▼ N CDPL The namespace of the Chemical Data Processing Library ► N Base Contains core framework classes and functions C Any A safe, type checked container for arbitrary data of variable type C ControlParameterContainer A class providing methods for the storage and lookup of control-parameter values C ControlParameterList A data structure for the storage and lookup of control-parameter values C DataFormat Provides meta-information about a particular data storage format C DataInputHandler A factory interface providing methods for the creation of Base::DataReader instances handling a particular object type and storage format C DataIOBase Provides infrastructure for the registration of I/O callback functions C DataIOManager A singleton class that serves as a global registry for Base::DataInputHandler and Base::DataOutputHandler implementation instances C DataOutputHandler A factory interface providing methods for the creation of Base::DataWriter instances handling a particular object type and storage format C DataReader An interface for reading data objects of a given type from an arbitrary data source C DataWriter An interface for writing data objects of a given type to an arbitrary data sink C Exception The root of the CDPL exception hierarchy C ValueError Thrown to indicate errors caused by some invalid value C NullPointerException Thrown when an operation requires or expects a valid pointer but a null pointer was provided C RangeError Thrown to indicate that a value is out of range C SizeError Thrown to indicate that the size of a (multidimensional) array is not correct C IndexError Thrown to indicate that an index is out of range C ItemNotFound Thrown to indicate that some requested data item could not be found C BadCast Thrown to indicate that a cast or conversion from a given source type to a requested target type is not possible C OperationFailed Thrown to indicate that some requested operation has failed (e.g. due to unfulfilled preconditions or other errors) C CalculationFailed Thrown to indicate that some requested calculation has failed C IOError Thrown to indicate that an I/O operation has failed because of physical (e.g. broken pipe) or logical (e.g. invalid file format) errors ► C LookupKey An unique lookup key for control-parameter and property values C HashFunc A functor class implementing the generation of hash codes for LookupKey instances C PropertyContainer A class providing methods for the storage and lookup of object properties ► N Biomol Contains classes and functions related to biological macromolecules C HierarchyView A data structure allowing a hierarchical view on biological macromolecules C HierarchyViewChain HierarchyViewChain C HierarchyViewFragment HierarchyViewFragment C HierarchyViewModel HierarchyViewModel C HierarchyViewNode HierarchyViewNode ► C MMCIFData A data structure for the storage of imported MMCIF data (see [MMCIF ]) C Category C Item C MMCIFMolecularGraphWriter C MMCIFMoleculeReader C MMTFMolecularGraphWriter A writer for molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF ] C MMTFMoleculeReader A reader for molecule data in the Macromolecular Transmission Format (MMTF) [MMTF ] C PDBData A data structure for the storage of imported PDB data records (see [CTFILE ]) C PDBMolecularGraphWriter A writer for molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB ] format C PDBMoleculeReader A reader for molecule data in the Brookhaven Protein Data Bank (PDB) [PDB ] format ► C ResidueDictionary A global dictionary for the lookup of meta-data associated with the residues in biological macromolecules C Entry C ResidueList Implements the extraction of residues in biological macromolecules ► N Chem Contains classes and functions related to chemistry C AmideImidicAcidTautomerization AmideImidicAcidTautomerizationRule C ANDMatchExpressionList ANDMatchExpressionList C ANDMatchExpressionList< ObjType, void > ANDMatchExpressionList C AromaticRingSet Implements the perception of aromatic rings in a molecular graph C AromaticSSSRSubset Implements the extraction of the aromatic rings in the SSSR of a molecular graph C AromaticSubstructure Implements the perception of aromatic atoms and bonds in a molecular graph C Atom Atom C Atom2DCoordinatesCalculator Atom2DCoordinatesCalculator C Atom3DCoordinatesFunctor Atom3DCoordinatesFunctor C AtomArray3DCoordinatesFunctor AtomArray3DCoordinatesFunctor C AtomBondMapping A data structure for the common storage of related atom to atom and bond to bond mappings C AtomConfigurationMatchExpression AtomConfigurationMatchExpression C AtomConformer3DCoordinatesFunctor AtomConformer3DCoordinatesFunctor C AtomContainer A common interface for data-structures that support a random access to stored Chem::Atom instances ► C AtomDictionary A global dictionary for the lookup of data associated with the atom types defined in namespace Chem::AtomType C Entry C AtomEnvironmentMatchExpression AtomEnvironmentMatchExpression C AtomMapping A data type for the storage and lookup of arbitrary atom to atom mappings C AtomSSSRRingSizeMatchExpression AtomSSSRRingSizeMatchExpression C AtomTypeMatchExpression AtomTypeMatchExpression C AutomorphismGroupSearch AutomorphismGroupSearch C BasicAtom