All Classes Interface Summary Class Summary Enum Summary Exception Summary
Class |
Description |
AbstractDepictor<T> |
|
AbstractDepictor.DepictorDot |
|
AbstractDepictor.DepictorLine |
|
AbstractDescriptorHandlerFP<U> |
|
AbstractDescriptorHandlerLongFP<U> |
|
AbstractDistribution |
This is the base class of univariate distributions.
|
AbstractDrawingObject |
|
AbstractExtendedDepictor<T,C> |
|
AbstractForceField |
|
AbstractParser |
A parser is used to load and save molecules from the filesystem.
|
AbstractScoringEngine |
this class is not thread safe!
|
AcceptorPoint |
|
Action |
Basic Interface for all editor actions
|
AddRingAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:03 PM
|
AliphaticPoint |
|
AMemorizedObject |
AMemorizedObject
|
AminoAcidLabeled |
AminoAcidLabeled
|
AminoAcidsLabeledContainer |
AminoAcidsLabeledContainer
The txt file was generated with com.actelion.research.chem.parsers.pdb.ProcessLabeledAminoAcids
|
AnalyticalParameterCalculatorSVM |
AnalyticalParameterCalculatorSVM
|
Angle |
Angle table, corresponds to the MMFFANG.PAR parameters table provided in
the MMFF literature.
|
Angle |
The angle type class provides static functions for getting angle and
stretch bend MMFF type.
|
Angle |
This class provides various operations on angles,
while making sure that the values is always in the rangle
from -pi >= v > pi.
|
AngleBend |
Angle bending energy term class.
|
AngleConstraint |
|
AnimatedGIFWriter |
|
AnimatedGIFWriter.GIFFrame |
|
ARegressionMethod<T extends ParameterRegressionMethod> |
ARegressionMethod
|
AromaticityResolver |
|
AromRingPoint |
|
ArrayUtils |
|
ArrayUtilsCalc |
|
Arrow |
|
ArrowAction |
Project:
User: rufenec
Date: 5/16/13
Time: 3:46 PM
|
Atom |
Atom table, corresponds to the MMFFPROP.PAR parameters table provided
in the MMFF literature.
|
Atom |
The Atom type class provides static functions to perform atom typing on
atoms in a Molecule.
|
AtomAssembler |
|
AtomComparator |
|
AtomFunctionAnalyzer |
|
AtomHighlightAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:13 PM
|
AtomicFloat |
|
AtomicGaussian |
|
AtomIndexLinkerId |
AtomIndexLinkerId
|
AtomLabelDialogBuilder |
|
AtomMapAction |
Project:
User: rufenec
Date: 5/22/13
Time: 4:00 PM
|
AtomQueryFeatureDialogBuilder |
|
AtomRecord |
ModelAtom
|
AtomTypeCalculator |
|
AtomTypeList |
|
AtomTypeMap |
|
Attribute |
Generic class to represent a named attribute/variable.
|
Attribute.Type |
The type of attributes.
|
AttributeDataset |
A dataset of fixed number of attributes.
|
AttributeVector |
A vector with attribute information.
|
AutoMapper |
Project:
User: rufenec
Date: 6/17/2014
Time: 10:04 AM
|
AxialStereoRule |
Handles attropisomery as well as chiral allenes
|
BadAtomTypeException |
The BadAtomTypeException is thrown when there is a bad atom type in a
molecule.
|
BadRingAromException |
The BadRingAromException is thrown when there is a problem with the MMFF
ring aromaticity assignment.
|
Base64 |
|
Base64.InputStream |
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 |
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.
|
BBDTree |
Balanced Box-Decomposition Tree.
|
BinaryDecoder |
|
BinaryEncoder |
|
BinarySOM |
|
BitArray128 |
|
BitArray128Factory |
|
BitUtils |
|
Bndk |
Bndk table, corresponds to the MMFFBNDK.PAR parameters table provided
in the MMFF literature.
|
BOMSkipper |
|
Bond |
Bond table, corresponds to the MMFFBOND.PAR parameters table provided
in the MMFF literature.
|
Bond |
The bond type class provides static functions for getting the MMFF bond
type (either by bond or by the atoms of a bond).
|
BondAngleSet |
|
BondBaseAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:07 PM
|
BondConstraint |
|
BondHighlightAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:07 PM
|
BondLengthSet |
|
BondQueryFeatureDialogBuilder |
|
BondRotationHelper |
|
BondsCalculator |
BondsCalculator is used to recreate the bonds and / or calculate the bonds orders
based on the 3D coordinates of the atoms
|
BondStretch |
Bond stretching energy term class.
|
BondVector2IdCode |
|
BoxCox |
BoxCox
|
BrowserControl |
|
BurtleHasher |
http://burtleburtle.net/bob/c/lookup3.c
-------------------------------------------------------------------------------
lookup3.c, by Bob Jenkins, May 2006, Public Domain.
|
BurtleHasherABC |
|
ByteArray |
|
ByteArrayArrayComparator |
|
ByteArrayComparator |
|
ByteVec |
ByteVec:
|
Canonizer |
|
CanonizerBaseValue |
|
CanonizerMesoHelper |
|
CanonizerUtil |
|
CanonizerUtil.IDCODE_TYPE |
|
CanonizerUtil.StrongHasher |
64 bit hash, derived from numerical recipes
Will move this class later to dd_core.
|
CDXConstants |
|
ChangeAtomAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:13 PM
|
ChangeAtomPropertiesAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:13 PM
|
ChangeChargeAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:13 PM
|
Charge |
|
Charge |
The charge class provides static functions for calculating formal and
partial charges on a molecule.
|
ChargedGroupDetector |
derives charged groups
|
ChargePoint |
|
ChemDrawCDX |
|
ChemicalRule |
A ChemicalRule is basically a chemical reaction (transformation) defined by a reaction substructure
and a product substructure with full stoichiometry and completely mapped atoms.
