
- set(double) - Method in class com.actelion.research.calc.Matrix
- set(double) - Method in class com.actelion.research.util.DoubleVec
- set(double[]) - Method in class com.actelion.research.util.DoubleVec
- set(double[][]) - Method in class com.actelion.research.calc.Matrix
- set(double[][], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(double[], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(double, double) - Method in class com.actelion.research.util.datamodel.PointDouble
- set(double, double, double) - Method in class com.actelion.research.chem.Coordinates
- set(float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
- set(float[][], float) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(float[], float) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Don't forget to set the hash code!
- set(int[]) - Method in class com.actelion.research.util.DoubleVec
- set(int[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(int, byte) - Method in class com.actelion.research.util.datamodel.ByteVec
-
Hash value has to be recalculated!
- set(int, double) - Method in class com.actelion.research.util.DoubleVec
- set(int, double) - Method in class smile.math.SparseArray
-
Sets or add an entry.
- set(int, int) - Method in class com.actelion.research.util.datamodel.IntArray
- set(int, int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Don't forget to set the hash code!
- set(int, int, double) - Method in class com.actelion.research.calc.Matrix
- set(int, int, double) - Method in class com.actelion.research.util.DoubleVec
- set(int, int, double) - Method in interface smile.math.matrix.DenseMatrix
-
Set the entry value at row i and column j.
- set(int, int, double) - Method in class smile.math.matrix.JMatrix
- set(int, int, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- set(short[][], short) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(Matrix) - Method in class com.actelion.research.calc.Matrix
- set(Matrix, int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- set(Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Copies x,y,z from c to this
- set(ExtendedMolecule, int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- set(ExtendedMolecule, int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- set(ExtendedMolecule, int) - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- set(Molecule3D) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- set(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCS
-
mol should contain equal or more bonds than frag.
- set(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCSFast
- set(StereoMolecule, StereoMolecule, boolean[]) - Method in class com.actelion.research.chem.mcs.MCS
-
mol should contain equal or more bonds than frag.
- set(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
-
Don't forget to set the hash code!
- set(PointDouble) - Method in class com.actelion.research.util.datamodel.PointDouble
- set(String, String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- set(String, String, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- set(List<PPNodeViz>) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- set(T, T) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- setAccessory(Component) - Method in class com.actelion.research.gui.editor.SwingEditorDialog
- setAccessory(Component) - Method in class com.actelion.research.gui.JDrawDialog
-
Deprecated.
- setActivationFunction(NeuralNetwork.ActivationFunction) - Method in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- setActive(boolean) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- setActive(boolean) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- setAlignment(int, int) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Sets the Alignment attribute of the VerticalFlowLayout object
- setAllAtomFlag(int, boolean) - Method in class com.actelion.research.chem.Molecule3D
- setAllAtoms(int) - Method in class com.actelion.research.chem.Molecule
-
Low level method for constructing/modifying a molecule from scratch.
- setAllBonds(int) - Method in class com.actelion.research.chem.Molecule
-
Low level method for constructing/modifying a molecule from scratch.
- setAllDataIn() - Method in class com.actelion.research.util.Pipeline
- setAllDataIn(boolean) - Method in interface com.actelion.research.util.IPipeline
- setAllDataIn(boolean) - Method in class com.actelion.research.util.Pipeline
-
has to be set true or
wereAllDataFetched()
will never become true. - setAllowDropOrPasteWhenDisabled(boolean) - Method in class com.actelion.research.gui.JChemistryView
- setAllowFragmentStatusChangeOnPasteOrDrop(boolean) - Method in class com.actelion.research.gui.JStructureView
-
When fragment status change on drop is allowed then dropping a fragment (molecule) on a molecule (fragment) inverts the status of the view's chemical object.
- setAllowQueryFeatures(boolean) - Method in class com.actelion.research.gui.editor.GenericDrawArea
-
If set to false then any query features will be removed from the molecule and any functionality that allows to define atom- or bond-query features won't be available.
- setAllowQueryFeatures(boolean) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.If set to false then any query features will be removed from the molecule and any functionality that allows to define atom- or bond-query features won't be available.
- setAllowQueryFeatures(boolean) - Method in class com.actelion.research.gui.JEditableStructureView
- setAlternateBackground(boolean) - Method in class com.actelion.research.gui.table.ChemistryRenderPanel
- setAlternateRowBackground(boolean) - Method in class com.actelion.research.gui.table.ChemistryCellRenderer
- setAnisou(String) - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- setArea(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- setAromatic(boolean) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setArrIndexParentNodes(int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- setArrInnerLayerArchitecture(int[]) - Method in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- setArrNode(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- setAssignParitiesToNitrogen(boolean) - Method in class com.actelion.research.chem.StereoMolecule
-
This is a policy setting for this StereoMolecule as molecule container.
- setAssumeChiralTrue(boolean) - Method in class com.actelion.research.chem.MolfileParser
-
Some software exports mol/sd-files with an unset chiral flag despite the original molecule is a pure enantiomer.
- setAtomAbnormalValence(int, int) - Method in class com.actelion.research.chem.Molecule
-
Set an atom's maximum valance to be different from the default one.
- setAtomAmino(int, String) - Method in class com.actelion.research.chem.Molecule3D
- setAtomBfactor(int, double) - Method in class com.actelion.research.chem.Molecule3D
- setAtomChainId(int, String) - Method in class com.actelion.research.chem.Molecule3D
- setAtomCharge(int, int) - Method in class com.actelion.research.chem.Molecule
- setAtomCIPParity(int, int) - Method in class com.actelion.research.chem.Molecule
-
The atom Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
- setAtomColor(int, int) - Method in class com.actelion.research.chem.Molecule
- setAtomColorSupported(boolean) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setAtomColorSupported(boolean) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setAtomColorSupported(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- setAtomConfigurationUnknown(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
This is a user applied information, rather than a calculated value.
- setAtomCustomLabel(int, byte[]) - Method in class com.actelion.research.chem.Molecule
-
If a custom atom label is set, a molecule depiction displays the custom label instead of the original one.
- setAtomCustomLabel(int, String) - Method in class com.actelion.research.chem.Molecule
-
If a custom atom label is set, a molecule depiction displays the custom label instead of the original one.
- setAtomDescription(int, String) - Method in class com.actelion.research.chem.Molecule3D
- setAtomESR(int, int, int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- setAtomFlag(int, int, boolean) - Method in class com.actelion.research.chem.Molecule3D
- setAtomFlags(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setAtomHighlightColors(int[]) - Method in class com.actelion.research.chem.AbstractDepictor
-
If you want this tructure view to also draw an atom background with specific colors for every atom, then you need to call this method before calling paint().
- setAtomHighlightColors(int[]) - Method in class com.actelion.research.gui.JStructureView
-
If you want this tructure view to also draw an atom background with specific colors for every atom, then you need to call this method before or just after one of the structureChanged() calls.
- setAtomicGaussians(List<AtomicGaussian>) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- setAtomicNo(int) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setAtomicNo(int, int) - Method in class com.actelion.research.chem.Molecule
-
Set an atom's atomic number and defines the isotop to be natural abundance.
- setAtomId(int) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setAtomId(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- setAtomIndexConnectionFlexophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- setAtomIndexFirstLinkerAtom(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- setAtomList(int, int[]) - Method in class com.actelion.research.chem.Molecule
-
Defines a list of allowed/excluded atomic numbers for sub-structure matching.
- setAtomList(int, int[], boolean) - Method in class com.actelion.research.chem.Molecule
-
Defines an atom list as query feature for substructure search
- setAtomMapNo(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Defines an atom mapping number within the context of a reaction.
- setAtomMarker(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Atom marking may be used for any external purpose
- setAtomMass(int, int) - Method in class com.actelion.research.chem.Molecule
-
Set atom to specific isotop or to have a natural isotop distribution
- setAtomName(int, String) - Method in class com.actelion.research.chem.Molecule3D
- setAtomParity(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
The atom parity is a calculated property available above/equal helper level cHelperParities.
- setAtomQueryFeature(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Introduce or remove an atom query feature and make sure, the molecule is flagged to be a sub-structure fragment (see setFragment()).
- setAtomRadical(int, int) - Method in class com.actelion.research.chem.Molecule
-
Sets an atom's radical state as singulet,dublet,triplet or none
- setAtoms(List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setAtomSelection(int, boolean) - Method in class com.actelion.research.chem.Molecule
- setAtomSequence(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setAtomStereoCenter(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
An atom is considered a stereo center, if it is a stereo center in at least in one of the molecule configurations represented by the ESR definitions.
- setAtomText(String[]) - Method in class com.actelion.research.chem.AbstractDepictor
-
Defines additional atom text to be displayed in top right position of some/all atom label.
- setAtomText(String[]) - Method in class com.actelion.research.gui.editor.GenericDrawArea
-
Defines additional atom text to be displayed in top right position of some/all atom label.
- setAtomText(String[]) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.Defines additional atom text to be displayed in top right position of some/all atom label.
- setAtomText(String[]) - Method in class com.actelion.research.gui.JStructureView
-
Defines additional atom text to be displayed in top right position of some/all atom labels.
- setAtomX(int, double) - Method in class com.actelion.research.chem.Molecule
- setAtomY(int, double) - Method in class com.actelion.research.chem.Molecule
- setAtomZ(int, double) - Method in class com.actelion.research.chem.Molecule
- setAttachedHydrogenCount(int, int) - Method in class com.actelion.research.chem.Molecule3D
-
Defines a number of attached hydrogens without known 3D-coordinates
- setAttributes(Attribute[]) - Method in class smile.regression.RegressionTrainer
-
Sets feature attributes.
- setAuthor(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setAuxiliaryInfo(String, Object) - Method in class com.actelion.research.chem.Molecule3D
- setAverageBondLength(Reaction, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- setBackground(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setBackground(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setBackgroundColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
- setBackgroundColor(Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setBackgroundColor(Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- setBase(IMolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- setBase(T) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- setBBData(Map<String, Map<String, List<String>>>) - Method in class com.actelion.research.chem.chemicalspaces.ChemicalSpaceCreator
- setBBs(Set<String>) - Method in class com.actelion.research.chem.chemicalspaces.ChemicalSpaceCreator
- setBiasProvider(MutationBiasProvider) - Method in class com.actelion.research.chem.Mutator
- setBiasReference(StereoMolecule) - Method in interface com.actelion.research.chem.MutationBiasProvider
- setBins(int) - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- setBit(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- setBit(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- setBit(int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Counts from the left to the right Don't forget to set the hash code!
- setBit(int[], int) - Static method in class com.actelion.research.util.BitUtils
- setBit(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- setBits(int, int) - Method in class com.actelion.research.util.datamodel.IntVec
- setBKColor(Color) - Method in class com.actelion.research.gui.wmf.MetaFile
- setBKColor(Color) - Method in class com.actelion.research.gui.wmf.WMF
- setBKMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setBKMode(int) - Method in class com.actelion.research.gui.wmf.WMF
- setBondAtom(int, int, int) - Method in class com.actelion.research.chem.Molecule
- setBondBackgroundHiliting(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Used for depiction only.
- setBondCIPParity(int, int) - Method in class com.actelion.research.chem.Molecule
-
The bond Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
- setBondESR(int, int, int) - Method in class com.actelion.research.chem.Molecule
-
MDL's enhanced stereo representation for BINAP type of stereo bonds.
- setBondForegroundHiliting(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Used for depiction only.
- setBondOrder(int, int) - Method in class com.actelion.research.chem.Molecule
-
Sets the bond type based on bond order without stereo orientation.
- setBondOrder(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setBondParity(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
The bond parity is a calculated property available above/equal helper level cHelperParities.
- setBondParityUnknownOrNone(int) - Method in class com.actelion.research.chem.Molecule
-
This hint/flag is set by CoordinateInventor for double bonds without given EZ-parity, because the new coordinates may imply a not intended EZ-parity.
- setBondQueryFeature(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
- setBondsMolecule(int) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- setBondTorsion(int, short) - Method in class com.actelion.research.chem.conf.Conformer
-
Sets the current bond torsion to be retrieved later.
- setBondType(int, int) - Method in class com.actelion.research.chem.Molecule
-
Defines a bond type combining bod order and stereo orientation.
- setBorderColor(Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- setBrushFillStyle(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setBrushHatch(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setBrushPattern(Image) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setBusyColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
- setButtonClip(GenericDrawContext, int) - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- setButtonClip(Graphics, int) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- setByte(int[], int, int) - Static method in class com.actelion.research.util.datamodel.IntVec
- setByte(int, int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Counts from the left to the right Don't forget to set the hash code!
- setBytes(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- setBytes(int, int, int) - Method in class com.actelion.research.util.datamodel.IntVec
- setC(double) - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- setCache(RigidFragmentCache) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
- setCaveat(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setCenter(Coordinates) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setCenter(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- setCenterData(boolean) - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- setCenterData(boolean) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- setCenterData(boolean) - Method in class com.actelion.research.calc.regression.linear.pls.RegressionModelCalculatorOptimumFactors
- setCenterData(boolean) - Method in class com.actelion.research.calc.regression.linear.pls.SimPLSLMOValidation
-
Deprecated.
- setCenterID(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- setCenterID(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- setCenterID(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- setCenterID(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- setCenterID(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- setCenterID(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- setCenterID(int) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- setCenterID(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- setChargeAtom(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- setChemistry(Object) - Method in class com.actelion.research.gui.table.ChemistryRenderPanel
- setChiralDrawPosition(int) - Method in class com.actelion.research.gui.JStructureView
- setChirality(int) - Method in class com.actelion.research.chem.Molecule
-
Sets the overall chirality of the molecule taking into account: Recognition of stereo centers and stereo bonds, defined ESR features, meso detection.
- setCIPParities() - Method in class com.actelion.research.chem.Canonizer
- setCisPep(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setClassification(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setClip(double, double, double, double) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- setClip(double, double, double, double) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- setClip(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setClip(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setClip(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setClip(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setClipBoardData(String, byte[]) - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
- setClipBoardData(String, byte[]) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
call this in order to get clipboard support
- setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.editor.GenericDrawArea
-
Call this after initialization to get clipboard support
- setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.Call this after initialization to get clipboard support
- setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.JStructureView
-
Call this in order to get clipboard support: setClipboardHandler(new ClipboardHandler());
- setClipRgn() - Method in class com.actelion.research.gui.wmf.MetaFile
- setClipRgn() - Method in class com.actelion.research.gui.wmf.WMF
- setCol(int, double) - Method in class com.actelion.research.calc.Matrix
- setCol(int, double[]) - Method in class com.actelion.research.calc.Matrix
- setCollectFragmentIdCodes(boolean) - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- setCollisionIntensity(double, double[][]) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- setColName(int, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- setColor(int) - Method in class com.actelion.research.chem.AbstractDepictor
- setColor(Color) - Method in class com.actelion.research.chem.AbstractDepictor
- setColor(Color) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- setColor(Color) - Method in class com.actelion.research.chem.Depictor2D
- setColor(Color) - Method in class com.actelion.research.chem.SVGDepictor
- setColor(Color) - Method in class com.actelion.research.gui.dock.ShadowBorder
- setColor(Color) - Method in class com.actelion.research.gui.generic.GenericDepictor
- setColor(Color) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- setColor(Color) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- setColor(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setColor(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setColor(Color) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- setColorMCS2Molecule(StereoMolecule, StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- setColorMolecule(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- setColorMoleculeFromBondIndex(StereoMolecule, int[], int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- setColors(Color, Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
-
Colors to be passed to Depictor.
- setComponentOrientation(ComponentOrientation) - Method in class com.actelion.research.gui.JScrollableMenu
- setComposite(Composite) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setCompound(int, T) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- setCompound(int, T) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- setCompound(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setCompoundFilter(MoleculeFilter) - Method in class com.actelion.research.gui.CompoundCollectionPane
- setCompoundList(Collection<T>) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- setCompoundList(Collection<T>) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- setConformationMode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- setContent(Reaction) - Method in class com.actelion.research.gui.JChemistryView
- setContent(Reaction) - Method in class com.actelion.research.gui.JEditableChemistryView
- setContent(Reaction, DrawingObjectList) - Method in class com.actelion.research.gui.JChemistryView
- setContent(Reaction, DrawingObjectList) - Method in class com.actelion.research.gui.JEditableChemistryView
- setContent(StereoMolecule) - Method in class com.actelion.research.gui.JChemistryView
- setContent(StereoMolecule[]) - Method in class com.actelion.research.gui.JChemistryView
- setContent(StereoMolecule[]) - Method in class com.actelion.research.gui.JEditableChemistryView
- setContent(StereoMolecule[], DrawingObjectList) - Method in class com.actelion.research.gui.JChemistryView
- setContent(StereoMolecule[], DrawingObjectList) - Method in class com.actelion.research.gui.JEditableChemistryView
- setContent(StereoMolecule, DrawingObjectList) - Method in class com.actelion.research.gui.JChemistryView
- setContentMinimumSize(Dimension) - Method in class com.actelion.research.gui.dock.Dockable
-
Sets the minimum size of the encapsulated content component and sets the minimum width of the dockable header.
- setContributions(double[]) - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- setController(SOMController) - Method in class com.actelion.research.calc.SelfOrganizedMap
- setCoord(Coordinates) - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- setCoordinates(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- setCoordinates(double, double, double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setCoordinates(double, double, double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- setCoordinates(float, float, float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IArrow
- setCoordinates(int, Coordinates) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies x,y,z from coords into this atom's coordinates
- setCoordinates(int, Coordinates) - Method in class com.actelion.research.chem.Molecule3D
- setCoordinates(Coordinates) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setCoordinates(String) - Method in class com.actelion.research.chem.shredder.Fragment3D
- setCoordinatesNull() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setCoordinatesNull(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- setCoordinatesReplace(int, Coordinates) - Method in class com.actelion.research.chem.conf.Conformer
-
Replaces the atom's Coordinates object by the given one
- setCorrectionFactor(double) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerIntVector
- setCreateFragments(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines whether new created structures are fragments of molecules.
- setCryst1(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setCurrentDirectory(File) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- setCurrentTool(int) - Method in class com.actelion.research.gui.editor.GenericEditorToolbar
- setCurrentTool(int) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- setCursor(int) - Method in interface com.actelion.research.gui.generic.GenericDialogHelper
- setCursor(int) - Method in class com.actelion.research.gui.swing.SwingDialogHelper
- setCustomTemplateList(List<InventorTemplate>) - Method in class com.actelion.research.chem.coords.CoordinateInventor
-
A custom template list contains substructures with predefined atom coordinates.
- setData(String, Object) - Method in class com.actelion.research.chem.StructureInfo
- setData(T) - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- setData(T) - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
- setDateDeposition(Date) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setDBRef(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setDBRef1DBRef2(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setDefaultAverageBondLength(double) - Static method in class com.actelion.research.chem.Molecule
-
When the molecule adds a new bond to a new atom or a new ring, then atoms are positioned such that the lengths of the new bonds are equal to the average length of existing bonds.
- setDeletable(boolean) - Method in class com.actelion.research.chem.AbstractDrawingObject
- setDescription(String) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Sets the human readable description of this filter.
- setDescription(String) - Method in class smile.data.Attribute
- setDescription(String) - Method in class smile.data.Dataset
-
Sets the detailed dataset description.
- setDescriptorHandlerFactory(DescriptorHandlerFactory) - Method in class com.actelion.research.chem.io.CompoundFileParser
-
If a requested descriptor is not available in a particuar compound record, the parser can create one itself, provided its DescriptorHandlerFactory knows the descriptor name.
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- setDirectionality(Coordinates) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- setDisableBorder(boolean) - Method in class com.actelion.research.gui.JStructureView
- setDiscreteFunction(double[]) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- setDisplayMode(int) - Method in class com.actelion.research.chem.AbstractDepictor
- setDisplayMode(int) - Method in class com.actelion.research.chem.ExtendedDepictor
- setDisplayMode(int) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setDisplayMode(int) - Method in class com.actelion.research.gui.JChemistryView
- setDisplayMode(int) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setDisplayMode(int) - Method in class com.actelion.research.gui.JStructureView
-
Sets the display mode for the Depictor.
- setDisplayMode(int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- setDisplayMode(int) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- setDisplayMode(int) - Method in class com.actelion.research.share.gui.editor.Model
- setDisplaySize(Dimension) - Method in class com.actelion.research.share.gui.editor.Model
- setDistanceHistogram(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- setDistanceTables(List<double[][]>) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
The distance tables which were generated from the conformations.
- setDistHist(int, int, byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- setDistHists(byte[], int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
-
Flat copy
- setDividerChangeListeners(Vector<DividerChangeListener>) - Method in class com.actelion.research.gui.dock.TreeRoot
- setDouble(double) - Method in class com.actelion.research.util.datamodel.IntegerDouble
- setDragEnabled(boolean) - Method in class com.actelion.research.gui.JMultiPanelTitle
- setDrawingObjects(DrawingObjectList) - Method in class com.actelion.research.chem.reaction.Reaction
- setDrawingObjects(DrawingObjectList) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setDrawingObjects(DrawingObjectList) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setE0(double) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- setEditable(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines, whether the list and individual structures can be edited.
- setEditable(boolean) - Method in interface com.actelion.research.gui.generic.GenericComboBox
- setEditable(boolean) - Method in class com.actelion.research.gui.JChemistryView
- setEditable(boolean) - Method in class com.actelion.research.gui.JStructureView
- setEditable(boolean) - Method in class com.actelion.research.gui.swing.SwingComboBox
- setEditable(boolean) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setElectronegativity(double) - Method in class com.actelion.research.chem.Element
- setELUSIVE(boolean) - Static method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- setELUSIVE(boolean) - Static method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- setELUSIVE(boolean) - Static method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- setEnabled(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
- setEnabled(boolean) - Method in interface com.actelion.research.gui.generic.GenericComponent
- setEnabled(boolean) - Method in class com.actelion.research.gui.JChemistryView
- setEnabled(boolean) - Method in class com.actelion.research.gui.JStructureView
- setEnabled(boolean) - Method in class com.actelion.research.gui.swing.SwingComponent
- setEnabled(boolean) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- setEnd(boolean) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setEnergy(double) - Method in class com.actelion.research.chem.conf.Conformer
- setEpsilon(double) - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- setErrorColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
- setESRType(int) - Method in class com.actelion.research.share.gui.editor.Model
- setEventConsumer(DialogEventConsumer) - Method in interface com.actelion.research.gui.generic.GenericComponent
- setEventConsumer(DialogEventConsumer) - Method in class com.actelion.research.gui.swing.SwingComponent
- setEventConsumer(DialogEventConsumer) - Method in class com.actelion.research.gui.swing.SwingDialog
- setExistingSet(long[][]) - Method in class com.actelion.research.chem.DiversitySelector
- setExpdata(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setExtension(String) - Method in class com.actelion.research.gui.JFileChooserOverwrite
- setExtensionListInDescription(boolean) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Determines whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
- setFactorIsomorphSymmetric(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setFactors(int) - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- setFactors(int) - Method in class com.actelion.research.calc.regression.linear.pls.PLSRegressionModelCalculator
- setFactorTextSize(double) - Method in class com.actelion.research.chem.AbstractDepictor
-
Sets a multiplication factor to the text size of all labels.
- setFailed() - Method in class com.actelion.research.calc.regression.ModelError
- setFalseNegative(int) - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- setFalsePositive(int) - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- setFieldData(String, String) - Method in class com.actelion.research.chem.SDFileMolecule
- setFileName(String) - Method in class com.actelion.research.gui.JImagePanel
- setFileSupport(int) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines, whether the popup menu contains 'Open' and/or 'Save' items.