BasicAtom C BasicBond BasicBond C BasicMolecule BasicMolecule C BasicReaction BasicReaction C BemisMurckoAnalyzer BemisMurckoAnalyzer C Bond Bond C BondConfigurationMatchExpression BondConfigurationMatchExpression C BondContainer A common interface for data-structures that support a random access to stored Chem::Bond instances C BondDirectionMatchExpression BondDirectionMatchExpression C BondMapping A data type for the storage and lookup of arbitrary bond to bond mappings C BondOrderCalculator BondOrderCalculator C BondReactionCenterStatusMatchExpression BondReactionCenterStatusMatchExpression C BondStereoFlagCalculator BondStereoFlagCalculator C BondSubstituentDirectionMatchExpression BondSubstituentDirectionMatchExpression C BRICSFragmentGenerator BRICSFragmentGenerator C CanonicalNumberingCalculator CanonicalNumberingCalculator C CDFMolecularGraphWriter A writer for molecular graph data in the native I/O format of the CDPL C CDFMoleculeReader A reader for molecule data in the native I/O format of the CDPL C CDFReactionReader A reader for reaction data in the native I/O format of the CDPL C CDFReactionWriter A writer for molecular graph data in the native I/O format of the CDPL C ChEMBLStandardizer Implementation of the ChEMBL structure preprocessing pipeline C CIPConfigurationLabeler CIPConfigurationLabeler C CIPPriorityCalculator CIPPriorityCalculator C CMLMolecularGraphWriter A writer for molecular graph data in the Chemical Markup Language [CML ] format C CMLMoleculeReader A Reader for molecule data in the Chemical Markup Language [CML ] format C CommonConnectedSubstructureSearch CommonConnectedSubstructureSearch C CompleteRingSet Implements the exhaustive perception of rings in a molecular graph C ComponentSet Implements the perception of molecular graph components C ConnectedSubstructureSet ConnectedSubstructureSet C CyclicSubstructure Implements the perception of ring atoms and bonds in a molecular graph C DefaultMultiConfMoleculeInputProcessor MultiConfMoleculeInputProcessor C DefaultTautomerGenerator DefaultTautomerGenerator C ElectronSystem Describes an electron system of a molecule in terms of involved atoms and their electron contributions C ElectronSystemList A data type for the storage of Chem::ElectronSystem objects C Entity3D Entity3D C Entity3DContainer A common interface for data-structures that support a random access to stored Chem::Entity3D instances C Entity3DCoordinatesFunctor Entity3DCoordinatesFunctor C Entity3DMapping A data type for the storage and lookup of arbitrary entity to entity mappings C ExtendedSSSR Implements the perception of the Extended Smallest Set of Smallest Rings (ESSSR) of a molecular graph C Fragment Fragment ► C FragmentGenerator FragmentGenerator C ExcludePattern C FragmentationRule C FragmentLink C FragmentList A data type for the storage of Chem::Fragment objects C GenericHydrogen13ShiftTautomerization GenericHydrogen13ShiftTautomerizationRule C GenericHydrogen15ShiftTautomerization GenericHydrogen15ShiftTautomerizationRule ► C HashCodeCalculator HashCodeCalculator C DefAtomHashSeedFunctor The default functor for the generation of atom hash seeds C DefBondHashSeedFunctor The default functor for the generation of bond hash seeds C Hydrogen3DCoordinatesCalculator Hydrogen3DCoordinatesCalculator C ImineEnamineTautomerization ImineEnamineTautomerizationRule C INCHIMolecularGraphWriter A writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI ] format C INCHIMoleculeReader A reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI ] format C JMEMolecularGraphWriter A writer for molecular graph data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEMoleculeReader A reader for molecule data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEReactionReader A reader for reaction data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEReactionWriter A writer for reaction data in the native I/O format of the JME Molecular Editor [JME ] java applet C KekuleStructureCalculator KekuleStructureCalculator C KeteneYnolTautomerization KeteneYnolTautomerizationRule C KetoEnolTautomerization KetoEnolTautomerizationRule C LactamLactimTautomerization LactamLactimTautomerizationRule C MatchConstraint MatchConstraint C MatchConstraintList MatchConstraintList C MatchExpression A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms C MatchExpression< ObjType, void > A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms C MatchExpressionList A container for the storage and evaluation of logical match expression lists C MaxCommonAtomSubstructureSearch MaxCommonAtomSubstructureSearch C MaxCommonBondSubstructureSearch MaxCommonBondSubstructureSearch C MOL2MolecularGraphWriter C MOL2MoleculeReader C MolecularGraph MolecularGraph C MolecularGraphComponentGroupingMatchExpression MolecularGraphComponentGroupingMatchExpression C Molecule Molecule C MOLMolecularGraphWriter A writer for molecular graph data in the MDL Mol-File [CTFILE ] format C MOLMoleculeReader A reader for molecule data in the MDL Mol-File [CTFILE ] format C MorganNumberingCalculator MorganNumberingCalculator C MultiConfMoleculeInputProcessor MultiConfMoleculeInputProcessor C MultiSubstructureSearch MultiSubstructureSearch C NitroAciTautomerization