CDPL.Chem Package Reference

Contains classes and functions related to chemistry. More...

Classes
class	ANDAtomMatchExpressionList
	ANDAtomMatchExpressionList. More...
class	ANDBondMatchExpressionList
	ANDBondMatchExpressionList. More...
class	ANDMolecularGraphMatchExpressionList
	ANDMolecularGraphMatchExpressionList. More...
class	ANDReactionMatchExpressionList
	ANDReactionMatchExpressionList. More...
class	AmideImidicAcidTautomerization
	AmideImidicAcidTautomerizationRule. More...
class	AromaticRingSet
	Implements the perception of aromatic rings in a molecular graph. More...
class	AromaticSSSRSubset
	Implements the extraction of the aromatic rings in the SSSR of a molecular graph. More...
class	AromaticSubstructure
	Implements the perception of aromatic atoms and bonds in a molecular graph. More...
class	Atom
	Atom. More...
class	Atom2DCoordinatesCalculator
	Atom2DCoordinatesCalculator. More...
class	Atom3DCoordinatesFunction
	A generic wrapper class used to store a user-defined Chem.Atom 3D-coordinates function. More...
class	Atom3DCoordinatesFunctor
	Atom3DCoordinatesFunctor. More...
class	AtomArray3DCoordinatesFunctor
	AtomArray3DCoordinatesFunctor. More...
class	AtomBondMapping
	A data structure for the common storage of related atom to atom and bond to bond mappings. More...
class	AtomConfiguration
	Provides constants that are used to specify the R/S configuration of atoms. More...
class	AtomConfigurationMatchExpression
	AtomConfigurationMatchExpression. More...
class	AtomConformer3DCoordinatesFunctor
	AtomConformer3DCoordinatesFunctor. More...
class	AtomContainer
	A common interface for data-structures that support a random access to stored Chem.Atom instances. More...
class	AtomDictionary
	A global dictionary for the lookup of data associated with the atom types defined in namespace Chem.AtomType. More...
class	AtomEnvironmentMatchExpression
	AtomEnvironmentMatchExpression. More...
class	AtomMapping
	A data type for the storage and lookup of arbitrary atom to atom mappings. More...
class	AtomMatchConstraint
	Provides numerical identifiers for built-in Chem.Atom matching constraints. More...
class	AtomMatchExpression
	A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	AtomMatchExpressionList
	A container for the storage and evaluation of logical match expression lists. More...
class	AtomMatchExpressionPtrAtomFunctor
class	AtomPredicate
	A generic wrapper class used to store a user-defined atom predicate. More...
class	AtomProperty
	Provides keys for built-in Chem.Atom properties. More...
class	AtomPropertyDefault
	Provides default values for built-in Chem.Atom properties. More...
class	AtomPropertyFlag
	Provides flags for the specification of basic Chem.Atom properties. More...
class	AtomType
	Provides constants for the specification of the chemical element or generic type of an atom. More...
class	AtomTypeMatchExpression
	AtomTypeMatchExpression. More...
class	AutomorphismGroupSearch
	AutomorphismGroupSearch. More...
class	BRICSAtomLabel
	Provides constants for the labeling of atoms in bonds matched by a BRICS fragmentation rule. More...
class	BRICSFragmentGenerator
	BRICSFragmentGenerator. More...
class	BRICSRuleID
	Provides constants for the identification of BRICS fragmentation rules. More...
class	BasicAtom
	BasicAtom. More...
class	BasicBond
	BasicBond. More...
class	BasicMolecule
	BasicMolecule. More...
class	BasicReaction
	BasicReaction. More...
class	BemisMurckoAnalyzer
	BemisMurckoAnalyzer. More...
class	Bond
	Bond. More...
class	BondConfiguration
	Provides constants that are used to specify the cis/trans configuration of bonds. More...
class	BondConfigurationMatchExpression
	BondConfigurationMatchExpression. More...
class	BondContainer
	A common interface for data-structures that support a random access to stored Chem.Bond instances. More...
class	BondDirection
	Provides constants for the specification of directional bonds in Daylight SMILES and SMARTS strings. More...
class	BondDirectionMatchExpression
	BondDirectionMatchExpression. More...
class	BondMapping
	A data type for the storage and lookup of arbitrary bond to bond mappings. More...
class	BondMatchConstraint
	Provides numerical identifiers for built-in Chem.Bond matching constraints and flags for the specification of bond orders. More...
class	BondMatchExpression
	A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	BondMatchExpressionList
	A container for the storage and evaluation of logical match expression lists. More...
class	BondMatchExpressionPtrBondFunctor
class	BondOrderCalculator
	BondOrderCalculator. More...
class	BondPredicate
	A generic wrapper class used to store a user-defined bond predicate. More...
class	BondProperty
	Provides keys for built-in Chem.Bond properties. More...
class	BondPropertyDefault
	Provides default values for built-in Chem.Bond properties. More...
class	BondPropertyFlag
	Provides flags for the specification of basic Chem.Bond properties. More...
class	BondReactionCenterStatusMatchExpression
	BondReactionCenterStatusMatchExpression. More...
class	BondStereoFlag
	Provides constants for the specification of stereo bonds in 2D depictions of chemical structures. More...
class	BondStereoFlagCalculator
	BondStereoFlagCalculator. More...
class	BondSubstituentDirectionMatchExpression
	BondSubstituentDirectionMatchExpression. More...
class	BoolAtom2Functor
class	BoolAtom4Functor
class	BoolAtomMappingFunctor
class	BoolBond2Functor
class	BoolConstMolecularGraphFunctor
class	BoolEntity3D2Functor
class	BoolEntity3D4Functor
class	BoolEntity3DMappingFunctor
class	BoolMolecularGraphAtomBondMappingFunctor
class	BoolMolecularGraphFunctor
class	BoolSTPairArrayFunctor
class	CDFBZ2MolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More...
class	CDFBZ2MolecularGraphWriter
class	CDFBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL. More...
class	CDFBZ2MoleculeReader
class	CDFBZ2ReactionInputHandler
	A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More...
class	CDFBZ2ReactionOutputHandler
	A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More...
class	CDFBZ2ReactionReader
class	CDFBZ2ReactionWriter
class	CDFGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More...
class	CDFGZMolecularGraphWriter
class	CDFGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL. More...
class	CDFGZMoleculeReader
class	CDFGZReactionInputHandler
	A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More...
class	CDFGZReactionOutputHandler
	A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More...
class	CDFGZReactionReader
class	CDFGZReactionWriter
class	CDFMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the native I/O format of the CDPL. More...
class	CDFMolecularGraphWriter
	A writer for molecular graph data in the native I/O format of the CDPL. More...
class	CDFMoleculeInputHandler
	A handler for the input of molecule data in the native I/O format of the CDPL. More...
class	CDFMoleculeReader
	A reader for molecule data in the native I/O format of the CDPL. More...
class	CDFReactionInputHandler
	A handler for the input of reaction data in the native I/O format of the CDPL. More...
class	CDFReactionOutputHandler
	A handler for the output of reaction data in the native I/O format of the CDPL. More...
class	CDFReactionReader
	A reader for reaction data in the native I/O format of the CDPL. More...
class	CDFReactionWriter
	A writer for molecular graph data in the native I/O format of the CDPL. More...
class	CIPConfigurationLabeler
	CIPConfigurationLabeler. More...
class	CIPDescriptor
	Provides constants for the specification of stereogenic atom/bond configurations determined by the CIP sequence rules. More...
class	CIPPriorityCalculator
	CIPPriorityCalculator. More...
class	CMLBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the Chemical Markup Language [CML] format. More...
class	CMLBZ2MolecularGraphWriter
class	CMLBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the Chemical Markup Language [CML] format. More...
class	CMLBZ2MoleculeReader
class	CMLGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the Chemical Markup Language [CML] format. More...
class	CMLGZMolecularGraphWriter
class	CMLGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the Chemical Markup Language [CML] format. More...
class	CMLGZMoleculeReader
class	CMLMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the Chemical Markup Language [CML] format. More...
class	CMLMolecularGraphWriter
	A writer for molecular graph data in the Chemical Markup Language [CML] format. More...
class	CMLMoleculeInputHandler
	A handler for the input of molecule data in the Chemical Markup Language [CML] format. More...
class	CMLMoleculeReader
	A Reader for molecule data in the Chemical Markup Language [CML] format. More...
class	CanonicalNumberingCalculator
	CanonicalNumberingCalculator. More...
class	ChEMBLStandardizer
	Implementation of the ChEMBL structure preprocessing pipeline. More...
class	CommonConnectedSubstructureSearch
	CommonConnectedSubstructureSearch. More...
class	CompleteRingSet
	Implements the exhaustive perception of rings in a molecular graph. More...
class	ComponentSet
	Implements the perception of molecular graph components. More...
class	CompoundMoleculeReader
	CompoundDataReader. More...
class	CompoundReactionReader
	CompoundDataReader. More...
class	ConnectedSubstructureSet
	ConnectedSubstructureSet. More...
class	ControlParameter
	Provides keys for built-in control-parameters. More...
class	ControlParameterDefault
	Provides default values for built-in control-parameters. More...
class	CyclicSubstructure
	Implements the perception of ring atoms and bonds in a molecular graph. More...
class	DataFormat
	Provides preinitialized Base.DataFormat objects for all supported chemical data formats. More...
class	DefaultMultiConfMoleculeInputProcessor
	MultiConfMoleculeInputProcessor. More...
class	DefaultTautomerGenerator
	DefaultTautomerGenerator. More...
class	DoubleAtom2Functor
class	DoubleAtom2UInt2Functor
class	DoubleAtom2UIntFunctor
class	DoubleAtomFunctor
class	DoubleDVectorFunctor
class	DoubleEntity3D2Functor
class	DoubleEntity3DFunctor
class	DoubleVector3D2AtomFunctor
class	ElectronSystem
	Describes an electron system of a molecule in terms of involved atoms and their electron contributions. More...
class	ElectronSystemList
	A data type for the storage of Chem.ElectronSystem objects. More...
class	Entity3D
	Entity3D. More...
class	Entity3DContainer
	A common interface for data-structures that support a random access to stored Chem.Entity3D instances. More...
class	Entity3DMapping
	A data type for the storage and lookup of arbitrary entity to entity mappings. More...
class	Entity3DProperty
	Provides keys for built-in Chem.Entity3D properties. More...
class	ExtendedSSSR
	Implements the perception of the Extended Smallest Set of Smallest Rings (ESSSR) of a molecular graph. More...
class	FileCDFBZ2MolecularGraphWriter
class	FileCDFBZ2MoleculeReader
class	FileCDFBZ2ReactionReader
class	FileCDFBZ2ReactionWriter
class	FileCDFGZMolecularGraphWriter
class	FileCDFGZMoleculeReader
class	FileCDFGZReactionReader
class	FileCDFGZReactionWriter
class	FileCDFMolecularGraphWriter
class	FileCDFMoleculeReader
class	FileCDFReactionReader
class	FileCDFReactionWriter
class	FileCMLBZ2MolecularGraphWriter
class	FileCMLBZ2MoleculeReader
class	FileCMLGZMolecularGraphWriter
class	FileCMLGZMoleculeReader
class	FileCMLMolecularGraphWriter
class	FileCMLMoleculeReader
class	FileINCHIMolecularGraphWriter
class	FileINCHIMoleculeReader
class	FileJMEMolecularGraphWriter
class	FileJMEMoleculeReader
class	FileJMEReactionReader
class	FileJMEReactionWriter
class	FileMOL2BZ2MolecularGraphWriter
class	FileMOL2BZ2MoleculeReader
class	FileMOL2GZMolecularGraphWriter
class	FileMOL2GZMoleculeReader
class	FileMOL2MolecularGraphWriter
class	FileMOL2MoleculeReader
class	FileMOLMolecularGraphWriter
class	FileMOLMoleculeReader
class	FileRDFBZ2ReactionReader
class	FileRDFBZ2ReactionWriter
class	FileRDFGZReactionReader
class	FileRDFGZReactionWriter
class	FileRDFReactionReader
class	FileRDFReactionWriter
class	FileRXNReactionWriter
class	FileSDFBZ2MolecularGraphWriter
class	FileSDFBZ2MoleculeReader
class	FileSDFGZMolecularGraphWriter
class	FileSDFGZMoleculeReader
class	FileSDFMolecularGraphWriter
class	FileSDFMoleculeReader
class	FileSMARTSMolecularGraphWriter
class	FileSMARTSMoleculeReader
class	FileSMARTSReactionReader
class	FileSMARTSReactionWriter
class	FileSMILESBZ2MolecularGraphWriter
class	FileSMILESBZ2MoleculeReader
class	FileSMILESBZ2ReactionReader
class	FileSMILESBZ2ReactionWriter
class	FileSMILESGZMolecularGraphWriter
class	FileSMILESGZMoleculeReader
class	FileSMILESGZReactionReader
class	FileSMILESGZReactionWriter
class	FileSMILESMolecularGraphWriter
class	FileSMILESMoleculeReader
class	FileSMILESReactionReader
class	FileSMILESReactionWriter
class	FileXYZBZ2MolecularGraphWriter
class	FileXYZBZ2MoleculeReader
class	FileXYZGZMolecularGraphWriter
class	FileXYZGZMoleculeReader
class	FileXYZMolecularGraphWriter
class	FileXYZMoleculeReader
class	Fragment
	Fragment. More...
class	FragmentGenerator
	FragmentGenerator. More...
class	FragmentList
	A data type for the storage of Chem.Fragment objects. More...
class	GenericHydrogen13ShiftTautomerization
	GenericHydrogen13ShiftTautomerizationRule. More...
class	GenericHydrogen15ShiftTautomerization
	GenericHydrogen15ShiftTautomerizationRule. More...
class	HashCodeCalculator
	HashCodeCalculator. More...
class	HybridizationState
	Provides constants for the specification of atom hybridization states. More...
class	Hydrogen3DCoordinatesCalculator
	Hydrogen3DCoordinatesCalculator. More...
class	INCHIMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	INCHIMolecularGraphWriter
	A writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	INCHIMoleculeInputHandler
	A handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	INCHIMoleculeReader
	A reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	INCHIReturnCode
	Provides constants that are used to describe the status of an InChI [INCHI] output or input operation. More...
class	ImineEnamineTautomerization
	ImineEnamineTautomerizationRule. More...
class	JMEMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEMolecularGraphWriter
	A writer for molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEMoleculeInputHandler
	A handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEMoleculeReader
	A reader for molecule data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionInputHandler
	A handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionOutputHandler
	A handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionReader
	A reader for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionWriter
	A writer for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	KekuleStructureCalculator