- setFill(long) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- setFill(long) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- setFixedAtoms(int[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- setFixedAtoms(int[]) - Method in interface com.actelion.research.chem.forcefield.ForceField
- setFlat(double[][]) - Method in class com.actelion.research.calc.Matrix
- setFlatness(double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setFlexible(boolean) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- setFocus(boolean) - Method in class com.actelion.research.gui.table.ChemistryRenderPanel
- setFont(int, boolean, boolean) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- setFont(int, boolean, boolean) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- setFont(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setFont(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setFont(String, double, boolean) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- setFont(String, double, boolean) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- setFontEscapement(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setFontSize(int) - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- setForegroundColor(Color, Color) - Method in class com.actelion.research.chem.AbstractDepictor
-
If the foreground color is set, the molecule is drawn in the foreground color except for non carbon atoms, which are drawn in atomicNo specific colors.
- setForegroundColor(Color, Color) - Method in class com.actelion.research.chem.ExtendedDepictor
- setForegroundColor(Color, Color) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- setFormat(String) - Method in class smile.data.DateAttribute
-
Sets the date format.
- setFormat(DateFormat) - Method in class smile.data.DateAttribute
-
Sets the date string formatter.
- setFractionLeaveOut(double) - Method in class com.actelion.research.calc.regression.linear.pls.SimPLSLMOValidation
-
Deprecated.
- setFractionLeaveOut(double) - Method in class com.actelion.research.util.datamodel.ModelXYCrossValidation
-
Deprecated.
- setFractionMTry(double) - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- setFragment(boolean) - Method in class com.actelion.research.chem.Molecule
-
Molecule objects may represent complete molecules or sub-structure fragments, depending on, whether they are flagges as being a fragment or not.
- setFragment(boolean) - Method in class com.actelion.research.chem.reaction.Reaction
-
Sets all reactants and products of this reaction to the given fragment state, i.e.
- setFragment(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- setFragment(byte[], int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setFragment(byte[], long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setFragment(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- setFragment(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcher
-
Defines the fragment to be used in isFragmentInMolecule(...) or findFragmentInMolecule(...).
- setFragment(StereoMolecule, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setFragment(StereoMolecule, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setFragment(String, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setFragment(String, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setFragmentNoColor(long) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- setFragmentNoColor(C) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- setFragmentNoColor(Color) - Method in class com.actelion.research.chem.ExtendedDepictor
- setFragmentNoColor(Color) - Method in class com.actelion.research.gui.JChemistryView
- setFragments(int) - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- setFragments(StereoMolecule[]) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setFragments(StereoMolecule[]) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setFragments(StereoMolecule[]) - Method in class com.actelion.research.share.gui.editor.Model
- setFragmentSymmetryConstraints(int[]) - Method in class com.actelion.research.chem.SSSearcher
-
If countMode is cCountModeUnique, then matches are considered distinct, if
- either the list of matching molecule atoms to the query fragment is a different one
- or if the mutual combination of fragment and molecule atom's symmetry rank is different (when the list of matched molecule atoms is the same)
For certain situations fragment atoms must be considered different, even if their symmetry rank is equal, e.g. - setFrequency(int) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- setFrequency(int) - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- setFrequencyOnePerMol(int) - Method in class com.actelion.research.chem.shredder.Fragment
- setFrequencySumAll(int) - Method in class com.actelion.research.chem.shredder.Fragment
- setFunctionalities(int[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setGamma(double) - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- setGamma(double) - Method in class com.actelion.research.calc.regression.svm.SVMRegression
- setGDIFillBrush() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setGDIFont() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setGDIFontDrawing(boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setGDIHollowBrush() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setGDIPen() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setGDIPenDrawing(boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setGDIPenWidthDrawing(boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setGrowBoost(double) - Method in class com.actelion.research.chem.Mutator
- setHash(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- setHash(int) - Method in class com.actelion.research.chem.properties.complexity.IndexHash
- setHeight(double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setHelix(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHelperValidity(int) - Method in class com.actelion.research.chem.Molecule
-
Use this method with extreme care.
- setHet(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHetAtomRecords(List<AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHgap(int) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Sets the Hgap attribute of the VerticalFlowLayout object
- setHighResolutionImageSource(ImageDataSource) - Method in class com.actelion.research.gui.JImagePanel
-
If this panel uses thumbnails and if this panel is not based on path names, then use this method to define the source for high resolution image data.
- setHighValue(float) - Method in class com.actelion.research.gui.JPruningBar
-
Updates the high value provided the new value is >= current low and <= current max.
- setHiliteBondSet(int[]) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setHiliteBondSet(int[]) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setHmId_Formula(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHmId_Name(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHmId_Site(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHmId_Synonyms(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHorizontalFill(boolean) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Sets the Hfill attribute of the VerticalFlowLayout object
- setHydrogenProtection(boolean) - Method in class com.actelion.research.chem.Molecule
-
Fragment's query features are checked for consistency and normalized during helper array creation.
- setId(int) - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
- setId(long) - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- setId(long) - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
- setID(int) - Method in class com.actelion.research.calc.Matrix
- setID(int) - Method in class com.actelion.research.gui.JPruningBar
- setID(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setIdcode(String) - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- setIdCode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- setIdCode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- setIdCode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- setIdCode(String) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- setIDCode(String) - Method in class com.actelion.research.gui.JStructureView
- setIDCode(String, String) - Method in class com.actelion.research.gui.JStructureView
- setIdentifier(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- setIdFlexophorePoint1(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- setIdFlexophorePoint2(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- setImage(String) - Method in class com.actelion.research.gui.JImagePanelFixedSize
- setImageData(byte[]) - Method in class com.actelion.research.gui.JImagePanel
-
If this uses thumbnails and if you use this method to provide the thumbnail, then you must also define a source for high resolution images with setHighResolutionImageSource().
- setImagePath(String) - Method in class com.actelion.research.gui.JImagePanel
- setImageProvider(ImageProvider) - Method in class com.actelion.research.share.gui.editor.Model
- setIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- setIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setIndex(int) - Method in class com.actelion.research.chem.properties.complexity.IndexHash
- setIndexOriginalAtom(int) - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- setIndexSphereVisualization(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setInitialState() - Method in class com.actelion.research.chem.docking.LigandPose
- setInstance(IStructureNameResolver) - Static method in class com.actelion.research.chem.name.StructureNameResolver
- setInteger(int) - Method in class com.actelion.research.util.datamodel.IntegerDouble
- setInteractionAtomType(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setInteractionType(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- setInteractionTypes(Molecule3D) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- setInternalDragAndDropIsMove(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines the behaviour for internal drag&drop.
- setJrnl(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setKernelType(int) - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- setKeywords(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setL1(long) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- setL2(long) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- setLambda(double) - Method in class com.actelion.research.calc.BoxCox
- setLambda(double) - Method in class com.actelion.research.calc.regression.gaussianprocess.GaussianProcessRegression
- setLambda(double) - Method in class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- setLambda(double) - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- setLambda(double) - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.PLSBoxCoxY
- setLambda(double) - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- setLargestFragmentOnly(boolean) - Method in class com.actelion.research.chem.StructureSearchSpecification
- setLayout(int[], int[]) - Method in interface com.actelion.research.gui.generic.GenericDialog
- setLayout(int[], int[]) - Method in class com.actelion.research.gui.swing.SwingDialog
- setLayouted(boolean) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- setLearningRate(double) - Method in class smile.regression.NeuralNetwork
-
Sets the learning rate.
- setLearningRate(double) - Method in class smile.regression.NeuralNetwork.Trainer
-
Sets the learning rate.
- setLi(List<T>) - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
- setLiConnect(List<int[]>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setLineWidth(double) - Method in class com.actelion.research.chem.AbstractDepictor
- setLineWidth(double) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- setLineWidth(double) - Method in class com.actelion.research.chem.Depictor2D
- setLineWidth(double) - Method in class com.actelion.research.chem.SVGDepictor
- setLineWidth(double) - Method in class com.actelion.research.gui.generic.GenericDepictor
- setLineWidth(double) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- setLineWidth(double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- setLineWidth(double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- setLineWidth(float) - Method in interface com.actelion.research.gui.generic.GenericDrawContext
- setLineWidth(float) - Method in class com.actelion.research.gui.swing.SwingDrawContext
- setLink(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setLinkerId(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- setLocaleFormat(Formatter.LocaleFormat) - Static method in class com.actelion.research.util.Formatter
- setLoopCount(int) - Method in class com.actelion.research.util.AnimatedGIFWriter
- setLowAndHigh(float, float, boolean) - Method in class com.actelion.research.gui.JPruningBar
-
Updates the low and high values simultaniously, provided the low <= high, low >= current min, and high <= current max.
- setLowValue(float) - Method in class com.actelion.research.gui.JPruningBar
-
Updates the low value provided the new value is >= current min and <= current high.
- setMapMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setMapMode(int) - Method in class com.actelion.research.gui.wmf.WMF
- setMapper(IReactionMapper) - Method in class com.actelion.research.share.gui.editor.Model
- setMappingIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setMappingIndex(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setMark(int, boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setMarkAll(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setMarked(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setMarkushStructure(MarkushStructure) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setMarkushStructure(MarkushStructure) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setMarkushStructure(MarkushStructure) - Method in class com.actelion.research.share.gui.editor.Model
- setMaster(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMasterCopy(DWARFileParser) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
If the file to be created shall resemble another DataWarrior file regarding file explanation, macro content, columns names, column properties, runtime properties (template), then one may define a master copy with this method that serves as a blue print.
- setMatchingInfoInQueryAndBase(SolutionCompleteGraph) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
-
Sets the color information for the visualization of the Flexophore PPPoints.
- setMatchingInfoInQueryAndBase(SolutionCompleteGraph) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- setMatchLimit(int, int) - Method in class com.actelion.research.chem.reaction.ReactionSearch
-
If the search shall be aborted once it exceed a given number of matches, then define the maximum number of matches with this method before starting the search.
- setMatchLimit(int, int) - Method in class com.actelion.research.chem.StructureSearch
-
If the search shall be aborted once it exceed a given number of matches, then define the maximum number of matches with this method before starting the search.
- setMaxAtoms(int) - Method in class com.actelion.research.chem.Molecule
-
Usually called automatically and hardly needed to be called.
- setMaxAtoms(int) - Method in class com.actelion.research.chem.Molecule3D
- setMaxBonds(int) - Method in class com.actelion.research.chem.Molecule
-
Usually called automatically and hardly needed to be called.
- setMaxConfs(int) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- setMaximumTextSize(int) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- setMaximumValue(float) - Method in class com.actelion.research.gui.JPruningBar
-
Updates the maximum value; may update low and high to stay within limits Sends PruningBarEvents in case of a successful change.
- setMaximumVisibleRows(int) - Method in class com.actelion.research.gui.JScrollablePopupMenu
- setMaxNodes(int) - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- setMaxNodes(int) - Method in class smile.regression.RandomForest.Trainer
-
Sets the maximum number of leaf nodes.
- setMaxNodes(int) - Method in class smile.regression.RegressionTree.Trainer
-
Sets the maximum number of leaf nodes in the tree.
- setMaxNumSolutions(int) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- setMaxTautomers(int) - Static method in class com.actelion.research.chem.TautomerHelper
- setMaxTotalCount(int) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- setMCSBondConstraints(List<Integer>) - Method in class com.actelion.research.chem.docking.LigandPose
-
for MCS docking:create array of bond indices that are allowed to be permuted
- setMCSReference(StereoMolecule) - Method in class com.actelion.research.chem.docking.DockingEngine
- setMdltyp(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMenuLocation(int, int) - Method in class com.actelion.research.gui.JScrollableMenu
- setMethod(String) - Method in class com.actelion.research.calc.regression.RegressionMethodContainer
- setMinAndMax(float, float) - Method in class com.actelion.research.gui.JPruningBar
-
Initializes the bar by setting min and low/max and high to the values given.
- setMinimumValue(float) - Method in class com.actelion.research.gui.JPruningBar
-
Updates the minimum value; may update low and high to stay within limits Sends PruningBarEvents in case of a successful change.
- setMode(int) - Method in class com.actelion.research.share.gui.editor.Model
- setModeFlexophore(byte) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setModeFlexophore(byte) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- setModeQuery(boolean) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- setModeQuery(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- setModRes(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMol(StereoMolecule) - Method in class com.actelion.research.chem.shredder.Fragment
- setMol(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.SSSearcher
-
Defines fragment and molecule before calling isFragmentInMolecule(...) or findFragmentInMolecule(...).
- setMolecule(byte[], int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setMolecule(byte[], long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setMolecule(int, StereoMolecule) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- setMolecule(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- setMolecule(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcher
-
Defines the molecule to be used in isFragmentInMolecule(...) or findFragmentInMolecule(...).
- setMolecule(StereoMolecule) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setMolecule(StereoMolecule) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setMolecule(StereoMolecule) - Method in interface com.actelion.research.jfx.gui.chem.IMoleculeView
- setMolecule(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setMolecule(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- setMolecule(StereoMolecule, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setMolecule(StereoMolecule, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setMolecule(String, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setMolecule(String, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setMoleculeColor(int) - Method in class com.actelion.research.chem.Molecule
-
Currently, this method only allows to switch the default atomic number dependent atom coloring off by passing cMoleculeColorNeutral.
- setMoleculeRegNo(int, int) - Method in class com.actelion.research.chem.reaction.DatabaseReaction
- setMolFile(String) - Method in class com.actelion.research.share.gui.editor.Model
- setMomentum(double) - Method in class smile.regression.NeuralNetwork
-
Sets the momentum factor.
- setMomentum(double) - Method in class smile.regression.NeuralNetwork.Trainer
-
Sets the momentum factor.
- setMtrix1(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMtrix2(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMtrix3(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setName(String) - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- setName(String) - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- setName(String) - Method in class com.actelion.research.chem.conf.Conformer
- setName(String) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setName(String) - Method in class com.actelion.research.chem.Molecule
- setName(String) - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- setName(String) - Method in class com.actelion.research.chem.reaction.Reaction
- setName(String) - Method in class smile.data.Attribute
- setName(String) - Method in class smile.data.Dataset
-
Sets the dataset name.
- setNeighbours(int) - Method in class com.actelion.research.calc.regression.knn.KNNRegression
- setNeighbours(int) - Method in class com.actelion.research.calc.regression.knn.ParameterKNN
- setNeighbours(List<Integer>) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- setNewMolecule() - Method in class com.actelion.research.share.gui.editor.Model
- setNodeSize(int) - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- setNodeSize(int) - Method in class smile.regression.RandomForest.Trainer
-
Sets the minimum size of leaf nodes.
- setNodeSize(int) - Method in class smile.regression.RegressionTree.Trainer
-
Sets the minimum size of leaf nodes.
- setNodesQuery(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
-
Only needed for the toString() method.
- setNu(double) - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- setNu(double) - Method in class com.actelion.research.calc.regression.svm.SVMRegression
- setNumEpochs(int) - Method in class smile.regression.NeuralNetwork.Trainer
-
Sets the number of epochs of stochastic learning.
- setNumFactors(int) - Method in class com.actelion.research.calc.regression.linear.pls.SimPLSLMOValidation
-
Deprecated.
- setNummdl(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setNumRandomFeatures(int) - Method in class smile.regression.RandomForest.Trainer
-
Sets the number of random selected features for splitting.
- setNumRegressionPoints(int) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setNumRepetitions(int) - Method in class com.actelion.research.calc.regression.linear.pls.SimPLSLMOValidation
-
Deprecated.
- setNumTrees(int) - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- setNumTrees(int) - Method in class smile.regression.RandomForest.Trainer
-
Sets the number of trees in the random forest.
- setObjective(IObjectiveCompleteGraph<T>) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- setObjectiveQueryBiased(boolean) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- setObsolete(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setOccurencesArray(int[]) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- setOpaqueBackground(boolean) - Method in class com.actelion.research.gui.JChemistryView
- setOpen(boolean) - Method in class smile.data.NominalAttribute
-
Sets if the string values of the nominal attribute is a open set.
- setOptimize3D(boolean) - Method in class com.actelion.research.chem.io.AbstractParser
- setOrigX1(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setOrigX2(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setOrigX3(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setOutdirectory(File) - Method in class com.actelion.research.chem.chemicalspaces.ChemicalSpaceCreator
- setOverruleColor(Color, Color) - Method in class com.actelion.research.chem.AbstractDepictor
-
If the overrule color is set, the entire molecule is drawn in the foreground color neglecting any atom color information.
- setOverruleColor(Color, Color) - Method in class com.actelion.research.chem.ExtendedDepictor
- setOverruleColor(Color, Color) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- setOverruleColors(Color, Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
-
Colors to be passed to Depictor.
- setOverruleForeground(Color) - Method in class com.actelion.research.gui.table.ChemistryRenderPanel
- setPaint(Paint) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setPaintMode() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setPaintMode() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setParameterCount(int) - Method in class com.actelion.research.calc.VectorSOM
- setParameterRegressionMethod(T) - Method in class com.actelion.research.calc.regression.ARegressionMethod
- setParent(TreeContainer) - Method in class com.actelion.research.gui.dock.TreeElement
- setParent(TreeContainer) - Method in class com.actelion.research.gui.dock.TreeRoot
- setParities() - Method in class com.actelion.research.chem.Canonizer
-
Creates parities based on atom indices of original molecule and copies them back into that molecule.
- setParitiesValid(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Atom stereo parities and bond E/Z-parities are properties that are usually perceived from up/down-bonds and atom coordinates, respectively.
- setPartialCharge(int, double) - Method in class com.actelion.research.chem.Molecule3D
- setPasteAndDropOptions(int) - Method in class com.actelion.research.gui.JChemistryView
-
fragment status change on drop is allowed then dropping a fragment (molecule) on a molecule (fragment) inverts the status of the view's chemical object.
- setPenStyle(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setPenWidth(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setPixel(int, int, Color) - Method in class com.actelion.research.gui.wmf.MetaFile
- setPixel(int, int, Color) - Method in class com.actelion.research.gui.wmf.WMF
- setPolyFillMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setPolyFillMode(int) - Method in class com.actelion.research.gui.wmf.WMF
- setPolyFillMode(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setPopupItemProvider(PopupItemProvider) - Method in class com.actelion.research.gui.JImagePanel
-
Use this, if you want the popup menu to contain more than just "Copy Full Image" and "Copy Visible".
- setPopupProvider(PopupProvider) - Method in class com.actelion.research.gui.dock.Dockable
- setPopupProvider(PopupProvider) - Method in class com.actelion.research.gui.dock.DockableHeader
- setPopupProvider(PopupProvider) - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- setPositionInContainer(int) - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
- setPPGaussians(List<PPGaussian>) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- setPPP(int, int[]) - Method in class com.actelion.research.chem.Molecule3D
- setPreferredSize(int, int, int) - Method in class com.actelion.research.chem.Mutator
- setPreviousAlignment(StereoMolecule[]) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- setPreviousPheSAResult(double[]) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- setProgressController(ProgressController) - Method in class com.actelion.research.calc.regression.ARegressionMethod
- setProperties(String) - Method in class com.actelion.research.gui.JMultiPanelView
- setProtAtomRecords(List<AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setQ0(double) - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- setQ1(double) - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- setQ2(double) - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- setQ3(double) - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- setQuery(byte[], byte[], byte[], long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
- setQuery(IMolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- setQuery(Reaction) - Method in class com.actelion.research.chem.reaction.SRSearcher
-
This defines the query reaction (or transformation).
- setQuery(Reaction, long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
-
This defines the query reaction (or transformation).
- setQuery(T) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- setRandomSeed(long) - Method in class com.actelion.research.chem.coords.CoordinateInventor
- setRandomSeed(long) - Method in class com.actelion.research.chem.SmilesParser
-
Depending on the parse() parameters, the SmilesParser may or may not generate new atom coordinates after parsing the SMILES.
- setReactant(int, StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reactor
-
Defines a real world reactant.
- setReaction(byte[], byte[], byte[], long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
- setReaction(Reaction) - Method in class com.actelion.research.chem.reaction.SRSearcher
- setReaction(Reaction) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setReaction(Reaction) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setReaction(Reaction) - Method in class com.actelion.research.share.gui.editor.Model
- setReaction(Reaction, long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
-
This defines the query reaction (or transformation).
- setReactionMapper(IReactionMapper) - Static method in class com.actelion.research.gui.editor.GenericDrawArea
- setReactionMapper(IReactionMapper) - Static method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setReactionMode(boolean) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setReactionMode(boolean) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setReactionMode(boolean) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- setReactionRegNo(int) - Method in class com.actelion.research.chem.reaction.DatabaseReaction
- setReactions(List<Reaction>) - Method in class com.actelion.research.chem.chemicalspaces.ChemicalSpaceCreator
- setReactionYield(int) - Method in class com.actelion.research.chem.reaction.DatabaseReaction
- setRearAtoms(int[][]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setRect(float, float, float, float) - Method in class com.actelion.research.share.gui.Arrow
- setRect(float, float, float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- setReferenceVector(int, int, String) - Method in class com.actelion.research.calc.BinarySOM
- setReferenceVector(int, int, String) - Method in class com.actelion.research.calc.SelfOrganizedMap
- setReferenceVector(int, int, String) - Method in class com.actelion.research.calc.VectorSOM
- setReferenceVector(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- setRemarks(HashMap<Integer, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setRenderingHint(RenderingHints.Key, Object) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setRenderingHints(Map<?, ?>) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setResourcePath(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Use this method before initializing the TorsionDB, if you want to open the resource files from an external location in the file system rather than from the project resources.
- setResSequence(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setRevdat(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setRing(boolean) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setRMSD(int) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
-
Sum of squared distances of the center to the other cluster members
- setRNDvalue(double) - Method in class com.actelion.research.util.datamodel.ByteVec
- setRNDvalue(double) - Method in class com.actelion.research.util.datamodel.IntVec
- setRNDvalue(double) - Method in class com.actelion.research.util.DoubleVec
- setRNDvalue(double, double) - Method in class com.actelion.research.util.datamodel.ByteVec
- setRNDvalue(double, double) - Method in class com.actelion.research.util.datamodel.IntVec
- setRNDvalue(double, double) - Method in class com.actelion.research.util.DoubleVec
- setRole(int) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setROP2(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setROP2(int) - Method in class com.actelion.research.gui.wmf.WMF
- setRotatableBonds(int[]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setRotation(double[][]) - Method in class com.actelion.research.chem.alignment3d.transformation.Rotation
- setRotationCenters(int[]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setRow(int, double) - Method in class com.actelion.research.calc.Matrix
- setRow(int, double[]) - Method in class com.actelion.research.calc.Matrix
-
Deep copy
- setRow(int, int[]) - Method in class com.actelion.research.calc.Matrix
- setRowCoordinates(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Puts the given encoded atom coordinates into the given column.
- setRowHeaderMinWidth(int) - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- setRowHeight(int) - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- setRowHeight(int, int) - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- setRowName(int, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- setRowStructure(StereoMolecule, int, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Calculates the canonical structure representation as idcode from mol and puts it into the given idcodeColumn.
- setRowStructure(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Puts the given idcode into the given column.
- setRowValue(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Puts the given value into the given column.
- setSamplingRates(double) - Method in class smile.regression.RandomForest.Trainer
-
Sets the sampling rate.
- setScale1(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setScale2(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setScale3(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setScaling(double) - Method in class com.actelion.research.chem.DepictorTransformation
- setScalingFactor(double) - Method in class com.actelion.research.chem.alignment3d.transformation.Scaling
- setScore(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setScore(double) - Method in class com.actelion.research.util.datamodel.ScorePoint
- setSeed(int) - Method in class smile.math.random.MersenneTwister
- setSeed(long) - Static method in class smile.math.Math
-
Initialize the random generator with a seed.