|
ChemicalRuleEnhancedReactionMapper |
|
ChemicalSpaceCreator |
|
ChemistryCellRenderer |
|
ChemistryDataFormats |
|
ChemistryFlavors |
|
ChemistryHelper |
|
ChemistryRenderPanel |
|
ChemPLP |
Implementation of ChemPLP scoring function as described in: doi: 10.1021/ci800298z
THIS SCORING FUNCTION REQUIRES EXPLICIT HYDROGENS TO BE PRESENT!
|
Cholesky |
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'.
|
CLARANS<T> |
Clustering Large Applications based upon RANdomized Search.
|
Classification |
|
ClassificationAttr |
Modest v.
|
ClassificationData |
|
CleanAction |
Project:
User: rufenec
Date: 1/28/13
Time: 10:09 AM
|
ClearAction |
Project:
User: rufenec
Date: 1/24/13
Time: 5:09 PM
|
ClipboardHandler |
Title: Actelion Library
|
ClipboardHelper |
Created by baerr on 7/28/14.
|
CLogPPredictor |
|
Clusterer<T> |
|
Clustering<T> |
Clustering interface.
|
ClusteringDistance |
Clustering distance measure.
|
ClusterNode |
|
ColorHelper |
|
ColorUtils |
Defines a color with some utility methods.
|
CombinationGenerator |
CombinationGenerator
|
ComboBoxColorItem |
|
CommandAction |
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
|
CommandLineParser |
CommandLineParser
Simple command line parser.
|
CommonSubGraphHelper |
|
CompleteGraphMatcher<T extends ICompleteGraph> |
CompleteGraphMatcher
|
CompleteLinkage |
Complete linkage.
|
Complex |
Complex number.
|
CompoundCollectionListener |
|
CompoundCollectionModel<T> |
|
CompoundCollectionPane<T> |
|
CompoundFileFilter |
A convenience implementation of FileFilter that filters out
all files except for those type extensions that it knows about.
|
CompoundFileHelper |
|
CompoundFileParser |
|
CompoundTableConstants |
|
ConformationRule |
|
ConformationSelfOrganizer |
|
Conformer |
|
ConformerGenerator |
This class generates 3D-conformers of a given molecule using the following strategy:
All rotatable, non-ring bonds are determined.
|
ConformerSet |
|
ConformerSetGenerator |
|
Constants |
The Constants class holds numerical constants that are reused in
multiple classes.
|
ConstantsAminoAcidsLabeled |
ConstantsAminoAcidsLabeled
|
ConstantsDWAR |
ConstantsDWAR
|
ConstantsFlexophore |
|
ConstantsFlexophoreGenerator |
|
ConstantsFlexophoreHardPPPoints |
|
ConstantsHistogram |
ConstantsHistogram
|
ConstantsRegressionMethods |
ConstantsRegressionMethods
|
ContainerBitArray |
|
ContainerBitArray.CapacityReachedError |
|
ContainerFragBondsSolutions |
|
ContainerListWithIntVec |
|
ContainerMemory<S extends AMemorizedObject> |
ContainerMemory
|
CoordinateInventor |
|
Coordinates |
Class to encapsulate 3D coordinates
|
CopyAction |
Project:
User: rufenec
Date: 5/16/13
Time: 3:31 PM
|
CorrelationCalculator |
|
CovRad |
CovRad table, used in the bond stretch empirical calculations of 'kb'
and 'r0'.
|
CreatorMolDistHistViz |
CreatorMolDistHistViz
|
Csv |
Basic CSV parser.
|
CursorHelper |
|
CutAction |
Project:
User: rufenec
Date: 5/16/13
Time: 3:43 PM
|
DatabaseReaction |
|
DataProcessor |
|
Dataset<E> |
A set of data objects.
|
DateAnalysis |
|
DateAttribute |
Data attribute.
|
Datum<T> |
An object of generic datum and optional weight.
|
Def |
Equivalence table, corresponds to MMFFDEF.PAR parameters table provided
in the MMFF literature.
|
DefaultCompoundCollectionModel<T> |
|
DefaultCompoundCollectionModel.IDCode |
This version of the DefaultCompoundCollectionModel collects
molecules as IDCodes.
|
DefaultCompoundCollectionModel.IDCodeWithName |
This version of the DefaultCompoundCollectionModel collects
molecules as String[2] with idcodes & idcoords (index 0) and molecule name (index 1).
|
DefaultCompoundCollectionModel.Molecule |
This version of the DefaultCompoundCollectionModel collects molecules as StereoMolecules.
|
DefaultCompoundCollectionModel.Native |
This version of the DefaultCompoundCollectionModel collects
IDCodes and StereoMolecules without conversion into their native type.
|
Delegator<T> |
|
DeleteAction |
Project:
User: rufenec
Date: 3/26/13
Time: 4:15 PM
|
DenseMatrix |
An abstract interface of dense matrix.
|
Depictor |
Deprecated. |
Depictor2D |
|
DepictorTransformation |
|
DescriptorConstants |
|
DescriptorEncoder |
DescriptorEncoder encodes int[] based descriptors
into byte arrays that may be used to instantiate Strings
|
DescriptorHandler<T,U> |
DescriptorHandler is the base Interface for any molecular descriptor
handling StereoMolecules or Reactions
|
DescriptorHandlerFactory |
|
DescriptorHandlerFFP512 |
|
DescriptorHandlerFlexophore |
DescriptorHandlerFlexophore
|
DescriptorHandlerFunctionalGroups |
|
DescriptorHandlerHashedCFp |
|
DescriptorHandlerIntVector<U> |
This is a descriptor handler, where the input object is an integer array
that typically represents counts of some sort.