	KekuleStructureCalculator. More...
class	KeteneYnolTautomerization
	KeteneYnolTautomerizationRule. More...
class	KetoEnolTautomerization
	KetoEnolTautomerizationRule. More...
class	LactamLactimTautomerization
	LactamLactimTautomerizationRule. More...
class	MDLDataFormatVersion
	Provides constants that are used to specify the connection table and Rxn-File version for the I/O of molecular graphs and reactions in MDL format [CTFILE]. More...
class	MDLParity
	Provides constants that are used to specify the MDL stereo parity of atoms. More...
class	MOL2BZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format. More...
class	MOL2BZ2MolecularGraphWriter
class	MOL2BZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format. More...
class	MOL2BZ2MoleculeReader
class	MOL2ChargeType
	Provides constants for the specification of the atom charge type in Tripos MOL2 files. More...
class	MOL2GZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format. More...
class	MOL2GZMolecularGraphWriter
class	MOL2GZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format. More...
class	MOL2GZMoleculeReader
class	MOL2MolecularGraphOutputHandler
	A handler for the output of molecular graph data in the Sybyl MOL2 format. More...
class	MOL2MolecularGraphWriter
class	MOL2MoleculeInputHandler
	A handler for the input of molecule data in the Sybyl MOL2 format. More...
class	MOL2MoleculeReader
class	MOL2MoleculeType
	Provides constants for the specification of the molecule type in Tripos MOL2 files. More...
class	MOLMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format. More...
class	MOLMolecularGraphWriter
	A writer for molecular graph data in the MDL Mol-File [CTFILE] format. More...
class	MOLMoleculeInputHandler
	A handler for the input of molecule data in the MDL Mol-File [CTFILE] format. More...
class	MOLMoleculeReader
	A reader for molecule data in the MDL Mol-File [CTFILE] format. More...
class	MatchConstraint
	MatchConstraint. More...
class	MatchConstraintList
	MatchConstraintList. More...
class	MaxCommonAtomSubstructureSearch
	MaxCommonAtomSubstructureSearch. More...
class	MaxCommonBondSubstructureSearch
	MaxCommonBondSubstructureSearch. More...
class	MolGraphMatchExpressionPtrMolGraphFunctor
class	MolecularGraph
	MolecularGraph. More...
class	MolecularGraphComponentGroupingMatchExpression
	MolecularGraphComponentGroupingMatchExpression. More...
class	MolecularGraphIOManager
	A singleton class that serves as a global registry for Chem.MolecularGraphInputHandler and Chem.MolecularGraphOutputHandler implementation instances. More...
class	MolecularGraphInputHandler
class	MolecularGraphMatchConstraint
	Provides numerical identifiers for built-in Chem.MolecularGraph matching constraints. More...
class	MolecularGraphMatchExpression
	A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	MolecularGraphMatchExpressionList
class	MolecularGraphOutputHandler
	A factory interface providing methods for the creation of Chem.MolecularGraphWriterBase instances for data output in a particular storage format. More...
class	MolecularGraphProperty
	Provides keys for built-in Chem.MolecularGraph properties. More...
class	MolecularGraphPropertyDefault
	Provides default values for built-in Chem.MolecularGraph properties. More...
class	MolecularGraphWriter
	Writer for molecule data in any supported format. More...
class	MolecularGraphWriterBase
	An interface for writing data objects of type Chem.MolecularGraph to an arbitrary data sink. More...
class	Molecule
	Molecule. More...
class	MoleculeIOManager
	A singleton class that serves as a global registry for Chem.MoleculeInputHandler and Chem.MoleculeOutputHandler implementation instances. More...
class	MoleculeInputHandler
	A factory interface providing methods for the creation of Chem.MoleculeReaderBase instances for reading data provided in a particular storage format. More...
class	MoleculeOutputHandler
class	MoleculeReader
	Reader for molecule data in any supported format. More...
class	MoleculeReaderBase
	An interface for reading data objects of type Chem.Molecule from an arbitrary data source. More...
class	MorganNumberingCalculator
	MorganNumberingCalculator. More...
class	MultiConfMoleculeInputProcessor
	MultiConfMoleculeInputProcessor. More...
class	MultiSubstructureSearch
	MultiSubstructureSearch. More...
class	NOTAtomMatchExpression
	NOTAtomMatchExpression. More...
class	NOTBondMatchExpression
	NOTBondMatchExpression. More...
class	NOTMolecularGraphMatchExpression
	NOTMolecularGraphMatchExpression. More...
class	NOTReactionMatchExpression
	NOTReactionMatchExpression. More...
class	NitroAciTautomerization
	NitroAciTautomerizationRule. More...
class	NitrosoOximeTautomerization
	NitrosoOximeTautomerizationRule. More...
class	ORAtomMatchExpressionList
	ORAtomMatchExpressionList. More...
class	ORBondMatchExpressionList
	ORBondMatchExpressionList. More...
class	ORMolecularGraphMatchExpressionList
	ORMolecularGraphMatchExpressionList. More...
class	ORReactionMatchExpressionList
	ORReactionMatchExpressionList. More...
class	PatternAtomTyper
	PatternAtomTyper. More...
class	PatternBasedTautomerizationRule
	PatternBasedTautomerizationRule. More...
class	PhosphinicAcidTautomerization
	PhosphinicAcidTautomerizationRule. More...
class	PiElectronSystemList
	Implements the perception of all pi electron systems present in a molecule. More...
class	ProtonationStateStandardizer
	Sets the protation state of molecules according to desired objectives. More...
class	RDFBZ2ReactionInputHandler
	A handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFBZ2ReactionOutputHandler
	A handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFBZ2ReactionReader
class	RDFBZ2ReactionWriter
class	RDFGZReactionInputHandler
	A handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFGZReactionOutputHandler
	A handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFGZReactionReader
class	RDFGZReactionWriter
class	RDFReactionInputHandler
	A handler for the input of reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFReactionOutputHandler
	A handler for the output of reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFReactionReader
	A reader for reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFReactionWriter
	A writer for reaction data in the MDL RD-File [CTFILE] format. More...
class	RECAPAtomLabel
	Provides constants for the labeling of atoms in bonds matched by a RECAP fragmentation rule. More...
class	RECAPFragmentGenerator
	RECAPFragmentGenerator. More...
class	RECAPRuleID
	Provides constants for the identification of RECAP fragmentation rules. More...
class	RXNReactionInputHandler
	A handler for the input of reaction data in the MDL Rxn-File [CTFILE] format. More...
class	RXNReactionOutputHandler
	A handler for the output of reaction data in the MDL Rxn-File [CTFILE] format. More...
class	RXNReactionReader
	A reader for reaction data in the MDL Rxn-File [CTFILE] format. More...
class	RXNReactionWriter
	A writer for reaction data in the MDL Rxn-File [CTFILE] format. More...
class	RadicalType
	Provides constants that are used to specify the degeneracy of the electronic state of radical atoms. More...
class	Reaction
	Reaction. More...
class	ReactionAtomMappingMatchExpression
	ReactionAtomMappingMatchExpression. More...
class	ReactionCenterStatus
	Provides flags that are used to describe state changes of atoms and bonds in a reaction center. More...
class	ReactionComponentGroupingMatchExpression
	ReactionComponentGroupingMatchExpression. More...
class	ReactionIOManager
	A singleton class that serves as a global registry for Chem.ReactionInputHandler and Chem.ReactionOutputHandler implementation instances. More...
class	ReactionInputHandler
	A factory interface providing methods for the creation of Chem.ReactionReaderBase instances for reading data provided in a particular storage format. More...
class	ReactionMatchConstraint
	Provides numerical identifiers for built-in Chem.Reaction matching constraints. More...
class	ReactionMatchExpression
	A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	ReactionMatchExpressionList
class	ReactionOutputHandler
	A factory interface providing methods for the creation of Chem.ReactionWriterBase instances for data output in a particular storage format. More...
class	ReactionProperty
	Provides keys for built-in Chem.Reaction properties. More...
class	ReactionPropertyDefault
	Provides default values for built-in Chem.Reaction properties. More...
class	ReactionReader
	Reader for reaction data in any supported format. More...
class	ReactionReaderBase
	An interface for reading data objects of type Chem.Reaction from an arbitrary data source. More...
class	ReactionRole
	Provides constants that are used to specify the role of molecules (components) in a chemical reaction. More...
class	ReactionSubstructureSearch
	ReactionSubstructureSearch. More...
class	ReactionWriter
	Writer for reaction data in any supported format. More...
class	ReactionWriterBase
	An interface for writing data objects of type Chem.Reaction to an arbitrary data sink. More...
class	Reactor
	Reactor. More...
class	ResonanceStructureGenerator
	ResonanceStructureGenerator. More...
class	SDFBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
class	SDFBZ2MolecularGraphWriter
class	SDFBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format. More...
class	SDFBZ2MoleculeReader
class	SDFGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
class	SDFGZMolecularGraphWriter
class	SDFGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format. More...
class	SDFGZMoleculeReader
class	SDFMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the MDL SD-File [CTFILE] format. More...
class	SDFMolecularGraphWriter
	A writer for molecular graph data in the MDL Mol-File [CTFILE] format. More...
class	SDFMoleculeInputHandler
	A handler for the input of molecule data in the MDL SD-File [CTFILE] format. More...
class	SDFMoleculeReader
	A Reader for molecule data in the MDL SD-File [CTFILE] format. More...
class	SMARTSMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSMolecularGraphWriter
	A writer for molecular graph data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSMoleculeInputHandler
	A handler for the input of molecule data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSMoleculeReader
	A reader for molecule data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionInputHandler
	A handler for the input of reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionOutputHandler
	A handler for the output of reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionReader
	A reader for reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionWriter
	A writer for reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMILESBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESBZ2MolecularGraphWriter
class	SMILESBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format. More...
class	SMILESBZ2MoleculeReader
class	SMILESBZ2ReactionInputHandler
	A handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESBZ2ReactionOutputHandler
	A handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESBZ2ReactionReader
class	SMILESBZ2ReactionWriter
class	SMILESGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESGZMolecularGraphWriter
class	SMILESGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format. More...
class	SMILESGZMoleculeReader
class	SMILESGZReactionInputHandler
	A handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESGZReactionOutputHandler
	A handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESGZReactionReader
class	SMILESGZReactionWriter
class	SMILESMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESMolecularGraphWriter
	A writer for molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESMoleculeInputHandler
	A handler for the input of molecule data in the Daylight SMILES [SMILES] format. More...
class	SMILESMoleculeReader
	A reader for molecule data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionInputHandler
	A handler for the input of reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionOutputHandler
	A handler for the output of reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionReader
	A reader for reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionWriter
	A writer for reaction data in the Daylight SMILES [SMILES] format. More...
class	SizeTypeAtomFunctor
class	SizeTypeAtomMolecularGraphFunctor
class	SmallestSetOfSmallestRings
	Implements the perception of the Smallest Set of Smallest Rings (SSSR) of a molecular graphs. More...
class	SpatialAtomAlignment
class	SpatialEntity3DAlignment
class	StereoDescriptor
	A data structure for the storage and retrieval of stereochemical information about atoms and bonds. More...
class	StereoisomerGenerator
	StereoisomerGenerator. More...
class	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]). More...
class	StringDataBlockEntry
	Represents a data item in the structure or reaction data block of a MDL SD- or RD-File data record (see [CTFILE]). More...
class	SubstructureHistogramCalculator
	SubstructureHistogramCalculator. More...
class	SubstructureSearch
	SubstructureSearch. More...
class	SulfenicAcidTautomerization
	SulfenicAcidTautomerizationRule. More...
class	SurfaceAtomExtractor
	SurfaceAtomExtractor. More...
class	SybylAtomType
	Provides constants for the specification of the Tripos Sybyl atom type. More...
class	SybylBondType
	Provides constants for the specification of the Tripos Sybyl bond type. More...
class	SymmetryClassCalculator
	SymmetryClassCalculator. More...
class	TautomerGenerator
	TautomerGenerator. More...
class	TautomerScore
	TautomerScore. More...
class	TautomerizationRule
	TautomerizationRule. More...
class	TautomerizationType
	Provides constants serving as identifiers for built-in Chem.TautomerizationRule implementations. More...
class	TopologicalAtomAlignment
class	TopologicalEntity3DAlignment
class	UInt64AtomFunctor
class	UInt64AtomMolecularGraphFunctor
class	UInt64BondFunctor
class	Vector2DAtomFunctor
class	Vector3DEntity3DFunctor
class	VoidMolecularGraphFunctor
class	VoidMoleculeMolecularGraphFunctor
class	XYZBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the XYZ format. More...
class	XYZBZ2MolecularGraphWriter
class	XYZBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the XYZ format. More...
class	XYZBZ2MoleculeReader
class	XYZGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the XYZ format. More...
class	XYZGZMolecularGraphWriter
class	XYZGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the XYZ format. More...
class	XYZGZMoleculeReader
class	XYZMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the XYZ format. More...
class	XYZMolecularGraphWriter
class	XYZMoleculeInputHandler
	A handler for the input of molecule data in the XYZ format. More...
class	XYZMoleculeReader