- setSeed(long) - Method in class smile.math.random.MersenneTwister
- setSeed(long) - Method in interface smile.math.random.RandomNumberGenerator
-
Initialize the random generator with a seed.
- setSeed(long) - Method in class smile.math.Random
-
Initialize the random generator with a seed.
- setSeed(long) - Method in class smile.math.random.UniversalGenerator
- setSelectable(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
- setSelected(boolean) - Method in class com.actelion.research.chem.AbstractDrawingObject
- setSelected(boolean) - Method in class com.actelion.research.gui.dock.Dockable
-
This panel draws its title bar differently if it is selected, which may be used to indicate to the user that this panel has the focus, or should get more attention than other simple internal frames.
- setSelected(boolean) - Method in class com.actelion.research.gui.dock.TreeLeaf
- setSelected(boolean) - Method in interface com.actelion.research.gui.generic.GenericCheckBox
- setSelected(boolean) - Method in class com.actelion.research.gui.swing.SwingCheckBox
- setSelected(boolean) - Method in class com.actelion.research.gui.table.ChemistryRenderPanel
- setSelected(boolean) - Method in class com.actelion.research.share.gui.Arrow
- setSelected(boolean) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- setSelected(boolean) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- setSelectedAtom(int) - Method in class com.actelion.research.share.gui.editor.Model
- setSelectedBond(int) - Method in class com.actelion.research.share.gui.editor.Model
- setSelectedDockable(Dockable) - Method in class com.actelion.research.gui.dock.TreeLeaf
- setSelectedDrawingObject(IDrawingObject) - Method in class com.actelion.research.share.gui.editor.Model
- setSelectedIndex(int) - Method in interface com.actelion.research.gui.generic.GenericComboBox
- setSelectedIndex(int) - Method in class com.actelion.research.gui.swing.SwingComboBox
- setSelectedItem(String) - Method in interface com.actelion.research.gui.generic.GenericComboBox
- setSelectedItem(String) - Method in class com.actelion.research.gui.swing.SwingComboBox
- setSelection(int) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
May be overridden to act on selection changes
- setSelectionModel(ListSelectionModel) - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- setSeparatorCol(String) - Static method in class com.actelion.research.calc.Matrix
- setSeparatorRow(String) - Static method in class com.actelion.research.calc.Matrix
- setSEQADV(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSEQRES(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSheet(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setShiftVector(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- setShowValidationError(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines whether a large red question mark is shown in case of a structure validation error.
- setSigma(double[]) - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- setSim(double) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- setSimilarity(double) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- setSimilarityContributions(double[]) - Method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer.AlignmentResult
- setSimilarityMappingNodes(float) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setSimilarityMappingNodes(int, float) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setSingleConformationModeQuery(boolean) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- setSingleUnknownAsRacemicParity() - Method in class com.actelion.research.chem.Canonizer
-
If the molecule contains exactly one stereo center and if that has unknown configuration, than assume that the configuration is meant to be racemic and update molecule accordingly.
- setSize(int) - Method in class com.actelion.research.chem.shredder.Fragment
- setSize(int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setSize(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setSizes(double[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- setSlope(double) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- setSlope(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setSlopeFragments(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setSlopeR2(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setSmallerSideAtomLists(int[][]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setSmiles(String) - Method in class com.actelion.research.share.gui.editor.Model
- setSource(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSplineFunction(FastSpline) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- setSplit(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSpotColors(Color, Color) - Static method in class com.actelion.research.gui.HeaderPaintHelper
- setSprsde(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSSBond(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSSSearcher(SSSearcher) - Method in class com.actelion.research.chem.mcs.MCS
- setState(double[]) - Method in class com.actelion.research.chem.docking.LigandPose
- setState(double[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- setState(double[]) - Method in interface com.actelion.research.chem.optimization.Evaluable
- setState(double[]) - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- setState(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- setStereoBondFromAtomParity(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- setStereoBondFromBondParity(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
In case bond is a BINAP kind of chiral bond with defined parity, then the preferred neighbour single bond is converted into a stereo bond to correctly reflect its defined parity.
- setStereoBondsFromParity() - Method in class com.actelion.research.chem.ExtendedMolecule
-
This converts one single bond per parity into a stereo up/down bond to correctly reflect the given parity.
- setStereoCenters() - Method in class com.actelion.research.chem.Canonizer
- setStereoProblem(int) - Method in class com.actelion.research.chem.Molecule
-
The stereo problem flag is set by the stereo recognition (available equal/above helper level cHelperParities) if an atom has over- or under-specified stereo bonds attached, i.e.
- setStretchBltMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setStretchBltMode(int) - Method in class com.actelion.research.gui.wmf.WMF
- setString(String, String) - Static method in class com.actelion.research.util.Prefs
- setStroke(long) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- setStroke(long) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- setStroke(Stroke) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setStructureSize(int) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines the width or height of individual structure cells, depending on whether the the CompoundCollectionPane is horizontal or vertical, respectively.
- setStyle(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setSuppressWarning(boolean) - Static method in class com.actelion.research.chem.TautomerHelper
- setSVMRegressionType(int) - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- setSymmetric(boolean) - Method in class smile.math.matrix.JMatrix
- setSymmetric(boolean) - Method in interface smile.math.matrix.Matrix
-
Sets if the matrix is symmetric.
- setTerminalC(boolean) - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- setText(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setText(String) - Method in class com.actelion.research.gui.ComboBoxColorItem
- setText(String) - Method in interface com.actelion.research.gui.generic.GenericLabel
- setText(String) - Method in interface com.actelion.research.gui.generic.GenericTextField
- setText(String) - Method in class com.actelion.research.gui.JMessageBar
- setText(String) - Method in class com.actelion.research.gui.swing.SwingLabel
- setText(String) - Method in class com.actelion.research.gui.swing.SwingTextField
- setTextAlign(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setTextAlign(int) - Method in class com.actelion.research.gui.wmf.WMF
- setTextCharacterExtra(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setTextCharacterExtra(int) - Method in class com.actelion.research.gui.wmf.WMF
- setTextColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
- setTextColor(Color) - Method in class com.actelion.research.gui.wmf.MetaFile
- setTextColor(Color) - Method in class com.actelion.research.gui.wmf.WMF
- setTextSize(int) - Method in class com.actelion.research.chem.AbstractDepictor
- setTextSize(int) - Method in class com.actelion.research.chem.Depictor
-
Deprecated.
- setTextSize(int) - Method in class com.actelion.research.chem.Depictor2D
- setTextSize(int) - Method in class com.actelion.research.chem.SVGDepictor
- setTextSize(int) - Method in class com.actelion.research.gui.generic.GenericDepictor
- setTextSize(int) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.calc.DataProcessor
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.conf.ConformerSetGenerator
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.docking.DockingEngine
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.docking.shape.ShapeDocking
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- setThreadMaster(ThreadMaster) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
If the conformer generation must be stopped from outside, for instance because of user intervention or because of a defined timeout, the provide a ThreadMaster with this method.
- setThreadMaster(ThreadMaster) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- setThreshSimilarityHardMatch(double) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- setTitle(int, String) - Method in class com.actelion.research.gui.JMultiPanelView
- setTitle(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setTitle(String) - Method in class com.actelion.research.gui.dock.Dockable
-
Sets a new title text of the dockable header.
- setTitle(String) - Method in class com.actelion.research.gui.dock.DockableHeader
- setTitle(String) - Method in class com.actelion.research.gui.JMultiPanelTitle
- setToFrontInTabbedPane(String) - Method in class com.actelion.research.gui.dock.JDockingPanel
- setToRacemate() - Method in class com.actelion.research.chem.Molecule
-
This is for compatibility with old MDL stereo representation that contained a 'chiral' flag to indicate that the molecule is not a racemate.
- setTorsionAtoms(int[][]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setTorsionIDs(String[]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setTransform(AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setTransformation(DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDepictor
- setTransparent(boolean) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setTrueNegative(int) - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- setTruePositive(int) - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- setUnique(int) - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- setUniqueFragmentsEstimated(int) - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- setUnknownParitiesToExplicitlyUnknown() - Method in class com.actelion.research.chem.Canonizer
-
Sets all atoms with TH-parity 'unknown' to explicitly defined 'unknown'.
- setUnknownParitiesToExplicitlyUnknown() - Method in class com.actelion.research.chem.StereoMolecule
-
Sets all atoms with TH-parity 'unknown' to explicitly defined 'unknown'.
- setupAtomAndBondFeatures(int) - Method in class com.actelion.research.chem.SSSearcher
- setUpdateMode(int) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- setUpdateMode(int) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- setUsed() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- setUsed(boolean) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- setUserData(Object) - Method in class com.actelion.research.chem.Molecule
- setUseRedColor(boolean) - Method in class com.actelion.research.gui.JPruningBar
- setUseSelfOrganizerIfAllFails(boolean) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
If a molecule has at least one rotatable bond if all permutations of torsions collide beyond a tolerated strain, then the standard behaviour of this class is to return that clashing conformer with the lowest strain.
If passing true to this method, the ConformerGenerator will use the ConformerSelfOrganizer in these cases to generate conformers. - setUseThumbNail(boolean) - Method in class com.actelion.research.gui.JImagePanel
- setValue(double) - Method in class com.actelion.research.util.Angle
- setValue(Reaction) - Method in class com.actelion.research.share.gui.editor.Model
- setValue(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setValue(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- setValue(StereoMolecule, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- setValues(String, double, int) - Method in class com.actelion.research.chem.TextDrawingObject
- setVerbose() - Method in class com.actelion.research.calc.SimilarityMulticore
- setVerbose(boolean) - Method in class com.actelion.research.calc.DataProcessor
- setVerbose(boolean) - Method in interface com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.IPPNodeSimilarity
- setVerbose(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- setVerbose(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- setVerbose(boolean) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- setVerbose(boolean) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- setVgap(int) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Sets the Vgap attribute of the VerticalFlowLayout object
- setViewportExt(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setViewportExt(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- setVolumes(List<Double>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setWeight(double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setWeight(double) - Method in class smile.data.Attribute
- setWeightDecay(double) - Method in class smile.regression.NeuralNetwork
-
Sets the weight decay factor.
- setWeightDecay(double) - Method in class smile.regression.NeuralNetwork.Trainer
-
Sets the weight decay factor.
- setWeights(List<Double>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setWindowExt(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setWindowExt(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- setWindowOrg(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setWindowOrg(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- setWMF(MetaFile, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setX(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setX(int, double) - Method in class com.actelion.research.chem.conf.Conformer
- setX(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setXORMode(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setXORMode(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setY(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setY(int, double) - Method in class com.actelion.research.chem.conf.Conformer
- setY(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setZ(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setZ(int, double) - Method in class com.actelion.research.chem.conf.Conformer
- sFactory - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- ShadowBorder - Class in com.actelion.research.gui.dock
- ShadowBorder() - Constructor for class com.actelion.research.gui.dock.ShadowBorder
-
Creates a border with a grey 1 pixel line on left and top and a 3 pixel (scaled to Hi-dpi factor) wide shadow on right and bottom.
- ShadowBorder(int, int, int, int) - Constructor for class com.actelion.research.gui.dock.ShadowBorder
-
Creates a border with a grey 1 pixel line on left and top and a 3 pixel wide shadow on right and bottom.
- shadowSize() - Static method in class com.actelion.research.gui.dock.ShadowBorder
- ShapeDocking - Class in com.actelion.research.chem.docking.shape
- ShapeDocking(ShapeVolume, Transformation) - Constructor for class com.actelion.research.chem.docking.shape.ShapeDocking
- ShapeVolume - Class in com.actelion.research.chem.phesa
- ShapeVolume() - Constructor for class com.actelion.research.chem.phesa.ShapeVolume
- ShapeVolume(ShapeVolume) - Constructor for class com.actelion.research.chem.phesa.ShapeVolume
- shareSameFragment(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
- shear(double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- shift(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- shift(int[], int) - Static method in class com.actelion.research.util.ArrayUtils
- SHIFTJIS_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SHORT_NAME - Static variable in class com.actelion.research.chem.descriptor.SimilarityCalculatorDoubleArray
- shortName - Variable in class com.actelion.research.chem.descriptor.SimilarityCalculatorInfo
- shortNameToName(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- show(int, int) - Method in interface com.actelion.research.gui.generic.GenericPopupMenu
- show(int, int) - Method in class com.actelion.research.gui.swing.SwingPopupMenu
- show(Component, int, int) - Method in class com.actelion.research.gui.JScrollablePopupMenu
- showBusyMessage(String) - Method in class com.actelion.research.gui.JMessageBar
- showDialog() - Method in interface com.actelion.research.gui.generic.GenericDialog
- showDialog() - Method in class com.actelion.research.gui.swing.SwingDialog
- showErrorMessage(String) - Method in interface com.actelion.research.calc.ProgressListener
- showErrorMessage(String) - Method in class com.actelion.research.gui.JMessageBar
- showErrorMessage(String) - Method in class com.actelion.research.gui.JProgressDialog
- showErrorMessage(String) - Method in class com.actelion.research.gui.JProgressPanel
- showHelpDialog() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- showHelpDialog() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- showHelpDialog(String) - Method in interface com.actelion.research.gui.generic.GenericDialogHelper
- showHelpDialog(String) - Method in class com.actelion.research.gui.swing.SwingDialogHelper
- showMessage(String) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- showMessage(String) - Method in class com.actelion.research.gui.FileHelper
- showMessage(String) - Method in interface com.actelion.research.gui.generic.GenericDialog
- showMessage(String) - Method in interface com.actelion.research.gui.generic.GenericDialogHelper
- showMessage(String) - Method in class com.actelion.research.gui.JProgressPanel
- showMessage(String) - Method in class com.actelion.research.gui.swing.SwingDialog
- showMessage(String) - Method in class com.actelion.research.gui.swing.SwingDialogHelper
- showText() - Method in class com.actelion.research.gui.JMessageBar
- showWarningMessage(String) - Method in class com.actelion.research.gui.JChemistryView
- showWarningMessage(String) - Method in class com.actelion.research.gui.JStructureView
- shrinkage() - Method in class smile.regression.GaussianProcessRegression
-
Returns the shrinkage parameter.
- shrinking - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- shuffle(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- shuffle(int[], Random) - Static method in class com.actelion.research.util.ArrayUtils
- shuffle(IntArray) - Static method in class com.actelion.research.util.datamodel.IntArray
- shuffle(T[]) - Static method in class com.actelion.research.util.ArrayUtils
- shuffleArray(IdentifiedObject[]) - Static method in class com.actelion.research.util.datamodel.IdentifiedObject
- shuffleRows() - Method in class com.actelion.research.calc.Matrix
- shutdown() - Static method in class smile.util.MulticoreExecutor
-
Shutdown the thread pool.
- siftDown(double[], int, int) - Static method in class smile.sort.SortUtils
-
To restore the max-heap condition when a node's priority is decreased.
- siftDown(float[], int, int) - Static method in class smile.sort.SortUtils
-
To restore the max-heap condition when a node's priority is decreased.
- siftDown(int[], int, int) - Static method in class smile.sort.SortUtils
-
To restore the max-heap condition when a node's priority is decreased.
- siftDown(T[], int, int) - Static method in class smile.sort.SortUtils
-
To restore the max-heap condition when a node's priority is decreased.
- siftUp(double[], int) - Static method in class smile.sort.SortUtils
-
To restore the max-heap condition when a node's priority is increased.
- siftUp(float[], int) - Static method in class smile.sort.SortUtils
-
To restore the max-heap condition when a node's priority is increased.
- siftUp(int[], int) - Static method in class smile.sort.SortUtils
-
To restore the max-heap condition when a node's priority is increased.
- siftUp(T[], int) - Static method in class smile.sort.SortUtils
-
To restore the max-heap condition when a node's priority is increased.
- SIGMOID - Static variable in class org.machinelearning.svm.libsvm.svm_parameter
- Sign(double, double) - Static method in class com.actelion.research.calc.Matrix
- signum(double) - Static method in class smile.math.Math
-
Returns the signum of the argument; zero if the argument is zero, 1.0 if the argument is greater than zero, -1.0 if the argument is less than zero.
- signum(float) - Static method in class smile.math.Math
-
Returns the signum function of the argument; zero if the argument is zero, 1.0f if the argument is greater than zero, -1.0f if the argument is less than zero.
- Silicon - Static variable in class com.actelion.research.chem.PeriodicTable
- SIMILARITY_MODE_CARBON - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- SIMILARITY_MODE_HARD_THRESH - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
-
Hard thresh means if the similarity of two atom types in a node to node comparison is below a threshold the complete node to node similarity becomes 0.
- SIMILARITY_MODE_HARD_THRESH_AVR - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- SIMILARITY_MODE_HARD_THRESH_OPTIMISTIC - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- SIMILARITY_MODE_SIMPLE - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- SIMILARITY_SCALING_SPLIT_SCORE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- SimilarityCalculatorDoubleArray - Class in com.actelion.research.chem.descriptor
-
SimilarityCalculatorDoubleArray Created by korffmo1 on 12.07.18.
- SimilarityCalculatorDoubleArray() - Constructor for class com.actelion.research.chem.descriptor.SimilarityCalculatorDoubleArray
- SimilarityCalculatorInfo - Class in com.actelion.research.chem.descriptor
- SimilarityCalculatorInfo(String, String) - Constructor for class com.actelion.research.chem.descriptor.SimilarityCalculatorInfo
- SimilarityGraphBasedReactionMapper - Class in com.actelion.research.chem.reaction.mapping
- SimilarityGraphBasedReactionMapper() - Constructor for class com.actelion.research.chem.reaction.mapping.SimilarityGraphBasedReactionMapper
- SimilarityMulticore<T> - Class in com.actelion.research.calc
-
SimilarityMulticore T is the descriptor object class
- SimilarityMulticore(ISimilarityCalculator<T>) - Constructor for class com.actelion.research.calc.SimilarityMulticore
- SimilarityMulticore(ISimilarityCalculator<T>, int) - Constructor for class com.actelion.research.calc.SimilarityMulticore
- SIMPLE_DATE_FORMAT - Static variable in class com.actelion.research.util.ConstantsDWAR
- SimpleCanonizer - Class in com.actelion.research.chem
- SimpleCanonizer(ExtendedMolecule) - Constructor for class com.actelion.research.chem.SimpleCanonizer
- SimpleMetalTerm - Class in com.actelion.research.chem.docking.scoring.chemscore
- SimplePharmacophorePoint - Class in com.actelion.research.chem.phesa.pharmacophore.pp
-
doesn't possess directionality terms (only a dummy vector) and is used to represent receptor pharmacophores (not dependent on a molecular conformation, as opposed to ligand-based pharmacophores)
- SimplePharmacophorePoint(int, Coordinates, IPharmacophorePoint.Functionality) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- SimplePharmacophorePoint(SimplePharmacophorePoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- simpleUpdateCoords(Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
-
Returns full transformation that moves/scales original molecule into viewRect.
- simpleValidateView(Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
- simpleValidateView(Rectangle2D.Double, int) - Method in class com.actelion.research.chem.SVGDepictor
- simpleValidateView(Rectangle2D.Double, int) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- SimPLS - Class in com.actelion.research.calc.regression.linear.pls
-
Title: SimPLS
- SimPLS() - Constructor for class com.actelion.research.calc.regression.linear.pls.SimPLS
- SimPLSLMOValidation - Class in com.actelion.research.calc.regression.linear.pls
-
Deprecated.
- SimPLSLMOValidation(Matrix, Matrix) - Constructor for class com.actelion.research.calc.regression.linear.pls.SimPLSLMOValidation
-
Deprecated.
- simPlsSave(Matrix, Matrix, int) - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
-
No explained variance is calculated.
- simPlsSave(Matrix, Matrix, Matrix, Matrix, int) - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- simPlsSaveExplainedVariance(Matrix, Matrix, int) - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
-
The explained variance is calculated.
- sin() - Method in class com.actelion.research.util.Angle
- sin() - Method in class smile.math.Complex
-
Returns the complex sine.
- sin(double) - Static method in class smile.math.Math
-
Returns the trigonometric sine of an angle.
- SingleLinkage - Class in smile.clustering.linkage
-
Single linkage.
- SingleLinkage(double[][]) - Constructor for class smile.clustering.linkage.SingleLinkage
-
Constructor.
- singular - Variable in class smile.math.matrix.LU
-
True if the matrix is singular.
- singular - Variable in class smile.math.matrix.QR
-
Indicate if the matrix is singular.
- SingularValueDecomposition - Class in com.actelion.research.calc
-
Singular Value Decomposition.
- SingularValueDecomposition(double[][], ProgressListener, ThreadMaster) - Constructor for class com.actelion.research.calc.SingularValueDecomposition
-
Construct the singular value decomposition
- sinh(double) - Static method in class smile.math.Math
-
Returns the hyperbolic sine of a double value.
- SiteParser - Class in com.actelion.research.chem.io.pdb.parser
-
SiteParser Site records specify residues comprising catalytic, co-factor, anti-codon, regulatory or other essential sites or environments surrounding ligands present in the structure.
- SiteParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.SiteParser
- size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- size - Variable in class smile.clustering.PartitionClustering
-
The number of samples in each cluster.
- size() - Method in class com.actelion.research.chem.coords.InventorFragment
- size() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Returns the total number of atoms in this force field.
- size() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- size() - Static method in class com.actelion.research.chem.PeriodicTable
- size() - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- size() - Method in class com.actelion.research.share.gui.Polygon
- size() - Method in class com.actelion.research.util.datamodel.ByteVec
- size() - Method in class com.actelion.research.util.datamodel.DoubleArray
- size() - Method in class com.actelion.research.util.datamodel.IntVec
- size() - Method in class com.actelion.research.util.datamodel.ModelXY
- size() - Method in class com.actelion.research.util.DoubleVec
- size() - Method in class com.actelion.research.util.hash.HashSetInt
- size() - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- size() - Method in class com.actelion.research.util.SortedList
- size() - Method in class smile.clustering.linkage.Linkage
-
Returns the proximity matrix size.
- size() - Method in class smile.data.AttributeVector
-
Returns the vector size.
- size() - Method in class smile.data.Dataset
-
Returns the size of dataset.
- size() - Method in class smile.data.NominalAttribute
-
Returns the number of nominal values.
- size() - Method in class smile.math.SparseArray
-
Returns the number of nonzero entries.
- size() - Method in class smile.regression.RandomForest
-
Returns the number of trees in the model.
- size() - Method in class smile.stat.distribution.Mixture
-
Returns the number of components in the mixture.
- SIZE_CUTOFF - Static variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- SIZE_RATIO - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- sizeAfterLastBitSet - Variable in class com.actelion.research.chem.properties.complexity.BitArray128
- sizeBits() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- sizeBits() - Method in class com.actelion.research.util.datamodel.IntVec
- sizeBytes() - Method in class com.actelion.research.util.datamodel.IntVec
- sizeContent() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- sizeContent(boolean) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- sizeOf(String) - Static method in class com.actelion.research.util.StringFunctions
-
https://stackoverflow.com/questions/4385623/bytes-of-a-string-in-java sizeof(string) = 8 + // object header used by the VM 8 + // 64-bit reference to char array (value) 8 + string.length() * 2 + // character array itself (object header + 16-bit chars) 4 + // offset integer 4 + // count integer 4 + // cached hash code
- sizeOf(List<String>) - Static method in class com.actelion.research.util.StringFunctions
- SizeOf - Class in com.actelion.research.util
-
13.02.2006 MvK
- SizeOf() - Constructor for class com.actelion.research.util.SizeOf
- sizePipe() - Method in class com.actelion.research.util.Pipeline
- Sketch - Class in com.actelion.research.util
-
Title: Actelion Java Library
- Sketch() - Constructor for class com.actelion.research.util.Sketch
- skip(Reader) - Static method in class com.actelion.research.io.BOMSkipper
-
Some text editors (e.g.