NitroAciTautomerizationRule C NitrosoOximeTautomerization NitrosoOximeTautomerizationRule C NOTMatchExpression NOTMatchExpression C NOTMatchExpression< ObjType, void > NOTMatchExpression C ORMatchExpressionList ORMatchExpressionList C ORMatchExpressionList< ObjType, void > ORMatchExpressionList ► C PatternAtomTyper PatternAtomTyper C Pattern ► C PatternBasedTautomerizationRule PatternBasedTautomerizationRule C BondOrderChange C PhosphinicAcidTautomerization PhosphinicAcidTautomerizationRule C PiElectronSystemList Implements the perception of all pi electron systems present in a molecule C PropertyMatchExpression PropertyMatchExpression C PropertyMatchExpression< ValueType, MatchFunc, ObjType, void > PropertyMatchExpression C ProtonationStateStandardizer Sets the protation state of molecules according to desired objectives C RDFReactionReader A reader for reaction data in the MDL RD-File [CTFILE ] format C RDFReactionWriter A writer for reaction data in the MDL RD-File [CTFILE ] format C Reaction Reaction C ReactionAtomMappingMatchExpression ReactionAtomMappingMatchExpression C ReactionComponentGroupingMatchExpression ReactionComponentGroupingMatchExpression C ReactionSubstructureSearch ReactionSubstructureSearch C Reactor Reactor C RECAPFragmentGenerator RECAPFragmentGenerator ► C ResonanceStructureGenerator ResonanceStructureGenerator C StructureData C RXNReactionReader A reader for reaction data in the MDL Rxn-File [CTFILE ] format C RXNReactionWriter A writer for reaction data in the MDL Rxn-File [CTFILE ] format C SDFMolecularGraphWriter A writer for molecular graph data in the MDL Mol-File [CTFILE ] format C SDFMoleculeReader A Reader for molecule data in the MDL SD-File [CTFILE ] format C SmallestSetOfSmallestRings Implements the perception of the Smallest Set of Smallest Rings (SSSR) of a molecular graphs C SMARTSMolecularGraphWriter A writer for molecular graph data in the Daylight SMARTS [SMARTS ] format C SMARTSMoleculeReader A reader for molecule data in the Daylight SMARTS [SMARTS ] format C SMARTSReactionReader A reader for reaction data in the Daylight SMARTS [SMARTS ] format C SMARTSReactionWriter A writer for reaction data in the Daylight SMARTS [SMARTS ] format C SMILESMolecularGraphWriter A writer for molecular graph data in the Daylight SMILES [SMILES ] format C SMILESMoleculeReader A reader for molecule data in the Daylight SMILES [SMILES ] format C SMILESReactionReader A reader for reaction data in the Daylight SMILES [SMILES ] format C SMILESReactionWriter A writer for reaction data in the Daylight SMILES [SMILES ] format C SpatialEntityAlignment SpatialEntityAlignment C StereoDescriptor A data structure for the storage and retrieval of stereochemical information about atoms and bonds C StereoisomerGenerator StereoisomerGenerator C StringDataBlockEntry Represents a data item in the structure or reaction data block of a MDL SD- or RD-File data record (see [CTFILE ]) C StringDataBlock An array of Chem::StringDataBlockEntry objects used to store the structure or reaction data block of a STRING SD- or RD-File data record (see [CTFILE ]) C SubstructureEditor SubstructureEditor ► C SubstructureHistogramCalculator SubstructureHistogramCalculator C Pattern C SubstructureSearch SubstructureSearch C SulfenicAcidTautomerization SulfenicAcidTautomerizationRule C SurfaceAtomExtractor SurfaceAtomExtractor C SymmetryClassCalculator SymmetryClassCalculator C TautomerGenerator TautomerGenerator C TautomerizationRule TautomerizationRule C TautomerScore TautomerScore C TopologicalEntityAlignment TopologicalEntityAlignment C XYZMolecularGraphWriter C XYZMoleculeReader ► N ConfGen Contains classes and functions related to conformer ensemble generation C CanonicalFragment CanonicalFragment C CFLMoleculeReader A reader for molecule data in the native I/O format of the CDPL C ConformerData C ConformerGenerator C ConformerGeneratorSettings C DGConstraintGenerator C DGConstraintGeneratorSettings C DGStructureGenerator C DGStructureGeneratorSettings C FragmentAssembler C FragmentAssemblerSettings C FragmentConformerGenerator ► C FragmentConformerGeneratorSettings C FragmentSettings C FragmentLibrary C FragmentLibraryEntry FragmentLibraryEntry C FragmentLibraryGenerator FragmentLibraryGenerator C RMSDConformerSelector C StructureGenerator C StructureGeneratorSettings C TorsionCategory C TorsionDriver C TorsionDriverSettings C TorsionLibrary ► C TorsionRule C AngleEntry C TorsionRuleMatch C TorsionRuleMatcher ► N Descr Contains classes and functions related to the generation and processing of pharmacophore and molecule descriptors C AtomAutoCorrelation3DVectorCalculator AtomAutoCorrelation3DVectorCalculator C AtomRDFCodeCalculator AtomRDFCodeCalculator C AutoCorrelation2DVectorCalculator AutoCorrelation2DVectorCalculator C AutoCorrelation3DVectorCalculator AutoCorrelation3DVectorCalculator C BCUTDescriptorCalculator BCUTDescriptorCalculator C BulkSimilarityCalculator C BurdenMatrixGenerator BurdenMatrixGenerator ► C CircularFingerprintGenerator CircularFingerprintGenerator C DefAtomIdentifierFunctor The functor for the generation of ECFP atom identifiers C DefBondIdentifierFunctor The default functor for the generation of bond identifiers