|
DescriptorHandlerLongCFP |
|
DescriptorHandlerLongFFP512 |
|
DescriptorHandlerLongPFP512 |
|
DescriptorHandlerPFP512 |
|
DescriptorHandlerPTree |
|
DescriptorHandlerReactionFP |
|
DescriptorHandlerShape |
|
DescriptorHandlerShapeOneConf |
|
DescriptorHandlerSkeletonSpheres |
|
DescriptorHandlerStandard2DFactory |
|
DescriptorHandlerStandardFactory |
|
DescriptorHelper |
|
DescriptorInfo |
|
Dfsb |
|
DialogEvent |
|
DialogEventConsumer |
|
DialogResult |
Return values from Dialog calls
|
DiastereoIDTest |
|
DiastereotopicAtomID |
|
DifferentiableFunction |
A differentiable function is a function whose derivative exists at each point
in its domain.
|
DifferentiableMultivariateFunction |
A differentiable function is a function whose derivative exists at each point
in its domain.
|
Distance<T> |
An interface to calculate a distance measure between two objects.
|
DistanceMetrics |
DistanceMetrics
|
DistanceRule |
|
DistHist |
|
DistHistEncoder |
|
DistHistHelper |
DistHistHelper
|
DistHistHelper.RangeStatistics |
|
Distribution |
Probability distribution of univariate random variable.
|
DiversitySelector |
|
DividerChangeListener |
|
Dockable |
A lightweight component derived from JPanel that features certain subcomponents
that make it look similar to a frame or internal frame.
|
DockableHeader |
|
DockingEngine |
|
DockingEngine.DockingResult |
|
DockingEngine.ScoringFunction |
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 |
|
DockingUtils |
|
DonorPoint |
|
DoubleArray |
DoubleArray
26 Jun 2010 MvK: Start implementation
|
DoubleFormat |
|
DoubleVec |
|
DownBondAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:51 PM
|
DragGlassPane |
Project:
User: rufenec
Date: 2/21/14
Time: 6:14 PM
|
DrawAction |
Basic class which handles all actions which interact with the drawing surface
|
DrawAreaEvent |
|
DrawAreaListener |
|
DrawConfig |
User: rufenec
Creation Date: 8/24/2016
|
DrawingObject |
Project:
User: rufenec
Date: 5/16/13
Time: 12:31 PM
|
DrawingObjectFactory |
|
DrawingObjectList |
|
DruglikenessPredictor |
|
DruglikenessPredictorWithIndex |
|
DrugScoreCalculator |
Created by rufenec on 26/10/15.
|
DWARFileCreator |
|
DWARFileParser |
|
Electrostatic |
Nonbonded electrostatic energy term class.
|
Element |
|
EmpiricalLigandStrain |
|
EncodeFunctions |
February 2018
Author: J.
|
EncoderFloatingPointNumbers |
|
EncoderIntegerNumbers |
Encodes integer numbers into a string.
|
EnergyTerm |
Interface class for energy terms.
|
Erf |
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.
|
ErrorHashMap |
ErrorHashMap
2005 MvK: Start implementation
|
Evaluable |
|
EvaluableFlexibleOverlap |
|
EvaluableOverlap |
|
EVD |
Eigen decomposition of a real matrix.
|
ExceptionConformationGenerationFailed |
|
ExhaustiveFragmentGeneratorAtoms |
|
ExhaustiveFragmentGeneratorBonds |
|
ExhaustiveFragmentGeneratorParallizer |
|
ExhaustiveFragmentsStatistics |
|
ExhaustiveMCSGeneratorParallel |
|
ExitVectorPoint |
|
ExponentialFamily |
The exponential family is a class of probability distributions sharing
a certain form.
|
ExponentialMap |
described in:
F.
|
ExtendedDepictor |
|
ExtendedMolecule |
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.
|
ExtendedMoleculeFunctions |
ExtendedMoleculeFunctions
|
FactorySolution |
FactorySolution
|
FastMolecularComplexityCalculator |
This is a fast version of the MolecularComplexityCalculator in the com.actelion.chem.properties.complexity
package.
|
FastSpline |
Represents a polynomial spline function.
|
FastSpline.Polynome |
|
FeatureCalculator |
calculates features for all atoms in a molecule:
H-bond acceptors/donors, negatively/positively ionizable, aromatic, lipophilic
|
FileHelper |
|
FingerPrintGenerator |
Generator of a path-based Fingerprint
Not thread safe!
|
FittingFunction |
|
FlexibleShapeAlignment |
Performs flexible Alignment of two Molecules that are prealigned.
|
FlexophoreCreateFunctions |
FlexophoreCreateFunctions
|
FlexophorePoint |
FlexophorePoint
|
ForceField |
|
ForceFieldChangeListener |
|
ForceFieldMMFF94 |
|
Formatter |
|
Formatter.LocaleFormat |
|
FormulaParser |
FormulaParser
|
FractalDimensionMolecule |
FractalDimensionMolecule
|
FractalDimensionMoleculeMain |
FractalDimensionMoleculeMain
|
Fragment |
Fragment
Jan 18, 2013 MvK Start implementation
|
Fragment3D |
|
FragmentAssociation |
Created by thomas on 9/23/16.
|
FragmentDefinedByBondsHasher |
|
FragmentDefinedByBondsIdCode |
|
Fragmenter3D |
|
Function |
An interface representing a univariate real function.
|
FunctionalGroupClassifier |
|
Gaussian3D |
|
GaussianDistribution |
The normal distribution or Gaussian distribution is a continuous probability
distribution that describes data that clusters around a mean.
|
GaussianKernel |
The Gaussian Mercer Kernel.
|
GaussianProcessRegression |
GaussianProcessRegression
|
GaussianProcessRegression<T> |
Gaussian Process for Regression.
|
GaussianProcessRegression.Trainer<T> |
Trainer for Gaussian Process for Regression.
|
GaussianRadialBasis |
Gaussian RBF.