- skipBytes(int) - Method in class com.actelion.research.util.LittleEndianDataInputStream
- skipUntilLineMatchesRegEx(StringReadChannel, String) - Static method in class com.actelion.research.io.StringReadChannel
- skipUntilLineMatchesRegEx(StringReadChannel, String, int) - Static method in class com.actelion.research.io.StringReadChannel
- skipUntilLineMatchesRegEx(InputStream, String) - Static method in class com.actelion.research.util.IO
- slice(double[], int[]) - Static method in class smile.math.Math
-
Returns a slice of data for given indices.
- slice(float[], int[]) - Static method in class smile.math.Math
-
Returns a slice of data for given indices.
- slice(int[], int[]) - Static method in class smile.math.Math
-
Returns a slice of data for given indices.
- slice(E[], int[]) - Static method in class smile.math.Math
-
Returns a slice of data for given indices.
- SlidingWindow - Class in com.actelion.research.calc.filter
-
SlidingWindow
- SlidingWindow(double[]) - Constructor for class com.actelion.research.calc.filter.SlidingWindow
- SlidingWindowDistHist - Class in com.actelion.research.chem.descriptor.flexophore
-
SlidingWindowDistHist Created by korffmo1 on 01.03.16.
- SlidingWindowDistHist(double[]) - Constructor for class com.actelion.research.chem.descriptor.flexophore.SlidingWindowDistHist
- SMARTS_MODE_GUESS - Static variable in class com.actelion.research.chem.SmilesParser
- SMARTS_MODE_IS_SMARTS - Static variable in class com.actelion.research.chem.SmilesParser
- SMARTS_MODE_IS_SMILES - Static variable in class com.actelion.research.chem.SmilesParser
- smile.clustering - package smile.clustering
- smile.clustering.linkage - package smile.clustering.linkage
- smile.data - package smile.data
- smile.math - package smile.math
- smile.math.distance - package smile.math.distance
- smile.math.kernel - package smile.math.kernel
- smile.math.matrix - package smile.math.matrix
- smile.math.random - package smile.math.random
- smile.math.rbf - package smile.math.rbf
- smile.math.special - package smile.math.special
- smile.regression - package smile.regression
- smile.sort - package smile.sort
- smile.stat.distribution - package smile.stat.distribution
- smile.util - package smile.util
- smile.validation - package smile.validation
- SmilesCreator - Class in com.actelion.research.chem
-
Deprecated.
- SmilesCreator() - Constructor for class com.actelion.research.chem.SmilesCreator
-
Deprecated.
- SmilesParser - Class in com.actelion.research.chem
- SmilesParser() - Constructor for class com.actelion.research.chem.SmilesParser
-
Creates a new SmilesParser that doesn't allow SMARTS features to be present in parsed strings.
- SmilesParser(int, boolean) - Constructor for class com.actelion.research.chem.SmilesParser
-
Creates a new SmilesParser that may or may not allow SMARTS features to be present in parsed strings.
- SmileUtils - Class in smile.util
-
Some useful functions.
- SmoothingSplineInterpolator - Class in com.actelion.research.util
-
Smoothing Spline Interpolator based on the algorithm described at http://www.qmw.ac.uk/~ugte133/book/11_tsd/splines.pdf
The Smoothing Spline is used to minimize Sum(sqr((Si-yi)/sigmai)) + lambda*Sum(sqr(S''i)) If lambda=0 (default), this is equivalent to the cubic spline interpolation If lambda=Infinity, this is equivalent to the least square fitting - SmoothingSplineInterpolator() - Constructor for class com.actelion.research.util.SmoothingSplineInterpolator
- sNastyFunction - Static variable in class com.actelion.research.chem.NastyFunctionDetector
- SolubilityPredictor - Class in com.actelion.research.chem.prediction
- SolubilityPredictor() - Constructor for class com.actelion.research.chem.prediction.SolubilityPredictor
- SolutionCompleteGraph - Class in com.actelion.research.util.graph.complete
-
SolutionCompleteGraph
- SolutionCompleteGraph() - Constructor for class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- solve(double[]) - Method in class smile.math.matrix.Cholesky
-
Solve the linear system A * x = b.
- solve(double[]) - Method in class smile.math.matrix.LU
-
Solve A * x = b.
- solve(double[], double[]) - Method in class smile.math.matrix.QR
-
Solve the least squares A*x = b.
- solve(double[], double[]) - Method in class smile.math.matrix.SVD
-
Solve the least squares A*x = b.
- solve(double[], double[], double[], double[]) - Static method in class smile.math.Math
-
Solve the tridiagonal linear set which is of diagonal dominance |bi| > |ai| + |ci|.
- solve(Matrix) - Method in class com.actelion.research.calc.LUDecomposition
-
Solve A*X = B
- solve(DenseMatrix) - Method in class smile.math.matrix.Cholesky
-
Solve the linear system A * X = B.
- solve(DenseMatrix) - Method in class smile.math.matrix.LU
-
Solve A * X = B.
- solve(DenseMatrix) - Method in class smile.math.matrix.QR
-
Solve the least squares A * X = B.
- solve(DenseMatrix) - Method in class smile.math.matrix.SVD
-
Solve the least squares A * X = B.
- SOLVENT_GROUP - Static variable in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- SOMController - Interface in com.actelion.research.calc
- sort() - Method in class com.actelion.research.util.datamodel.IntArray
- sort() - Method in class smile.sort.IntHeapSelect
-
Sort the smallest values.
- sort(double[]) - Static method in class smile.sort.QuickSort
-
Sorts the specified array into ascending numerical order.
- sort(double[][]) - Static method in class smile.math.Math
-
Sorts each variable and returns the index of values in ascending order.
- sort(double[], double[]) - Static method in class smile.math.matrix.JMatrix
-
Sort eigenvalues.
- sort(double[], double[]) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(double[], double[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(double[], double[], DenseMatrix) - Static method in class smile.math.matrix.JMatrix
-
Sort eigenvalues and eigenvectors.
- sort(double[], int[]) - Static method in class smile.sort.QuickSort
-
Besides sorting the array arr, the array brr will be also rearranged as the same order of arr.
- sort(double[], int[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(double[], Object[]) - Static method in class smile.sort.QuickSort
-
Besides sorting the array arr, the array brr will be also rearranged as the same order of arr.
- sort(double[], Object[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(float[]) - Static method in class smile.sort.QuickSort
-
Sorts the specified array into ascending numerical order.
- sort(float[], float[]) - Static method in class smile.sort.QuickSort
-
Besides sorting the array arr, the array brr will be also rearranged as the same order of arr.
- sort(float[], float[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(float[], int[]) - Static method in class smile.sort.QuickSort
-
Besides sorting the array arr, the array brr will be also rearranged as the same order of arr.
- sort(float[], int[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(float[], Object[]) - Static method in class smile.sort.QuickSort
-
Besides sorting the array arr, the array brr will be also rearranged as the same order of arr.
- sort(float[], Object[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(int[]) - Static method in class smile.sort.QuickSort
-
Sorts the specified array into ascending numerical order.
- sort(int[], int[]) - Static method in class smile.sort.QuickSort
-
Besides sorting the array arr, the array brr will be also rearranged as the same order of arr.
- sort(int[], int[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(int[], Object[]) - Static method in class smile.sort.QuickSort
-
Besides sorting the array arr, the array brr will be also rearranged as the same order of arr.
- sort(int[], Object[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(Attribute[], double[][]) - Static method in class smile.util.SmileUtils
-
Sorts each variable and returns the index of values in ascending order.
- sort(T[]) - Static method in class smile.sort.QuickSort
-
Sorts the specified array into ascending order.
- sort(T[], int[]) - Static method in class smile.sort.QuickSort
-
Besides sorting the array arr, the array brr will be also rearranged as the same order of arr.
- sort(T[], int[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(T[], int[], int, Comparator<T>) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- sort(T[], Object[]) - Static method in class smile.sort.QuickSort
-
Besides sorting the array arr, the array brr will be also rearranged as the same order of arr.
- sort(T[], Object[], int) - Static method in class smile.sort.QuickSort
-
This is an effecient implementation Quick Sort algorithm without recursive.
- SortedList<T extends java.lang.Comparable<? super T>> - Class in com.actelion.research.util
- SortedList() - Constructor for class com.actelion.research.util.SortedList
- SortedList(Comparator) - Constructor for class com.actelion.research.util.SortedList
- SortedPair - Class in com.actelion.research.chem.forcefield.mmff
-
SortedPair class is used in the Separation table.
- SortedPair(int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.SortedPair
-
Construct a new SortedPair.
- SortedStringList - Class in com.actelion.research.chem
- SortedStringList() - Constructor for class com.actelion.research.chem.SortedStringList
- sortInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- sortRows(int) - Method in class com.actelion.research.calc.Matrix
- SortUtils - Class in smile.sort
-
Some useful functions such as swap and swif-down used in many sorting algorithms.
- SP2_AMINE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- SparseArray - Class in smile.math
-
Sparse array of double values.
- SparseArray() - Constructor for class smile.math.SparseArray
-
Constructor.
- SparseArray.Entry - Class in smile.math
-
The entry in a sparse array of double values.
- spearman(double[], double[]) - Static method in class smile.math.Math
-
The Spearman Rank Correlation Coefficient is a form of the Pearson coefficient with the data converted to rankings (ie.
- spearman(float[], float[]) - Static method in class smile.math.Math
-
The Spearman Rank Correlation Coefficient is a form of the Pearson coefficient with the data converted to rankings (ie.
- spearman(int[], int[]) - Static method in class smile.math.Math
-
The Spearman Rank Correlation Coefficient is a form of the Pearson coefficient with the data converted to rankings (ie.
- SPEC - Static variable in class com.actelion.research.chem.prediction.MolecularPropertyHelper
- SpecialField(String, String, String, String, String) - Constructor for class com.actelion.research.chem.io.DWARFileParser.SpecialField
- SPECIFIC - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- SplineFunction - Class in com.actelion.research.chem.interactionstatistics
-
Class used to represent a Protein Ligand Function
- SplineFunction() - Constructor for class com.actelion.research.chem.interactionstatistics.SplineFunction
- split(Matrix, int) - Static method in class com.actelion.research.calc.MatrixFunctions
-
Splits the matrix row wise into two matrices.
- splitCol(Matrix, int) - Static method in class com.actelion.research.calc.MatrixFunctions
- sqr(double) - Static method in class smile.math.Math
-
Returns x * x.
- sqrt(double) - Static method in class smile.math.Math
-
Returns the correctly rounded positive square root of a double value.
- squaredDistance(double[], double[]) - Static method in class smile.math.Math
-
The squared Euclidean distance.
- squaredDistance(float[], float[]) - Static method in class smile.math.Math
-
The squared Euclidean distance.
- squaredDistance(int[], int[]) - Static method in class smile.math.Math
-
The squared Euclidean distance.
- squaredDistance(SparseArray, SparseArray) - Static method in class smile.math.Math
-
The Euclidean distance.
- SRC_AND - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
- SRC_COPY - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
- SRC_PAINT - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
- SRCAND - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRCCOPY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRCERASE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRCINVERT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRCPAINT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRSearcher - Class in com.actelion.research.chem.reaction
-
The SRSearcher class handles reaction-sub-structure searches.
- SRSearcher() - Constructor for class com.actelion.research.chem.reaction.SRSearcher
- SSSearcher - Class in com.actelion.research.chem
- SSSearcher() - Constructor for class com.actelion.research.chem.SSSearcher
-
Instantiates a SSSearcher object for running sub-structure searches with one or more sub-structure fragments on one or more molecules.
- SSSearcher(int) - Constructor for class com.actelion.research.chem.SSSearcher
-
Instantiates a SSSearcher object for running sub-structure searches with one or more sub-structure fragments on one or more molecules.
- SSSearcherWithIndex - Class in com.actelion.research.chem
- SSSearcherWithIndex() - Constructor for class com.actelion.research.chem.SSSearcherWithIndex
- SSSearcherWithIndex(int) - Constructor for class com.actelion.research.chem.SSSearcherWithIndex
- STABILIZED - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- standard() - Static method in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- standardize(double[]) - Static method in class smile.math.Math
-
Standardizes an array to mean 0 and variance 1.
- standardize(double[][]) - Static method in class smile.math.Math
-
Standardizes each column of a matrix to 0 mean and unit variance.
- standardize(StereoMolecule, int) - Static method in class com.actelion.research.chem.MoleculeStandardizer
-
Standardises a molecule and fixes some structural errors.
- start() - Method in class com.actelion.research.chem.reaction.ReactionSearch
- start() - Method in class com.actelion.research.chem.StructureSearch
- start() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
- start() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXPage
- start() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXReactionStep
- START_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- startAnimation(int) - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
-
In order for a button to support an animation, it need additional images to follow after its normal appearance.
- startProgress(String, int, int) - Method in class com.actelion.research.calc.DataProcessor
- startProgress(String, int, int) - Method in interface com.actelion.research.calc.ProgressListener
- startProgress(String, int, int) - Method in class com.actelion.research.gui.JProgressDialog
- startProgress(String, int, int) - Method in class com.actelion.research.gui.JProgressPanel
- startSubMenu(String) - Method in interface com.actelion.research.gui.generic.GenericPopupMenu
- startSubMenu(String) - Method in class com.actelion.research.gui.swing.SwingPopupMenu
- startWrite(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
- stateChanged() - Method in interface com.actelion.research.chem.forcefield.ForceFieldChangeListener
- stateChanged(ChangeEvent) - Method in class com.actelion.research.gui.dock.TreeLeaf
- StatisticalTorsionPotential - Class in com.actelion.research.chem.conf.torsionstrain
- StatisticalTorsionTerm - Class in com.actelion.research.chem.conf.torsionstrain
-
Represents a torsion potential as a function of the angle, derived from statistical torsion distributions from the COD/CSD The dihedral angle is defined by a atom sequence of 4 atoms.
- StatisticsOverview - Class in com.actelion.research.calc.statistics
-
StatisticsOverview Some basic statistics about the given data 28 Jun 2010 MvK: Start implementation
- StatisticsOverview() - Constructor for class com.actelion.research.calc.statistics.StatisticsOverview
- StatisticsOverview(DoubleArray) - Constructor for class com.actelion.research.calc.statistics.StatisticsOverview
- stbn - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Stbn - Class in com.actelion.research.chem.forcefield.mmff.table
- Stbn(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Stbn
- step() - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
- STEREO_ANGLE_LIMIT - Static variable in class com.actelion.research.chem.ExtendedMolecule
- StereoIsomerEnumerator - Class in com.actelion.research.chem
- StereoIsomerEnumerator(StereoMolecule, boolean) - Constructor for class com.actelion.research.chem.StereoIsomerEnumerator
-
If the passed molecule has stereo-chemically undefined configurations (double bonds, stereo centers) or/and one or more AND/OR groups of defined relative stereo configurations, then it represents multiple stereo isomers.
- StereoMolecule - Class in com.actelion.research.chem
- StereoMolecule() - Constructor for class com.actelion.research.chem.StereoMolecule
- StereoMolecule(int, int) - Constructor for class com.actelion.research.chem.StereoMolecule
- StereoMolecule(Molecule) - Constructor for class com.actelion.research.chem.StereoMolecule
- stop() - Method in class com.actelion.research.chem.reaction.SRSearcher
- stop() - Method in class com.actelion.research.chem.SSSearcher
-
Asks the substructure search to stop without completing as soon as possible.
- stop() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- stopAnimation() - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
- stopProgress() - Method in interface com.actelion.research.calc.ProgressListener
- stopProgress() - Method in class com.actelion.research.gui.JProgressDialog
-
Sets progress back to zero, hides the progress bar, but keeps the dialog open.
- stopProgress() - Method in class com.actelion.research.gui.JProgressPanel
- stopProgress(String) - Method in class com.actelion.research.calc.DataProcessor
- stopScrolling() - Method in class com.actelion.research.gui.ScrollPaneAutoScrollerWhenDragging
- storeState() - Method in class com.actelion.research.gui.editor.GenericDrawArea
- storeState() - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- StraightLineRule - Class in org.openmolecules.chem.conf.so
- StraightLineRule(int[]) - Constructor for class org.openmolecules.chem.conf.so.StraightLineRule
- StrainTerm - Class in com.actelion.research.chem.docking.scoring.idoscore
-
knowledge-based term for the internal strain of a ligand, composed of the pair-potentials (only atoms further away than 3 bonds from each other)
- StrainTerm(StereoMolecule) - Constructor for class com.actelion.research.chem.docking.scoring.idoscore.StrainTerm
- STRATEGY_ADAPTIVE_RANDOM - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- STRATEGY_LIKELY_RANDOM - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- STRATEGY_LIKELY_SYSTEMATIC - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- STRATEGY_PURE_RANDOM - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- STRETCH_ANDSCANS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- STRETCH_DELETESCANS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- STRETCH_ORSCANS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- StretchBend - Class in com.actelion.research.chem.forcefield.mmff
-
Stretch bending energy term class.
- StretchBend(Tables, MMFFMolecule, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Constructs a new stretch bend object.
- stretchBlt(int, int, int, int, int, int, int, int, int, int[], int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- stretchBlt(int, int, int, int, int, int, int, int, int, int[], int, int) - Method in class com.actelion.research.gui.wmf.WMF
- string(int) - Method in class smile.data.AttributeDataset.Row
-
Returns an element value in string format.
- STRING - smile.data.Attribute.Type
-
String attribute.
- String2DoubleArray - Class in com.actelion.research.util.convert
- String2DoubleArray() - Constructor for class com.actelion.research.util.convert.String2DoubleArray
- StringFunctions - Class in com.actelion.research.util
- StringFunctions() - Constructor for class com.actelion.research.util.StringFunctions
- StringReadChannel - Class in com.actelion.research.io
-
StringReadChannel 2007 MvK: Start implementation 25.06.2009 MvK: implementation changed 12.02.2014 MvK: added charset encoding to handle Umlaute.
- StringReadChannel(ReadableByteChannel) - Constructor for class com.actelion.research.io.StringReadChannel
- stringToColor(String) - Static method in class com.actelion.research.gui.hidpi.ColorUtils
- stringToDoubleArray(String) - Static method in class com.actelion.research.calc.VectorSOM
- stripIsotopInfo() - Method in class com.actelion.research.chem.Molecule
-
Removes all isotop information, i.e.
- stripSmallFragments() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Removes all unconnected fragments except for the largest one.
- stripSmallFragments(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Removes all unconnected fragments except for the largest one.
- stripStereoInformation() - Method in class com.actelion.research.chem.StereoMolecule
-
Removes defined and implicit stereo information from the molecule.
- up/down-bonds are converted to double bonds
- stereo centers are flagged to be unknown
- double bonds with implicit stereo configurations are converted into cross bonds
- all atom and bond ESR assignments are removed
- parity and CIP helper state is set to invalid, such that stereo calculation is redone, if needed. - strokeLine(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- strokeLine(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- StrokeLineCap<T> - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 4:20 PM
- StrokeLineJoin - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 4:20 PM
- StrongHasher() - Constructor for class com.actelion.research.chem.CanonizerUtil.StrongHasher
- StructureAssembler - Class in com.actelion.research.chem.io.pdb.parser
- StructureAssembler(List<int[]>, List<AtomRecord>, List<AtomRecord>) - Constructor for class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- StructureCalculator - Class in com.actelion.research.chem.descriptor.flexophore.calculator
-
Utility function based on the molecule's connections (groups, rings,...)
- StructureCalculator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- structureChanged() - Method in class com.actelion.research.gui.JStructureView
-
Should only be called if JStructureView's internal Molecule is changed from outside as: theStructureView.getMolecule().setFragment(false); The caller is responsible to update displayMol also, if it is different from the molecule.
- structureChanged(StereoMolecule) - Method in class com.actelion.research.gui.CompoundCollectionPane
- structureChanged(StereoMolecule) - Method in class com.actelion.research.gui.JStructureView
-
Updates the molecule used for display, drag & drop and clipboard transfer.
- structureChanged(StereoMolecule) - Method in interface com.actelion.research.gui.StructureListener
- structureChanged(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.gui.JStructureView
-
Updates both molecules used for display and for drag & drop/clipboard transfer.
- StructureInfo - Class in com.actelion.research.chem
- StructureInfo() - Constructor for class com.actelion.research.chem.StructureInfo
- StructureInfo(String, String, String, float, String) - Constructor for class com.actelion.research.chem.StructureInfo
- StructureListener - Interface in com.actelion.research.gui
- StructureNameResolver - Class in com.actelion.research.chem.name
-
Created by thomas on 7/13/17.
- StructureNameResolver() - Constructor for class com.actelion.research.chem.name.StructureNameResolver
- StructureSearch - Class in com.actelion.research.chem
- StructureSearch(StructureSearchSpecification, StructureSearchDataSource, StructureSearchController, ProgressController, DescriptorHandlerFactory) - Constructor for class com.actelion.research.chem.StructureSearch
-
This contructs a new structure search, which upon calling start() runs a multithreaded structure search on the structure rows provided by dataSource.
- StructureSearchController - Interface in com.actelion.research.chem
- StructureSearchDataSource - Interface in com.actelion.research.chem
- StructureSearchSpecification - Class in com.actelion.research.chem
- StructureSearchSpecification(int, byte[][], Object[], String, float) - Constructor for class com.actelion.research.chem.StructureSearchSpecification
-
Creates a complete specification for a substructure or similarity search with one or more query fragments or molecules.
- StructureTransferData - Class in com.actelion.research.chem
- StructureTransferData() - Constructor for class com.actelion.research.chem.StructureTransferData
- StructureTransferData(ExtendedMolecule, StructureInfo) - Constructor for class com.actelion.research.chem.StructureTransferData
- sub(double) - Method in interface smile.math.matrix.DenseMatrix
-
In place element-wise subtraction A = A - x
- sub(double) - Method in class smile.math.matrix.JMatrix
- sub(double, DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
Element-wise addition C = A - x
- sub(double, DenseMatrix) - Method in class smile.math.matrix.JMatrix
- sub(double, JMatrix) - Method in class smile.math.matrix.JMatrix
- sub(int, int) - Method in class com.actelion.research.util.datamodel.ModelXYIndex
- sub(int, int, double) - Method in interface smile.math.matrix.DenseMatrix
-
A[i][j] -= x
- sub(int, int, double) - Method in class smile.math.matrix.JMatrix
- sub(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- sub(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Subtracts that vector from this vector by component.
- sub(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
-
Substraction
- sub(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
-
Substraction
- sub(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
-
Substraction
- sub(List<Integer>) - Method in class com.actelion.research.util.datamodel.ModelXYClassLabel
- sub(List<Integer>) - Method in class com.actelion.research.util.datamodel.ModelXYIndex
- sub(List<Integer>, ModelXYClassLabel) - Method in class com.actelion.research.util.datamodel.ModelXYClassLabel
- sub(List<Integer>, ModelXYIndex) - Method in class com.actelion.research.util.datamodel.ModelXYIndex
-
Rows are copied from this into target.
- sub(DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
In place subtraction A = A - B
- sub(DenseMatrix) - Method in class smile.math.matrix.JMatrix
- sub(DenseMatrix, DenseMatrix) - Method in interface smile.math.matrix.DenseMatrix
-
C = A - B
- sub(DenseMatrix, DenseMatrix) - Method in class smile.math.matrix.JMatrix
- sub(JMatrix) - Method in class smile.math.matrix.JMatrix
- sub(JMatrix, JMatrix) - Method in class smile.math.matrix.JMatrix
- subC(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- SubFlexophoreGenerator - Class in com.actelion.research.chem.descriptor.flexophore.generator
-
SubFlexophoreGenerator
- SubFlexophoreGenerator(int, int, int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- SubFlexophoreGenerator(SubFlexophoreGenerator) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- SubFlexophoreGenerator.ViolatedConditionsCount - Class in com.actelion.research.chem.descriptor.flexophore.generator
- SubGraphExtractor - Class in com.actelion.research.chem.descriptor.flexophore.redgraph
-
SubGraphExtractor Creates substructures by fragmentation and summarizes them.