C FeatureAutoCorrelation3DVectorCalculator FeatureAutoCorrelation3DVectorCalculator C FeatureRDFCodeCalculator FeatureRDFCodeCalculator C MACCSFingerprintGenerator Generation of 166 bit MACCS key fingerprints C MolecularComplexityCalculator MolecularComplexityCalculator C MoleculeAutoCorr2DDescriptorCalculator MoleculeAutoCorr2DDescriptorCalculator C MoleculeAutoCorr3DDescriptorCalculator MoleculeAutoCorr3DDescriptorCalculator C MoleculeRDFDescriptorCalculator MoleculeRDFDescriptorCalculator C NPoint2DPharmacophoreFingerprintGenerator NPoint2DPharmacophoreFingerprintGenerator C NPoint3DPharmacophoreFingerprintGenerator NPoint3DPharmacophoreFingerprintGenerator C NPointPharmacophoreFingerprintGenerator NPointPharmacophoreFingerprintGenerator ► C PathFingerprintGenerator PathFingerprintGenerator C DefAtomDescriptorFunctor The default functor for the generation of atom descriptors C DefBondDescriptorFunctor The default functor for the generation of bond descriptors C PharmacophoreAutoCorr3DDescriptorCalculator PharmacophoreAutoCorr3DDescriptorCalculator C PharmacophoreRDFDescriptorCalculator PharmacophoreRDFDescriptorCalculator C PubChemFingerprintGenerator Generation of 881 bit PubChem fingerprints C RDFCodeCalculator RDFCodeCalculator C TanimotoSimilarity Functor class for calculating Tanimoto Similarities [CITB ] of bitsets and vectors C CosineSimilarity Functor class for calculating Cosine Similarities [WCOS ] of bitsets and vectors C EuclideanSimilarity Functor class for calculating the Euclidean Similarity [GSIM ] of bitsets C ManhattanSimilarity Functor class for calculating the Manhattan Similarity [GSIM ] of bitsets C DiceSimilarity Functor class for calculating the Dice Similarity [GSIM ] of bitsets C TverskySimilarity Functor class for calculating the Tversky Similarity [GSIM ] of bitsets C HammingDistance Functor class for calculating the Hamming Distance [WHAM , CITB ] between bitsets C ManhattanDistance Functor class for calculating the Manhattan Distance [MADI ] between bitsets and vectors C EuclideanDistance Functor class for calculating the Euclidean Distance [CITB ] between bitsets and vectors ► N ForceField Contains classes and functions related to molecular force fields C ElasticPotential C Error C ParameterizationFailed C GradientVectorTraits C GradientVectorTraits< Math::VectorArray< V > > C GradientVectorTraits< std::vector< V > > C MMFF94AngleBendingInteraction C MMFF94AngleBendingInteractionParameterizer ► C MMFF94AngleBendingParameterTable C Entry ► C MMFF94AromaticAtomTypeDefinitionTable C Entry C MMFF94AromaticSSSRSubset Implements the extraction of all rings in the SSSR of a molecular graph that are aromatic according to MMFF94 conventions ► C MMFF94AtomTypePropertyTable C Entry C MMFF94AtomTyper ► C MMFF94BondChargeIncrementTable C Entry C MMFF94BondStretchingInteraction C MMFF94BondStretchingInteractionParameterizer ► C MMFF94BondStretchingParameterTable C Entry ► C MMFF94BondStretchingRuleParameterTable C Entry C MMFF94BondTyper C MMFF94ChargeCalculator ► C MMFF94DefaultStretchBendParameterTable C Entry C MMFF94ElectrostaticInteraction C MMFF94ElectrostaticInteractionParameterizer C MMFF94EnergyCalculator ► C MMFF94FormalAtomChargeDefinitionTable C Entry C MMFF94GradientCalculator C MMFF94HeavyToHydrogenAtomTypeMap C MMFF94InteractionData C MMFF94InteractionParameterizer C MMFF94OutOfPlaneBendingInteraction C MMFF94OutOfPlaneBendingInteractionParameterizer ► C MMFF94OutOfPlaneBendingParameterTable C Entry ► C MMFF94PartialBondChargeIncrementTable C Entry ► C MMFF94PrimaryToParameterAtomTypeMap C Entry C MMFF94StretchBendInteraction C MMFF94StretchBendInteractionParameterizer ► C MMFF94StretchBendParameterTable C Entry ► C MMFF94SymbolicAtomTypePatternTable C Entry C MMFF94SymbolicToNumericAtomTypeMap C MMFF94TorsionInteraction C MMFF94TorsionInteractionParameterizer ► C MMFF94TorsionParameterTable C Entry C MMFF94VanDerWaalsInteraction C MMFF94VanDerWaalsInteractionParameterizer ► C MMFF94VanDerWaalsParameterTable C Entry ► C UFFAtomTypePropertyTable C Entry ► N GRAIL Contains classes and functions related to the GRAIL method [GRAIL ] C AtomDensityGridCalculator AtomDensityGridCalculator C BindingAffinityCalculator BindingAffinityCalculator C BuriednessGridCalculator BuriednessGridCalculator C BuriednessScore BuriednessScore ► C FeatureInteractionScoreGridCalculator FeatureInteractionScoreGridCalculator C MaxScoreFunctor C ScoreSumFunctor C GeneralizedBellAtomDensity GeneralizedBellAtomDensity C GRAILDataSetGenerator GRAILDataSetGenerator C GRAILDescriptorCalculator GRAILDescriptorCalculator C GRAILXDescriptorCalculator GRAILXDescriptorCalculator ► N Grid Contains classes and functions related to grid based data representation and processing C RegularGrid RegularGrid C RegularGridSet RegularGridSet C AttributedGrid AttributedGrid C CDFDRegularGridReader A reader for spatial regular grid data in the native I/O format of the CDPL C CDFDRegularGridSetReader A reader for spatial regular grid set data in the native I/O format of the CDPL C CDFDRegularGridSetWriter A writer for spatial regular grid set data in the native I/O format of the CDPL C CDFDRegularGridWriter A writer for spatial regular grid data in the