|
GenericCanvas |
|
GenericCheckBox |
|
GenericComboBox |
|
GenericComponent |
|
GenericDepictor |
|
GenericDialog |
|
GenericDialogHelper |
|
GenericDrawArea |
|
GenericDrawContext |
|
GenericEditorToolbar |
|
GenericKeyEvent |
|
GenericKeyListener |
|
GenericLabel |
|
GenericMouseEvent |
|
GenericMouseListener |
|
GenericPolygon |
|
GenericPopupMenu |
|
GenericRectangle |
|
GenericShape |
|
GenericTextField |
|
GeometryCalculator |
Utility class to perform 3D geometry calculations on molecules
|
GeometryCalculator |
Utility class to perform 3D geometry calculations on molecules
|
GeomFactory |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:15 PM
|
GhostPreview |
|
GlobularityCalculator |
|
Graph |
|
GraphicsContextImpl |
Project:
User: rufenec
Date: 11/24/2014
Time: 6:24 PM
|
HashSetInt |
HashSetInt
|
HBTerm |
|
HeaderMouseAdapter |
|
HeaderPaintHelper |
|
HerschbachLaurie |
Table for Herschbach-Laurie version of Badger's rule.
|
HetNameParser |
HetNameParser
|
HetSynonymParser |
HetSynonymParser
|
HiDPIHelper |
|
HiDPIIcon |
Created by thomas on 07/12/15.
|
HiDPIIconButton |
Created by sandert on 04/12/15.
|
HiDPIToggleButton |
Created by thomas on 07/12/15.
|
HiDPIUtil |
|
HierarchicalClustering |
Agglomerative Hierarchical Clustering.
|
Histogram |
Histogram
|
HistogramMatchCalculator |
HistogramMatchCalculator
|
HoseCodeCreator |
|
HungarianAlgorithm |
|
HydrogenHandler |
|
IArrow |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:28 PM
|
IAtomPropertiesDialog |
Project:
User: rufenec
Date: 11/24/2014
Time: 5:03 PM
|
IAtomQueryFeaturesDialog |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:53 PM
|
IBitArray |
|
IBitArrayFactory<T extends IBitArray> |
|
IBondQueryFeaturesDialog |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:57 PM
|
ICalculateModel |
ICalculateModel
|
ICalculateYHat |
ICalculateYHat
|
IChangeListener |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:25 PM
|
IClipboardHandler |
|
IColor |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:21 PM
|
ICompleteGraph |
ICompleteGraph
|
ICursor |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:21 PM
|
IDCodeCoord |
IDCodeCoord
Apr 12, 2012 MvK: Start implementation
|
IDCodeParser |
|
IDCodeParserWithoutCoordinateInvention |
Typically you should use IDCodeParser instead of this class.
|
IdentifiedObject<T> |
IdentifiedObject
Nov 2, 2011 MvK: Start implementation
|
IDepictor<T> |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:26 PM
|
IDescriptorHandlerFlexophore |
|
IDialog |
|
IdoScore |
|
IDrawContext<T> |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:22 PM
|
IDrawingObject |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:28 PM
|
IFactory<S extends AMemorizedObject> |
IFactory
|
IIdentifiedObject<T> |
IIdentifiedObject
Nov 4, 2011 MvK: Start implementation
|
IKeyCode |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:17 PM
|
IKeyEvent |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:20 PM
|
ImageClipboardHandler |
|
ImageClipboardHandler.ImageSelection |
|
ImageDataSource |
This is a source for high resolution image data requested by JImagePanel
|
ImageProvider<T> |
Created by rufenec on 08/05/15.
|
IModelCloneable<T> |
IModelClonable
|
IMolDistHist |
|
IMoleculeView |
|
IMouseEvent |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:19 PM
|
IncrementTable |
|
IncrementTableWithIndex |
|
IndexCoordinates |
|
IndexHash |
|
InputObjectFracDimCalc |
InputObjectFracDimCalc
|
IntArray |
|
IntArrayComparator |
|
IntegerDouble |
IntegerDouble
Oct 24, 2011 MvK: Start implementation
|
IntegerHistogram |
IntegerHistogram
|
InteractionAtomTypeCalculator |
|
InteractionAtomTypeCalculator.AtomFlagCount |
|
InteractionAtomTypeCalculator.AtomPropertyMask |
|
InteractionAtomTypeCalculator.AtomPropertyShift |
|
InteractionAtomTypeCalculator.FunctionalGroup |
|
InteractionDistanceStatistics |
|
InteractionSimilarityTable |
distance gives the distance of the point of highest potential.
|
InteractionSimilarityTable.InteractionDescriptor |
|
InteractionTerm |
ProteinLigandTerm is used to represent the energy between 2 atoms.
|
InteractionTypeMap |
|
IntHeapSelect |
This class tracks the smallest values seen thus far in a stream of values.
|
IntQueue |
Implementation for a FIFO of int.
|
IntQueue |
Implementation for a FIFO of int.
|
IntVec |
|
INumericalDataColumn |
|
InventorAngle |
Created by thomas on 9/23/16.
|
InventorChain |
Created by thomas on 9/23/16.
|
InventorCharge |
Created by thomas on 9/28/16.
|
InventorDefaultTemplateList |
|
InventorFragment |
|
InventorTemplate |
|
IO |
IO
2003 MvK: Start implementation
|
IObjectiveCompleteGraph<T extends ICompleteGraph> |
IObjectiveCompleteGraph
|
IonizableGroupDetector |
derives potentially ionizable Groups, independent of the chosen explicit protonation state
|
IonizableGroupDetector2D |
|
IPharmacophorePoint |
|
IPharmacophorePoint.Functionality |
|
IPipeline<T> |
IPipeline
Interface to connect several Runable in a pipeline
Mar 27, 2012 MvK: Start implementation
Oct 9 2012 MvK: wereAllDataFetched() added.
|
IPolygon |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:45 PM
|
IPPNode |
|
IPPNodeSimilarity |
IPPNodeSimilarity
|
IReactionArrow |
Project:
User: rufenec
Date: 11/24/2014
Time: 5:49 PM
|
IReactionMapper |
|
IRectangle2D |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:17 PM
|
ISimilarityCalculator<T> |
|
ISimilarityHandlerFactory |
|
IsomericSmilesCreator |
|
IsotopeHelper |
|
IStructureNameResolver |
Created by thomas on 7/13/17.