- SubGraphExtractor() - Constructor for class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor
- SubGraphIndices - Class in com.actelion.research.chem.descriptor.flexophore.redgraph
-
SubGraphIndices A class to handle indices in a molecular graph.
- SubGraphIndices() - Constructor for class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- SubStructSearchExhaustiveTreeWalker - Class in com.actelion.research.chem.mcs
- SubStructSearchExhaustiveTreeWalker() - Constructor for class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- SubstructureFilter - Class in com.actelion.research.chem
- SubstructureFilter(StereoMolecule) - Constructor for class com.actelion.research.chem.SubstructureFilter
- SubstructureFilter(StereoMolecule, int) - Constructor for class com.actelion.research.chem.SubstructureFilter
- subtract(double) - Method in class com.actelion.research.calc.Matrix
- subtract(double) - Method in class com.actelion.research.util.Angle
- subtract(Matrix) - Method in class com.actelion.research.calc.Matrix
- subtract(Angle) - Method in class com.actelion.research.util.Angle
- subtractByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- subtractFromCols(Matrix) - Method in class com.actelion.research.calc.Matrix
- suggestBondType(int, int) - Method in class com.actelion.research.chem.Molecule
-
Suggests either cBondTypeSingle or cBondTypeMetalLigand whatever seems more appropriate for a new bond between the two atoms.
- suggestNewX2AndY2(int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- SULFONAMIDE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- SULFONATE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- SULFONE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- SULFOXIDE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- Sulfur - Static variable in class com.actelion.research.chem.PeriodicTable
- sum() - Method in class com.actelion.research.util.datamodel.DoubleArray
- sum() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the sum of all elements in the matrix.
- sum() - Method in class smile.math.matrix.JMatrix
- sum(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- sum(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- sum(double[]) - Static method in class com.actelion.research.util.ArrayUtils
- sum(double[]) - Static method in class smile.math.Math
-
Returns the sum of an array.
- sum(float[]) - Static method in class smile.math.Math
-
Returns the sum of an array.
- sum(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- sum(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- sum(int[]) - Static method in class smile.math.Math
-
Returns the sum of an array.
- sum(long[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- summarizeAlkaneCluster(MolDistHistViz, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Summarizes alkane cluster.
- summary() - Method in class smile.data.AttributeDataset
-
Returns statistic summary.
- summary() - Method in class smile.data.AttributeVector
-
Returns statistic summary.
- SummaryFragments - Class in com.actelion.research.chem.properties.complexity
- SummaryFragments(ResultFragmentsStatistic) - Constructor for class com.actelion.research.chem.properties.complexity.SummaryFragments
- supportsImplicitHydrogen(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Whether an atom may be considered to carry implicit hydrogen atoms depends on the atomicNo of that atom.
- suspendEncoding() - Method in class com.actelion.research.util.Base64.OutputStream
-
Suspends encoding of the stream.
- SV - Variable in class org.machinelearning.svm.libsvm.svm_model
- sv_coef - Variable in class org.machinelearning.svm.libsvm.svm_model
- sv_indices - Variable in class org.machinelearning.svm.libsvm.svm_model
- svbksb(double[][], double[], double[][], int, int, double[], double[]) - Static method in class com.actelion.research.util.NumericalRecipes
- svd() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the singular value decomposition.
- svd() - Method in class smile.math.matrix.JMatrix
- svd(boolean) - Method in interface smile.math.matrix.DenseMatrix
-
Returns the singular value decomposition.
- svd(int) - Method in interface smile.math.matrix.Matrix
-
Find k largest approximate singular triples of a matrix by the Lanczos algorithm.
- svd(int, double, int) - Method in interface smile.math.matrix.Matrix
-
Find k largest approximate singular triples of a matrix by the Lanczos algorithm.
- SVD - Class in smile.math.matrix
-
Singular Value Decomposition.
- SVD(DenseMatrix, DenseMatrix, double[]) - Constructor for class smile.math.matrix.SVD
-
Constructor.
- svdcmp(double[][], int, int, double[], double[][]) - Static method in class com.actelion.research.util.NumericalRecipes
- SVGDepictor - Class in com.actelion.research.chem
- SVGDepictor(StereoMolecule, int, String) - Constructor for class com.actelion.research.chem.SVGDepictor
- SVGDepictor(StereoMolecule, String) - Constructor for class com.actelion.research.chem.SVGDepictor
- svm - Class in com.actelion.research.calc.regression.svm
- svm - Class in org.machinelearning.svm.libsvm
- svm() - Constructor for class com.actelion.research.calc.regression.svm.svm
- svm() - Constructor for class org.machinelearning.svm.libsvm.svm
- svm_check_parameter(svm_problem, svm_parameter) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_check_parameter(svm_problem, svm_parameter) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_check_probability_model(svm_model) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_check_probability_model(svm_model) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_cross_validation(svm_problem, svm_parameter, int, double[]) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_cross_validation(svm_problem, svm_parameter, int, double[]) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_get_labels(svm_model, int[]) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_get_labels(svm_model, int[]) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_get_nr_class(svm_model) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_get_nr_class(svm_model) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_get_nr_sv(svm_model) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_get_nr_sv(svm_model) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_get_sv_indices(svm_model, int[]) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_get_sv_indices(svm_model, int[]) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_get_svm_type(svm_model) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_get_svm_type(svm_model) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_get_svr_probability(svm_model) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_get_svr_probability(svm_model) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_load_model(BufferedReader) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_load_model(BufferedReader) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_load_model(String) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_load_model(String) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_model - Class in org.machinelearning.svm.libsvm
- svm_model() - Constructor for class org.machinelearning.svm.libsvm.svm_model
- svm_node - Class in org.machinelearning.svm.libsvm
- svm_node() - Constructor for class org.machinelearning.svm.libsvm.svm_node
- svm_parameter - Class in org.machinelearning.svm.libsvm
- svm_parameter() - Constructor for class org.machinelearning.svm.libsvm.svm_parameter
- svm_predict(svm_model, svm_node[]) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_predict(svm_model, svm_node[]) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_predict_probability(svm_model, svm_node[], double[]) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_predict_probability(svm_model, svm_node[], double[]) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_predict_values(svm_model, svm_node[], double[]) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_predict_values(svm_model, svm_node[], double[]) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_print_interface - Interface in org.machinelearning.svm.libsvm
- svm_problem - Class in org.machinelearning.svm.libsvm
- svm_problem() - Constructor for class org.machinelearning.svm.libsvm.svm_problem
- svm_save_model(String, svm_model) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_save_model(String, svm_model) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_set_print_string_function(svm_print_interface) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_set_print_string_function(svm_print_interface) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_train(svm_problem, svm_parameter) - Static method in class org.machinelearning.svm.libsvm.svm
- svm_train(svm_problem, svm_parameter, ProgressController) - Static method in class com.actelion.research.calc.regression.svm.svm
- svm_type - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- SVM_TYPE_C - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- SVM_TYPE_EPSILON_SVR - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- SVM_TYPE_NU - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- SVM_TYPE_NU_SVR - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- SVM_TYPE_ONE_CLASS - Static variable in class com.actelion.research.calc.regression.svm.SVMParameterHelper
- SVMParameterHelper - Class in com.actelion.research.calc.regression.svm
-
SVMParameterHelper
- SVMParameterHelper() - Constructor for class com.actelion.research.calc.regression.svm.SVMParameterHelper
- SVMRegression - Class in com.actelion.research.calc.regression.svm
-
SVMRegression Calculates the SVM regression for one Y column.
- SVMRegression() - Constructor for class com.actelion.research.calc.regression.svm.SVMRegression
- SVMRegression(ParameterSVM) - Constructor for class com.actelion.research.calc.regression.svm.SVMRegression
- swap(double[], double[]) - Static method in class smile.math.Math
-
Swap two arrays.
- swap(double[], int, int) - Static method in class smile.math.Math
-
Swap two elements of an array.
- swap(double[], int, int) - Static method in class smile.sort.SortUtils
-
Swap two positions.
- swap(float[], float[]) - Static method in class smile.math.Math
-
Swap two arrays.
- swap(float[], int, int) - Static method in class smile.math.Math
-
Swap two elements of an array.
- swap(float[], int, int) - Static method in class smile.sort.SortUtils
-
Swap two positions.
- swap(int[], int[]) - Static method in class smile.math.Math
-
Swap two arrays.
- swap(int[], int, int) - Static method in class smile.math.Math
-
Swap two elements of an array.
- swap(int[], int, int) - Static method in class smile.sort.SortUtils
-
Swap two positions.
- swap(E[], E[]) - Static method in class smile.math.Math
-
Swap two arrays.
- swap(Object[], int, int) - Static method in class smile.math.Math
-
Swap two elements of an array.
- swap(Object[], int, int) - Static method in class smile.sort.SortUtils
-
Swap two positions.
- swapAtoms(int, int) - Method in class com.actelion.research.chem.Molecule
-
Swaps two atoms' indexes/locations in the atom table.
- swapAtoms(int, int) - Method in class com.actelion.research.chem.Molecule3D
- swapBonds(int, int) - Method in class com.actelion.research.chem.Molecule
-
Swaps two bonds' indexes/locations in the atom table.
- swapNodes(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- swapRows(int, int) - Method in class com.actelion.research.calc.Matrix
- SwingCheckBox - Class in com.actelion.research.gui.swing
- SwingCheckBox(String) - Constructor for class com.actelion.research.gui.swing.SwingCheckBox
- SwingComboBox - Class in com.actelion.research.gui.swing
- SwingComboBox() - Constructor for class com.actelion.research.gui.swing.SwingComboBox
- SwingComponent - Class in com.actelion.research.gui.swing
- SwingComponent(JComponent) - Constructor for class com.actelion.research.gui.swing.SwingComponent
- SwingDialog - Class in com.actelion.research.gui.swing
- SwingDialog(Dialog, String) - Constructor for class com.actelion.research.gui.swing.SwingDialog
- SwingDialog(Frame, String) - Constructor for class com.actelion.research.gui.swing.SwingDialog
- SwingDialogHelper - Class in com.actelion.research.gui.swing
- SwingDialogHelper(SwingEditorArea) - Constructor for class com.actelion.research.gui.swing.SwingDialogHelper
- SwingDrawContext - Class in com.actelion.research.gui.swing
- SwingDrawContext(Graphics2D) - Constructor for class com.actelion.research.gui.swing.SwingDrawContext
- SwingEditorArea - Class in com.actelion.research.gui.editor
- SwingEditorArea(StereoMolecule, int) - Constructor for class com.actelion.research.gui.editor.SwingEditorArea
- SwingEditorDialog - Class in com.actelion.research.gui.editor
- SwingEditorDialog(Dialog, Reaction) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a modal chemical editor dialog to edit a chemical reaction.
- SwingEditorDialog(Dialog, Reaction, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a modal chemical editor dialog to edit a chemical reaction.
- SwingEditorDialog(Dialog, StereoMolecule) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a modal chemical editor dialog to edit a single molecule, which may, of course, consist of multiple disconnected fragments.
- SwingEditorDialog(Dialog, StereoMolecule[], Dialog.ModalityType) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a modal chemical editor dialog to edit multiple molecules in one editor pane.
- SwingEditorDialog(Dialog, StereoMolecule, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a chemical editor dialog to edit a single molecule, which may, of course, consist of multiple disconnected fragments.
- SwingEditorDialog(Frame, Reaction) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a modal chemical editor dialog to edit a chemical reaction.
- SwingEditorDialog(Frame, Reaction, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a modal chemical editor dialog to edit a chemical reaction.
- SwingEditorDialog(Frame, StereoMolecule) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a modal chemical editor dialog to edit a single molecule, which may, of course, consist of multiple disconnected fragments.
- SwingEditorDialog(Frame, StereoMolecule[], Dialog.ModalityType) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a modal chemical editor dialog to edit multiple molecules in one editor pane.
- SwingEditorDialog(Frame, StereoMolecule, Dialog.ModalityType) - Constructor for class com.actelion.research.gui.editor.SwingEditorDialog
-
Creates a chemical editor dialog to edit a single molecule, which may, of course, consist of multiple disconnected fragments.
- SwingEditorPanel - Class in com.actelion.research.gui.editor
- SwingEditorPanel(Reaction) - Constructor for class com.actelion.research.gui.editor.SwingEditorPanel
-
Creates a chemical editor panel to edit the given chemical reaction.
- SwingEditorPanel(StereoMolecule) - Constructor for class com.actelion.research.gui.editor.SwingEditorPanel
-
Creates a chemical editor panel to edit the given molecule.
- SwingEditorPanel(StereoMolecule[]) - Constructor for class com.actelion.research.gui.editor.SwingEditorPanel
-
Creates a chemical editor panel to edit multiple molecules.
- SwingEditorPanel(StereoMolecule, int) - Constructor for class com.actelion.research.gui.editor.SwingEditorPanel
-
Creates a chemical editor panel to draw a molecule, reaction, or set of molecules, depending on the mode.
- SwingEditorToolbar - Class in com.actelion.research.gui.editor
- SwingEditorToolbar(SwingEditorArea, int) - Constructor for class com.actelion.research.gui.editor.SwingEditorToolbar
- SwingKeyHandler - Class in com.actelion.research.gui.swing
- SwingKeyHandler() - Constructor for class com.actelion.research.gui.swing.SwingKeyHandler
- SwingLabel - Class in com.actelion.research.gui.swing
- SwingLabel(String) - Constructor for class com.actelion.research.gui.swing.SwingLabel
- SwingMouseHandler - Class in com.actelion.research.gui.swing
- SwingMouseHandler() - Constructor for class com.actelion.research.gui.swing.SwingMouseHandler
- SwingPopupMenu - Class in com.actelion.research.gui.swing
- SwingPopupMenu(JComponent, DialogEventConsumer) - Constructor for class com.actelion.research.gui.swing.SwingPopupMenu
- SwingTextField - Class in com.actelion.research.gui.swing
- SwingTextField(int, int) - Constructor for class com.actelion.research.gui.swing.SwingTextField
- SWISS - com.actelion.research.util.Formatter.LocaleFormat
- switchBit(int) - Method in class com.actelion.research.util.datamodel.IntVec
- symbol(int) - Static method in class com.actelion.research.chem.PeriodicTable
- SYMBOL_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SYMMETRY_C1C1_OR_C1D1 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
- SYMMETRY_C1D2 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
- SYMMETRY_D1D1 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
- SYMMETRY_D1D2_OR_D2D2 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
- SymmetryCalculator - Class in com.actelion.research.chem.properties.complexity
- SymmetryCalculator() - Constructor for class com.actelion.research.chem.properties.complexity.SymmetryCalculator
- SymmetryCorrectedRMSDCalculator - Class in com.actelion.research.chem.conf
-
employing RMSD calculation using a HungarianAlgorithm for the atom assignment to correct for overestimated RMSD values obtained by conventional methods for molecules with symmetric substructures based on: dx.doi.org/10.1021/ci400534h
- SymmetryCorrectedRMSDCalculator(Conformer, Conformer) - Constructor for class com.actelion.research.chem.conf.SymmetryCorrectedRMSDCalculator
- Synthon - Class in com.actelion.research.chem.combinatorialspace
-
a Synthon is a reaction-specific representation of a building block, already encoding structural changes that occur upon the reaction (e.g.
- Synthon(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.combinatorialspace.Synthon
- SynthonCreator - Class in com.actelion.research.chem.chemicalspaces.synthon
- SynthonCreator() - Constructor for class com.actelion.research.chem.chemicalspaces.synthon.SynthonCreator
- SynthonReactor - Class in com.actelion.research.chem.chemicalspaces.synthon
- SynthonReactor() - Constructor for class com.actelion.research.chem.chemicalspaces.synthon.SynthonReactor
- systemExec(String[]) - Static method in class com.actelion.research.util.Platform
-
Wrapper for Runtime.exec() that allows different handling by platform This method fixes forking issues in Windows when starting Mercury (by default new processes do not seem to be forked correctly)
T
- T - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- TA_BASELINE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_BOTTOM - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_CENTER - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_LEFT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_NOUPDATECP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_RIGHT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_TOP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_UPDATECP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TAB_STRING - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- table - Variable in class com.actelion.research.chem.forcefield.mmff.Separation
- table - Variable in class com.actelion.research.chem.forcefield.mmff.table.Def
- table(String) - Static method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Returns a table given a table name.
- tableChanged(TableModelEvent) - Method in class com.actelion.research.gui.table.JTableWithRowNumbers
- TableModelString - Class in com.actelion.research.util.datamodel.table
-
TableModelText Data model for an only text containing table
- TableModelString() - Constructor for class com.actelion.research.util.datamodel.table.TableModelString
- TableModelString(int, int) - Constructor for class com.actelion.research.util.datamodel.table.TableModelString
- TableModelString(List<String>, List<String>) - Constructor for class com.actelion.research.util.datamodel.table.TableModelString
- Tables - Class in com.actelion.research.chem.forcefield.mmff
-
A collection of tables with the official parameters of the MMFF94/MMFF94s force field variants.
- Tables(String, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.Tables
-
Construct a new Tables object.
- TAG_AAS_ABBR1 - Static variable in class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
- TAG_AAS_NAME - Static variable in class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
- TAG_ACTIVATION_FCT - Static variable in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- TAG_ACTNO - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_ANISOU - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ATOM - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ATOMS - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_AUTHOR - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_BONDS - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_BONDS_AT_MAX_FRAGS_CALC - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_C - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_CACHE_SIZE - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_CAVEAT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_CISPEP - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_COEF0 - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_COMPLEXITY - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_COMPND - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_CONECT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_CONFORMERSET - Static variable in class com.actelion.research.util.ConstantsDWAR
-
Contains the idcode and the 3d coordinates.
- TAG_COOR - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_COOR2 - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_COOR3D - Static variable in class com.actelion.research.util.ConstantsDWAR
-
Can be one or multiple sets of 3D coordinates.
- TAG_CRYST1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_DBREF - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_DBREF1_DBREF2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_DEGREE - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_END - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ENDMDL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_EPSILON - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_EXPDTA - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_FACTORS - Static variable in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- TAG_FORMUL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_FRACTAL_DIM - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_FREQUENCY - Static variable in class com.actelion.research.chem.shredder.Fragment
- TAG_FREQUENCY_ONE_PER_MOLECULE - Static variable in class com.actelion.research.chem.shredder.Fragment
- TAG_GAMMA - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_HEADER - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HELIX - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HET - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HETATM - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HETNAM - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HETSYN - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ID - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_ID_QUERY - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_IDCODE - Static variable in class com.actelion.research.util.ConstantsDWAR
-
Deprecated.
- TAG_IDCODE2 - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_INNERLAYER_ARCITECTURE - Static variable in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- TAG_JRNL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_KERNEL - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_KEYWDS - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_LAMBDA - Static variable in class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- TAG_LAMBDA - Static variable in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- TAG_LIGAND_EFFICIENCY - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_LINK - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MASTER - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MAX_NODES - Static variable in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- TAG_MAX_NUM_UNIQUE_FRAGMENTS_CALC - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_MAXIMUM_SLOPE - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_MDLTYP - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MEAN - Static variable in class com.actelion.research.calc.statistics.StatisticsOverview
- TAG_MEDIAN - Static variable in class com.actelion.research.calc.statistics.StatisticsOverview
- TAG_MESSAGE - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_MODEL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ModelExhaustiveStatistics - Static variable in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- TAG_MODRES - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MTRIX1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MTRIX2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MTRIX3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MTRY - Static variable in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- TAG_MultipleNonOverlapSolution - Static variable in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- TAG_MW - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_NAME - Static variable in class com.actelion.research.calc.regression.ParameterRegressionMethod
- TAG_NAME - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_NAMES - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_NEIGHBOURS - Static variable in class com.actelion.research.calc.regression.knn.ParameterKNN
- TAG_NODE_SIZE - Static variable in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- TAG_NR_WEIGHT - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_NU - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_NUM_BONDS_AT_MAXIMUM_FREQ - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_NUM_BONDS_AT_MAXIMUM_SLOPE - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_NUMMDL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_OBSOLTE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ORIGX1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ORIGX2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ORIGX3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_P - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_PERCENTILE05 - Static variable in class com.actelion.research.calc.statistics.StatisticsOverview
- TAG_PERCENTILE95 - Static variable in class com.actelion.research.calc.statistics.StatisticsOverview
- TAG_PROBABILITY - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_QUERY_IDENTIFIER - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_RATIO_NON_SYMMETRIC_ATOMS - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_RATIO_USED_BONDS_UP_TO_MAX_FREQ - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_REACTION_CODE - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_REACTION_COORD - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_REACTION_DRAW_OBJ - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_REACTION_MAPPING - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_RECORD_NO - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_RELATIVE_FREQUNCY - Static variable in class com.actelion.research.chem.shredder.Fragment
- TAG_REMARK - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK_N - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK0 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ResultFragmentsStatistic - Static variable in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- TAG_REVDAT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SCALE1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SCALE2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SCALE3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SDV - Static variable in class com.actelion.research.calc.statistics.StatisticsOverview
- TAG_SEQADV - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SEQRES - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SHEET - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SHRINKING - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_SIMILARITY - Static variable in class com.actelion.research.chem.descriptor.DescriptorHelper
- TAG_SITE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SIZE - Static variable in class com.actelion.research.chem.shredder.Fragment
- TAG_SMILES - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_SOURCE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SOURCE - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_SPLIT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SPRSDE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SSBOND - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_STRING - Static variable in class com.actelion.research.calc.regression.ParameterRegressionMethod
- TAG_STRUCTURE_EXCLUDE - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_STRUCTURE_INCLUDE - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_SUM_UNIQUE_FRAGMENTS_CALC - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_SUM_UNIQUE_FRAGMENTS_UNTIL_MAX - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_SVM_TYPE - Static variable in class com.actelion.research.calc.regression.svm.ParameterSVM
- TAG_TER - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_TEST_CLASS - Static variable in enum com.actelion.research.calc.classification.ClassificationAttr
- TAG_TITLE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_TREES - Static variable in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- TAG_VIZ_INFO_ENCODED - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- tail(int) - Method in class smile.data.AttributeDataset
-
Returns the last few rows.
- tail(int) - Method in class smile.data.AttributeVector
-
Shows the last few rows.
- tan() - Method in class com.actelion.research.util.Angle
- tan() - Method in class smile.math.Complex
-
Returns the complex tangent.
- tan(double) - Static method in class smile.math.Math
-
Returns the trigonometric tangent of an angle.
- tanh(double) - Static method in class smile.math.Math
-
Returns the hyperbolic tangent of a double value.
- TANH - smile.regression.NeuralNetwork.ActivationFunction
-
Hyperbolic tangent activation function: f(v)=tanh(v)
- TANIMOTO - Static variable in class com.actelion.research.util.datamodel.ByteVec
- TANIMOTO - Static variable in class com.actelion.research.util.DoubleVec
- TANIMOTO_INV - Static variable in class com.actelion.research.util.datamodel.ByteVec
- TANIMOTO_INV - Static variable in class com.actelion.research.util.DoubleVec
- tau - Variable in class smile.math.matrix.QR
-
The diagonal of R for this implementation.
- TAUTOMER - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- TautomerHelper - Class in com.actelion.research.chem
- TautomerHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.TautomerHelper
- test() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- test(double[][], double[]) - Method in class smile.regression.RandomForest
-
Test the model on a validation dataset.