native I/O format of the CDPL C SpatialGrid SpatialGrid ► N Math Contains classes and functions related to mathematics C MatrixReference C Vector C Matrix C RotationMatrix C ScalingMatrix C TranslationMatrix C BFGSMinimizer Fletcher's implementation of the BFGS method C CommonType C DirectAssignmentProxy C Expression C VectorExpression C MatrixExpression C QuaternionExpression C GridExpression C VectorContainer C MatrixContainer C QuaternionContainer C GridContainer C ScalarBinaryAssignmentFunctor C ScalarAssignment C ScalarAdditionAssignment C ScalarSubtractionAssignment C ScalarMultiplicationAssignment C ScalarDivisionAssignment C ScalarUnaryFunctor C ScalarNegation C ScalarConjugation C ScalarRealUnaryFunctor C ScalarReal C ScalarImaginary C ScalarBinaryFunctor C ScalarAddition C ScalarSubtraction C ScalarMultiplication C ScalarDivision C VectorScalarBinaryFunctor C VectorInnerProduct C VectorAngleCosine C VectorBooleanBinaryFunctor C VectorEquality C Scalar3VectorBooleanTernaryFunctor C VectorToleranceEquality C VectorBinaryFunctor C VectorCrossProduct C VectorScalarUnaryFunctor C VectorElementSum C VectorScalarRealUnaryFunctor C VectorNorm1 C VectorNorm2 C VectorNormInfinity C VectorScalarIndexUnaryFunctor C VectorNormInfinityIndex C MatrixBooleanBinaryFunctor C MatrixEquality C Scalar3MatrixBooleanTernaryFunctor C MatrixToleranceEquality C MatrixScalarUnaryFunctor C MatrixElementSum C MatrixTrace C MatrixScalarRealUnaryFunctor C MatrixNorm1 C MatrixNormFrobenius C MatrixNormInfinity C VectorMatrixUnaryFunctor C DiagonalMatrixFromVector C CrossProductMatrixFromVector C MatrixVectorBinaryFunctor C MatrixVectorProduct C VectorMatrixProduct C MatrixBinaryFunctor C MatrixProduct C QuaternionBooleanBinaryFunctor C QuaternionEquality C Scalar3QuaternionBooleanTernaryFunctor C QuaternionToleranceEquality C QuaternionScalarUnaryFunctor C QuaternionElementSum C QuaternionScalarRealUnaryFunctor C QuaternionNorm C QuaternionNorm2 C QuaternionUnaryFunctor C QuaternionUnreal C QuaternionConjugate C Scalar1QuaternionBinaryFunctor C Scalar1QuaternionAddition C Scalar1QuaternionSubtraction C Scalar2QuaternionBinaryFunctor C Scalar2QuaternionAddition C Scalar2QuaternionSubtraction C QuaternionInverse C QuaternionBinaryFunctor C QuaternionProduct C Scalar3QuaternionTernaryFunctor C QuaternionDivision C Scalar13QuaternionTernaryFunctor C ScalarQuaternionDivision C QuaternionVectorBinaryFunctor C QuaternionVectorRotation C GridBooleanBinaryFunctor C GridEquality C Scalar3GridBooleanTernaryFunctor C GridToleranceEquality C GridScalarUnaryFunctor C GridElementSum C GridReference C Grid C ZeroGrid C ScalarGrid C GridTemporaryTraits< GridReference< G > > C GridTemporaryTraits< const GridReference< G > > C GridUnary C GridUnaryTraits C GridBinary1 C GridBinary1Traits C Scalar1GridBinary C Scalar1GridBinaryTraits C Scalar2GridBinary C Scalar2GridBinaryTraits C KabschAlgorithm Implementation of the Kabsch algorithm [KABA ] C InitListMatrix C SparseMatrix C BoundedVector C BoundedMatrix C CMatrix C ZeroMatrix C ScalarMatrix C IdentityMatrix C VectorTemporaryTraits< MatrixReference< M > > C VectorTemporaryTraits< const MatrixReference< M > > C MatrixTemporaryTraits< MatrixReference< M > > C MatrixTemporaryTraits< const MatrixReference< M > > C Range C Lower C UnitLower C Upper C UnitUpper C TriangularAdapter C VectorTemporaryTraits< TriangularAdapter< M, Tri > > C VectorTemporaryTraits< const TriangularAdapter< M, Tri > > C MatrixTemporaryTraits< TriangularAdapter< M, Tri > > C MatrixTemporaryTraits< const TriangularAdapter< M, Tri > > C MatrixUnary C MatrixUnaryTraits C VectorMatrixUnary C VectorMatrixUnaryTraits C MatrixBinary1 C MatrixBinary1Traits C MatrixBinary2 C MatrixBinary2Traits C VectorMatrixBinary C VectorMatrixBinaryTraits C Matrix1VectorBinary C Matrix1VectorBinaryTraits C Matrix2VectorBinary C Matrix2VectorBinaryTraits C Scalar1MatrixBinary C Scalar1MatrixBinaryTraits C Scalar2MatrixBinary C Scalar2MatrixBinaryTraits C MatrixTranspose C VectorTemporaryTraits< MatrixTranspose< M > > C VectorTemporaryTraits< const MatrixTranspose< M > > C MatrixTemporaryTraits< MatrixTranspose< M > > C MatrixTemporaryTraits< const MatrixTranspose< M > > C MatrixRow C MatrixColumn C MatrixRange C MatrixSlice C VectorTemporaryTraits< MatrixRow< M > > C VectorTemporaryTraits< const MatrixRow< M > > C MatrixTemporaryTraits< MatrixRow< M > > C MatrixTemporaryTraits< const MatrixRow< M > > C VectorTemporaryTraits< MatrixColumn< M > > C VectorTemporaryTraits< const MatrixColumn< M > > C MatrixTemporaryTraits< MatrixColumn< M > > C MatrixTemporaryTraits< const MatrixColumn< M > > C VectorTemporaryTraits< MatrixRange< M > > C VectorTemporaryTraits< const MatrixRange< M > > C MatrixTemporaryTraits< MatrixRange< M > > C MatrixTemporaryTraits< const MatrixRange< M > > C VectorTemporaryTraits< MatrixSlice< M > > C VectorTemporaryTraits< const MatrixSlice< M > > C MatrixTemporaryTraits< MatrixSlice< M > > C MatrixTemporaryTraits< const MatrixSlice< M > > C MinimizerVariableArrayTraits C MinimizerVariableArrayTraits< VectorArray< V > > C MinimizerVariableArrayTraits< std::vector< V > > C MLRModel Performs Multiple Linear Regression [WLIREG ] on a set of data points C QuaternionReference