|
IValidationListener |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:27 PM
|
JAtomLabelDialog |
Deprecated. |
JAtomQueryFeatureDialog |
Deprecated. |
JBondQueryFeatureDialog |
Deprecated. |
JBrowseButtons |
|
JChemistryView |
|
JComboBoxWithColor |
|
JDockingPanel |
|
JDrawArea |
Deprecated. |
JDrawDialog |
Deprecated. |
JDrawPanel |
Deprecated. |
JDrawToolbar |
Deprecated. |
JEditableChemistryView |
|
JEditableStructureView |
|
JFileChooserOverwrite |
|
JFXCanvasDepictor |
Project:
User: rufenec
Date: 10/12/11
Time: 6:00 PM
|
JImagePanel |
|
JImagePanelFixedSize |
|
JLoginDialog |
|
JMatrix |
A pure Java implementation of DenseMatrix whose data is stored in a single 1D array of
doubles in column major order.
|
JMessageBar |
|
JMultiPanelTitle |
|
JMultiPanelView |
|
JPopupButton |
|
JProgressDialog |
|
JProgressPanel |
|
JPruningBar |
Lightweight Slider for maintaining two values within given limits
|
JScrollableMenu |
|
JScrollablePopupMenu |
|
JScrollablePopupMenu.ScrollPopupMenuLayout |
|
JStructureView |
|
JTableWithRowNumbers |
|
JTextDrawingObjectDialog |
Deprecated. |
KabschAlignment |
described in: DOI 10.1002/jcc.20110 "Using Quaternions to Calculate RMSD"
|
KMeans |
K-Means clustering.
|
KNNRegression |
KNNRegression
kNN regression seems to be very inappropriate for regression problems.
|
Lanczos |
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.
|
LigandPose |
|
LinearRegression |
LinearRegression
2009 MvK: Start implementation
|
Linkage |
A measure of dissimilarity between clusters (i.e.
|
Linker |
Linker
|
ListInteger<T> |
ListInteger
|
ListWithIntVec |
|
ListWithIntVecIdCode |
|
LittleEndianDataInputStream |
|
LittleEndianDataOutputStream |
|
Logarithm |
Logarithm
Mar 14, 2013 MvK Start implementation
|
LookAndFeelHelper |
|
LU |
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.
|
LUDecomposition |
LU Decomposition.
|
MappingScorer |
|
MarkushStructure |
|
MatchFlexophoreNodesMain |
|
Math |
A collection of useful mathematical functions.
|
MathHelper |
|
Matrix |
|
Matrix |
An abstract interface of matrix.
|
Matrix2SVMNodeConverter |
Matrix2SVMNodeConverter
|
MatrixBasedHistogram |
MatrixBasedHistogram
|
MatrixFunctions |
Title: MatrixFunctions
|
MatrixMultiplication<A,B> |
Matrix multiplication interface.
|
MatrixTests |
MatrixData
|
MCS |
|
MCSFast |
|
MCSFunctions |
|
MCSReactionMapper |
|
MDHIndexTables |
|
MedianRegression |
MedianRegression
|
MedianStatisticFunctions |
MedianStatisticFunctions
Aug 5, 2011 MvK: Start implementation
|
MercerKernel<T> |
A Mercer Kernel is a kernel that is positive semi-definite.
|
MersenneTwister |
|
MetaFile |
|
MetalTerm |
|
Metric<T> |
A metric function defines a distance between elements of a set.
|
MetropolisMonteCarloHelper |
|
MinimumSpanningTree |
MinimumSpanningTree
Kruskal's algorithm
|
Mixture |
A finite mixture model is a probabilistic model for density estimation using a
mixture distribution.
|
Mixture.Component |
A component in the mixture distribution is defined by a distribution
and its weight in the mixture.
|
MMFFExternalPositionConstraint |
|
MMFFMolecule |
MMFF molecule is a wrapper class for the ExtendedMolecule.
|
MMFFPositionConstraint |
|
Model |
Project:
User: rufenec
Date: 1/24/13
Time: 5:02 PM
|
Model.AtomHighlightCallback |
|
Model.BondHighlightCallback |
|
ModelError |
ModelError
This class is a data model for the error.
|
ModelExhaustiveStatistics |
|
ModelMedianDouble |
|
ModelMedianFloat |
|
ModelMedianInteger |
ModelMedianInteger
Feb 9, 2012 MvK: Start implementation
|
ModelMedianLong |
ModelMedianInteger
Feb 14, 2017 MvK: Start implementation
|
ModelParser |
ModelParser
|
ModelSampleFragments |
|
ModelSolutionSimilarity |
|
ModelStatisticsOverview |
ModelStatisticsOverview
|
ModelStatisticsOverviewMedian |
ModelStatisticsOverviewMedian
|
ModelXY |
ModelDataXY
X and Y are assumed to have the same row dim.
|
ModelXYClassLabel |
ModelXYClassLabel
|
ModelXYColTags |
ModelXYColTags
|
ModelXYCrossValidation |
Deprecated. |
ModelXYIndex |
ModelDataXY
|
Mol2FileParser |
|
MolDistHist |
|
MolDistHistEncoder |
|
MolDistHistViz |
Class for Flexophore visualization and atom tracking.
|
MolDistHistVizEncoder |
|
MolDistHistVizFrag |
|
MolecularComplexityCalculator |
|
MolecularFlexibilityCalculator |
|
MolecularFormula |
|
MolecularPropertyHelper |
|
MolecularShapeCalculator |
|
MolecularVolume |
|
Molecule |
|
Molecule3D |
|
Molecule3DFunctions |
|
MoleculeAutoMapper |
|
MoleculeDataFormats |
Deprecated. |
MoleculeDragAdapter |
|
MoleculeDropAdapter |
|
MoleculeFilter |
|
MoleculeGrid |
Class used to speed up the calculation of neighbours by creating a grid.