Functions
int	getMaxAtomMappingID (AtomContainer cntnr)
int	getMaxComponentGroupID (AtomContainer cntnr)
bool	calcCentroid (AtomContainer cntnr, Atom3DCoordinatesFunction coords_func, Math.Vector3D ctr)
None	copyAtomsIf (AtomContainer cntnr, Molecule mol, AtomPredicate pred, bool append=False)
None	copyAtomsIf (AtomContainer cntnr, Fragment frag, AtomPredicate pred, bool append=False)
int	createAtomTypeMask (AtomContainer cntnr, Util.BitSet mask, int type, bool reset=True, bool strict=True)
None	addConformation (AtomContainer cntnr, Math.Vector3DArray coords)
None	transformConformation (AtomContainer cntnr, int conf_idx, Math.Matrix4D mtx)
None	getConformation (AtomContainer cntnr, int conf_idx, Math.Vector3DArray coords, bool append=False)
None	applyConformation (AtomContainer cntnr, int conf_idx)
None	transform2DCoordinates (AtomContainer cntnr, Math.Matrix3D mtx)
None	get2DCoordinates (AtomContainer cntnr, Math.Vector2DArray coords, bool append=False)
None	set2DCoordinates (AtomContainer cntnr, Math.Vector2DArray coords)
None	get3DCoordinates (AtomContainer cntnr, Math.Vector3DArray coords, Atom3DCoordinatesFunction coords_func, bool append=False)
bool	hasCoordinates (AtomContainer cntnr, int dim)
None	transformConformations (AtomContainer cntnr, Math.Matrix4D mtx)
int	getNumConformations (AtomContainer cntnr)
bool	alignConformations (AtomContainer cntnr, Util.BitSet ref_atoms, Math.Vector3DArray ref_coords)
bool	alignConformations (AtomContainer cntnr, AtomContainer ref_atoms, Math.Vector3DArray ref_coords)
bool	alignConformations (AtomContainer cntnr, Util.BitSet ref_atoms)
bool	alignConformations (AtomContainer cntnr, AtomContainer ref_atoms)
None	clearConformations (AtomContainer cntnr)
bool	calcCenterOfMass (AtomContainer cntnr, Atom3DCoordinatesFunction coords_func, Math.Vector3D ctr)
None	copyAtomsIfNot (AtomContainer cntnr, Molecule mol, AtomPredicate pred, bool append=False)
None	copyAtomsIfNot (AtomContainer cntnr, Fragment frag, AtomPredicate pred, bool append=False)
None	calcBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func, bool reset=True)
bool	insideBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func)
bool	intersectsBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func)
None	clearMOL2SubstructureID (Atom atom)
bool	hasMOL2SubstructureID (Atom atom)
int	getMOL2SubstructureID (Atom atom)
None	setMOL2SubstructureID (Atom atom, int id)
None	clearAtomMappingID (Atom atom)
bool	hasAtomMappingID (Atom atom)
int	getAtomMappingID (Atom atom)
None	setAtomMappingID (Atom atom, int id)
None	clearComponentGroupID (Atom atom)
bool	hasComponentGroupID (Atom atom)
int	getComponentGroupID (Atom atom)
None	setComponentGroupID (Atom atom, int id)
int	getTopologicalDistance (Atom atom1, Atom atom2, MolecularGraph molgraph)
None	clearMOL2Charge (Atom atom)
bool	hasMOL2Charge (Atom atom)
float	getMOL2Charge (Atom atom)
None	setMOL2Charge (Atom atom, float charge)
int	calcFormalCharge (Atom atom, MolecularGraph molgraph)
None	clearFormalCharge (Atom atom)
bool	hasFormalCharge (Atom atom)
int	getFormalCharge (Atom atom)
None	setFormalCharge (Atom atom, int charge)
None	clearMOL2Name (Atom atom)
bool	hasMOL2Name (Atom atom)
str	getMOL2Name (Atom atom)
None	setMOL2Name (Atom atom, str name)
None	clearMOL2SubstructureName (Atom atom)
bool	hasMOL2SubstructureName (Atom atom)
str	getMOL2SubstructureName (Atom atom)
None	setMOL2SubstructureName (Atom atom, str name)
None	clearName (Atom atom)
bool	hasName (Atom atom)
str	getName (Atom atom)
None	setName (Atom atom, str name)
None	clearIsotope (Atom atom)
bool	hasIsotope (Atom atom)
int	getIsotope (Atom atom)
None	setIsotope (Atom atom, int isotope)
int	getGenericType (Atom atom)
None	clearRadicalType (Atom atom)
bool	hasRadicalType (Atom atom)
int	getRadicalType (Atom atom)
None	setRadicalType (Atom atom, int type)
int	perceiveSybylType (Atom atom, MolecularGraph molgraph)
None	clearSybylType (Atom atom)
bool	hasSybylType (Atom atom)
int	getSybylType (Atom atom)
None	setSybylType (Atom atom, int type)
None	clearType (Atom atom)
str	getSymbolForType (Atom atom)
bool	hasType (Atom atom)
int	getType (Atom atom)
None	setType (Atom atom, int type)
None	clearMOL2SubstructureSubtype (Atom atom)
bool	hasMOL2SubstructureSubtype (Atom atom)
str	getMOL2SubstructureSubtype (Atom atom)
None	setMOL2SubstructureSubtype (Atom atom, str subtype)
int	perceiveHybridizationState (Atom atom, MolecularGraph molgraph)
None	clearHybridizationState (Atom atom)
bool	hasHybridizationState (Atom atom)
int	getHybridizationState (Atom atom)
None	setHybridizationState (Atom atom, int state)
bool	isInFragmentOfSize (Atom atom, FragmentList frag_list, int size)
None	clearMDLStereoCareFlag (Atom atom)
bool	hasMDLStereoCareFlag (Atom atom)
bool	getMDLStereoCareFlag (Atom atom)
None	setMDLStereoCareFlag (Atom atom, bool flag)
None	clearRingFlag (Atom atom)
bool	hasRingFlag (Atom atom)
bool	getRingFlag (Atom atom)
None	setRingFlag (Atom atom, bool in_ring)
None	clearStereoCenterFlag (Atom atom)
bool	hasStereoCenterFlag (Atom atom)
bool	getStereoCenterFlag (Atom atom)
None	setStereoCenterFlag (Atom atom, bool is_center)
None	clearAromaticityFlag (Atom atom)
bool	hasAromaticityFlag (Atom atom)
bool	getAromaticityFlag (Atom atom)
None	setAromaticityFlag (Atom atom, bool aromatic)
str	generateMatchExpressionString (Atom atom, MolecularGraph molgraph)
None	clearMatchExpressionString (Atom atom)
bool	hasMatchExpressionString (Atom atom)
str	getMatchExpressionString (Atom atom)
None	setMatchExpressionString (Atom atom, str expr_str)
None	clearSymbol (Atom atom)
int	getTypeForSymbol (Atom atom)
bool	hasSymbol (Atom atom)
str	getSymbol (Atom atom)
None	setSymbol (Atom atom, str symbol)
None	clearMOL2SubstructureChain (Atom atom)
bool	hasMOL2SubstructureChain (Atom atom)
str	getMOL2SubstructureChain (Atom atom)
None	setMOL2SubstructureChain (Atom atom, str chain)
AtomMatchExpression	generateMatchExpression (Atom atom, MolecularGraph molgraph)
None	clearMatchExpression (Atom atom)
bool	hasMatchExpression (Atom atom)
AtomMatchExpression	getMatchExpression (Atom atom)
None	setMatchExpression (Atom atom, AtomMatchExpression expr)
None	clearCIPConfiguration (Atom atom)
bool	hasCIPConfiguration (Atom atom)
int	getCIPConfiguration (Atom atom)
None	setCIPConfiguration (Atom atom, int config)
int	calcConfiguration (Atom atom, MolecularGraph molgraph, StereoDescriptor descr, Math.Vector3DArray coords)
None	clearCanonicalNumber (Atom atom)
bool	hasCanonicalNumber (Atom atom)
int	getCanonicalNumber (Atom atom)
None	setCanonicalNumber (Atom atom, int num)
None	clearMorganNumber (Atom atom)
bool	hasMorganNumber (Atom atom)
int	getMorganNumber (Atom atom)
None	setMorganNumber (Atom atom, int num)
bool	isStereoCenter (Atom atom, MolecularGraph molgraph, bool check_asym=True, bool check_inv_n=True, bool check_quart_n=True, bool check_plan_n=True, bool check_amide_n=True, bool check_res_ctrs=True)
StereoDescriptor	calcStereoDescriptor (Atom atom, MolecularGraph molgraph, int dim=1)
None	clearStereoDescriptor (Atom atom)
bool	hasStereoDescriptor (Atom atom)
StereoDescriptor	getStereoDescriptor (Atom atom)
None	setStereoDescriptor (Atom atom, StereoDescriptor descr)
int	getConnectedAtomsAndBonds (Atom atom, MolecularGraph molgraph, list atoms, list bonds, Atom excl_atom)
int	getIncidentBonds (Atom atom, MolecularGraph molgraph, list bonds, Atom excl_atom)
None	clear2DCoordinates (Atom atom)
bool	has2DCoordinates (Atom atom)
Math.Vector2D	get2DCoordinates (Atom atom)
None	set2DCoordinates (Atom atom, Math.Vector2D coords)
Math.Vector3D	getConformer3DCoordinates (Atom atom, int conf_idx)
int	getConnectedAtoms (Atom atom, MolecularGraph molgraph, list atoms, Atom excl_atom)
None	markReachableAtoms (Atom atom, MolecularGraph molgraph, Util.BitSet atom_mask, bool reset=True)
None	clearSymmetryClass (Atom atom)
bool	hasSymmetryClass (Atom atom)
int	getSymmetryClass (Atom atom)
None	setSymmetryClass (Atom atom, int class_id)
int	getNumContainingFragments (Atom atom, FragmentList frag_list)
None	getContainingFragments (Atom atom, FragmentList frag_list, FragmentList cont_frag_list)
None	clearMatchConstraints (Atom atom)
bool	hasMatchConstraints (Atom atom)
MatchConstraintList	getMatchConstraints (Atom atom)
None	setMatchConstraints (Atom atom, MatchConstraintList constr)
None	clearReactionCenterStatus (Atom atom)
bool	hasReactionCenterStatus (Atom atom)
int	getReactionCenterStatus (Atom atom)
None	setReactionCenterStatus (Atom atom, int status)
int	getSizeOfLargestContainingFragment (Atom atom, FragmentList frag_list)
int	getSizeOfSmallestContainingFragment (Atom atom, FragmentList frag_list)
int	getEnvironment (Atom atom, MolecularGraph molgraph, int max_dist, Fragment env, bool append=False)
int	calcImplicitHydrogenCount (Atom atom, MolecularGraph molgraph)
None	clearImplicitHydrogenCount (Atom atom)
bool	hasImplicitHydrogenCount (Atom atom)
int	getImplicitHydrogenCount (Atom atom)
None	setImplicitHydrogenCount (Atom atom, int count)
None	clearUnpairedElectronCount (Atom atom)
bool	hasUnpairedElectronCount (Atom atom)
int	getUnpairedElectronCount (Atom atom)
None	setUnpairedElectronCount (Atom atom, int count)
None	clear3DCoordinatesArray (Atom atom)
bool	has3DCoordinatesArray (Atom atom)
Math.Vector3DArray	get3DCoordinatesArray (Atom atom)
None	set3DCoordinatesArray (Atom atom, Math.Vector3DArray coords_array)
int	calcMDLParity (Atom atom, MolecularGraph molgraph)
StereoDescriptor	calcStereoDescriptorFromMDLParity (Atom atom, MolecularGraph molgraph)
None	clearMDLParity (Atom atom)
bool	hasMDLParity (Atom atom)
int	getMDLParity (Atom atom)
None	setMDLParity (Atom atom, int parity)
None	clearCIPPriority (Atom atom)
bool	hasCIPPriority (Atom atom)
int	getCIPPriority (Atom atom)
None	setCIPPriority (Atom atom, int priority)
int	perceiveSybylType (Bond bond, MolecularGraph molgraph)
None	clearSybylType (Bond bond)
bool	hasSybylType (Bond bond)
int	getSybylType (Bond bond)
None	setSybylType (Bond bond, int type)
bool	isInFragmentOfSize (Bond bond, FragmentList frag_list, int size)
None	clearRingFlag (Bond bond)
bool	hasRingFlag (Bond bond)
bool	getRingFlag (Bond bond)
None	setRingFlag (Bond bond, bool in_ring)
None	clear2DStereoFlag (Bond bond)
bool	has2DStereoFlag (Bond bond)
int	get2DStereoFlag (Bond bond)
None	set2DStereoFlag (Bond bond, int flag)
None	clearStereoCenterFlag (Bond bond)
bool	hasStereoCenterFlag (Bond bond)
bool	getStereoCenterFlag (Bond bond)
None	setStereoCenterFlag (Bond bond, bool is_center)
None	clearAromaticityFlag (Bond bond)
bool	hasAromaticityFlag (Bond bond)
bool	getAromaticityFlag (Bond bond)
None	setAromaticityFlag (Bond bond, bool aromatic)
str	generateMatchExpressionString (Bond bond, MolecularGraph molgraph)
None	clearMatchExpressionString (Bond bond)
bool	hasMatchExpressionString (Bond bond)
str	getMatchExpressionString (Bond bond)
None	setMatchExpressionString (Bond bond, str expr_str)
BondMatchExpression	generateMatchExpression (Bond bond, MolecularGraph molgraph)
None	clearMatchExpression (Bond bond)
bool	hasMatchExpression (Bond bond)
BondMatchExpression	getMatchExpression (Bond bond)
None	setMatchExpression (Bond bond, BondMatchExpression expr)
None	clearCIPConfiguration (Bond bond)
bool	hasCIPConfiguration (Bond bond)
int	getCIPConfiguration (Bond bond)
None	setCIPConfiguration (Bond bond, int config)
int	calcConfiguration (Bond bond, MolecularGraph molgraph, StereoDescriptor descr, Math.Vector3DArray coords)
None	clearDirection (Bond bond)
bool	hasDirection (Bond bond)
int	getDirection (Bond bond)
None	setDirection (Bond bond, int dir)
None	clearOrder (Bond bond)
bool	hasOrder (Bond bond)
int	getOrder (Bond bond)
None	setOrder (Bond bond, int order)
bool	isStereoCenter (Bond bond, MolecularGraph molgraph, bool check_asym=True, bool check_term_n=True, bool check_order=True, int min_ring_size=8)
StereoDescriptor	calcStereoDescriptor (Bond bond, MolecularGraph molgraph, int dim=1)
None	clearStereoDescriptor (Bond bond)
bool	hasStereoDescriptor (Bond bond)
StereoDescriptor	getStereoDescriptor (Bond bond)
None	setStereoDescriptor (Bond bond, StereoDescriptor descr)
int	getNumContainingFragments (Bond bond, FragmentList frag_list)
None	getContainingFragments (Bond bond, FragmentList frag_list, FragmentList cont_frag_list)
None	clearMatchConstraints (Bond bond)
bool	hasMatchConstraints (Bond bond)
MatchConstraintList	getMatchConstraints (Bond bond)
None	setMatchConstraints (Bond bond, MatchConstraintList constr)
None	clearReactionCenterStatus (Bond bond)
bool	hasReactionCenterStatus (Bond bond)
int	getReactionCenterStatus (Bond bond)
None	setReactionCenterStatus (Bond bond, int status)
int	getSizeOfLargestContainingFragment (Bond bond, FragmentList frag_list)
int	getSizeOfSmallestContainingFragment (Bond bond, FragmentList frag_list)
None	clearSMILESMolWriteAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESMolWriteAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESMolWriteAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
None	setSMILESMolWriteAtomMappingIDParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearSMILESRxnWriteAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESRxnWriteAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESRxnWriteAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
None	setSMILESRxnWriteAtomMappingIDParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr)
bool	getMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr)
None	setMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr, bool output)
None	clearXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr)
bool	hasXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr)
bool	getXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr)
None	setXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr, bool is_name)
None	clearSMILESWriteIsotopeParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESWriteIsotopeParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESWriteIsotopeParameter (Base.ControlParameterContainer cntnr)
None	setSMILESWriteIsotopeParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr)
bool	hasMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr)
int	getMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr)
None	setMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr, int type)
None	clearMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr)
bool	hasMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr)
int	getMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr)
None	setMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr, int type)
None	clearOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr)
bool	hasOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr)
bool	getOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr)
None	setOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr, bool deplete)
None	clearSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr)
int	getSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr)
None	setSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr, int min_size)
None	clearMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr)
str	getMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr)
None	setMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr, str tag)