C Quaternion C RealQuaternion C QuaternionTemporaryTraits< const QuaternionReference< Q > > C QuaternionTemporaryTraits< QuaternionReference< Q > > C QuaternionVectorAdapter C CVector C VectorTemporaryTraits< QuaternionVectorAdapter< Q > > C VectorTemporaryTraits< const QuaternionVectorAdapter< Q > > C QuaternionUnary1 C QuaternionUnary1Traits C QuaternionUnary2 C QuaternionUnary2Traits C QuaternionBinary1 C QuaternionBinary1Traits C QuaternionBinary2 C QuaternionBinary2Traits C Scalar1QuaternionBinary1 C Scalar1QuaternionBinary1Traits C Scalar1QuaternionBinary2 C Scalar1QuaternionBinary2Traits C Scalar2QuaternionBinary1 C Scalar2QuaternionBinary1Traits C Scalar2QuaternionBinary2 C Scalar2QuaternionBinary2Traits C Scalar3QuaternionTernary C Scalar3QuaternionTernaryTraits C Scalar13QuaternionTernary C Scalar13QuaternionTernaryTraits C GridCoordinatesMatrixTransformTraits C GridCoordinatesTransformTraits C GridCoordinatesTransformTraits< CMatrix< T, 4, 4 > > C GridCoordinatesTransformTraits< BoundedMatrix< T, 4, 4 > > C RegularSpatialGrid C Slice C SparseContainerElement C TypeTraits< SparseContainerElement< C > > C ScalarAbsImpl C ScalarAbsImpl< false > C ScalarTraits C TypeTraits C ComplexTraits C TypeTraits< std::complex< T > > C VectorTemporaryTraits C MatrixTemporaryTraits C QuaternionTemporaryTraits C GridTemporaryTraits C IsScalar C IsScalar< std::complex< T > > C VectorReference C InitListVector C SparseVector C ZeroVector C UnitVector C ScalarVector C VectorTemporaryTraits< const VectorReference< V > > C VectorTemporaryTraits< VectorReference< V > > C HomogenousCoordsAdapter C VectorQuaternionAdapter C QuaternionTemporaryTraits< VectorQuaternionAdapter< V > > C QuaternionTemporaryTraits< const VectorQuaternionAdapter< V > > C VectorTemporaryTraits< HomogenousCoordsAdapter< V > > C VectorTemporaryTraits< const HomogenousCoordsAdapter< V > > C VectorArray An array for storing generic vector objects C VectorArrayAlignmentCalculator C VectorUnary C VectorUnaryTraits C VectorBinary1 C VectorBinary1Traits C VectorBinary2 C VectorBinary2Traits C Scalar1VectorBinary C Scalar1VectorBinaryTraits C Scalar2VectorBinary C Scalar2VectorBinaryTraits C QuaternionVectorBinary C QuaternionVectorBinaryTraits C VectorElementAccessor C VectorElementAccessor< const E > C VectorIteratorTraits C VectorIteratorTraits< const E > C VectorRange C VectorSlice C VectorTemporaryTraits< VectorRange< V > > C VectorTemporaryTraits< const VectorRange< V > > C VectorTemporaryTraits< VectorSlice< V > > C VectorTemporaryTraits< const VectorSlice< V > > ► N MolProp Contains classes and functions related to the calculation/preciction of physicochemical molecular properties C AtomHydrophobicityCalculator Implements Greene's algorithm [CATA ] for the calculation of atom hydrophobicities C ElementHistogram A data type for the storage of element histograms of chemical compounds C HBondAcceptorAtomTyper C HBondDonorAtomTyper C LogSCalculator LogSCalculator C MassComposition A data type for the storage of mass percent compositions of chemical compounds C MHMOPiChargeCalculator MHMOPiChargeCalculator C PEOESigmaChargeCalculator PEOESigmaChargeCalculator C TPSACalculator TPSACalculator C XLogPCalculator XLogPCalculator ► N Pharm Contains classes and functions related to pharmacophore perception and pharmacophore applications C AromaticFeatureGenerator AromaticFeatureGenerator C BasicFeature BasicFeature C BasicPharmacophore BasicPharmacophore C CationPiInteractionConstraint CationPiInteractionConstraint C CationPiInteractionScore CationPiInteractionScore C CDFFeatureContainerWriter A writer for feature container data in the native I/O format of the CDPL C CDFPharmacophoreReader A reader for pharmacophore data in the native I/O format of the CDPL C DefaultInteractionAnalyzer DefaultInteractionAnalyzer C DefaultPharmacophoreGenerator DefaultPharmacophoreGenerator C Feature Feature C FeatureContainer FeatureContainer C FeatureDistanceConstraint FeatureDistanceConstraint C FeatureDistanceScore FeatureDistanceScore C FeatureGenerator FeatureGenerator C FeatureGeometryMatchFunctor FeatureGeometryMatchFunctor C FeatureInteractionScore FeatureInteractionScore C FeatureInteractionScoreCombiner FeatureInteractionScoreCombiner C FeatureMapping A data type for the storage and lookup of arbitrary feature to feature mappings C FeaturePairDistanceMatchFunctor FeaturePairDistanceMatchFunctor C FeaturePositionMatchFunctor FeaturePositionMatchFunctor C FeatureSet FeatureSet C FeatureTypeHistogram A data type for the storage of feature type histograms of pharmacophores C FeatureTypeMatchFunctor FeatureTypeMatchFunctor C FileScreeningHitCollector FileScreeningHitCollector C HBondAcceptorFeatureGenerator HBondAcceptorFeatureGenerator C HBondDonorFeatureGenerator HBondDonorFeatureGenerator C HBondingInteractionConstraint HBondingInteractionConstraint C HBondingInteractionScore HBondingInteractionScore C HydrophobicAtomFeatureGenerator HydrophobicAtomFeatureGenerator C HydrophobicFeatureGenerator HydrophobicFeatureGenerator C HydrophobicInteractionConstraint HydrophobicInteractionConstraint C HydrophobicInteractionScore HydrophobicInteractionScore C InteractionAnalyzer InteractionAnalyzer C