|
MoleculeNeutralizer |
|
MoleculeStandardizer |
MoleculeStandardizer
|
MoleculeTransferable |
|
MoleculeView |
Project:
User: rufenec
Date: 10/12/11
Time: 4:03 PM
|
MoleculeViewSkin |
Project:
User: rufenec
Date: 10/12/11
Time: 4:10 PM
|
MolfileCreator |
|
MolfileParser |
|
MolfileV3Creator |
This class generates an MDL molfile version 3.0 from a StereoMolecule
as described by MDL in 'CTFile Formats June 2005'.
|
MultCoordFragIndex |
|
MulticoreExecutor |
Utility class to run tasks in a thread pool on multi-core systems.
|
MultiPanelDragListener |
|
MultipleNonOverlapSolution |
|
MultivariateFunction |
An interface representing a multivariate real function.
|
Mutation |
|
MutationBiasProvider |
|
Mutator |
|
NamedSubstituents |
|
NastyFunctionDetector |
|
NativeClipboardAccessor |
|
NativeMDLReactionReader |
|
NegativeReceptorImage |
|
NegativeReceptorImage.InteractionProbe |
|
NegativeReceptorImageCreator |
|
NeuralNetwork |
Multilayer perceptron neural network for regression.
|
NeuralNetwork.ActivationFunction |
|
NeuralNetwork.Trainer |
Trainer for neural networks.
|
NeuralNetworkParameterHelper |
NeuralNetworkParameterHelper
|
NeuralNetworkRegression |
NeuralNetworkRegression
|
NewBondAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:28 PM
|
NewChainAction |
Project:
User: rufenec
Date: 3/26/13
Time: 3:42 PM
|
NominalAttribute |
Nominal attribute.
|
NumericalRecipes |
|
NumericAttribute |
Numeric attribute.
|
ObjectiveBlurFlexophoreHardMatchUncovered |
ObjectiveBlurFlexophoreHardMatchUncovered
The weighting of the coverage is hard.
|
ObjectiveExhaustiveStatistics |
|
ODEFileParser |
|
OnlineRegression<T> |
Regression model with online learning capability.
|
OptimizerLBFGS |
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
|
OutOfPlane |
Out of plane energy term class.
|
OutOfPlane |
|
ParameterGaussianProcess |
ParameterGaussianProcess
|
ParameterizedStringList |
|
ParameterKNN |
ParameterKNN
|
ParameterMedian |
ParameterMedian
|
ParameterNeuralNetwork |
ParameterNeuralNetwork
|
ParameterPLS |
ParameterPLS
|
ParameterPLSBoxCox |
ParameterPLSBoxCox
|
ParameterRandomForest |
ParameterRandomForest
|
ParameterRegressionMethod |
ParameterRegressionMethod
|
ParameterSVM |
ParameterSVM
|
PartitionClustering<T> |
Abstract class of partition clustering.
|
PasteAction |
Project:
User: rufenec
Date: 5/16/13
Time: 3:39 PM
|
PDBCoordEntryFile |
PDBCoordEntryFile
|
PDBFileParser |
PDBFileParser
|
PeriodicTable |
|
PeriodicTable |
|
PharmacophoreCalculator |
|
PharmacophoreNode |
A PharmacophoreNode represents a node in a PharmacophoreTree.
|
PharmacophorePointFactory |
|
PharmacophoreTree |
A PharmacophoreTree closely follows the concepts of FeatureTrees as described by Rarey and Dixon
(DOI:10.1023/a:1008068904628).
|
PharmacophoreTree.BiGramInt |
container of an undirected edge
|
PharmacophoreTreeGenerator |
Generates a PharmacophoreTree from a StereoMolecule.
|
PharmGraphGenerator |
|
PheSAAlignment |
|
PheSAAlignment.axis |
|
PheSAAlignment.PheSAResult |
|
PheSAAlignmentOptimizer |
|
PheSAAlignmentOptimizer.AlignmentResult |
|
PheSAMolecule |
|
Pipeline<T> |
Pipeline
Enables concurrent access to a queue.
|
Pipeline2FileWriter<T> |
Modest v.
|
PlaneRule |
|
Platform |
Requires JRE 1.6
|
PLPTerm |
piecewise linear potential (PLP) as described in doi:10.1021/ci800298z
parameters from model 3 (M3)
|
PLSBoxCoxY |
PLSBoxCoxY
|
PLSRegressionModelCalculator |
PLSRegressionModelCalculator
|
PointDouble |
|
PointUtils |
|
PolarSurfaceAreaPredictor |
This class predicts the topological polar surface area (TPSA) of a molecule as a sum of
contributions of its polar atom-types.
|
Polygon |
|
PopupItemProvider |
|
PopupProvider |
|
PositionConstraint |
|
PotentialEnergyTerm |
|
PPGaussian |
|
PPNode |
|
PPNodeRGroup |
PPNodeStructure
|
PPNodeSimilarity |
PPNodeSimilarity
|
PPNodeViz |
Pharmacophore node with information about corresponding atoms in the molecule used for construction.
|
PPNodeVizTriangle |
|
PPTriangle |
|
PPTriangleCreator |
|
PPTriangleMatcher |
|
PrecisionAndRecall |
PrecisionAndRecall
|
Prefs |
|
ProbeScanning |
scans a receptor binding site for interaction points using a probe atom
|
ProbeScanning.Probe |
|
ProgressController |
|
ProgressListener |
|
PropertyCalculator |
|
ProteinSynthesizer |
|
PruningBarEvent |
|
PruningBarListener |
|
QR |
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.
|
Quaternion |
|
QuickMathCalculator |
|
QuickSelect |
Selection is asking for the k th smallest element out of n elements.
|
QuickSort |
Quicksort is a well-known sorting algorithm that, on average, makes O(n log n)
comparisons to sort n items.