None	clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
bool	hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
bool	getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
None	setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)
None	clearCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
bool	hasCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
bool	getCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
None	setCheckLineLengthParameter (Base.ControlParameterContainer cntnr, bool check)
None	clearSMILESWriteKekuleFormParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESWriteKekuleFormParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESWriteKekuleFormParameter (Base.ControlParameterContainer cntnr)
None	setSMILESWriteKekuleFormParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearSMILESWriteCanonicalFormParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESWriteCanonicalFormParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESWriteCanonicalFormParameter (Base.ControlParameterContainer cntnr)
None	setSMILESWriteCanonicalFormParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr)
bool	hasCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr)
int	getCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr)
None	setCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr, int dim)
None	clearMDLCTABVersionParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLCTABVersionParameter (Base.ControlParameterContainer cntnr)
int	getMDLCTABVersionParameter (Base.ControlParameterContainer cntnr)
None	setMDLCTABVersionParameter (Base.ControlParameterContainer cntnr, int version)
None	clearMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr)
int	getMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr)
None	setMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr, int version)
None	clearConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr)
bool	hasConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr)
str	getConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr)
None	setConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr, str pattern)
None	clearSMILESWriteBondStereoParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESWriteBondStereoParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESWriteBondStereoParameter (Base.ControlParameterContainer cntnr)
None	setSMILESWriteBondStereoParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearSMILESWriteRingBondStereoParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESWriteRingBondStereoParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESWriteRingBondStereoParameter (Base.ControlParameterContainer cntnr)
None	setSMILESWriteRingBondStereoParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearSMILESWriteAtomStereoParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESWriteAtomStereoParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESWriteAtomStereoParameter (Base.ControlParameterContainer cntnr)
None	setSMILESWriteAtomStereoParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr)
bool	getMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr)
None	setMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr, bool update)
None	clearMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr)
bool	hasMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr)
MultiConfMoleculeInputProcessor	getMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr)
None	setMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr, MultiConfMoleculeInputProcessor proc)
None	clearRecordSeparatorParameter (Base.ControlParameterContainer cntnr)
bool	hasRecordSeparatorParameter (Base.ControlParameterContainer cntnr)
str	getRecordSeparatorParameter (Base.ControlParameterContainer cntnr)
None	setRecordSeparatorParameter (Base.ControlParameterContainer cntnr, str sep)
None	clearSMILESWriteAromaticBondsParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESWriteAromaticBondsParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESWriteAromaticBondsParameter (Base.ControlParameterContainer cntnr)
None	setSMILESWriteAromaticBondsParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearSMILESWriteSingleBondsParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESWriteSingleBondsParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESWriteSingleBondsParameter (Base.ControlParameterContainer cntnr)
None	setSMILESWriteSingleBondsParameter (Base.ControlParameterContainer cntnr, bool write)
None	clearMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
bool	hasMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	setMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)
None	clearXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
bool	hasXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
bool	getXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	setXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)
None	clearMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr)
bool	getMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr)
None	setMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr, bool trunc)
None	clearMDLTrimLinesParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLTrimLinesParameter (Base.ControlParameterContainer cntnr)
bool	getMDLTrimLinesParameter (Base.ControlParameterContainer cntnr)
None	setMDLTrimLinesParameter (Base.ControlParameterContainer cntnr, bool trim)
None	clearMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
bool	hasMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
None	setMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
None	clearMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr)
bool	hasMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr)
None	setMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
None	clearMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr)
bool	hasMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr)
None	setMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr, bool output)
None	clearMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr)
bool	getMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr)
None	setMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr, bool trunc)
None	clearMDLTrimStringsParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLTrimStringsParameter (Base.ControlParameterContainer cntnr)
bool	getMDLTrimStringsParameter (Base.ControlParameterContainer cntnr)
None	setMDLTrimStringsParameter (Base.ControlParameterContainer cntnr, bool trim)
None	clearINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr)
bool	hasINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr)
str	getINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr)
None	setINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr, str opts)
None	clearINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr)
bool	hasINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr)
str	getINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr)
None	setINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr, str opts)
None	clearXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr)
bool	hasXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr)
bool	getXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr)
None	setXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr, bool perceive)
None	clearCDFWriteSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
bool	hasCDFWriteSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
bool	getCDFWriteSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
None	setCDFWriteSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr, bool single_prec)
None	clearJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr)
bool	hasJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr)
bool	getJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr)
None	setJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr, bool separate)
None	clearSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr)
str	getSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr)
None	setSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr, str format)
None	clearSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr)
bool	hasSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr)
None	setSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr, bool no_subset)
None	clearOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr)
bool	hasOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr)
bool	getOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr)
None	setOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr, bool output)
None	clearMultiConfImportParameter (Base.ControlParameterContainer cntnr)
bool	hasMultiConfImportParameter (Base.ControlParameterContainer cntnr)
bool	getMultiConfImportParameter (Base.ControlParameterContainer cntnr)
None	setMultiConfImportParameter (Base.ControlParameterContainer cntnr, bool multi_conf)
None	clearMultiConfExportParameter (Base.ControlParameterContainer cntnr)
bool	hasMultiConfExportParameter (Base.ControlParameterContainer cntnr)
bool	getMultiConfExportParameter (Base.ControlParameterContainer cntnr)
None	setMultiConfExportParameter (Base.ControlParameterContainer cntnr, bool multi_conf)
None	clearBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr)
bool	hasBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr)
bool	getBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr)
None	setBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr, bool fix)
None	clearMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr)
bool	getMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr)
None	setMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr, bool output)
None	clearMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr)
bool	hasMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr)
bool	getMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr)
None	setMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr, bool ignore)
None	clearXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr)
bool	hasXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr)
bool	getXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr)
None	setXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr, bool perceive)
bool	calcCentroid (Entity3DContainer cntnr, Math.Vector3D ctr)
None	transform3DCoordinates (Entity3DContainer cntnr, Math.Matrix4D mtx)
bool	align3DCoordinates (Entity3DContainer cntnr, Entity3DContainer ref_entities, Math.Vector3DArray ref_coords)
None	get3DCoordinates (Entity3DContainer cntnr, Math.Vector3DArray coords, bool append=False)
None	set3DCoordinates (Entity3DContainer cntnr, Math.Vector3DArray coords)
None	calcGeometricalDistanceMatrix (Entity3DContainer cntnr, Math.DMatrix mtx)
None	calcBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max, bool reset=True)
bool	insideBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max)
bool	intersectsBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max)
None	clear3DCoordinates (Entity3D entity)
bool	has3DCoordinates (Entity3D entity)
Math.Vector3D	get3DCoordinates (Entity3D entity)
None	set3DCoordinates (Entity3D entity, Math.Vector3D coords)
bool	containsFragmentWithBond (FragmentList frag_list, Bond bond)
bool	containsFragmentWithMinSize (FragmentList frag_list, int min_size)
bool	isAromatic (Fragment ring, MolecularGraph molgraph, Util.BitSet arom_bond_mask)
bool	isNotAromatic (Fragment ring, MolecularGraph molgraph)
bool	makeHydrogenDeplete (Fragment frag)
	Removes all explicit hydrogen atoms from the fragment frag. More...
bool	makeOrdinaryHydrogenDeplete (Fragment frag, int flags)
	Removes all explicit ordinary hydrogen atoms from the fragment frag. More...
None	removeAtomsIf (Fragment frag, AtomPredicate pred)
None	removeAtomsIfNot (Fragment frag, AtomPredicate pred)
None	clearMDLScalingFactor1 (MolecularGraph molgraph)
bool	hasMDLScalingFactor1 (MolecularGraph molgraph)
int	getMDLScalingFactor1 (MolecularGraph molgraph)
None	setMDLScalingFactor1 (MolecularGraph molgraph, int factor)
None	clearMDLScalingFactor2 (MolecularGraph molgraph)
bool	hasMDLScalingFactor2 (MolecularGraph molgraph)
float	getMDLScalingFactor2 (MolecularGraph molgraph)
None	setMDLScalingFactor2 (MolecularGraph molgraph, float factor)
object	generateINCHI (MolecularGraph molgraph, str options='/WarnOnEmptyStructure/AuxNone/NEWPSOFF', int dim=0)
FragmentList	perceiveSSSR (MolecularGraph molgraph)
FragmentList	perceiveSSSR (MolecularGraph molgraph, bool overwrite)
None	clearSSSR (MolecularGraph molgraph)
bool	hasSSSR (MolecularGraph molgraph)
FragmentList	getSSSR (MolecularGraph molgraph)
None	setSSSR (MolecularGraph molgraph, FragmentList sssr)
object	generateSMILES (MolecularGraph molgraph, bool canonical=False, bool ord_h_deplete=True, int atom_flags=2147483648, int bond_flags=2147483648)
None	clearStructureData (MolecularGraph molgraph)
bool	hasStructureData (MolecularGraph molgraph)
StringDataBlock	getStructureData (MolecularGraph molgraph)
None	setStructureData (MolecularGraph molgraph, StringDataBlock data)
int	calcHashCode (MolecularGraph molgraph, int atom_flags=2147483648, int bond_flags=2147483648, bool ord_h_deplete=True)
None	clearHashCode (MolecularGraph molgraph)
bool	hasHashCode (MolecularGraph molgraph)
int	getHashCode (MolecularGraph molgraph)
None	setHashCode (MolecularGraph molgraph, int hash_code)
None	clearMDLProgramName (MolecularGraph molgraph)
bool	hasMDLProgramName (MolecularGraph molgraph)
str	getMDLProgramName (MolecularGraph molgraph)
None	setMDLProgramName (MolecularGraph molgraph, str name)
None	clearName (MolecularGraph molgraph)
bool	hasName (MolecularGraph molgraph)
str	getName (MolecularGraph molgraph)
None	setName (MolecularGraph molgraph, str name)
None	clearMOL2ChargeType (MolecularGraph molgraph)
bool	hasMOL2ChargeType (MolecularGraph molgraph)
int	getMOL2ChargeType (MolecularGraph molgraph)
None	setMOL2ChargeType (MolecularGraph molgraph, int type)
None	clearMOL2MoleculeType (MolecularGraph molgraph)
bool	hasMOL2MoleculeType (MolecularGraph molgraph)
int	getMOL2MoleculeType (MolecularGraph molgraph)
None	setMOL2MoleculeType (MolecularGraph molgraph, int type)
Fragment	perceiveCyclicSubstructure (MolecularGraph molgraph)
Fragment	perceiveCyclicSubstructure (MolecularGraph molgraph, bool overwrite)
None	clearCyclicSubstructure (MolecularGraph molgraph)
bool	hasCyclicSubstructure (MolecularGraph molgraph)
Fragment	getCyclicSubstructure (MolecularGraph molgraph)
None	setCyclicSubstructure (MolecularGraph molgraph, Fragment substruct)
Fragment	perceiveAromaticSubstructure (MolecularGraph molgraph)
Fragment	perceiveAromaticSubstructure (MolecularGraph molgraph, bool overwrite)
None	clearAromaticSubstructure (MolecularGraph molgraph)
bool	hasAromaticSubstructure (MolecularGraph molgraph)
Fragment	getAromaticSubstructure (MolecularGraph molgraph)
None	setAromaticSubstructure (MolecularGraph molgraph, Fragment substruct)
None	canonicalize (MolecularGraph molgraph, bool atoms=True, bool atom_nbrs=True, bool bonds=True, bool bond_atoms=False)
None	canonicalize (MolecularGraph molgraph, ForceField.InteractionFilterFunction2 func, bool atoms=True, bool atom_nbrs=True, bool bonds=True, bool bond_atoms=False)
None	clearMDLChiralFlag (MolecularGraph molgraph)