InteractionConstraintConnector InteractionConstraintConnector C InteractionPharmacophoreGenerator InteractionPharmacophoreGenerator C IonicInteractionConstraint IonicInteractionConstraint C IonicInteractionScore IonicInteractionScore C NegIonizableFeatureGenerator NegIonizableFeatureGenerator C OrthogonalPiPiInteractionConstraint OrthogonalPiPiInteractionConstraint C OrthogonalPiPiInteractionScore OrthogonalPiPiInteractionScore C ParallelPiPiInteractionConstraint ParallelPiPiInteractionConstraint C ParallelPiPiInteractionScore ParallelPiPiInteractionScore C PatternBasedFeatureGenerator PatternBasedFeatureGenerator C Pharmacophore Pharmacophore C PharmacophoreAlignment PharmacophoreAlignment C PharmacophoreFitScore PharmacophoreFitScore C PharmacophoreFitScreeningScore PharmacophoreFitScreeningScore C PharmacophoreGenerator PharmacophoreGenerator C PMLFeatureContainerWriter A writer for feature container data in the native I/O format of LigandScout C PMLPharmacophoreReader A reader for pharmacophore data in the native I/O format of LigandScout C PosIonizableFeatureGenerator PosIonizableFeatureGenerator C PSDMolecularGraphOutputHandler A handler for the output of molecular graph dara in the PSD-format of the CDPL C PSDMolecularGraphWriter A writer for molecular graph data in the PSD-format of the CDPL C PSDMoleculeInputHandler A handler for the input of molecule data in the PSD-format of the CDPL C PSDMoleculeReader A reader for molecule data in the PSD-format of the CDPL C PSDPharmacophoreInputHandler A handler for the input of pharmacophore data in the PSD-format of the CDPL C PSDPharmacophoreReader A reader for pharmacophore data in the PSD-format of the CDPL C PSDScreeningDBAccessor A class for accessing pharmacophore screening databases in the built-in optimized format C PSDScreeningDBCreator A class for the creation of optimized pharmacophore screening databases C ScreeningDBAccessor A class for accessing the data stored in pharmacophore screening databases C ScreeningDBCreator A class for the creation of optimized pharmacophore screening databases ► C ScreeningProcessor ScreeningProcessor C SearchHit C SpatialFeatureMapping SpatialFeatureMapping C XBondAcceptorFeatureGenerator XBondAcceptorFeatureGenerator C XBondDonorFeatureGenerator XBondDonorFeatureGenerator C XBondingInteractionConstraint XBondingInteractionConstraint C XBondingInteractionScore XBondingInteractionScore ► N Shape Contains classes and functions related to molecular shape representation and processing C AlignmentResult C ExactGaussianShapeOverlapFunction C FastGaussianShapeAlignment C FastGaussianShapeOverlapFunction ► C GaussianShape A data type for the descripton of arbitrary shapes composed of spheres approximated by gaussian functions C Element C GaussianShapeAlignment C GaussianShapeAlignmentStartGenerator C GaussianShapeFunction ► C GaussianShapeFunctionAlignment C Result C GaussianShapeGenerator C GaussianShapeOverlapFunction C GaussianShapeSet C PrincipalAxesAlignmentStartGenerator C TotalOverlapTanimotoScore C ShapeTanimotoScore C ColorTanimotoScore C TanimotoComboScore C TotalOverlapTverskyScore C ShapeTverskyScore C ColorTverskyScore C TverskyComboScore C ReferenceTotalOverlapTverskyScore C ReferenceShapeTverskyScore C ReferenceColorTverskyScore C ReferenceTverskyComboScore C AlignedTotalOverlapTverskyScore C AlignedShapeTverskyScore C AlignedColorTverskyScore C AlignedTverskyComboScore C ScreeningProcessor C ScreeningSettings ► N Util Contains general purpose algorithms, containers, functors and other classes C Array A dynamic array class providing amortized constant time access to arbitrary elements C BronKerboschAlgorithm Implementation of the Bron-Kerbosch clique-detection algorithm [BKA ] C CompoundDataReader CompoundDataReader C CompressedDataReader CompressedDataReader C CompressedDataWriter CompressedDataWriter C CompressionAlgoTraits C CompressionAlgoTraits< GZIP > C CompressionAlgoTraits< BZIP2 > C CompressionStreamBase C DecompressionIStream C CompressionOStream C CompressedIOStream C DefaultDataInputHandler DefaultDataInputHandler C DefaultDataOutputHandler DefaultDataOutputHandler C Dereferencer An unary functor for the dereferenciation of pointers without null pointer checking C NullCheckDereferencer An unary functor for the dereferenciation of pointers with null pointer checking ► C DGCoordinatesGeneratorBase Base for classes dedicated to the generation of coordinates that fulfill user-provided point distance (and volume) constraints [ASPE ] C DistanceConstraint C DGCoordinatesGenerator Generic implementation for generation of coordinates that fulfill user-provided point distance constraints [ASPE ] ► C DGCoordinatesGenerator< 3, T > Specialized implementation for the generation of 3D coordinates that fulfill user-provided point distance and volume constraints [ASPE ] C VolumeConstraint C FileDataReader FileDataReader C FileDataWriter FileDataWriter C FileRemover C IndexedElementIterator A STL compatible random access iterator for container elements accessible by index C IndirectArray A dynamic array class for the storage of object pointers with an indirected query interface C MapDefaultValue C MapDefaultValue< ValueType, false > C Map A unique