|
RadialBasisFunction |
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||).
|
Random |
This is a high quality random number generator as a replacement of
the standard Random class of Java system.
|
RandomForest |
Random forest for regression.
|
RandomForest.Trainer |
Trainer for random forest.
|
RandomForestRegression |
RandomForestRegression
|
RandomNumberGenerator |
Random number generator interface.
|
RDFileParser |
Quick and dirty RD-File parser that reads non-hierarchical RD-Files.
|
Reaction |
|
ReactionArrow |
|
ReactionCenterMapper |
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.
|
ReactionClassifier |
|
ReactionDragAdapter |
|
ReactionDropAdapter |
|
ReactionEncoder |
|
ReactionSearch |
|
ReactionSearchDataSource |
|
ReactionSearchSpecification |
|
ReactionTransferable |
|
Reactor |
|
Regression<T> |
Regression analysis includes any techniques for modeling and analyzing
the relationship between a dependent variable and one or more independent
variables.
|
RegressionMeasure |
An abstract interface to measure the regression performance.
|
RegressionMethodContainer |
RegressionMethodContainer
|
RegressionModelCalculatorOptimumFactors |
RegressionModelCalculatorOptimumFactors
|
RegressionTrainer<T> |
Abstract regression model trainer.
|
RegressionTree |
Decision tree for regression.
|
RegressionTree.NodeOutput |
An interface to calculate node output.
|
RegressionTree.Trainer |
Trainer for regression tree.
|
RemarkParser |
RemarkParser
|
REPTerm |
repulsive term, see PLPTerm for reference
|
Residue |
ModelGroupAtoms
handles a group of atoms, e.g.
|
ResultFracDimCalc |
ResultFracDimCalc
|
ResultFragmentsStatistic |
|
ResultObjective |
|
RigidFragment |
|
RigidFragmentCache |
This class implements a thread-save, concurrent cache of rigid fragments' 3D-atom-coordinates.
|
RigidFragmentCache.CacheEntry |
|
RigidFragmentProvider |
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.
|
RingBoolean |
|
RingCollection |
|
RMSE |
Root mean squared error.
|
RootAtomPairSource |
|
RotatableBond |
A RotatableBond knows the two rigid fragments within a molecule
that are connected by this bond.
|
Rotation |
|
RotationDerivatives |
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!
|
RunBondVector2IdCode |
|
RXNFileCreator |
|
RXNFileParser |
|
RXNFileV3Creator |
|
ScaffoldHelper |
|
ScaledEditorKit |
|
ScaledHTML |
|
ScaledStyleSheet |
|
ScaleLabel |
Contains shown label, the relative position on the scale and the numerical value
|
ScaleLabelCreator |
|
Scaling |
|
ScorePoint |
|
ScoringTask |
|
ScrollPaneAutoScrollerWhenDragging |
|
Sdf |
The Sdf class provides helper functions for dealing with the SDF file
format.
|
Sdf.OnMolecule |
|
SDFileMolecule |
|
SDFileMoleculeDropAdapter |
|
SDFileMoleculeTransferable |
|
SDFileParser |
|
Search |
The search class provides binary searching on arrays.
|
Searchable |
Interface that must be implemented for array objects that can be
searched by the binary search function.
|
SelectionAction |
Project:
User: rufenec
Date: 1/24/13
Time: 5:57 PM
|
Selector<T> |
Created with IntelliJ IDEA.
|
SelfOrganizedConformer |
|
SelfOrganizedMap |
|
Separation |
The Separation class is an efficient storage of an adjacency matrix
representing how many degrees of separation there are between any two
atoms.
|
Separation.Relation |
Relation class shows the relationship between two atoms A1 and A2.
|
ShadowBorder |
|
ShapeDocking |
|
ShapeVolume |
|
SimilarityCalculatorDoubleArray |
SimilarityCalculatorDoubleArray
Created by korffmo1 on 12.07.18.
|
SimilarityCalculatorInfo |
|
SimilarityGraphBasedReactionMapper |
|
SimilarityMulticore<T> |
SimilarityMulticore
T is the descriptor object class
|
SimpleCanonizer |
|
SimpleMetalTerm |
|
SimplePharmacophorePoint |
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)
|
SimPLS |
Title: SimPLS
|
SimPLSLMOValidation |
Deprecated. |
SingleLinkage |
Single linkage.
|
SingularValueDecomposition |
Singular Value Decomposition.
|
SiteParser |
SiteParser
Site records specify residues comprising catalytic, co-factor, anti-codon, regulatory or other
essential sites or environments surrounding ligands present in the structure.
|
SizeOf |
13.02.2006 MvK
|
Sketch |
Title: Actelion Java Library
|
SlidingWindow |
SlidingWindow
|
SlidingWindowDistHist |
SlidingWindowDistHist
Created by korffmo1 on 01.03.16.
|
SmilesCreator |
Deprecated. |
SmilesParser |
|
SmileUtils |
Some useful functions.
|
SmoothingSplineInterpolator |
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
|
SolubilityPredictor |
|
SolutionCompleteGraph |
SolutionCompleteGraph
|
SOMController |
|
SortedList<T extends java.lang.Comparable<? super T>> |
|
SortedPair |
SortedPair class is used in the Separation table.
|
SortedStringList |
|
SortUtils |
Some useful functions such as swap and swif-down used in many sorting
algorithms.
|
SparseArray |
Sparse array of double values.
|
SparseArray.Entry |
The entry in a sparse array of double values.
|
SplineFunction |
Class used to represent a Protein Ligand Function
|
SRSearcher |
The SRSearcher class handles reaction-sub-structure searches.
|
SSSearcher |
|
SSSearcherWithIndex |
|
StatisticalTorsionPotential |
|
StatisticalTorsionTerm |
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 |
StatisticsOverview
Some basic statistics about the given data
28 Jun 2010 MvK: Start implementation
|
Stbn |
|
StereoIsomerEnumerator |
|
StereoMolecule |
|
StraightLineRule |
|
StrainTerm |
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)
|
StretchBend |
Stretch bending energy term class.