bool	hasMDLChiralFlag (MolecularGraph molgraph)
bool	getMDLChiralFlag (MolecularGraph molgraph)
None	setMDLChiralFlag (MolecularGraph molgraph, bool flag)
None	calcCanonicalNumbering (MolecularGraph molgraph, bool overwrite, int atom_flags=2147483648, int bond_flags=2147483648)
None	calcMorganNumbering (MolecularGraph molgraph, bool overwrite)
bool	containsMolecularGraph (MolecularGraph molgraph, MolecularGraph sub_molgraph, bool atoms=True, bool bonds=True)
None	clearMDLCTABVersion (MolecularGraph molgraph)
bool	hasMDLCTABVersion (MolecularGraph molgraph)
int	getMDLCTABVersion (MolecularGraph molgraph)
None	setMDLCTABVersion (MolecularGraph molgraph, int version)
MolecularGraphMatchExpression	generateMatchExpression (MolecularGraph molgraph)
MolecularGraphMatchExpression	generateMatchExpression (MolecularGraph molgraph, bool overwrite)
None	clearMatchExpression (MolecularGraph molgraph)
bool	hasMatchExpression (MolecularGraph molgraph)
MolecularGraphMatchExpression	getMatchExpression (MolecularGraph molgraph)
None	setMatchExpression (MolecularGraph molgraph, MolecularGraphMatchExpression expr)
None	addConformation (MolecularGraph molgraph, Math.Vector3DArray coords, float energy)
None	setConformation (MolecularGraph molgraph, int conf_idx, Math.Vector3DArray coords, float energy)
None	clearTimestamp (MolecularGraph molgraph)
bool	hasTimestamp (MolecularGraph molgraph)
int	getTimestamp (MolecularGraph molgraph)
None	setTimestamp (MolecularGraph molgraph, int time)
None	clearStoichiometricNumber (MolecularGraph molgraph)
bool	hasStoichiometricNumber (MolecularGraph molgraph)
float	getStoichiometricNumber (MolecularGraph molgraph)
None	setStoichiometricNumber (MolecularGraph molgraph, float num)
None	clearMDLRegistryNumber (MolecularGraph molgraph)
bool	hasMDLRegistryNumber (MolecularGraph molgraph)
int	getMDLRegistryNumber (MolecularGraph molgraph)
None	setMDLRegistryNumber (MolecularGraph molgraph, int reg_no)
None	extractReactionCenter (MolecularGraph molgraph, Fragment rxn_center)
None	kekulizeBonds (MolecularGraph molgraph)
None	calcFormalCharges (MolecularGraph molgraph, bool overwrite)
None	clearConformerEnergies (MolecularGraph molgraph)
bool	hasConformerEnergies (MolecularGraph molgraph)
Util.DArray	getConformerEnergies (MolecularGraph molgraph)
None	setConformerEnergies (MolecularGraph molgraph, Util.DArray energies)
None	calcMDLParities (MolecularGraph molgraph, bool overwrite)
None	calcAtomStereoDescriptorsFromMDLParities (MolecularGraph molgraph, bool overwrite)
None	calcCIPPriorities (MolecularGraph molgraph, bool overwrite)
None	calcBasicProperties (MolecularGraph molgraph, bool overwrite)
None	setAtomSymbolsFromTypes (MolecularGraph molgraph, bool overwrite)
None	perceiveSybylAtomTypes (MolecularGraph molgraph, bool overwrite)
None	perceiveSymmetryClasses (MolecularGraph molgraph, bool overwrite, int atom_flags=2147483648, int bond_flags=2147483648, bool inc_impl_h=True)
None	calc2DCoordinates (MolecularGraph molgraph, bool overwrite)
None	calcHydrogen3DCoordinates (MolecularGraph molgraph, bool undef_only=True)
None	perceiveHybridizationStates (MolecularGraph molgraph, bool overwrite)
None	setRingFlags (MolecularGraph molgraph, bool overwrite)
None	calcBond2DStereoFlags (MolecularGraph molgraph, bool overwrite)
None	setAromaticityFlags (MolecularGraph molgraph, bool overwrite)
FragmentList	getAromaticRings (MolecularGraph molgraph)
FragmentList	perceiveRings (MolecularGraph molgraph)
FragmentList	perceiveRings (MolecularGraph molgraph, bool overwrite)
None	clearRings (MolecularGraph molgraph)
bool	hasRings (MolecularGraph molgraph)
FragmentList	getRings (MolecularGraph molgraph)
None	setRings (MolecularGraph molgraph, FragmentList rings)
None	generateMatchExpressionStrings (MolecularGraph molgraph, bool overwrite)
None	clearMDLUserInitials (MolecularGraph molgraph)
bool	hasMDLUserInitials (MolecularGraph molgraph)
str	getMDLUserInitials (MolecularGraph molgraph)
None	setMDLUserInitials (MolecularGraph molgraph, str initials)
None	setAtomTypesFromSymbols (MolecularGraph molgraph, bool overwrite)
ElectronSystemList	perceivePiElectronSystems (MolecularGraph molgraph)
ElectronSystemList	perceivePiElectronSystems (MolecularGraph molgraph, bool overwrite)
None	clearPiElectronSystems (MolecularGraph molgraph)
bool	hasPiElectronSystems (MolecularGraph molgraph)
ElectronSystemList	getPiElectronSystems (MolecularGraph molgraph)
None	setPiElectronSystems (MolecularGraph molgraph, ElectronSystemList pi_systems)
None	generateMatchExpressions (MolecularGraph molgraph, bool overwrite)
None	calcBondCIPConfigurations (MolecularGraph molgraph, bool overwrite)
None	calcAtomCIPConfigurations (MolecularGraph molgraph, bool overwrite)
FragmentList	perceiveComponentGroups (MolecularGraph molgraph)
FragmentList	perceiveComponentGroups (MolecularGraph molgraph, bool overwrite)
None	clearComponentGroups (MolecularGraph molgraph)
bool	hasComponentGroups (MolecularGraph molgraph)
FragmentList	getComponentGroups (MolecularGraph molgraph)
None	setComponentGroups (MolecularGraph molgraph, FragmentList comp_groups)
None	perceiveBondOrders (MolecularGraph molgraph, bool overwrite)
None	perceiveBondStereoCenters (MolecularGraph molgraph, bool overwrite, bool check_asym=True, bool check_term_n=True, bool check_order=True, int min_ring_size=8)
None	perceiveAtomStereoCenters (MolecularGraph molgraph, bool overwrite, bool check_asym=True, bool check_inv_n=True, bool check_quart_n=True, bool check_plan_n=True, bool check_amide_n=True, bool check_res_ctrs=True)
None	calcBondStereoDescriptors (MolecularGraph molgraph, bool overwrite, int dim=1, bool check_stc_flag=True)
None	calcAtomStereoDescriptors (MolecularGraph molgraph, bool overwrite, int dim=1, bool check_stc_flag=True)
None	getContainedFragments (MolecularGraph molgraph, FragmentList frag_list, FragmentList cont_frag_list, bool append=False, bool atoms=True, bool bonds=True)
None	translateFragments (MolecularGraph src_molgraph, FragmentList src_frag_list, MolecularGraph tgt_molgraph, FragmentList tgt_frag_list, bool append=False)
None	getContainingFragments (MolecularGraph molgraph, FragmentList frag_list, FragmentList cont_frag_list, bool append=False, bool atoms=True, bool bonds=True)
None	splitIntoFragments (MolecularGraph molgraph, FragmentList frag_list, Util.BitSet split_bond_mask, bool append=False)
FragmentList	perceiveComponents (MolecularGraph molgraph)
FragmentList	perceiveComponents (MolecularGraph molgraph, bool overwrite)
None	clearComponents (MolecularGraph molgraph)
bool	hasComponents (MolecularGraph molgraph)
FragmentList	getComponents (MolecularGraph molgraph)
None	setComponents (MolecularGraph molgraph, FragmentList comps)
None	setBondMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr, bool overwrite)
None	setAtomMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr, bool overwrite)
None	clearMatchConstraints (MolecularGraph molgraph)
bool	hasMatchConstraints (MolecularGraph molgraph)
MatchConstraintList	getMatchConstraints (MolecularGraph molgraph)
None	setMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr)
None	calcImplicitHydrogenCounts (MolecularGraph molgraph, bool overwrite)
None	initSubstructureSearchTarget (MolecularGraph molgraph, bool overwrite)
FragmentList	getAromaticSSSRSubset (MolecularGraph molgraph)
FragmentList	extractSSSRSubset (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph)
FragmentList	extractSSSRSubset (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, bool overwrite)
None	translateFragment (MolecularGraph src_molgraph, Fragment src_frag, MolecularGraph tgt_molgraph, Fragment tgt_frag, bool append=False)
None	clearComment (MolecularGraph molgraph)
bool	hasComment (MolecularGraph molgraph)
str	getComment (MolecularGraph molgraph)
None	setComment (MolecularGraph molgraph, str comment)
int	getCompleteBondCount (MolecularGraph molgraph)
None	clearConformationIndex (MolecularGraph molgraph)
bool	hasConformationIndex (MolecularGraph molgraph)
int	getConformationIndex (MolecularGraph molgraph)
None	setConformationIndex (MolecularGraph molgraph, int index)
Math.ULMatrix	extractTopologicalDistanceSubMatrix (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, bool overwrite)
None	extractTopologicalDistanceSubMatrix (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, Math.ULMatrix mtx)
None	generateBondMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
Math.ULMatrix	calcTopologicalDistanceMatrix (MolecularGraph molgraph, bool overwrite)
None	calcTopologicalDistanceMatrix (MolecularGraph molgraph, Math.ULMatrix mtx)
None	clearTopologicalDistanceMatrix (MolecularGraph molgraph)
bool	hasTopologicalDistanceMatrix (MolecularGraph molgraph)
Math.ULMatrix	getTopologicalDistanceMatrix (MolecularGraph molgraph)
None	setTopologicalDistanceMatrix (MolecularGraph molgraph, Math.ULMatrix mtx)
Math.DMatrix	calcGeometricalDistanceMatrix (MolecularGraph molgraph, bool overwrite)
None	clearGeometricalDistanceMatrix (MolecularGraph molgraph)
bool	hasGeometricalDistanceMatrix (MolecularGraph molgraph)
Math.DMatrix	getGeometricalDistanceMatrix (MolecularGraph molgraph)
None	setGeometricalDistanceMatrix (MolecularGraph molgraph, Math.DMatrix mtx)
None	generateIncidenceMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
None	generateBondAtomTypeMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
None	generateBondElectronMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
None	generateAdjacencyMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
object	generateINCHIKey (MolecularGraph molgraph)
None	clearMDLEnergy (MolecularGraph molgraph)
bool	hasMDLEnergy (MolecularGraph molgraph)
float	getMDLEnergy (MolecularGraph molgraph)
None	setMDLEnergy (MolecularGraph molgraph, float energy)
float	getConformationEnergy (MolecularGraph molgraph, int conf_idx)
None	initSubstructureSearchQuery (MolecularGraph molgraph, bool overwrite)
None	clearMDLDimensionality (MolecularGraph molgraph)
bool	hasMDLDimensionality (MolecularGraph molgraph)
int	getMDLDimensionality (MolecularGraph molgraph)
None	setMDLDimensionality (MolecularGraph molgraph, int dim)
bool	makeHydrogenDeplete (Molecule mol, bool corr_impl_h_count=True)
	Removes all explicit hydrogen atoms from the molecule mol. More...
bool	makeOrdinaryHydrogenDeplete (Molecule mol, int flags, bool corr_impl_h_count=True)
	Removes all explicit ordinary hydrogen atoms from the molecule mol. More...
bool	makeHydrogenComplete (Molecule mol, bool corr_impl_h_count=True)
	Converts all implicit hydrogens of the molecule mol to explicit hydrogen atoms. More...
None	removeAtomsIf (Molecule mol, AtomPredicate pred)
None	connectAtoms (Molecule mol, Atom3DCoordinatesFunction coords_func, float dist_tol=0.3, int atom_idx_offs=0)
None	connectAtoms (Molecule mol, float dist_tol=0.3, int atom_idx_offs=0)
None	removeAtomsIfNot (Molecule mol, AtomPredicate pred)
int	getMaxAtomMappingID (Reaction rxn)
int	getMaxComponentGroupID (Reaction rxn)
object	generateSMILES (Reaction rxn, bool canonical=False, bool ord_h_deplete=True, int atom_flags=2147483648, int bond_flags=2147483648)
None	clearReactionData (Reaction rxn)
bool	hasReactionData (Reaction rxn)
StringDataBlock	getReactionData (Reaction rxn)
None	setReactionData (Reaction rxn, StringDataBlock data)
None	clearMDLMoleculeRecord (Reaction rxn)
bool	hasMDLMoleculeRecord (Reaction rxn)
Molecule	getMDLMoleculeRecord (Reaction rxn)
None	setMDLMoleculeRecord (Reaction rxn, Molecule mol_rec)
int	calcHashCode (Reaction rxn, int role_mask=7, int atom_flags=2147483648, int bond_flags=2147483648, bool ord_h_deplete=True)
None	clearMDLProgramName (Reaction rxn)
bool	hasMDLProgramName (Reaction rxn)
str	getMDLProgramName (Reaction rxn)
None	setMDLProgramName (Reaction rxn, str name)
None	clearName (Reaction rxn)
bool	hasName (Reaction rxn)
str	getName (Reaction rxn)
None	setName (Reaction rxn, str name)
AtomMapping	perceiveAtomMapping (Reaction rxn)
AtomMapping	perceiveAtomMapping (Reaction rxn, bool overwrite)
None	clearAtomMapping (Reaction rxn)
bool	hasAtomMapping (Reaction rxn)
AtomMapping	getAtomMapping (Reaction rxn)
None	setAtomMapping (Reaction rxn, AtomMapping mapping)
None	clearMDLRXNFileVersion (Reaction rxn)
bool	hasMDLRXNFileVersion (Reaction rxn)
int	getMDLRXNFileVersion (Reaction rxn)
None	setMDLRXNFileVersion (Reaction rxn, int version)
ReactionMatchExpression	generateMatchExpression (Reaction rxn)
ReactionMatchExpression	generateMatchExpression (Reaction rxn, bool overwrite)
None	clearMatchExpression (Reaction rxn)
bool	hasMatchExpression (Reaction rxn)
ReactionMatchExpression	getMatchExpression (Reaction rxn)
None	setMatchExpression (Reaction rxn, ReactionMatchExpression expr)
None	clearTimestamp (Reaction rxn)
bool	hasTimestamp (Reaction rxn)
int	getTimestamp (Reaction rxn)
None	setTimestamp (Reaction rxn, int time)
None	clearMDLRegistryNumber (Reaction rxn)
bool	hasMDLRegistryNumber (Reaction rxn)
int	getMDLRegistryNumber (Reaction rxn)
None	setMDLRegistryNumber (Reaction rxn, int reg_no)
None	clearMDLInternalRegistryNumber (Reaction rxn)
bool	hasMDLInternalRegistryNumber (Reaction rxn)
str	getMDLInternalRegistryNumber (Reaction rxn)
None	setMDLInternalRegistryNumber (Reaction rxn, str reg_no)
None	clearMDLExternalRegistryNumber (Reaction rxn)
bool	hasMDLExternalRegistryNumber (Reaction rxn)
str	getMDLExternalRegistryNumber (Reaction rxn)
None	setMDLExternalRegistryNumber (Reaction rxn, str reg_no)
None	calcBasicProperties (Reaction rxn, bool overwrite)
None	clearMDLUserInitials (Reaction rxn)
bool	hasMDLUserInitials (Reaction rxn)
str	getMDLUserInitials (Reaction rxn)
None	setMDLUserInitials (Reaction rxn, str initials)
None	generateMatchExpressions (Reaction rxn, bool overwrite)
FragmentList	perceiveComponentGroups (Reaction rxn)
FragmentList	perceiveComponentGroups (Reaction rxn, bool overwrite)
None	clearComponentGroups (Reaction rxn)
bool	hasComponentGroups (Reaction rxn)
FragmentList	getComponentGroups (Reaction rxn)
None	setComponentGroups (Reaction rxn, FragmentList comp_groups)
None	setBondMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite)
None	setAtomMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite)
None	clearMatchConstraints (Reaction rxn)
bool	hasMatchConstraints (Reaction rxn)
MatchConstraintList	getMatchConstraints (Reaction rxn)
None	setMatchConstraints (Reaction rxn, MatchConstraintList constr)
None	setComponentMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite)
None	initSubstructureSearchTarget (Reaction rxn, bool overwrite)
None	clearComment (Reaction rxn)
bool	hasComment (Reaction rxn)
str	getComment (Reaction rxn)
None	setComment (Reaction rxn, str comment)
None	initSubstructureSearchQuery (Reaction rxn, bool overwrite)
None	extendBoundingBox (Math.Vector3D min, Math.Vector3D max, Math.Vector3D coords, bool reset=False)
bool	insideBoundingBox (Math.Vector3D min, Math.Vector3D max, Math.Vector3D coords)
int	sybylToAtomType (int sybyl_type)
str	getSybylBondTypeString (int sybyl_type)
str	getSybylAtomTypeString (int sybyl_type)
bool	atomTypesMatch (int qry_type, int tgt_type)
Molecule	parseSMILES (str smiles)
bool	parseSMILES (str smiles, Molecule mol)
Molecule	parseSMARTS (str smarts, bool init_qry=True)
bool	parseSMARTS (str smarts, Molecule mol, bool init_qry=True)