- test(double[][], double[], RegressionMeasure[]) - Method in class smile.regression.RandomForest
-
Test the model on a validation dataset.
- test(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
- test00() - Static method in class com.actelion.research.calc.MatrixTests
- test01() - Static method in class com.actelion.research.calc.BoxCox
- test01() - Static method in class com.actelion.research.calc.MatrixTests
- test01() - Static method in class com.actelion.research.util.datamodel.ByteVec
- test02() - Static method in class com.actelion.research.calc.MatrixTests
- test03() - Static method in class com.actelion.research.calc.MatrixTests
- test04() - Static method in class com.actelion.research.calc.MatrixTests
- test05() - Static method in class com.actelion.research.calc.MatrixTests
- test06() - Static method in class com.actelion.research.calc.MatrixTests
- test07() - Static method in class com.actelion.research.calc.MatrixTests
- test08() - Static method in class com.actelion.research.calc.MatrixTests
- testChiralDia - Class in com.actelion.research.chem.contrib
- testChiralDia() - Constructor for class com.actelion.research.chem.contrib.testChiralDia
- testDescriptor01X() - Static method in class com.actelion.research.calc.MatrixTests
- testDescriptor01Y() - Static method in class com.actelion.research.calc.MatrixTests
- testDiaID - Class in com.actelion.research.chem.contrib
- testDiaID() - Constructor for class com.actelion.research.chem.contrib.testDiaID
- testFolder(String, String, String, Sdf.OnMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.Sdf
-
Tests an entire pair of folders, one containing SDF files and the other containing reference files.
- testHoses - Class in com.actelion.research.chem.contrib
- testHoses() - Constructor for class com.actelion.research.chem.contrib.testHoses
- testLonglyX() - Static method in class com.actelion.research.calc.MatrixTests
-
http://itl.nist.gov/div898/strd/lls/data/LINKS/DATA/Longley.dat
- testLonglyY() - Static method in class com.actelion.research.calc.MatrixTests
-
http://www.itl.nist.gov/div898/strd/lls/data/Longley.shtml Y Matrix
- testMain01() - Static method in class com.actelion.research.calc.MatrixTests
- testMainHenrion() - Static method in class com.actelion.research.calc.MatrixTests
- testMatrix_XWine() - Static method in class com.actelion.research.calc.MatrixTests
- testMatrix_YWine() - Static method in class com.actelion.research.calc.MatrixTests
-
Validation data for PLS from Abdi, PLS, Encyclopedia of Social Sciences Reasearch Methods (2003).
- testMatrix02() - Static method in class com.actelion.research.calc.MatrixTests
- testMatrixHenrion01() - Static method in class com.actelion.research.calc.MatrixTests
- testS1() - Static method in class com.actelion.research.util.datamodel.ByteVec
- testSimple1X(int) - Static method in class com.actelion.research.calc.MatrixTests
- testSimple1Y() - Static method in class com.actelion.research.calc.MatrixTests
- testSimple2X(int) - Static method in class com.actelion.research.calc.MatrixTests
- testTakeda1() - Static method in class com.actelion.research.util.datamodel.ByteVec
- TetrahedralStereoRule - Class in org.openmolecules.chem.conf.so
- TetrahedralStereoRule(StereoMolecule, int[]) - Constructor for class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- TEXT_EXTENSION_LABEL - Static variable in class com.actelion.research.util.AnimatedGIFWriter
- TextClipboardHandler - Class in com.actelion.research.gui.clipboard
- TextDrawingObject - Class in com.actelion.research.chem
- TextDrawingObject() - Constructor for class com.actelion.research.chem.TextDrawingObject
- TextDrawingObject(String) - Constructor for class com.actelion.research.chem.TextDrawingObject
- TextDrawingObject(String, double, double) - Constructor for class com.actelion.research.chem.TextDrawingObject
- TextDrawingObject(String, double, double, double, int) - Constructor for class com.actelion.research.chem.TextDrawingObject
- TextDrawingObjectDialogBuilder - Class in com.actelion.research.gui.editor
- TextDrawingObjectDialogBuilder(GenericDialogHelper, TextDrawingObject) - Constructor for class com.actelion.research.gui.editor.TextDrawingObjectDialogBuilder
- textOut(int, int, String) - Method in class com.actelion.research.gui.wmf.MetaFile
- textOut(int, int, String) - Method in class com.actelion.research.gui.wmf.WMF
- theta(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns 'theta0' the equilibrium angle for a given index in the table.
- theta(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns 'theta0' the ideal angle given a molecule and three connected atoms which form an angle.
- theta0 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- theta0 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- thinSize() - Static method in class com.actelion.research.gui.dock.ShadowBorder
- threadMaster - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- ThreadMaster - Interface in com.actelion.research.calc
- threadMustDie() - Method in class com.actelion.research.calc.DataProcessor
- threadMustDie() - Method in interface com.actelion.research.calc.ThreadMaster
- threadMustDie() - Method in class com.actelion.research.gui.JProgressDialog
- threadMustDie() - Method in class com.actelion.research.gui.JProgressPanel
- THRESH_HISTOGRAM_SIMILARITY - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- THRESH_HISTOGRAM_SIMILARITY - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- THRESH_SIMILARITY_COMPARISON_NODE - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- THRESH_SIMILARITY_HARD_MATCH - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
-
Similarity value distribution of the interaction table (April 2020).
- TIE_BREAK_FREE_VALENCE_ATOMS - Static variable in class com.actelion.research.chem.Canonizer
- times(double) - Method in class smile.math.Complex
-
Scalar multiplication.* Returns this * b.
- times(Complex) - Method in class smile.math.Complex
-
Returns this * b.
- timestamp - Variable in class smile.data.Datum
-
Timestamp of datum in case of transactional data.
- TINY - Static variable in class com.actelion.research.calc.Matrix
- TINY_FACTOR - Static variable in class com.actelion.research.calc.histogram.ConstantsHistogram
- TINY04 - Static variable in class com.actelion.research.calc.Matrix
- TINY08 - Static variable in class com.actelion.research.calc.Matrix
- TINY16 - Static variable in class com.actelion.research.calc.Matrix
- to(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns a vector that points from this vector to that vector.
- toArray() - Method in class com.actelion.research.calc.Matrix
- toArray() - Method in class com.actelion.research.chem.SortedStringList
- toArray() - Method in class com.actelion.research.chem.UniqueStringList
- toArray() - Method in class com.actelion.research.util.datamodel.ByteVec
- toArray() - Method in class com.actelion.research.util.datamodel.IntVec
- toArray() - Method in class com.actelion.research.util.DoubleVec
- toArray(double[]) - Method in class smile.data.Dataset
-
Returns an array containing the response variable of the elements in this dataset in proper sequence (from first to last element).
- toArray(int[]) - Method in class smile.data.Dataset
-
Returns an array containing the class labels of the elements in this dataset in proper sequence (from first to last element).
- toArray(E[]) - Method in class smile.data.Dataset
-
Returns an array containing all of the elements in this dataset in proper sequence (from first to last element); the runtime type of the returned array is that of the specified array.
- toArray(String[]) - Method in class smile.data.Dataset
-
Returns an array containing the string names of the elements in this dataset in proper sequence (from first to last element).
- toArray(Timestamp[]) - Method in class smile.data.Dataset
-
Returns an array containing the timestamps of the elements in this dataset in proper sequence (from first to last element).
- toArray(List<String>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toArray(T[]) - Method in class com.actelion.research.util.SortedList
- toArray(T[]) - Method in class com.actelion.research.util.UniqueList
- toArrayStrStr(List<List<String>>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toBinaryString() - Method in class com.actelion.research.util.datamodel.ByteVec
- toBinaryStringDense() - Method in class com.actelion.research.util.datamodel.ByteVec
- toByteArray(double[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toByteArray(int) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toByteArray(int[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toByteArray(long) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toBytes(String, int) - Static method in class com.actelion.research.util.BinaryDecoder
-
Convenience method to directly decode a String-encoded byte array.
- toDate(double) - Method in class smile.data.DateAttribute
-
Retruns the date object from internal double encoding.
- toDegrees() - Method in class com.actelion.research.util.Angle
- toDegrees(double) - Static method in class smile.math.Math
-
Converts an angle measured in radians to an approximately equivalent angle measured in degrees.
- toDoubleArray(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toDoubleArray(List<Double>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toDoubleBitWise() - Method in class com.actelion.research.util.datamodel.IntVec
- toIntArray(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toIntArray(Collection<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Converts a List of Integer to an int[]
- toIntArray(Collection<Integer>) - Static method in class com.actelion.research.util.ArrayUtils
-
Converts a List of Integer to an int[]
- toIntByteWise() - Method in class com.actelion.research.util.datamodel.IntVec
- toIntegerListX() - Method in class com.actelion.research.util.datamodel.ModelXY
- toInts(String, int) - Static method in class com.actelion.research.util.BinaryDecoder
-
Convenience method to directly decode a String-encoded int array.
- tol - Variable in class smile.math.matrix.SVD
-
Threshold of estimated roundoff.
- toList() - Method in class com.actelion.research.util.datamodel.IntArray
- toList() - Method in class com.actelion.research.util.hash.HashSetInt
- toList(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toList(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- toList(int[]) - Static method in class com.actelion.research.util.datamodel.IntArray
- toList(int[], List<Integer>) - Static method in class com.actelion.research.util.ArrayUtils
- toList(String[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toList(String[]) - Static method in class com.actelion.research.util.ArrayUtils
- toList(T[]) - Static method in class com.actelion.research.util.ArrayUtils
- TOLX - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- toMolecule() - Method in class com.actelion.research.chem.conf.Conformer
-
Copies this Conformer's atom coordinates to the associated molecule.
- toMolecule(StereoMolecule) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies this Conformer's atom coordinates to the given molecule.
- TOOL_CHAINCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_CTEXTCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_CURSOR_BASE - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_DELETECURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_FISTCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_HANDCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_HANDPLUSCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_LASSOCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_LASSOPLUSCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_POINTERCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_SELECTRECTCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_SELECTRECTPLUSCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_ZOOMCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- ToolbarSelectionChange - Interface in com.actelion.research.share.gui.editor.actions
-
Created by rufenec on 5/3/16.
- toolChanged(int) - Method in class com.actelion.research.gui.editor.GenericDrawArea
- toolChanged(int) - Method in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- TOP - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- toQuaternion() - Method in class com.actelion.research.chem.alignment3d.transformation.ExponentialMap
- toRadians(double) - Static method in class smile.math.Math
-
Converts an angle measured in degrees to an approximately equivalent angle measured in radians.
- toRow() - Method in class com.actelion.research.calc.Matrix
- torsion - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Torsion - Class in com.actelion.research.chem.forcefield.mmff.table
- Torsion - Class in com.actelion.research.chem.forcefield.mmff.type
-
The torsion type class provides a static function for getting the torsion type of a torsion angle.
- Torsion() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Torsion
- Torsion(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion
- TORSION_GREEN - Static variable in class com.actelion.research.chem.conf.TorsionDB
- TORSION_NOT_FOUND - Static variable in class com.actelion.research.chem.conf.TorsionDB
- TORSION_RED - Static variable in class com.actelion.research.chem.conf.TorsionDB
- TORSION_YELLOW - Static variable in class com.actelion.research.chem.conf.TorsionDB
- Torsion.Kb - Class in com.actelion.research.chem.forcefield.mmff.table
- TorsionAngle - Class in com.actelion.research.chem.forcefield.mmff
-
Torsional Angle energy term class.
- TorsionAngle(Tables, MMFFMolecule, int, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Construct a new torsion angle energy term.
- TorsionConstraint - Class in com.actelion.research.chem.potentialenergy
- TorsionConstraint(Conformer, int[], double, double) - Constructor for class com.actelion.research.chem.potentialenergy.TorsionConstraint
-
Term that forces a torsion angle with a harmonic potential to a range of acceptable values (range given by the width)
- TorsionDB - Class in com.actelion.research.chem.conf
- TorsionDescriptor - Class in com.actelion.research.chem.conf
- TorsionDescriptor(float[], float[]) - Constructor for class com.actelion.research.chem.conf.TorsionDescriptor
- TorsionDescriptorHelper - Class in com.actelion.research.chem.conf
- TorsionDescriptorHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.TorsionDescriptorHelper
- TorsionDescriptorHelper(StereoMolecule, int[]) - Constructor for class com.actelion.research.chem.conf.TorsionDescriptorHelper
- TorsionDetail - Class in com.actelion.research.chem.conf
- TorsionDetail() - Constructor for class com.actelion.research.chem.conf.TorsionDetail
-
This creates an empty torsion classification detail, which multiply can be used to classify the environment of a rotatable bond.
- TorsionPrediction - Class in com.actelion.research.chem.conf
- TorsionPrediction(StereoMolecule, int[]) - Constructor for class com.actelion.research.chem.conf.TorsionPrediction
- TorsionRelevanceHelper - Class in com.actelion.research.chem.conf
- TorsionRelevanceHelper() - Constructor for class com.actelion.research.chem.conf.TorsionRelevanceHelper
- TorsionRule - Class in org.openmolecules.chem.conf.so
- TorsionRule(short[], short[], short[][], int[], int[], int) - Constructor for class org.openmolecules.chem.conf.so.TorsionRule
- TorsionSet - Class in org.openmolecules.chem.conf.gen
- TorsionSet(int[], int[], int[], int[], double) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSet
-
Creates a new conformer description from torsion and conformer indexes.
- TorsionSet(TorsionSet) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSet
-
Deep-Copy constructor not including collision intensities
- TorsionSetEliminationRule - Class in org.openmolecules.chem.conf.gen
- TorsionSetEliminationRule(long[], long[], double) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
- TorsionSetStrategy - Class in org.openmolecules.chem.conf.gen
-
Knowing all rotatable bonds of an underlying molecule and knowing those rigid fragments that are connected by them, the TorsionSetStrategy provides a mechanism to deliver valid and unique torsion sets, each effectively defining an individual conformer.
- TorsionSetStrategy(RotatableBond[], RigidFragment[]) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- TorsionSetStrategyAdaptiveRandom - Class in org.openmolecules.chem.conf.gen
- TorsionSetStrategyAdaptiveRandom(RotatableBond[], RigidFragment[], boolean, boolean, long) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategyAdaptiveRandom
-
This torsion set strategy produces random sets of torsion indices until a torsion set collides.
- TorsionSetStrategyLikelySystematic - Class in org.openmolecules.chem.conf.gen
-
TorsionSetStrategy that systematically creates all possible TorsionSets in batches while keeping a focus on the likelyhood of individual torsions.
- TorsionSetStrategyLikelySystematic(RotatableBond[], RigidFragment[]) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategyLikelySystematic
- TorsionSetStrategyRandom - Class in org.openmolecules.chem.conf.gen
- TorsionSetStrategyRandom(RotatableBond[], RigidFragment[], boolean, long) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
-
This simple TorsionSetStrategy produces random sets of torsion indexes in a loop.
- toShortString(long, int) - Static method in class com.actelion.research.util.DoubleFormat
-
Converts the value with the given exponent into a short string representation using the scientific notation if it is more compact.
- toSortedArray() - Method in class com.actelion.research.chem.UniqueStringList
- toSortedArray(T[]) - Method in class com.actelion.research.util.UniqueList
- toSortedString(List<String>) - Static method in class com.actelion.research.util.StringFunctions
- toString() - Method in class com.actelion.research.calc.classification.PrecisionAndRecall
- toString() - Method in class com.actelion.research.calc.histogram.Histogram
-
First row: bins, upper border.
- toString() - Method in class com.actelion.research.calc.histogram.IntegerHistogram
- toString() - Method in class com.actelion.research.calc.Matrix
- toString() - Method in class com.actelion.research.calc.regression.gaussianprocess.ParameterGaussianProcess
- toString() - Method in class com.actelion.research.calc.regression.knn.ParameterKNN
- toString() - Method in class com.actelion.research.calc.regression.linear.pls.boxcox.ParameterPLSBoxCox
- toString() - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- toString() - Method in class com.actelion.research.calc.regression.median.ParameterMedian
- toString() - Method in class com.actelion.research.calc.regression.ModelError
- toString() - Method in class com.actelion.research.calc.regression.neuralnetwork.ParameterNeuralNetwork
- toString() - Method in class com.actelion.research.calc.regression.randomforest.ParameterRandomForest
- toString() - Method in class com.actelion.research.calc.regression.svm.ParameterSVM
- toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianLong
- toString() - Method in class com.actelion.research.calc.statistics.ModelStatisticsOverview
- toString() - Method in class com.actelion.research.calc.statistics.ModelStatisticsOverviewMedian
- toString() - Method in class com.actelion.research.calc.statistics.StatisticsOverview
- toString() - Method in class com.actelion.research.chem.AbstractDrawingObject
- toString() - Method in class com.actelion.research.chem.alignment3d.transformation.Quaternion
- toString() - Method in class com.actelion.research.chem.conf.ConformerSet
- toString() - Method in class com.actelion.research.chem.conf.TorsionDescriptor
- toString() - Method in class com.actelion.research.chem.Coordinates
- toString() - Method in class com.actelion.research.chem.DepictorTransformation
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- toString() - Method in class com.actelion.research.chem.DrawingObjectList
- toString() - Method in class com.actelion.research.chem.Element
- toString() - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
- toString() - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- toString() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns a string form of this vector.
- toString() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- toString() - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- toString() - Method in class com.actelion.research.chem.io.pdb.converter.AminoAcidLabeled
- toString() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- toString() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- toString() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- toString() - Method in class com.actelion.research.chem.Molecule3D
- toString() - Method in class com.actelion.research.chem.Mutation
- toString() - Method in class com.actelion.research.chem.PeriodicTable
- toString() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- toString() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- toString() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- toString() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- toString() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- toString() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- toString() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- toString() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- toString() - Method in class com.actelion.research.chem.SDFileMolecule
- toString() - Method in class com.actelion.research.chem.StructureSearchSpecification
- toString() - Method in class com.actelion.research.chem.SVGDepictor
- toString() - Method in class com.actelion.research.gui.ComboBoxColorItem
- toString() - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- toString() - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- toString() - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- toString() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- toString() - Method in class com.actelion.research.util.Angle
- toString() - Method in class com.actelion.research.util.CommandLineParser
- toString() - Method in class com.actelion.research.util.datamodel.ByteVec
-
Converts a byte into its decimal.
- toString() - Method in class com.actelion.research.util.datamodel.DoubleArray
- toString() - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- toString() - Method in class com.actelion.research.util.datamodel.IntArray
- toString() - Method in class com.actelion.research.util.datamodel.IntegerDouble
- toString() - Method in class com.actelion.research.util.datamodel.IntVec
- toString() - Method in class com.actelion.research.util.datamodel.ScorePoint
- toString() - Method in class com.actelion.research.util.datamodel.table.TableModelString
- toString() - Method in class com.actelion.research.util.DoubleVec
- toString() - Method in class com.actelion.research.util.ErrorHashMap
- toString() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- toString() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- toString() - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
- toString() - Method in class org.openmolecules.chem.conf.so.ConformationRule
- toString() - Method in class org.openmolecules.chem.conf.so.DistanceRule
- toString() - Method in class org.openmolecules.chem.conf.so.PlaneRule
- toString() - Method in class org.openmolecules.chem.conf.so.StraightLineRule
- toString() - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- toString() - Method in class org.openmolecules.chem.conf.so.TorsionRule
- toString() - Method in class smile.clustering.CLARANS
- toString() - Method in class smile.clustering.KMeans
- toString() - Method in class smile.clustering.linkage.CompleteLinkage
- toString() - Method in class smile.clustering.linkage.SingleLinkage
- toString() - Method in class smile.clustering.linkage.UPGMALinkage
- toString() - Method in class smile.clustering.linkage.UPGMCLinkage
- toString() - Method in class smile.clustering.linkage.WardLinkage
- toString() - Method in class smile.clustering.linkage.WPGMALinkage
- toString() - Method in class smile.clustering.linkage.WPGMCLinkage
- toString() - Method in class smile.data.Attribute
- toString() - Method in class smile.data.AttributeDataset.Row
- toString() - Method in class smile.data.AttributeDataset
- toString() - Method in class smile.data.AttributeVector
- toString() - Method in class smile.math.Complex
- toString() - Method in class smile.math.kernel.GaussianKernel
- toString() - Method in class smile.math.matrix.JMatrix
- toString() - Method in class smile.math.rbf.GaussianRadialBasis
- toString() - Method in class smile.stat.distribution.GaussianDistribution
- toString() - Method in class smile.stat.distribution.Mixture
- toString() - Method in class smile.validation.RMSE
- toString(boolean) - Method in interface smile.math.matrix.Matrix
-
Returns the string representation of matrix.
- toString(boolean[]) - Static method in class com.actelion.research.util.StringFunctions
- toString(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(byte[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toString(byte[]) - Static method in class com.actelion.research.util.StringFunctions
- toString(byte[], int) - Static method in class com.actelion.research.util.BinaryEncoder
-
Convenience method to directly encode a byte array into a String Uses 6 bits per character using 64 characters from '@' (ASCII 64).
- toString(byte[], String) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toString(double) - Static method in class com.actelion.research.util.DoubleFormat
-
Converts a double value into a String representation in scientific format rounded to 5 significant digits, e.g.
- toString(double) - Method in class smile.data.Attribute
-
Returns the string representation of a double value of this attribute.
- toString(double) - Method in class smile.data.DateAttribute
- toString(double) - Method in class smile.data.NominalAttribute
- toString(double) - Method in class smile.data.NumericAttribute
- toString(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(double[]) - Static method in class com.actelion.research.util.StringFunctions
- toString(double[][]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[], DecimalFormat) - Static method in class com.actelion.research.util.ArrayUtils
- toString(double[], NumberFormat) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[], NumberFormat) - Static method in class com.actelion.research.util.StringFunctions
- toString(double, int) - Static method in class com.actelion.research.util.DoubleFormat
-
Converts a double value into a String representation in scientific format rounded to a definable number of digits, e.g.
- toString(double, int, boolean) - Static method in class com.actelion.research.util.DoubleFormat
-
Converts a double value into a String representation in scientific format rounded to a definable number of digits, e.g.
- toString(float[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(float[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(float[], NumberFormat) - Static method in class com.actelion.research.util.StringFunctions
- toString(int) - Method in class com.actelion.research.calc.Matrix
- toString(int) - Method in class com.actelion.research.calc.regression.linear.pls.SimPLS
- toString(int) - Method in class com.actelion.research.util.datamodel.ByteVec
- toString(int) - Method in class com.actelion.research.util.datamodel.IntVec
- toString(int) - Method in class com.actelion.research.util.DoubleVec
- toString(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(int[][]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(int[][], String) - Static method in class com.actelion.research.util.StringFunctions
- toString(int[], int) - Static method in class com.actelion.research.util.BinaryEncoder
-
Convenience method to directly encode an int array into a String Uses 6 bits per character using 64 characters from '@' (ASCII 64).
- toString(int[], String) - Static method in class com.actelion.research.util.StringFunctions
- toString(int, int) - Method in class smile.data.AttributeDataset
-
Stringify dataset.
- toString(int, int) - Method in class smile.data.AttributeVector
-
Stringify the vector.