sorted associative container that maps keys to values C MultiFormatDataReader MultiFormatDataReader C MultiFormatDataWriter MultiFormatDataWriter C MultiMapDefaultValue C MultiMapDefaultValue< ValueType, false > C MultiMap A multiple sorted associative container that maps keys to values ► C ObjectPool A data structure that caches instances of type T up to a user specified amount C DefaultConstructor C DefaultDestructor ► C ObjectStack ObjectStack C DefaultConstructor C PropertyValue An unary functor that retrieves the value of a given property from the Base::PropertyContainer instance provided as argument C PropertyValueProduct A binary functor that calculates the product of two property values retrieved from a pair of Base::PropertyContainer instances passed as argument C StreamDataReader A helper class that implements Base::DataReader for std::istream based data readers ► N Vis Contains classes and functions related to data visualization C Brush Specifies the fill pattern and fill color of shapes C CairoFontMetrics Implements the FontMetrics interface for the Cairo rendering backend C CairoPointerTraits C CairoPointerTraits< cairo_t > Specialization of CairoPointerTraits for the object type cairo_t C CairoPointerTraits< cairo_surface_t > Specialization of CairoPointerTraits for the object type cairo_surface_t C CairoPointerTraits< cairo_pattern_t > Specialization of CairoPointerTraits for the object type cairo_pattern_t C CairoPointer A smart pointer managing the lifetime of allocated Cairo data structures C CairoRenderer2D Implements the Renderer2D interface on top of the Cairo 2D Graphics Library C ClipPathPrimitive2D A graphics primitive representing a clipping region in 2D space C Color Specifies a color in terms of its red, green and blue components and an alpha-channel for transparency C ColorTable A container for the storage and lookup of Vis::Color objects that are associated with a numeric identifier C EllipsePrimitive2D A graphics primitive representing a ellipse C Font Specifies a font for drawing text C FontMetrics An interface class with methods that provide information about the metrics of a font C GraphicsPrimitive2D The abstract base class of all 2D graphics primitives C ImageWriter C Line2D Specifies a line segment in 2D space C LinePrimitive2D A graphics primitive representing a single line C LineSegmentListPrimitive2D A graphics primitive representing a list of disjoint line segments C Path2D Provides a container for painting operations, enabling arbitrary graphical shapes to be constructed and reused C Path2DConverter Provides an interface for classes that implement the conversion of Vis::Path2D objects into rendering backend specific path descriptions or drawing operations C PathPrimitive2D A graphics primitive representing an arbitrary path in 2D space C PDFMolecularGraphWriter Creates 2D structure diagrams of molecular graphs in the Portable Document Format (PDF) [WPDF ] C PDFReactionWriter Creates 2D depictions of chemical reactions in the Portable Document Format (PDF) [WPDF ] C Pen Specifies how to draw lines and outlines of shapes C PNGMolecularGraphWriter Creates 2D structure diagrams of molecular graphs in the Portable Network Graphics (PNG) [WPNG ] format C PNGReactionWriter Creates 2D depictions of chemical reactions in the Portable Network Graphics (PNG) [WPNG ] format C PointArray2D Stores a set of points in 2D space C PointListPrimitive2D A graphics primitive representing a list of points C PolygonPrimitive2D A graphics primitive representing a polygon C PolylinePrimitive2D A graphics primitive representing a set of connected line segments C PSMolecularGraphWriter Creates 2D structure diagrams of molecular graphs in the PostScript (PS) [WPS ] format C PSReactionWriter Creates 2D depictions of chemical reactions in the PostScript (PS) [WPS ] format C QtFontMetrics Implements the FontMetrics interface for the Qt rendering backend C QtObjectFactory Provides methods for the creation of QFont, QColor, QPen and QBrush objects from Font , Color , Pen and Brush instances C QtRenderer2D Implements the Renderer2D interface on top of the Qt Toolkit C ReactionView2D Implements the 2D visualization of chemical reactions C Rectangle2D Specifies an axis aligned rectangular area in 2D space C Renderer2D An interface that provides methods for low level 2D drawing operations C SizeSpecification Specifies the value and type of a size attribute and defines how the value may change during processing steps ► C StructureGridView2D Implements the 2D visualization of multiple chemical structures arranged in a grid C Cell Data structure storing the contents of a grid cell C StructureView2D Implements the 2D visualization of chemical structures C SVGMolecularGraphWriter Creates 2D structure diagrams of molecular graphs in the Scalable Vector Graphics (SVG) [WSVG ] format C SVGReactionWriter Creates 2D depictions of chemical reactions in the Scalable Vector Graphics (SVG) [WSVG ] format C TextBlockPrimitive2D A graphics primitive representing a block of styled text C TextLabelPrimitive2D A graphics primitive representing a text label C View2D The abstract base of classes implementing the 2D visualization of data objects 
1.9.1