Detailed Description

Contains classes and functions related to chemistry.

Function Documentation

getMaxAtomMappingID() [1/2]

int CDPL.Chem.getMaxAtomMappingID

(

AtomContainer

cntnr

)

Parameters

cntnr

Returns

getMaxComponentGroupID() [1/2]

int CDPL.Chem.getMaxComponentGroupID

(

AtomContainer

cntnr

)

Parameters

cntnr

Returns

calcCentroid() [1/2]

bool CDPL.Chem.calcCentroid	(	AtomContainer	cntnr,
		Atom3DCoordinatesFunction	coords_func,
		Math.Vector3D	ctr
	)

Parameters

cntnr
coords_func
ctr

Returns

copyAtomsIf() [1/2]

None CDPL.Chem.copyAtomsIf	(	AtomContainer	cntnr,
		Molecule	mol,
		AtomPredicate	pred,
		bool	append = False
	)

Parameters

cntnr
mol
pred
append

copyAtomsIf() [2/2]

None CDPL.Chem.copyAtomsIf	(	AtomContainer	cntnr,
		Fragment	frag,
		AtomPredicate	pred,
		bool	append = False
	)

Parameters

cntnr
frag
pred
append

createAtomTypeMask()

int CDPL.Chem.createAtomTypeMask	(	AtomContainer	cntnr,
		Util.BitSet	mask,
		int	type,
		bool	reset = True,
		bool	strict = True
	)

Parameters

cntnr
mask
type
reset
strict

Returns

addConformation() [1/2]

None CDPL.Chem.addConformation	(	AtomContainer	cntnr,
		Math.Vector3DArray	coords
	)

Parameters

cntnr
coords

transformConformation()

None CDPL.Chem.transformConformation	(	AtomContainer	cntnr,
		int	conf_idx,
		Math.Matrix4D	mtx
	)

Parameters

cntnr
conf_idx
mtx

getConformation()

None CDPL.Chem.getConformation	(	AtomContainer	cntnr,
		int	conf_idx,
		Math.Vector3DArray	coords,
		bool	append = False
	)

Parameters

cntnr
conf_idx
coords
append

applyConformation()

None CDPL.Chem.applyConformation	(	AtomContainer	cntnr,
		int	conf_idx
	)

Parameters

cntnr
conf_idx

transform2DCoordinates()

None CDPL.Chem.transform2DCoordinates	(	AtomContainer	cntnr,
		Math.Matrix3D	mtx
	)

Parameters

cntnr
mtx

get2DCoordinates() [1/2]

None CDPL.Chem.get2DCoordinates	(	AtomContainer	cntnr,
		Math.Vector2DArray	coords,
		bool	append = False
	)

Parameters

cntnr
coords
append

set2DCoordinates() [1/2]

None CDPL.Chem.set2DCoordinates	(	AtomContainer	cntnr,
		Math.Vector2DArray	coords
	)

Parameters

cntnr
coords

get3DCoordinates() [1/3]

None CDPL.Chem.get3DCoordinates	(	AtomContainer	cntnr,
		Math.Vector3DArray	coords,
		Atom3DCoordinatesFunction	coords_func,
		bool	append = False
	)

Parameters

cntnr
coords
coords_func
append

hasCoordinates()

bool CDPL.Chem.hasCoordinates	(	AtomContainer	cntnr,
		int	dim
	)