- toString(int, int, int) - Method in class com.actelion.research.calc.Matrix
- toString(long) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- toString(long, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- toString(ResultFragmentsStatistic) - Static method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- toString(DoubleArray, String) - Static method in class com.actelion.research.calc.statistics.StatisticsOverview
- toString(DoubleArray, String, String) - Static method in class com.actelion.research.calc.statistics.StatisticsOverview
- toString(IntArray, String) - Static method in class com.actelion.research.calc.statistics.StatisticsOverview
- toString(Exception) - Static method in class com.actelion.research.util.StringFunctions
- toString(Object[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(Object[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(String) - Method in class com.actelion.research.util.datamodel.IntArray
- toString(String[], String) - Static method in class com.actelion.research.util.StringFunctions
- toString(Collection<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(Collection<String>, String) - Static method in class com.actelion.research.util.StringFunctions
- toString(Date) - Method in class smile.data.DateAttribute
-
Generate the date string.
- toString(List<ModelMedianDouble>) - Static method in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- toString(List<ModelMedianFloat>) - Static method in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- toString(List<Double>, NumberFormat) - Static method in class com.actelion.research.util.StringFunctions
- toString(List<String>) - Static method in class com.actelion.research.util.StringFunctions
- toStringArray() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
-
The array part of the object.
- toStringArray(List<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringArray(List<String>) - Static method in class com.actelion.research.util.ArrayUtils
- toStringBinary() - Method in class com.actelion.research.calc.Matrix
- toStringBinary() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- toStringBinary() - Method in class com.actelion.research.util.datamodel.IntVec
- toStringBinary(int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringBinary(int) - Static method in class com.actelion.research.util.datamodel.IntVec
- toStringBinary(int) - Static method in class com.actelion.research.util.StringFunctions
- toStringBinary(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringBinary(int, boolean) - Static method in class com.actelion.research.util.datamodel.IntVec
- toStringBinary(long) - Static method in class com.actelion.research.util.StringFunctions
- toStringBinaryDense() - Method in class com.actelion.research.util.datamodel.IntVec
- toStringBytes() - Method in class com.actelion.research.util.datamodel.IntVec
- toStringFileNameCompatible(double) - Static method in class com.actelion.research.util.StringFunctions
- toStringFormatted(int[][]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringFormatted(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringForValueTable() - Method in class com.actelion.research.chem.Element
- toStringHeader() - Static method in class com.actelion.research.calc.statistics.StatisticsOverview
- toStringHeader() - Static method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- toStringHex() - Method in class com.actelion.research.util.datamodel.IntVec
- toStringHex(String) - Static method in class com.actelion.research.util.StringFunctions
- toStringHists() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- toStringHistsIndexed() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- toStringInevitable() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- toStringInt(List<Integer>) - Static method in class com.actelion.research.util.StringFunctions
- toStringInt(List<Integer>, String) - Static method in class com.actelion.research.util.StringFunctions
- toStringIntArrays(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringInteger(List<Integer>, String) - Static method in class com.actelion.research.util.StringFunctions
- toStringIntegerList(List<Integer>, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Writes a list into a string with line terminators.
- toStringInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- toStringLaTex() - Method in class com.actelion.research.util.datamodel.table.TableModelString
-
\begin{table}[] \begin{tabular}{lllllllll} & 0.20 & 0.30 & 0.40 & 0.50 & 0.60 & 0.70 & 0.80 & 0.90 \\ Gaussian process regression & 1.3550 & 1.3059 & 1.3818 & 1.4046 & 1.5150 & 1.4804 & 1.4579 & 1.6223 \\ KNN regression & 1.6776 & 1.7294 & 1.8899 & 2.1573 & 2.3484 & 2.6003 & 2.6931 & 2.8232 \\ Median & 1.6730 & 1.7421 & 1.9217 & 2.3378 & 2.7606 & 3.2241 & 3.6768 & 4.5243 \\ PLS & 1.4264 & 1.2870 & 1.2131 & 1.2989 & 1.3866 & 1.3830 & 1.4414 & 1.1730 \\ PLS Power & 1.4886 & 1.3616 & 1.4954 & 1.7442 & 2.2339 & 2.3904 & 2.1669 & 2.6130 \\ Random Forest regression & 1.6746 & 1.6848 & 1.8421 & 2.0106 & 2.2479 & 2.3896 & 2.5420 & 2.6523 \\ SVM regression & 1.5580 & 1.4634 & 1.5879 & 1.6687 & 1.8423 & 1.9769 & 1.8803 & 1.9618 \end{tabular} \end{table}
- toStringLong() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- toStringLong(List<Long>, String) - Static method in class com.actelion.research.util.StringFunctions
- toStringLongHardPPPoint() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- toStringLongList(List<Long>, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringLongPPNode() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- toStringNoBrackets(Collection<Integer>, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- toStringNoDigits(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringParameter() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- toStringParameter() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- toStringParameter() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- toStringPPNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Only nodes without coordinates
- toStringPPPoints(int) - Static method in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- toStringPure(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringPure(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringRecentSimilarityResults() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- toStringRow(int, int) - Method in class com.actelion.research.calc.Matrix
- toStringRowNumber(int, String) - Method in class com.actelion.research.calc.Matrix
- toStringShort() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- toStringShort() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- toStringShortMessage() - Method in class com.actelion.research.util.ErrorHashMap
- toStringSpaceDelimited() - Method in class com.actelion.research.chem.Coordinates
- toStringString() - Method in class com.actelion.research.util.datamodel.ByteVec
-
Converts the bytes into chars.
- toStringTabNL(String[][]) - Static method in class com.actelion.research.util.StringFunctions
-
Elements are separated by tabs and rows are separated by newline.
- toStringValues(IntegerDouble[], NumberFormat) - Static method in class com.actelion.research.util.datamodel.IntegerDouble
- toStringValues(List<IntegerDouble>, NumberFormat) - Static method in class com.actelion.research.util.datamodel.IntegerDouble
- toStringVizInfoEncoded(MolDistHistViz) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
-
Encodes the structure information, that it can be written to an DWAR file.
- toStringWithColTags(List<String>, DecimalFormat, String) - Method in class com.actelion.research.calc.Matrix
- toStringWithRowTags(List<String>, DecimalFormat, String) - Method in class com.actelion.research.calc.Matrix
- TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
- TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
- TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
- TotalSurfaceAreaPredictor - Class in com.actelion.research.chem.prediction
- TotalSurfaceAreaPredictor() - Constructor for class com.actelion.research.chem.prediction.TotalSurfaceAreaPredictor
- ToxicityPredictor - Class in com.actelion.research.chem.prediction
- ToxicityPredictor() - Constructor for class com.actelion.research.chem.prediction.ToxicityPredictor
- trace() - Method in interface smile.math.matrix.Matrix
-
Returns the matrix trace.
- train(double[][], double[]) - Method in class smile.regression.NeuralNetwork.Trainer
- train(double[][], double[]) - Method in class smile.regression.RandomForest.Trainer
- train(double[][], double[]) - Method in class smile.regression.RegressionTree.Trainer
- train(int[][], double[]) - Method in class smile.regression.RegressionTree.Trainer
- train(T[], double[]) - Method in class smile.regression.GaussianProcessRegression.Trainer
- train(T[], double[]) - Method in class smile.regression.RegressionTrainer
-
Learns a regression model with given training data.
- train(T[], double[], T[]) - Method in class smile.regression.GaussianProcessRegression.Trainer
-
Learns a Gaussian Process with given subset of regressors.
- Trainer(int) - Constructor for class smile.regression.RandomForest.Trainer
-
Constructor.
- Trainer(int) - Constructor for class smile.regression.RegressionTree.Trainer
-
Constructor.
- Trainer(int...) - Constructor for class smile.regression.NeuralNetwork.Trainer
-
Constructor.
- Trainer(int, int) - Constructor for class smile.regression.RegressionTree.Trainer
-
Constructor.
- Trainer(Attribute[], int) - Constructor for class smile.regression.RandomForest.Trainer
-
Constructor.
- Trainer(Attribute[], int) - Constructor for class smile.regression.RegressionTree.Trainer
-
Constructor.
- Trainer(MercerKernel<T>, double) - Constructor for class smile.regression.GaussianProcessRegression.Trainer
-
Constructor.
- Trainer(NeuralNetwork.ActivationFunction, int...) - Constructor for class smile.regression.NeuralNetwork.Trainer
-
Constructor.
- TransferableDockable - Class in com.actelion.research.gui.dock
- TransferableDockable(Dockable) - Constructor for class com.actelion.research.gui.dock.TransferableDockable
- transform(Matrix, BoxCox) - Static method in class com.actelion.research.calc.BoxCox
- transform(Transformation) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- transform(Transformation) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- transform(Transformation) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- transform(AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- Transformation - Interface in com.actelion.research.chem.alignment3d.transformation
- TransformationSequence - Class in com.actelion.research.chem.alignment3d.transformation
- TransformationSequence() - Constructor for class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- TransformationSequence(Quaternion) - Constructor for class com.actelion.research.chem.alignment3d.transformation.TransformationSequence
- transformGaussians(Transformation) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- transformGaussians(Transformation) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- transformGaussians(List<? extends Gaussian3D>, Transformation) - Static method in class com.actelion.research.chem.phesa.ShapeVolume
- transformMolecule(Molecule, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- transformMolecules(Molecule[], double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- transformReaction(Reaction, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- transformX(double) - Method in class com.actelion.research.chem.DepictorTransformation
- transformY(double) - Method in class com.actelion.research.chem.DepictorTransformation
- translate(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- translate(double, double) - Method in class com.actelion.research.chem.coords.InventorFragment
- translate(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- translate(double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- translate(double, double, double) - Method in class com.actelion.research.chem.conf.Conformer
-
Translate this conformer's coordinates by adding the dx,dy,dz shifts to all atom coordinates.
- translate(double, double, double) - Method in class com.actelion.research.chem.Molecule
-
Translate this molecule's 3D-coordinates by adding the dx,dy,dz shifts to all atom coordinates.
- translate(int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- translate(int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- translate(Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Translate a Molecule
- translate(StereoMolecule, Coordinates) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Translate a Molecule
- translateCoords(double, double) - Method in class com.actelion.research.chem.Molecule
- translateFontName(String) - Method in class com.actelion.research.gui.wmf.MetaFile
- translateFontName(String) - Method in class com.actelion.research.gui.wmf.WMF
- translateInit(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- translateLigand(Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- translateMol(StereoMolecule, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- translateRef(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- translateTHParity(int, int[]) - Method in class com.actelion.research.chem.StereoMolecule
-
This method translates the parity of a stereo center, if its neighbour atoms are assigned new atom indexes, or are assigned to a matching fragment or molecule with different atom indexes.
- translateToCOM(Coordinates) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- translateToCOM(Coordinates) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- Translation - Class in com.actelion.research.chem.alignment3d.transformation
- Translation(double[]) - Constructor for class com.actelion.research.chem.alignment3d.transformation.Translation
- Translation(double, double, double) - Constructor for class com.actelion.research.chem.alignment3d.transformation.Translation
- Translation(Coordinates) - Constructor for class com.actelion.research.chem.alignment3d.transformation.Translation
- TRANSLATION - Static variable in interface com.actelion.research.chem.alignment3d.transformation.Transformation
- TRANSPARENCY_COLOR_NONE - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- TRANSPARENCY_INDEX_NONE - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- TRANSPARENCY_INDEX_SET - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- TRANSPARENT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TRANSPARENT - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- transpose() - Method in interface smile.math.matrix.DenseMatrix
-
Returns the matrix transpose.
- transpose() - Method in class smile.math.matrix.JMatrix
- transpose() - Method in interface smile.math.matrix.Matrix
-
Returns the matrix transpose.
- transpose(double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- transpose(double[][]) - Static method in class smile.math.Math
-
Returns the matrix transpose.
- TreeContainer - Class in com.actelion.research.gui.dock
- TreeContainer() - Constructor for class com.actelion.research.gui.dock.TreeContainer
- TreeElement - Class in com.actelion.research.gui.dock
- TreeElement() - Constructor for class com.actelion.research.gui.dock.TreeElement
- TreeFork - Class in com.actelion.research.gui.dock
- TreeFork(TreeLeaf, TreeLeaf, int, double, Vector<DividerChangeListener>) - Constructor for class com.actelion.research.gui.dock.TreeFork
-
Constructor to create a fork element that is inserted between the specified parent and its former oldLeaf to carry newLeaf at the specified position.
- TreeLeaf - Class in com.actelion.research.gui.dock
- TreeLeaf(Dockable, JDockingPanel, boolean) - Constructor for class com.actelion.research.gui.dock.TreeLeaf
-
Constructor to create a leaf element with a visible component on the screen.
- TreeMatcher - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
Finds the optimal matching of nodes between two PharmacophoreTrees employing a dynamic programing scheme termed as "match-search" algorithm in the original publication (DOI:10.1023/a:1008068904628).
- TreeMatcher(PharmacophoreTree, PharmacophoreTree) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- TreeMatcher.FeatureMatch - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
TODO: don't add null-matches!
- TreeMatcher.TreeMatching - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- TreeMatching() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- TreeRoot - Class in com.actelion.research.gui.dock
- TreeRoot(JComponent, TreeElement) - Constructor for class com.actelion.research.gui.dock.TreeRoot
-
Constructor to create a root element to which the first leaf should be connected.
- TreeUtils - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- TreeUtils() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
- treeWalkBFS(int, int, List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
Walks a subtree of the PharmacophoreTree in breadth-first manner starting from a deleted edge and a designated head node.
- Triangle - Class in com.actelion.research.calc.geometry
-
Triangle Created by korffmo1 on 04.06.17.
- Triangle() - Constructor for class com.actelion.research.calc.geometry.Triangle
- trim(int) - Method in class smile.regression.RandomForest
-
Trims the tree model set to a smaller size in case of over-fitting.
- TRUE - com.actelion.research.chem.forcefield.mmff.RingBoolean
- trueNegative - Variable in class com.actelion.research.calc.classification.PrecisionAndRecall
- truePositive - Variable in class com.actelion.research.calc.classification.PrecisionAndRecall
- tryAutoMapReaction() - Method in class com.actelion.research.share.gui.editor.Model
- TVERSKY_COEFFICIENT - Static variable in class com.actelion.research.chem.phesa.PheSAAlignment
- TWO_PI - Variable in class com.actelion.research.util.Angle
- type - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- type - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- TYPE_BACKBONE_NO_STEREO - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_BRAVAIS_PEARSON - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_CODE - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_DRAGGED - Static variable in class com.actelion.research.gui.PruningBarEvent
- TYPE_EXACT_NO_STEREO - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_EXACT_NO_STEREO - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_EXACT_STRICT - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_EXACT_STRICT - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_HILITE_ATOM_CHANGED - Static variable in class com.actelion.research.gui.editor.DrawAreaEvent
- TYPE_HILITE_BOND_CHANGED - Static variable in class com.actelion.research.gui.editor.DrawAreaEvent
- TYPE_LONG_NAME - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_MARKUSH - Static variable in class com.actelion.research.chem.ExtendedDepictor
- TYPE_MOLECULE_CHANGED - Static variable in class com.actelion.research.gui.editor.DrawAreaEvent
- TYPE_MOLECULES - Static variable in class com.actelion.research.chem.ExtendedDepictor
- TYPE_NAME - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_NO_REACTION - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_NO_STRUCTURE - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_NONE - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_REACTION - Static variable in class com.actelion.research.chem.ExtendedDepictor
- TYPE_RETRON - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_SELECTION_CHANGED - Static variable in class com.actelion.research.gui.editor.DrawAreaEvent
- TYPE_SIMILARITY - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_SIMILARITY - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_SPEARMAN - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_STRING - Static variable in class com.actelion.research.chem.reaction.ReactionArrow
- TYPE_STRING - Static variable in class com.actelion.research.chem.TextDrawingObject
- TYPE_SUBREACTION - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_SUBSTRUCTURE - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_TAUTOMER - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_TAUTOMER_NO_STEREO - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_TYPED - Static variable in class com.actelion.research.gui.PruningBarEvent
U
- U - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- U - Variable in class smile.math.matrix.SVD
-
Arrays for internal storage of left singular vectors U.
- ulp(double) - Static method in class smile.math.Math
-
Returns the size of an ulp of the argument.
- ulp(float) - Static method in class smile.math.Math
-
* Returns the size of an ulp of the argument.
- UndoAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 3/26/13 Time: 4:39 PM
- UndoAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.UndoAction
- undock(String) - Method in class com.actelion.research.gui.dock.JDockingPanel
- undock(String, boolean) - Method in class com.actelion.research.gui.dock.JDockingPanel
- undockAll() - Method in class com.actelion.research.gui.dock.JDockingPanel
- undoStep() - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
- unique(int[]) - Static method in class smile.math.Math
-
Find unique elements of vector.
- unique(String[]) - Static method in class smile.math.Math
-
Find unique elements of vector.
- UniqueFragmentEstimator - Class in com.actelion.research.chem.properties.complexity
- UniqueFragmentEstimator() - Constructor for class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- UniqueFragmentEstimator(int) - Constructor for class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- UniqueList<T extends java.lang.Comparable<? super T>> - Class in com.actelion.research.util
- UniqueList() - Constructor for class com.actelion.research.util.UniqueList
- UniqueList(Comparator) - Constructor for class com.actelion.research.util.UniqueList
- UniqueStringList - Class in com.actelion.research.chem
- UniqueStringList() - Constructor for class com.actelion.research.chem.UniqueStringList
- unit() - Method in class com.actelion.research.chem.Coordinates
- unitC() - Method in class com.actelion.research.chem.Coordinates
- unitize(double[]) - Static method in class smile.math.Math
-
Unitize an array so that L2 norm of x = 1.
- unitize1(double[]) - Static method in class smile.math.Math
-
Unitize an array so that L1 norm of x is 1.
- unitize2(double[]) - Static method in class smile.math.Math
-
Unitize an array so that L2 norm of x = 1.
- UniversalGenerator - Class in smile.math.random
-
The so called "Universal Generator" based on multiplicative congruential method, which originally appeared in "Toward a Universal Random Number Generator" by Marsaglia, Zaman and Tsang.
- UniversalGenerator() - Constructor for class smile.math.random.UniversalGenerator
-
Initialize Random with default seed.
- UniversalGenerator(int) - Constructor for class smile.math.random.UniversalGenerator
-
Initialize Random with a specified integer seed
- UniversalGenerator(long) - Constructor for class smile.math.random.UniversalGenerator
-
Initialize Random with a specified long seed
- UNKNOWN - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- UnknownParityAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 3/26/13 Time: 4:33 PM
- UnknownParityAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.UnknownParityAction
- UnparametrizedAtomTypeException - Exception in com.actelion.research.chem.descriptor.flexophore
- UnparametrizedAtomTypeException() - Constructor for exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
- UnparametrizedAtomTypeException(String) - Constructor for exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
- unsetBit(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- unsetBit(int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Don't forget to set the hash code!
- unsetBit(int[], int) - Static method in class com.actelion.research.util.BitUtils
- UpBondAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:49 PM
- UpBondAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.UpBondAction
- update(boolean) - Method in class com.actelion.research.gui.dock.DockableHeader
- update(int, int, double) - Method in interface smile.math.matrix.DenseMatrix
-
Set the entry value at row i and column j.
- update(Conformer) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- update(Conformer) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- update(StereoMolecule) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- update(StereoMolecule) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- update(Graphics) - Method in class com.actelion.research.gui.JDrawToolbar
-
Deprecated.
- update(Graphics) - Method in class com.actelion.research.gui.JPruningBar
- update(Graphics) - Method in class com.actelion.research.gui.table.ChemistryRenderPanel
- UPDATE_CHECK_COORDS - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- UPDATE_CHECK_COORDS - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- UPDATE_CHECK_VIEW - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- UPDATE_CHECK_VIEW - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- UPDATE_INVENT_COORDS - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- UPDATE_INVENT_COORDS - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- UPDATE_NONE - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- UPDATE_NONE - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- UPDATE_REDRAW - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- UPDATE_REDRAW - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- UPDATE_SCALE_COORDS - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- UPDATE_SCALE_COORDS - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- UPDATE_SCALE_COORDS_USE_FRAGMENTS - Static variable in class com.actelion.research.gui.editor.GenericDrawArea
- UPDATE_SCALE_COORDS_USE_FRAGMENTS - Static variable in class com.actelion.research.gui.JDrawArea
-
Deprecated.
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- updateAtomIndeces(int[]) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- updateChildElement(Component, TreeElement) - Method in class com.actelion.research.gui.dock.TreeContainer
- updateChildElement(Component, TreeElement) - Method in class com.actelion.research.gui.dock.TreeFork
- updateChildElement(Component, TreeElement) - Method in class com.actelion.research.gui.dock.TreeRoot
- updateCOM() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- updateCoordinates(Coordinates) - Method in class com.actelion.research.chem.docking.scoring.ProbeScanning.Probe
- updateCoordinates(Coordinates[]) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- updateCoordinates(Coordinates[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AcceptorPoint
- updateCoordinates(Coordinates[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
- updateCoordinates(Coordinates[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.AromRingPoint
- updateCoordinates(Coordinates[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint
- updateCoordinates(Coordinates[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.DonorPoint
- updateCoordinates(Coordinates[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.ExitVectorPoint
- updateCoordinates(Coordinates[]) - Method in interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint
- updateCoordinates(Coordinates[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
- updateCoordinates(Coordinates[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.pp.SimplePharmacophorePoint
- updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- updateCoordinates(List<? extends Gaussian3D>, Coordinates[]) - Method in class com.actelion.research.chem.phesa.ShapeVolume
- updateCoords(GenericDrawContext, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.ExtendedDepictor
- updateCoords(IDrawContext<T>, Rectangle2D.Double, int) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- updateCoords(T, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
-
Returns full transformation that moves/scales original molecule into viewRect.
- updateCoords(T, Rectangle2D.Double, int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- updateDividerChangeListeners(Vector<DividerChangeListener>) - Method in class com.actelion.research.gui.dock.TreeFork
- updateGradient() - Method in interface com.actelion.research.chem.forcefield.ForceField
-
updates the gradient of the ForceField and returns the gradient scale
- updateGradient() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Minimise the current molecule using default parameter values for the number of iterations, energy tolerance and gradient tolerance.
- updateGrid(StereoMolecule) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- updateLigandCoordinates() - Method in class com.actelion.research.chem.docking.LigandPose
- updateProgress(int) - Method in class com.actelion.research.calc.DataProcessor
- updateProgress(int) - Method in interface com.actelion.research.calc.ProgressListener
- updateProgress(int) - Method in class com.actelion.research.gui.JProgressDialog
-
Update progress status in an absolute or relative way.
- updateProgress(int) - Method in class com.actelion.research.gui.JProgressPanel
- updateProgress(int, String) - Method in interface com.actelion.research.calc.ProgressListener
- updateProgress(int, String) - Method in class com.actelion.research.gui.JProgressDialog
-
Update progress status in an absolute or relative way.
- updateProgress(int, String) - Method in class com.actelion.research.gui.JProgressPanel
- updateReference(Object, Object, double) - Method in class com.actelion.research.calc.BinarySOM
- updateReference(Object, Object, double) - Method in class com.actelion.research.calc.SelfOrganizedMap
- updateReference(Object, Object, double) - Method in class com.actelion.research.calc.VectorSOM
- updateRenderer(JComponent, String) - Static method in class com.actelion.research.gui.hidpi.ScaledHTML
- updateState() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- updateState() - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
- updateState() - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- updateUI() - Method in class com.actelion.research.gui.dock.Dockable
-
Updates the UI.
- updateUI() - Method in class com.actelion.research.gui.dock.DockableHeader
- updateUI() - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
- updateUI() - Method in class com.actelion.research.gui.hidpi.HiDPIToggleButton
- updateUI() - Method in class com.actelion.research.gui.JScrollableMenu
- updateWeights(Map<Integer, List<Integer>>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- UPGMALinkage - Class in smile.clustering.linkage
-
Unweighted Pair Group Method with Arithmetic mean (also known as average linkage).