|
String2DoubleArray |
|
StringFunctions |
|
StringReadChannel |
StringReadChannel
2007 MvK: Start implementation
25.06.2009 MvK: implementation changed
12.02.2014 MvK: added charset encoding to handle Umlaute.
|
StrokeLineCap<T> |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:20 PM
|
StrokeLineJoin |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:20 PM
|
StructureAssembler |
|
StructureCalculator |
Utility function based on the molecule's connections (groups, rings,...)
|
StructureInfo |
|
StructureListener |
|
StructureNameResolver |
Created by thomas on 7/13/17.
|
StructureSearch |
|
StructureSearchController |
|
StructureSearchDataSource |
|
StructureSearchSpecification |
|
StructureTransferData |
|
SubFlexophoreGenerator |
SubFlexophoreGenerator
|
SubFlexophoreGenerator.ViolatedConditionsCount |
|
SubGraphExtractor |
SubGraphExtractor
Creates substructures by fragmentation and summarizes them.
|
SubGraphIndices |
SubGraphIndices
A class to handle indices in a molecular graph.
|
SubStructSearchExhaustiveTreeWalker |
|
SubstructureFilter |
|
SummaryFragments |
|
SVD |
Singular Value Decomposition.
|
SVGDepictor |
|
svm |
|
svm |
|
svm_model |
|
svm_node |
|
svm_parameter |
|
svm_print_interface |
|
svm_problem |
|
SVMParameterHelper |
SVMParameterHelper
|
SVMRegression |
SVMRegression
Calculates the SVM regression for one Y column.
|
SwingCheckBox |
|
SwingComboBox |
|
SwingComponent |
|
SwingDialog |
|
SwingDialogHelper |
|
SwingDrawContext |
|
SwingEditorArea |
|
SwingEditorDialog |
|
SwingEditorPanel |
|
SwingEditorToolbar |
|
SwingKeyHandler |
|
SwingLabel |
|
SwingMouseHandler |
|
SwingPopupMenu |
|
SwingTextField |
|
SymmetryCalculator |
|
SymmetryCorrectedRMSDCalculator |
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
|
Synthon |
a Synthon is a reaction-specific representation of a building block, already encoding structural changes
that occur upon the reaction (e.g.
|
SynthonCreator |
|
SynthonReactor |
|
TableModelString |
TableModelText
Data model for an only text containing table
|
Tables |
A collection of tables with the official parameters of the
MMFF94/MMFF94s force field variants.
|
TautomerHelper |
|
testChiralDia |
|
testDiaID |
|
testHoses |
|
TetrahedralStereoRule |
|
TextClipboardHandler |
TextDrawingObject |
|
TextDrawingObjectDialogBuilder |
|
ThreadMaster |
|
ToolbarSelectionChange |
Created by rufenec on 5/3/16.
|
Torsion |
|
Torsion |
The torsion type class provides a static function for getting the
torsion type of a torsion angle.
|
TorsionAngle |
Torsional Angle energy term class.
|
TorsionConstraint |
|
TorsionDB |
|
TorsionDescriptor |
|
TorsionDescriptorHelper |
|
TorsionDetail |
|
TorsionPrediction |
|
TorsionRelevanceHelper |
|
TorsionRule |
|
TorsionSet |
|
TorsionSetEliminationRule |
|
TorsionSetStrategy |
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.
|
TorsionSetStrategyAdaptiveRandom |
|
TorsionSetStrategyLikelySystematic |
TorsionSetStrategy that systematically creates all possible TorsionSets in
batches while keeping a focus on the likelyhood of individual torsions.
|
TorsionSetStrategyRandom |
|
TotalSurfaceAreaPredictor |
|
ToxicityPredictor |
|
TransferableDockable |
|
Transformation |
|
TransformationSequence |
|
Translation |
|
TreeContainer |
|
TreeElement |
|
TreeFork |
|
TreeLeaf |
|
TreeMatcher |
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.FeatureMatch |
TODO: don't add null-matches!
|
TreeMatcher.TreeMatching |
|
TreeRoot |
|
TreeUtils |
|
Triangle |
Triangle
Created by korffmo1 on 04.06.17.
|
UndoAction |
Project:
User: rufenec
Date: 3/26/13
Time: 4:39 PM
|
UniqueFragmentEstimator |
|
UniqueList<T extends java.lang.Comparable<? super T>> |
|
UniqueStringList |
|
UniversalGenerator |
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.
|
UnknownParityAction |
Project:
User: rufenec
Date: 3/26/13
Time: 4:33 PM
|
UnparametrizedAtomTypeException |
|
UpBondAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:49 PM
|
UPGMALinkage |
Unweighted Pair Group Method with Arithmetic mean (also known as average linkage).
|
UPGMCLinkage |
Unweighted Pair Group Method using Centroids (also known as centroid linkage).
|
VanDerWaals |
|
VanDerWaals |
Nonbonded van der Waals energy term class.
|
VDWRadii |
|
Vector3 |
The Vector3 class provides common vector operations used throughout the
MMFF codebase.
|
VectorSimilarity |
|
VectorSOM |
|
VerticalFlowLayout |
A vertical flow layout is similar to a flow layuot but it layouts the
components vertically instead of horizontally.
|
VolumeGaussian |
|
WardLinkage |
Ward's linkage.
|
WMF |
|
WMFConstants |
|
WMFGraphics |
|
WMFGraphics2D |
|
WPGMALinkage |
Weighted Pair Group Method with Arithmetic mean.
|
WPGMCLinkage |
Weighted Pair Group Method using Centroids (also known as median linkage).
|
XY |
XY
|
XYIndex |
Modest v.
|
ZoomRotateAction |
Project:
User: rufenec
Date: 4/28/2014
Time: 12:39 PM
|