Parameters

cntnr
dim

Returns

transformConformations()

None CDPL.Chem.transformConformations	(	AtomContainer	cntnr,
		Math.Matrix4D	mtx
	)

Parameters

cntnr
mtx

getNumConformations()

int CDPL.Chem.getNumConformations

(

AtomContainer

cntnr

)

Parameters

cntnr

Returns

alignConformations() [1/4]

bool CDPL.Chem.alignConformations	(	AtomContainer	cntnr,
		Util.BitSet	ref_atoms,
		Math.Vector3DArray	ref_coords
	)

Parameters

cntnr
ref_atoms
ref_coords

Returns

alignConformations() [2/4]

bool CDPL.Chem.alignConformations	(	AtomContainer	cntnr,
		AtomContainer	ref_atoms,
		Math.Vector3DArray	ref_coords
	)

Parameters

cntnr
ref_atoms
ref_coords

Returns

alignConformations() [3/4]

bool CDPL.Chem.alignConformations	(	AtomContainer	cntnr,
		Util.BitSet	ref_atoms
	)

Parameters

cntnr
ref_atoms

Returns

alignConformations() [4/4]

bool CDPL.Chem.alignConformations	(	AtomContainer	cntnr,
		AtomContainer	ref_atoms
	)

Parameters

cntnr
ref_atoms

Returns

clearConformations()

None CDPL.Chem.clearConformations

(

AtomContainer

cntnr

)

Parameters

cntnr

calcCenterOfMass()

bool CDPL.Chem.calcCenterOfMass	(	AtomContainer	cntnr,
		Atom3DCoordinatesFunction	coords_func,
		Math.Vector3D	ctr
	)

Parameters

cntnr
coords_func
ctr

Returns

copyAtomsIfNot() [1/2]

None CDPL.Chem.copyAtomsIfNot	(	AtomContainer	cntnr,
		Molecule	mol,
		AtomPredicate	pred,
		bool	append = False
	)

Parameters

cntnr
mol
pred
append

copyAtomsIfNot() [2/2]

None CDPL.Chem.copyAtomsIfNot	(	AtomContainer	cntnr,
		Fragment	frag,
		AtomPredicate	pred,
		bool	append = False
	)

Parameters

cntnr
frag
pred
append

calcBoundingBox() [1/2]

None CDPL.Chem.calcBoundingBox	(	AtomContainer	cntnr,
		Math.Vector3D	min,
		Math.Vector3D	max,
		Atom3DCoordinatesFunction	coords_func,
		bool	reset = True
	)

Parameters

cntnr
min
max
coords_func
reset

insideBoundingBox() [1/3]

bool CDPL.Chem.insideBoundingBox	(	AtomContainer	cntnr,
		Math.Vector3D	min,
		Math.Vector3D	max,
		Atom3DCoordinatesFunction	coords_func
	)

Parameters

cntnr
min
max
coords_func

Returns

intersectsBoundingBox() [1/2]

bool CDPL.Chem.intersectsBoundingBox	(	AtomContainer	cntnr,
		Math.Vector3D	min,
		Math.Vector3D	max,
		Atom3DCoordinatesFunction	coords_func
	)

Parameters

cntnr
min
max
coords_func

Returns

clearMOL2SubstructureID()

None CDPL.Chem.clearMOL2SubstructureID

(

Atom

atom

)

Parameters

atom

hasMOL2SubstructureID()

bool CDPL.Chem.hasMOL2SubstructureID

(

Atom

atom

)

Parameters

atom

Returns

getMOL2SubstructureID()

int CDPL.Chem.getMOL2SubstructureID

(

Atom

atom

)

Parameters

atom

Returns

setMOL2SubstructureID()

None CDPL.Chem.setMOL2SubstructureID	(	Atom	atom,
		int	id
	)

Parameters

atom
id

clearAtomMappingID()

None CDPL.Chem.clearAtomMappingID

(

Atom

atom

)

Parameters

atom

hasAtomMappingID()

bool CDPL.Chem.hasAtomMappingID

(

Atom

atom

)

Parameters

atom

Returns

getAtomMappingID()

int CDPL.Chem.getAtomMappingID

(

Atom

atom

)

Parameters

atom

Returns

setAtomMappingID()

None CDPL.Chem.setAtomMappingID	(	Atom	atom,
		int	id
	)

Parameters

atom
id

clearComponentGroupID()

None CDPL.Chem.clearComponentGroupID

(

Atom

atom

)

Parameters

atom

hasComponentGroupID()

bool CDPL.Chem.hasComponentGroupID

(

Atom

atom

)

Parameters

atom

Returns

getComponentGroupID()

int CDPL.Chem.getComponentGroupID

(

Atom

atom

)

Parameters

atom

Returns

setComponentGroupID()

None CDPL.Chem.setComponentGroupID	(	Atom	atom,
		int	id
	)

Parameters

atom
id

getTopologicalDistance()

int CDPL.Chem.getTopologicalDistance	(	Atom	atom1,
		Atom	atom2,
		MolecularGraph	molgraph
	)

Parameters

atom1
atom2
molgraph

Returns

clearMOL2Charge()

None CDPL.Chem.clearMOL2Charge

(

Atom

atom

)

Parameters

atom

hasMOL2Charge()

bool CDPL.Chem.hasMOL2Charge

(

Atom

atom

)

Parameters

atom

Returns

getMOL2Charge()

float CDPL.Chem.getMOL2Charge

(

Atom

atom

)

Parameters

atom

Returns

setMOL2Charge()

None CDPL.Chem.setMOL2Charge	(	Atom	atom,
		float	charge
	)

Parameters

atom
charge

calcFormalCharge()

int CDPL.Chem.calcFormalCharge	(	Atom	atom,
		MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

clearFormalCharge()

None CDPL.Chem.clearFormalCharge

(

Atom

atom

)

Parameters

atom

hasFormalCharge()

bool CDPL.Chem.hasFormalCharge

(

Atom

atom

)

Parameters

atom

Returns

getFormalCharge()

int CDPL.Chem.getFormalCharge

(

Atom

atom

)

Parameters

atom

Returns

setFormalCharge()

None CDPL.Chem.setFormalCharge	(	Atom	atom,
		int	charge
	)

Parameters

atom
charge

clearMOL2Name()

None CDPL.Chem.clearMOL2Name

(

Atom

atom

)

Parameters

atom

hasMOL2Name()

bool CDPL.Chem.hasMOL2Name

(

Atom

atom

)

Parameters

atom

Returns

getMOL2Name()

str CDPL.Chem.getMOL2Name

(

Atom

atom

)

Parameters

atom

Returns

setMOL2Name()

None CDPL.Chem.setMOL2Name	(	Atom	atom,
		str	name
	)

Parameters

atom
name

clearMOL2SubstructureName()

None CDPL.Chem.clearMOL2SubstructureName

(

Atom

atom

)

Parameters

atom

hasMOL2SubstructureName()

bool CDPL.Chem.hasMOL2SubstructureName

(

Atom

atom

)

Parameters

atom

Returns

getMOL2SubstructureName()

str CDPL.Chem.getMOL2SubstructureName

(

Atom

atom

)

Parameters

atom

Returns

setMOL2SubstructureName()

None CDPL.Chem.setMOL2SubstructureName	(	Atom	atom,
		str	name
	)

Parameters

atom
name

clearName() [1/3]

None CDPL.Chem.clearName

(

Atom

atom

)

Parameters

atom

hasName() [1/3]

bool CDPL.Chem.hasName

(

Atom

atom

)

Parameters

atom

Returns

getName() [1/3]

str CDPL.Chem.getName

(

Atom

atom

)

Parameters

atom

Returns

setName() [1/3]

None CDPL.Chem.setName	(	Atom	atom,
		str	name
	)

Parameters

atom
name

clearIsotope()

None CDPL.Chem.clearIsotope

(

Atom

atom

)

Parameters

atom

hasIsotope()

bool CDPL.Chem.hasIsotope

(

Atom

atom

)

Parameters

atom

Returns

getIsotope()

int CDPL.Chem.getIsotope

(

Atom

atom

)

Parameters

atom

Returns

setIsotope()

None CDPL.Chem.setIsotope	(	Atom	atom,
		int	isotope
	)

Parameters

atom
isotope

getGenericType()

int CDPL.Chem.getGenericType

(

Atom

atom

)

Parameters

atom

Returns

clearRadicalType()

None CDPL.Chem.clearRadicalType

(

Atom

atom

)

Parameters

atom

hasRadicalType()

bool CDPL.Chem.hasRadicalType

(

Atom

atom

)

Parameters

atom

Returns

getRadicalType()

int CDPL.Chem.getRadicalType

(

Atom

atom

)

Parameters

atom

Returns

setRadicalType()

None CDPL.Chem.setRadicalType	(	Atom	atom,
		int	type
	)

Parameters

atom
type

perceiveSybylType() [1/2]

int CDPL.Chem.perceiveSybylType	(	Atom	atom,
		MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

clearSybylType() [1/2]

None CDPL.Chem.clearSybylType

(

Atom

atom

)

Parameters

atom

hasSybylType() [1/2]

bool CDPL.Chem.hasSybylType

(

Atom

atom

)

Parameters

atom

Returns

getSybylType() [1/2]

int CDPL.Chem.getSybylType

(

Atom

atom

)

Parameters

atom

Returns

setSybylType() [1/2]

None CDPL.Chem.setSybylType	(	Atom	atom,
		int	type
	)

Parameters

atom
type

clearType()

None CDPL.Chem.clearType

(

Atom

atom

)

Parameters

atom

getSymbolForType()

str CDPL.Chem.getSymbolForType

(

Atom

atom

)

Parameters

atom

Returns

hasType()

bool CDPL.Chem.hasType

(

Atom

atom

)

Parameters

atom

Returns

getType()

int CDPL.Chem.getType

(

Atom

atom

)

Parameters

atom

Returns

setType()

None CDPL.Chem.setType	(	Atom	atom,
		int	type
	)

Parameters

atom
type

clearMOL2SubstructureSubtype()

None CDPL.Chem.clearMOL2SubstructureSubtype

(

Atom

atom

)

Parameters

atom

hasMOL2SubstructureSubtype()

bool CDPL.Chem.hasMOL2SubstructureSubtype

(

Atom

atom

)

Parameters

atom

Returns

getMOL2SubstructureSubtype()

str CDPL.Chem.getMOL2SubstructureSubtype

(

Atom

atom

)

Parameters

atom

Returns

setMOL2SubstructureSubtype()

None CDPL.Chem.setMOL2SubstructureSubtype	(	Atom	atom,
		str	subtype
	)

Parameters

atom
subtype

perceiveHybridizationState()

int CDPL.Chem.perceiveHybridizationState	(	Atom	atom,
		MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

clearHybridizationState()

None CDPL.Chem.clearHybridizationState

(

Atom

atom

)

Parameters

atom

hasHybridizationState()

bool CDPL.Chem.hasHybridizationState

(

Atom

atom

)

Parameters

atom

Returns

getHybridizationState()

int CDPL.Chem.getHybridizationState

(

Atom

atom

)

Parameters

atom

Returns

setHybridizationState()

None CDPL.Chem.setHybridizationState	(	Atom	atom,
		int	state
	)

Parameters

atom
state

isInFragmentOfSize() [1/2]

bool CDPL.Chem.isInFragmentOfSize	(	Atom	atom,
		FragmentList	frag_list,
		int	size
	)

Parameters

atom
frag_list
size

Returns

clearMDLStereoCareFlag()

None CDPL.Chem.clearMDLStereoCareFlag

(

Atom

atom

)

Parameters

atom

hasMDLStereoCareFlag()

bool CDPL.Chem.hasMDLStereoCareFlag

(

Atom

atom

)

Parameters

atom

Returns

getMDLStereoCareFlag()

bool CDPL.Chem.getMDLStereoCareFlag

(

Atom

atom

)

Parameters

atom

Returns

setMDLStereoCareFlag()

None CDPL.Chem.setMDLStereoCareFlag	(	Atom	atom,
		bool	flag
	)

Parameters

atom
flag

clearRingFlag() [1/2]

None CDPL.Chem.clearRingFlag

(

Atom

atom

)

Parameters

atom

hasRingFlag() [1/2]

bool CDPL.Chem.hasRingFlag

(

Atom

atom

)

Parameters

atom

Returns

getRingFlag() [1/2]

bool CDPL.Chem.getRingFlag

(

Atom

atom

)

Parameters

atom

Returns

setRingFlag() [1/2]

None CDPL.Chem.setRingFlag	(	Atom	atom,
		bool	in_ring
	)

Parameters

atom
in_ring

clearStereoCenterFlag() [1/2]

None CDPL.Chem.clearStereoCenterFlag

(

Atom

atom

)

Parameters

atom

hasStereoCenterFlag() [1/2]

bool CDPL.Chem.hasStereoCenterFlag

(

Atom

atom

)