- UPGMALinkage(double[][]) - Constructor for class smile.clustering.linkage.UPGMALinkage
-
Constructor.
- UPGMCLinkage - Class in smile.clustering.linkage
-
Unweighted Pair Group Method using Centroids (also known as centroid linkage).
- UPGMCLinkage(double[][]) - Constructor for class smile.clustering.linkage.UPGMCLinkage
-
Constructor.
- upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- upperTriangle(Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
- URL_SAFE - Static variable in class com.actelion.research.util.Base64
-
Encode using Base64-like encoding that is URL- and Filename-safe as described in Section 4 of RFC3548: http://www.faqs.org/rfcs/rfc3548.html.
- usedMemory() - Static method in class com.actelion.research.util.SizeOf
- usedMemoryMB() - Static method in class com.actelion.research.util.SizeOf
- USER_INPUT_EXPECTED - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- USER_INPUT_NONE - Static variable in class com.actelion.research.util.AnimatedGIFWriter.GIFFrame
- usesThumbNail() - Method in class com.actelion.research.gui.JImagePanel
V
- V - Variable in class com.actelion.research.calc.regression.linear.pls.SimPLS
- V - Variable in class smile.math.matrix.SVD
-
Arrays for internal storage of right singular vectors V.
- v1 - Variable in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- v1 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- v2 - Variable in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- v2 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- v3 - Variable in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- v3 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- val(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the VAL type of an atom given its MMFF type.
- valid(Tables, MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Checks if a Stretch Bend is valid
- validate() - Method in class com.actelion.research.chem.ExtendedMolecule
- validate() - Method in class com.actelion.research.chem.MarkushStructure
-
Check the validity of a defined Markush structure.
- validate() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Checks, whether this specification is correctly defining a search.
- validate() - Method in class com.actelion.research.chem.StereoMolecule
- validate() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
Checks, whether this specification is correctly defining a search.
- validateBondType(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
- validateBondType(int, int) - Method in class com.actelion.research.chem.Molecule
- validateMapping() - Method in class com.actelion.research.chem.reaction.Reaction
-
Removes mapping numbers that are only used on one side of the reaction.
- validateMemberIndex(int, int) - Method in class com.actelion.research.chem.RingCollection
-
Adds or subtracts the ring size from index to move it into the valid range from 0 to ringSize-1.
- validateView(GenericDrawContext, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.ExtendedDepictor
- validateView(T, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
-
A depictor maintains a DepictorTransformation object, which defines translation and scaling of molecule coordinates into the viewRect.
- validateView(T, Rectangle2D.Double, int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- VALIDATION_ERROR_AMBIGUOUS_CONFIGURATION - Static variable in class com.actelion.research.chem.StereoMolecule
- VALIDATION_ERROR_ESR_CENTER_UNKNOWN - Static variable in class com.actelion.research.chem.StereoMolecule
- VALIDATION_ERROR_OVER_UNDER_SPECIFIED - Static variable in class com.actelion.research.chem.StereoMolecule
- VALIDATION_ERRORS_STEREO - Static variable in class com.actelion.research.chem.StereoMolecule
- value - Variable in class com.actelion.research.util.ScaleLabel
- value - Variable in class org.machinelearning.svm.libsvm.svm_node
- value(double) - Method in class com.actelion.research.util.FastSpline.Polynome
- value(double) - Method in class com.actelion.research.util.FastSpline
-
Compute the value for the function.
- valueInvalidated() - Method in interface com.actelion.research.share.gui.editor.listeners.IValidationListener
- valueInvalidated() - Method in class com.actelion.research.share.gui.editor.Model
- valueOf(String) - Static method in enum com.actelion.research.calc.classification.ClassificationAttr
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.docking.DockingEngine.ScoringFunction
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage.InteractionProbe
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.forcefield.mmff.RingBoolean
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.forcefield.mmff.Separation.Relation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint.Functionality
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.phesa.PheSAAlignment.axis
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.share.gui.DialogResult
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.util.Formatter.LocaleFormat
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum smile.clustering.ClusteringDistance
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum smile.data.Attribute.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Method in class smile.data.Attribute
-
Returns the double value of a string of this attribute.
- valueOf(String) - Method in class smile.data.DateAttribute
- valueOf(String) - Method in class smile.data.NominalAttribute
-
Returns the ordinal value of a string value.
- valueOf(String) - Method in class smile.data.NumericAttribute
- valueOf(String) - Static method in enum smile.regression.NeuralNetwork.ActivationFunction
-
Returns the enum constant of this type with the specified name.
- valueOf(Date) - Method in class smile.data.DateAttribute
-
Returns the double value representation of a data object.
- valueProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- valueProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- values() - Static method in enum com.actelion.research.calc.classification.ClassificationAttr
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.docking.DockingEngine.ScoringFunction
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.docking.receptorpharmacophore.NegativeReceptorImage.InteractionProbe
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.forcefield.mmff.RingBoolean
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.forcefield.mmff.Separation.Relation
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint.Functionality
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.phesa.PheSAAlignment.axis
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.share.gui.DialogResult
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.util.Formatter.LocaleFormat
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum smile.clustering.ClusteringDistance
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum smile.data.Attribute.Type
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Method in class smile.data.NominalAttribute
-
Returns the string values of nominal attribute.
- values() - Static method in enum smile.regression.NeuralNetwork.ActivationFunction
-
Returns an array containing the constants of this enum type, in the order they are declared.
- VanDerWaals - Class in com.actelion.research.chem.forcefield.mmff.table
- VanDerWaals - Class in com.actelion.research.chem.forcefield.mmff
-
Nonbonded van der Waals energy term class.
- VanDerWaals(Tables, MMFFMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.VanDerWaals
-
Construct a new van der Waals energy term.
- VanDerWaals(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- var() - Method in interface smile.stat.distribution.Distribution
-
The variance of distribution.
- var() - Method in class smile.stat.distribution.GaussianDistribution
- var() - Method in class smile.stat.distribution.Mixture
- var(double[]) - Static method in class smile.math.Math
-
Returns the variance of an array.
- var(float[]) - Static method in class smile.math.Math
-
Returns the variance of an array.
- var(int[]) - Static method in class smile.math.Math
-
Returns the variance of an array.
- VARIABLE_PITCH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- VDW_RADIUS - Static variable in interface com.actelion.research.chem.conf.VDWRadii
-
VDW Radii indexed by atomic numbers, taken from DOI: 10.1039/c3dt50599e Santiago Alvarez: A cartography of the van der Waals territories Published on 01 May 2013 on http://pubs.rsc.org | doi:10.1039/C3DT50599E (in a few cases no value was given (marked ??), where we use estimated values)
- VDW_TOLERANCE_HYDROGEN - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- VDW_TOLERANCE_OTHER - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- VDWRadii - Interface in com.actelion.research.chem.conf
- vdws - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- vector() - Method in class smile.data.AttributeVector
-
Returns the data vector.
- Vector3 - Class in com.actelion.research.chem.forcefield.mmff
-
The Vector3 class provides common vector operations used throughout the MMFF codebase.
- Vector3() - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector with default coordinates.
- Vector3(double[], int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector from three consecutive doubles in a positions array.
- Vector3(double[], int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector starting at atom1 position and ending at atom2 position.
- Vector3(double, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector with given x, y and z coordinates.
- Vector3(ExtendedMolecule, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector from the x, y, z coordinates of an atom in a molecule.
- Vector3(ExtendedMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a vector that represents the line travelling from the position of atom1 to the position of atom2.
- Vector3(MMFFMolecule, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector from the x, y, z coordinates of an atom in a molecule.
- Vector3(MMFFMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a vector that represents the line travelling from the position of atom1 to the position of atom2.
- Vector3(Vector3) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Copy constructor, copies the x,y,z coordinates from another vector.
- VectorSimilarity - Class in com.actelion.research.calc
- VectorSimilarity() - Constructor for class com.actelion.research.calc.VectorSimilarity
- VectorSOM - Class in com.actelion.research.calc
- VectorSOM() - Constructor for class com.actelion.research.calc.VectorSOM
- VectorSOM(int, int, int) - Constructor for class com.actelion.research.calc.VectorSOM
- vecvec2Matrix(Vector<Vector<Double>>, Matrix) - Static method in class com.actelion.research.calc.MatrixFunctions
-
Converts a vector of vectors into doubles, each vector results in a row in the matrix.
- VERBOSE - Static variable in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- VERBOSE - Static variable in class com.actelion.research.calc.regression.svm.SVMRegression
- VERBOSE - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- VERBOSE - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- version - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- version - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- VERSION - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- VERSION - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- VERSION - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- VERSION_INTERACTION_TABLES - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- VerticalFlowLayout - Class in com.actelion.research.gui
-
A vertical flow layout is similar to a flow layuot but it layouts the components vertically instead of horizontally.
- VerticalFlowLayout() - Constructor for class com.actelion.research.gui.VerticalFlowLayout
-
Constructor for the VerticalFlowLayout object
- VerticalFlowLayout(int, int) - Constructor for class com.actelion.research.gui.VerticalFlowLayout
-
Constructor for the VerticalFlowLayout object
- VerticalFlowLayout(int, int, int, int, boolean) - Constructor for class com.actelion.research.gui.VerticalFlowLayout
-
Constructor for the VerticalFlowLayout object
- vibrateLigand(Molecule3D, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- VIEW_HEIGHT - Static variable in class com.actelion.research.gui.JMultiPanelView
- ViolatedConditionsCount() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- visibilityChanged(Dockable, boolean) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
This is called when a Dockable's visibility changes, i.e.
- when a new Dockable is docked
- when a new Dockable is undocked
- when the user drags & docks a Dockable
- when the user actively switches tabs in a tabbed pane
It may be overridden in order to react on a visibility change due to the user selecting a different tab of dragging & docking a Dockable. - volume - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- VolumeGaussian - Class in com.actelion.research.chem.phesa
- VolumeGaussian(int, int, Coordinates, Coordinates, int) - Constructor for class com.actelion.research.chem.phesa.VolumeGaussian
- VolumeGaussian(VolumeGaussian) - Constructor for class com.actelion.research.chem.phesa.VolumeGaussian
W
- WardLinkage - Class in smile.clustering.linkage
-
Ward's linkage.
- WardLinkage(double[][]) - Constructor for class smile.clustering.linkage.WardLinkage
-
Constructor.
- weakCompareAndSet(float, float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
- weight - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- weight - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- weight - Variable in class smile.data.Datum
-
Optional weight of this datum.
- weight_label - Variable in class org.machinelearning.svm.libsvm.svm_parameter
- well_depth - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- wereAllDataFetched() - Method in interface com.actelion.research.util.IPipeline
-
Has to be true when all data were fetched.
- wereAllDataFetched() - Method in class com.actelion.research.util.Pipeline
-
Returns true if all data in was set and the queue is empty.
- WHAT_CANCEL - Static variable in class com.actelion.research.gui.editor.DialogEvent
- WHAT_ITEM_SELECTED - Static variable in class com.actelion.research.gui.editor.DialogEvent
- WHAT_OK - Static variable in class com.actelion.research.gui.editor.DialogEvent
- WHAT_STATE_TOGGLED - Static variable in class com.actelion.research.gui.editor.DialogEvent
- whichMax(double[]) - Static method in class smile.math.Math
-
Returns the index of maximum value of an array.
- whichMax(float[]) - Static method in class smile.math.Math
-
Returns the index of maximum value of an array.
- whichMax(int[]) - Static method in class smile.math.Math
-
Returns the index of maximum value of an array.
- whichMin(double[]) - Static method in class smile.math.Math
-
Returns the index of minimum value of an array.
- whichMin(float[]) - Static method in class smile.math.Math
-
Returns the index of minimum value of an array.
- whichMin(int[]) - Static method in class smile.math.Math
-
Returns the index of minimum value of an array.
- WHITE - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- WHITENESS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- WINDING - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- windowActivated(WindowEvent) - Method in class com.actelion.research.gui.JLoginDialog
- windowClosed(WindowEvent) - Method in class com.actelion.research.gui.JLoginDialog
- windowClosing(WindowEvent) - Method in class com.actelion.research.gui.JLoginDialog
- windowDeactivated(WindowEvent) - Method in class com.actelion.research.gui.JLoginDialog
- windowDeiconified(WindowEvent) - Method in class com.actelion.research.gui.JLoginDialog
- windowIconified(WindowEvent) - Method in class com.actelion.research.gui.JLoginDialog
- windowOpened(WindowEvent) - Method in class com.actelion.research.gui.JLoginDialog
- WMF - Class in com.actelion.research.gui.wmf
- WMF() - Constructor for class com.actelion.research.gui.wmf.WMF
- WMFConstants - Interface in com.actelion.research.gui.wmf
- WMFGraphics - Class in com.actelion.research.gui.wmf
- WMFGraphics(MetaFile, int, int, Color, Color) - Constructor for class com.actelion.research.gui.wmf.WMFGraphics
- WMFGraphics2D - Class in com.actelion.research.gui.wmf
- WMFGraphics2D(WMF, int, int, Color, Color) - Constructor for class com.actelion.research.gui.wmf.WMFGraphics2D
- WPGMALinkage - Class in smile.clustering.linkage
-
Weighted Pair Group Method with Arithmetic mean.
- WPGMALinkage(double[][]) - Constructor for class smile.clustering.linkage.WPGMALinkage
-
Constructor.
- WPGMCLinkage - Class in smile.clustering.linkage
-
Weighted Pair Group Method using Centroids (also known as median linkage).
- WPGMCLinkage(double[][]) - Constructor for class smile.clustering.linkage.WPGMCLinkage
-
Constructor.
- write(byte[]) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- write(byte[], int, int) - Method in class com.actelion.research.util.Base64.OutputStream
-
Calls
Base64.OutputStream.write(int)
repeatedly until len bytes are written. - write(byte[], int, int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- write(double[], int) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Writes the contents of this vector to the specified positions in a positions array.
- write(int) - Method in class com.actelion.research.util.Base64.OutputStream
-
Writes the byte to the output stream after converting to/from Base64 notation.
- write(int) - Method in class com.actelion.research.util.BinaryEncoder
-
Encodes and writes one data value
- write(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- write(BufferedImage, OutputStream) - Method in class com.actelion.research.util.AnimatedGIFWriter
- write(BufferedWriter) - Method in class com.actelion.research.calc.BinarySOM
- write(BufferedWriter) - Method in class com.actelion.research.calc.SelfOrganizedMap
- write(BufferedWriter) - Method in class com.actelion.research.calc.VectorSOM
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomCharge
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomCIP
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomEnhGroup
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomEnhStereoType
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomIsotope
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomRadical
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondAttach
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondDisplay
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondType
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPElement
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPPoint2D
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPProducts
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPReactants
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPShowAtomStereo
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPShowBondStereo
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPShowEnhAtomStereo
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPText
- write(DataOutput, ChemDrawCDX.CDXNode) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- write(File) - Method in class com.actelion.research.calc.Matrix
- write(File) - Method in class com.actelion.research.calc.regression.linear.pls.ParameterPLS
- write(File) - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- write(File, boolean, int) - Method in class com.actelion.research.calc.Matrix
- write(File, double[]) - Static method in class com.actelion.research.util.IO
- write(File, int[]) - Static method in class com.actelion.research.util.IO
- write(File, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- write(File, String) - Static method in class com.actelion.research.util.IO
- write(File, String, boolean) - Static method in class com.actelion.research.util.IO
- write(File, DecimalFormat, boolean) - Method in class com.actelion.research.calc.Matrix
- write(File, List<String>) - Static method in class com.actelion.research.util.IO
-
Writes each string in a separate line
- write(OutputStream) - Method in class com.actelion.research.calc.Matrix
- write(OutputStream, NumberFormat) - Method in class com.actelion.research.calc.Matrix
- write(String) - Method in class com.actelion.research.calc.Matrix
- write(String) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- write(String, boolean) - Method in class com.actelion.research.calc.Matrix
- write(String, boolean, int) - Method in class com.actelion.research.calc.Matrix
- write(String, boolean, int, int) - Method in class com.actelion.research.calc.Matrix
- write(String, String) - Static method in class com.actelion.research.util.IO
- write(String, String, boolean) - Static method in class com.actelion.research.util.IO
- WRITE_DW_FILE - Static variable in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- WRITE_DW_FRAGMENT_FILE - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- write2Channel(FileChannel, String) - Method in class com.actelion.research.util.IO
- write2String() - Method in class com.actelion.research.calc.regression.ParameterRegressionMethod
- write2String() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- write2String() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- write2String() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- write2String() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- write2String() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- write2String() - Method in class com.actelion.research.util.datamodel.IntArray
- write2String() - Method in class com.actelion.research.util.datamodel.IntVec
- writeAnimatedGIF(AnimatedGIFWriter.GIFFrame[], OutputStream) - Method in class com.actelion.research.util.AnimatedGIFWriter
-
Writes an array of GIFFrame as an animated GIF
- writeAnimatedGIF(BufferedImage[], int[], OutputStream) - Method in class com.actelion.research.util.AnimatedGIFWriter
-
Writes an array of BufferedImage as an animated GIF
- writeAnimatedGIF(List<AnimatedGIFWriter.GIFFrame>, OutputStream) - Method in class com.actelion.research.util.AnimatedGIFWriter
-
Writes a list of GIFFrame as an animated GIF
- writeAsLineBase64Encoded() - Method in class com.actelion.research.calc.Matrix
- writeBitmap(int[], int, int) - Method in class com.actelion.research.gui.wmf.WMF
- writeBitStringDense(File, List<IntVec>) - Static method in class com.actelion.research.util.datamodel.IntVec
- writeBoolean(boolean) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeByte(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeBytes(String) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeChar(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeChars(String) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeColor(Color) - Method in class com.actelion.research.gui.wmf.WMF
- writeContent(StereoMolecule) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- writeContent(StereoMolecule, ClipboardContent) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- writeCTAB(StereoMolecule, double) - Static method in class com.actelion.research.chem.MolfileV3Creator
- writeCurrentRow() - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Call this once per row after setting individual cell content with the respective setRowXXXX() methods.
- writeDouble(double) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeEnd() - Method in class com.actelion.research.chem.io.DWARFileCreator
- writeFloat(float) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeFrame(OutputStream, AnimatedGIFWriter.GIFFrame) - Method in class com.actelion.research.util.AnimatedGIFWriter
- writeFrame(OutputStream, BufferedImage) - Method in class com.actelion.research.util.AnimatedGIFWriter
- writeFrame(OutputStream, BufferedImage, int) - Method in class com.actelion.research.util.AnimatedGIFWriter
- writeHeader(int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Call this after defining columns and specifying column properties
- writeHistogram(String, Matrix, boolean, int, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- writeInt(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeInteger(int) - Method in class com.actelion.research.gui.wmf.WMF
- writeIntegerList(File, List<Integer>) - Static method in class com.actelion.research.util.IO
- writeL(Writer, String, int) - Static method in class com.actelion.research.chem.io.AbstractParser
- writeLong(long) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeMolfile(Writer) - Method in class com.actelion.research.chem.MolfileCreator
- writeMolfile(Writer) - Method in class com.actelion.research.chem.MolfileV3Creator
- writeMolSketchFile(Molecule, OutputStream) - Static method in class com.actelion.research.util.Sketch
- writeMolSketchFile(Molecule, String) - Static method in class com.actelion.research.util.Sketch
- writeQuadraticSymmetricMatrixPairwise(Matrix, File) - Static method in class com.actelion.research.calc.MatrixFunctions
- writeR(Writer, String, int) - Static method in class com.actelion.research.chem.io.AbstractParser
- writeReactionSketchFile(Reaction, OutputStream) - Static method in class com.actelion.research.util.Sketch
- writeReactionSketchFile(Reaction, String) - Static method in class com.actelion.research.util.Sketch
- writeRecordHeader(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- writeRXNfile(Writer) - Method in class com.actelion.research.chem.io.RXNFileCreator
- writeRXNfile(Writer) - Method in class com.actelion.research.chem.io.RXNFileV3Creator
- writeSerialized(File) - Method in class com.actelion.research.calc.Matrix
- writeShort(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeTabDelimitedTable(String) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
Writes a TAB delimited text file that can be opened for debug or other purposes by DataWarrior containing idcode, idcoords, multiple conformer likelihoods
- writeTemplate(ArrayList<String>) - Method in class com.actelion.research.chem.io.DWARFileCreator
- writeTextFile(String, int) - Method in class com.actelion.research.chem.AtomTypeList
-
Writes this AtomTypeList into a TAB-delimited text file in human readable form.
- writeTypeFile(String) - Method in class com.actelion.research.chem.AtomTypeList
- writeUTF(String) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeWMF(OutputStream) - Method in class com.actelion.research.gui.wmf.WMF
- writeWord(int) - Method in class com.actelion.research.gui.wmf.WMF
X
- x - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorDot
- x - Variable in class com.actelion.research.chem.Coordinates
- x - Variable in class com.actelion.research.chem.forcefield.mmff.Vector3
- x - Variable in class com.actelion.research.util.datamodel.PointDouble
- x - Variable in class org.machinelearning.svm.libsvm.svm_problem
- x - Variable in class smile.data.Datum
-
Immutable datum object.
- x - Variable in class smile.math.SparseArray.Entry
-
The value of entry.
- x() - Method in class smile.data.AttributeDataset
-
Returns the array of data items.
- X - com.actelion.research.chem.phesa.PheSAAlignment.axis
- X - Variable in class com.actelion.research.util.datamodel.ModelXY
- x1 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
- x2 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
- xax(double[]) - Method in interface smile.math.matrix.DenseMatrix
-
Returns x' * A * x.
- XY - Class in com.actelion.research.util.datamodel
-
XY
- XY(double[], double[]) - Constructor for class com.actelion.research.util.datamodel.XY
- XYIndex - Class in com.actelion.research.util.datamodel
-
Modest v.
- XYIndex(double[], double[]) - Constructor for class com.actelion.research.util.datamodel.XYIndex
- XYIndex(double[], double[], int) - Constructor for class com.actelion.research.util.datamodel.XYIndex
Y
- y - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorDot
- y - Variable in class com.actelion.research.chem.Coordinates
- y - Variable in class com.actelion.research.chem.forcefield.mmff.Vector3
- y - Variable in class com.actelion.research.util.datamodel.PointDouble
- y - Variable in class org.machinelearning.svm.libsvm.svm_problem
- y - Variable in class smile.clustering.PartitionClustering
-
The cluster labels of data.
- y - Variable in class smile.data.Datum
-
Class label or real-valued response.
- y() - Method in class smile.data.Dataset
-
Returns the response values.
- Y - com.actelion.research.chem.phesa.PheSAAlignment.axis
- Y - Variable in class com.actelion.research.util.datamodel.ModelXY
- y1 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
- y2 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
Z
- z - Variable in class com.actelion.research.chem.Coordinates
- z - Variable in class com.actelion.research.chem.forcefield.mmff.Vector3
- Z - com.actelion.research.chem.phesa.PheSAAlignment.axis
- ZERO_NODE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- zeroGradient() - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- zeroGradient() - Method in interface com.actelion.research.chem.forcefield.ForceField
-
zeroes out gradient for fixed atoms
- zeroGradient() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- zeros(int, int) - Static method in interface smile.math.matrix.Matrix
-
Returns all-zero matrix.
- zoomAndRotate(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- zoomAndRotate(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- zoomAndRotate(double, double, boolean) - Method in class com.actelion.research.chem.Molecule
- zoomAndRotateInit(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- zoomAndRotateInit(double, double) - Method in class com.actelion.research.chem.Molecule
- zoomAndRotateInit(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- ZoomRotateAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 4/28/2014 Time: 12:39 PM
- ZoomRotateAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
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