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
Created by korffmo1 on 17.04.18.
|
| 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
Created by korffmo1 on 11.04.18.
|
| 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
Created by korffmo1 on 19.02.16.
|
| 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
|
| DescriptorHandlerBinarySkelSpheres |
DescriptorHandlerBinarySkelSpheres
This descriptor is a binary representation of the Skeleton Spheres descriptor.
|
| DescriptorHandlerFactory |
|
| DescriptorHandlerFFP512 |
|
| DescriptorHandlerFlexophore |
DescriptorHandlerFlexophore
29 Jan 2009 MvK: Start implementation
15 Oct 2012 MvK renamed DescriptorHandler3DMM2PPInteract-->DescriptorHandlerFlexophore
19 Apr 2013 MvK major changes in Flexophore encoding decoding
25 Apr 2013 MvK Flexophore version changed --> 3.0
07 May 2013 MvK bug fixes in encoding.
|
| 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
Created by korffmo1 on 13.09.17.
|
| 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.
|
| FlexophoreAtomContributionColors |
|
| FlexophoreCreateFunctions |
FlexophoreCreateFunctions
|
| FlexophorePoint |
FlexophorePoint
|
| ForceField |
|
| ForceFieldChangeListener |
|
| ForceFieldMMFF94 |
|
| Formatter |
|
| Formatter.LocaleFormat |
|
| FormulaParser |
FormulaParser
Created by korffmo1 on 11.04.18.
|
| 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
Created by korffmo1 on 10.04.18.
|
| HetSynonymParser |
HetSynonymParser
Created by korffmo1 on 11.04.18.
|
| 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
Created by korffmo1 on 02.03.16.
|
| 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
Created by korffmo1 on 22.03.18.
|
| ListUtils |
ListUtils
|
| 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.
|
| MatrixSparse |
MatrixSparse
|
| MatrixTests |
MatrixData
|
| MCHelper |
|
| 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 |
|
| MMP |
|
| MMP.MoleculeIndex |
|
| MMPairs |
|
| MMPEnumerator |
|
| MMPFragmenter |
|
| MMPFragmenter.MoleculeIndexID |
|
| MMPFragments |
|
| MMPPropertyCalculator |
|
| MMPReader |
|
| MMPReader.MatchedMolecularPair |
|
| MMPServices |
|
| MMPUniqueFragments |
|
| 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
Created by korffmo1 on 11.04.18.
|
| 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
|
| ModelXYIndexHelper |
ModelXYIndexHelper
|
| Mol2FileParser |
|
| MolDistHist |
|
| MolDistHistEncoder |
|
| MolDistHistViz |
Class for Flexophore visualization and atom tracking.
|
| MolDistHistVizEncoder |
|
| MolDistHistVizFrag |
|
| MolDistHistVizHiddenPPPoints |
|
| 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
Created by korffmo1 on 20.03.18.
|
| PDBFileParser |
PDBFileParser
Created by korffmo1 on 20.03.18.
|
| 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
Created by korffmo1 on 09.04.18.
|
| 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 |
|
| ScaleClasses |
Modest v.
|
| 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 |
|
| SimpleCombinatorialHit |
|
| 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)
|
| SimpleSynthon |
|
| 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
Created by korffmo1 on 01.03.16.
|
| 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.
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| TautomerHelper |
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| testChiralDia |
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| testDiaID |
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| testHoses |
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| TetrahedralStereoRule |
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| TextClipboardHandler |
| TextDrawingObject |
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| TextDrawingObjectDialogBuilder |
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| ThreadMaster |
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| TimeDelta |
TimeDelta:
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| ToolbarSelectionChange |
Created by rufenec on 5/3/16.
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| Torsion |
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| Torsion |
The torsion type class provides a static function for getting the
torsion type of a torsion angle.
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| TorsionAngle |
Torsional Angle energy term class.
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| TorsionConstraint |
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| TorsionDB |
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| TorsionDescriptor |
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| TorsionDescriptorHelper |
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| TorsionDetail |
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| TorsionPrediction |
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| TorsionRelevanceHelper |
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| TorsionRule |
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| TorsionSet |
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| TorsionSetEliminationRule |
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| 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.
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| TorsionSetStrategyAdaptiveRandom |
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| TorsionSetStrategyLikelySystematic |
TorsionSetStrategy that systematically creates all possible TorsionSets in
batches while keeping a focus on the likelyhood of individual torsions.
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| TorsionSetStrategyRandom |
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| TotalSurfaceAreaPredictor |
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| ToxicityPredictor |
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| TransferableDockable |
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| Transformation |
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| TransformationSequence |
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| Translation |
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| TreeContainer |
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| TreeElement |
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| TreeFork |
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| TreeLeaf |
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| 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).
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| TreeMatcher.FeatureMatch |
TODO: don't add null-matches!
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| TreeMatcher.TreeMatching |
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| TreeRoot |
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| TreeUtils |
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| Triangle |
Triangle
Created by korffmo1 on 04.06.17.
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| UndoAction |
Project:
User: rufenec
Date: 3/26/13
Time: 4:39 PM
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| UniqueFragmentEstimator |
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| UniqueList<T extends java.lang.Comparable<? super T>> |
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| UniqueStringList |
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| 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.
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| UnknownParityAction |
Project:
User: rufenec
Date: 3/26/13
Time: 4:33 PM
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| UnparametrizedAtomTypeException |
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| UpBondAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:49 PM
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| UPGMALinkage |
Unweighted Pair Group Method with Arithmetic mean (also known as average linkage).
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| UPGMCLinkage |
Unweighted Pair Group Method using Centroids (also known as centroid linkage).
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| VanDerWaals |
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| VanDerWaals |
Nonbonded van der Waals energy term class.
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| VDWRadii |
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| Vector3 |
The Vector3 class provides common vector operations used throughout the
MMFF codebase.
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| VectorSimilarity |
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| VectorSOM |
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| VerticalFlowLayout |
A vertical flow layout is similar to a flow layuot but it layouts the
components vertically instead of horizontally.
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| VolumeGaussian |
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| WardLinkage |
Ward's linkage.
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| WMF |
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| WMFConstants |
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| WMFGraphics |
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| WMFGraphics2D |
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| WPGMALinkage |
Weighted Pair Group Method with Arithmetic mean.
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| WPGMCLinkage |
Weighted Pair Group Method using Centroids (also known as median linkage).
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| XY |
XY
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| XYIndex |
Modest v.
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| ZoomRotateAction |
Project:
User: rufenec
Date: 4/28/2014
Time: 12:39 PM
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