Parameters

atom

Returns

getStereoCenterFlag() [1/2]

bool CDPL.Chem.getStereoCenterFlag

(

Atom

atom

)

Parameters

atom

Returns

setStereoCenterFlag() [1/2]

None CDPL.Chem.setStereoCenterFlag	(	Atom	atom,
		bool	is_center
	)

Parameters

atom
is_center

clearAromaticityFlag() [1/2]

None CDPL.Chem.clearAromaticityFlag

(

Atom

atom

)

Parameters

atom

hasAromaticityFlag() [1/2]

bool CDPL.Chem.hasAromaticityFlag

(

Atom

atom

)

Parameters

atom

Returns

getAromaticityFlag() [1/2]

bool CDPL.Chem.getAromaticityFlag

(

Atom

atom

)

Parameters

atom

Returns

setAromaticityFlag() [1/2]

None CDPL.Chem.setAromaticityFlag	(	Atom	atom,
		bool	aromatic
	)

Parameters

atom
aromatic

generateMatchExpressionString() [1/2]

str CDPL.Chem.generateMatchExpressionString	(	Atom	atom,
		MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

clearMatchExpressionString() [1/2]

None CDPL.Chem.clearMatchExpressionString

(

Atom

atom

)

Parameters

atom

hasMatchExpressionString() [1/2]

bool CDPL.Chem.hasMatchExpressionString

(

Atom

atom

)

Parameters

atom

Returns

getMatchExpressionString() [1/2]

str CDPL.Chem.getMatchExpressionString

(

Atom

atom

)

Parameters

atom

Returns

setMatchExpressionString() [1/2]

None CDPL.Chem.setMatchExpressionString	(	Atom	atom,
		str	expr_str
	)

Parameters

atom
expr_str

clearSymbol()

None CDPL.Chem.clearSymbol

(

Atom

atom

)

Parameters

atom

getTypeForSymbol()

int CDPL.Chem.getTypeForSymbol

(

Atom

atom

)

Parameters

atom

Returns

hasSymbol()

bool CDPL.Chem.hasSymbol

(

Atom

atom

)

Parameters

atom

Returns

getSymbol()

str CDPL.Chem.getSymbol

(

Atom

atom

)

Parameters

atom

Returns

setSymbol()

None CDPL.Chem.setSymbol	(	Atom	atom,
		str	symbol
	)

Parameters

atom
symbol

clearMOL2SubstructureChain()

None CDPL.Chem.clearMOL2SubstructureChain

(

Atom

atom

)

Parameters

atom

hasMOL2SubstructureChain()

bool CDPL.Chem.hasMOL2SubstructureChain

(

Atom

atom

)

Parameters

atom

Returns

getMOL2SubstructureChain()

str CDPL.Chem.getMOL2SubstructureChain

(

Atom

atom

)

Parameters

atom

Returns

setMOL2SubstructureChain()

None CDPL.Chem.setMOL2SubstructureChain	(	Atom	atom,
		str	chain
	)

Parameters

atom
chain

generateMatchExpression() [1/6]

AtomMatchExpression CDPL.Chem.generateMatchExpression	(	Atom	atom,
		MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

clearMatchExpression() [1/4]

None CDPL.Chem.clearMatchExpression

(

Atom

atom

)

Parameters

atom

hasMatchExpression() [1/4]

bool CDPL.Chem.hasMatchExpression

(

Atom

atom

)

Parameters

atom

Returns

getMatchExpression() [1/4]

AtomMatchExpression CDPL.Chem.getMatchExpression

(

Atom

atom

)

Parameters

atom

Returns

setMatchExpression() [1/4]

None CDPL.Chem.setMatchExpression	(	Atom	atom,
		AtomMatchExpression	expr
	)

Parameters

atom
expr

clearCIPConfiguration() [1/2]

None CDPL.Chem.clearCIPConfiguration

(

Atom

atom

)

Parameters

atom

hasCIPConfiguration() [1/2]

bool CDPL.Chem.hasCIPConfiguration

(

Atom

atom

)

Parameters

atom

Returns

getCIPConfiguration() [1/2]

int CDPL.Chem.getCIPConfiguration

(

Atom

atom

)

Parameters

atom

Returns

setCIPConfiguration() [1/2]

None CDPL.Chem.setCIPConfiguration	(	Atom	atom,
		int	config
	)

Parameters

atom
config

calcConfiguration() [1/2]

int CDPL.Chem.calcConfiguration	(	Atom	atom,
		MolecularGraph	molgraph,
		StereoDescriptor	descr,
		Math.Vector3DArray	coords
	)

Parameters

atom
molgraph
descr
coords

Returns

clearCanonicalNumber()

None CDPL.Chem.clearCanonicalNumber

(

Atom

atom

)

Parameters

atom

hasCanonicalNumber()

bool CDPL.Chem.hasCanonicalNumber

(

Atom

atom

)

Parameters

atom

Returns

getCanonicalNumber()

int CDPL.Chem.getCanonicalNumber

(

Atom

atom

)

Parameters

atom

Returns

setCanonicalNumber()

None CDPL.Chem.setCanonicalNumber	(	Atom	atom,
		int	num
	)

Parameters

atom
num

clearMorganNumber()

None CDPL.Chem.clearMorganNumber

(

Atom

atom

)

Parameters

atom

hasMorganNumber()

bool CDPL.Chem.hasMorganNumber

(

Atom

atom

)

Parameters

atom

Returns

getMorganNumber()

int CDPL.Chem.getMorganNumber

(

Atom

atom

)

Parameters

atom

Returns

setMorganNumber()

None CDPL.Chem.setMorganNumber	(	Atom	atom,
		int	num
	)

Parameters

atom
num

isStereoCenter() [1/2]

bool CDPL.Chem.isStereoCenter	(	Atom	atom,
		MolecularGraph	molgraph,
		bool	check_asym = True,
		bool	check_inv_n = True,
		bool	check_quart_n = True,
		bool	check_plan_n = True,
		bool	check_amide_n = True,
		bool	check_res_ctrs = True
	)

Parameters

atom
molgraph
check_asym
check_inv_n
check_quart_n
check_plan_n
check_amide_n
check_res_ctrs

Returns

calcStereoDescriptor() [1/2]

StereoDescriptor CDPL.Chem.calcStereoDescriptor	(	Atom	atom,
		MolecularGraph	molgraph,
		int	dim = 1
	)

Parameters

atom
molgraph
dim

Returns

clearStereoDescriptor() [1/2]

None CDPL.Chem.clearStereoDescriptor

(

Atom

atom

)

Parameters

atom

hasStereoDescriptor() [1/2]

bool CDPL.Chem.hasStereoDescriptor

(

Atom

atom

)

Parameters

atom

Returns

getStereoDescriptor() [1/2]

StereoDescriptor CDPL.Chem.getStereoDescriptor

(

Atom

atom

)

Parameters

atom

Returns

setStereoDescriptor() [1/2]

None CDPL.Chem.setStereoDescriptor	(	Atom	atom,
		StereoDescriptor	descr
	)

Parameters

atom
descr

getConnectedAtomsAndBonds()

int CDPL.Chem.getConnectedAtomsAndBonds	(	Atom	atom,
		MolecularGraph	molgraph,
		list	atoms,
		list	bonds,
		Atom	excl_atom
	)

Parameters

atom
molgraph
atoms
bonds
excl_atom

Returns

getIncidentBonds()

int CDPL.Chem.getIncidentBonds	(	Atom	atom,
		MolecularGraph	molgraph,
		list	bonds,
		Atom	excl_atom
	)

Parameters

atom
molgraph
bonds
excl_atom

Returns

clear2DCoordinates()

None CDPL.Chem.clear2DCoordinates

(

Atom

atom

)

Parameters

atom

has2DCoordinates()

bool CDPL.Chem.has2DCoordinates

(

Atom

atom

)

Parameters

atom

Returns

get2DCoordinates() [2/2]

Math.Vector2D CDPL.Chem.get2DCoordinates

(

Atom

atom

)

Parameters

atom

Returns

set2DCoordinates() [2/2]

None CDPL.Chem.set2DCoordinates	(	Atom	atom,
		Math.Vector2D	coords
	)

Parameters

atom
coords

getConformer3DCoordinates()

Math.Vector3D CDPL.Chem.getConformer3DCoordinates	(	Atom	atom,
		int	conf_idx
	)

Parameters

atom
conf_idx

Returns

getConnectedAtoms()

int CDPL.Chem.getConnectedAtoms	(	Atom	atom,
		MolecularGraph	molgraph,
		list	atoms,
		Atom	excl_atom
	)

Parameters

atom
molgraph
atoms
excl_atom

Returns

markReachableAtoms()

None CDPL.Chem.markReachableAtoms	(	Atom	atom,
		MolecularGraph	molgraph,
		Util.BitSet	atom_mask,
		bool	reset = True
	)

Parameters

atom
molgraph
atom_mask
reset

clearSymmetryClass()

None CDPL.Chem.clearSymmetryClass

(

Atom

atom

)

Parameters

atom

hasSymmetryClass()

bool CDPL.Chem.hasSymmetryClass

(

Atom

atom

)

Parameters

atom

Returns

getSymmetryClass()

int CDPL.Chem.getSymmetryClass

(

Atom

atom

)

Parameters

atom

Returns

setSymmetryClass()

None CDPL.Chem.setSymmetryClass	(	Atom	atom,
		int	class_id
	)

Parameters

atom
class_id

getNumContainingFragments() [1/2]

int CDPL.Chem.getNumContainingFragments	(	Atom	atom,
		FragmentList	frag_list
	)

Parameters

atom
frag_list

Returns

getContainingFragments() [1/3]

None CDPL.Chem.getContainingFragments	(	Atom	atom,
		FragmentList	frag_list,
		FragmentList	cont_frag_list
	)

Parameters

atom
frag_list
cont_frag_list

clearMatchConstraints() [1/4]

None CDPL.Chem.clearMatchConstraints

(

Atom

atom

)

Parameters

atom

hasMatchConstraints() [1/4]

bool CDPL.Chem.hasMatchConstraints

(

Atom

atom

)

Parameters

atom

Returns

getMatchConstraints() [1/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

Atom

atom

)

Parameters

atom

Returns

setMatchConstraints() [1/4]

None CDPL.Chem.setMatchConstraints	(	Atom	atom,
		MatchConstraintList	constr
	)

Parameters

atom
constr

clearReactionCenterStatus() [1/2]

None CDPL.Chem.clearReactionCenterStatus

(

Atom

atom

)

Parameters

atom

hasReactionCenterStatus() [1/2]

bool CDPL.Chem.hasReactionCenterStatus

(

Atom

atom

)

Parameters

atom

Returns

getReactionCenterStatus() [1/2]

int CDPL.Chem.getReactionCenterStatus

(

Atom

atom

)

Parameters

atom

Returns

setReactionCenterStatus() [1/2]

None CDPL.Chem.setReactionCenterStatus	(	Atom	atom,
		int	status
	)

Parameters

atom
status

getSizeOfLargestContainingFragment() [1/2]

int CDPL.Chem.getSizeOfLargestContainingFragment	(	Atom	atom,
		FragmentList	frag_list
	)

Parameters

atom
frag_list

Returns

getSizeOfSmallestContainingFragment() [1/2]

int CDPL.Chem.getSizeOfSmallestContainingFragment	(	Atom	atom,
		FragmentList	frag_list
	)

Parameters

atom
frag_list

Returns

getEnvironment()

int CDPL.Chem.getEnvironment	(	Atom	atom,
		MolecularGraph	molgraph,
		int	max_dist,
		Fragment	env,
		bool	append = False
	)

Parameters

atom
molgraph
max_dist
env
append

Returns

calcImplicitHydrogenCount()

int CDPL.Chem.calcImplicitHydrogenCount	(	Atom	atom,
		MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

clearImplicitHydrogenCount()

None CDPL.Chem.clearImplicitHydrogenCount

(

Atom

atom

)

Parameters

atom

hasImplicitHydrogenCount()

bool CDPL.Chem.hasImplicitHydrogenCount

(

Atom

atom

)

Parameters

atom

Returns

getImplicitHydrogenCount()

int CDPL.Chem.getImplicitHydrogenCount

(

Atom

atom

)

Parameters

atom

Returns

setImplicitHydrogenCount()

None CDPL.Chem.setImplicitHydrogenCount	(	Atom	atom,
		int	count
	)

Parameters

atom
count

clearUnpairedElectronCount()

None CDPL.Chem.clearUnpairedElectronCount

(

Atom

atom

)

Parameters

atom

hasUnpairedElectronCount()

bool CDPL.Chem.hasUnpairedElectronCount

(

Atom

atom

)

Parameters

atom

Returns

getUnpairedElectronCount()

int CDPL.Chem.getUnpairedElectronCount

(

Atom

atom

)

Parameters

atom

Returns

setUnpairedElectronCount()

None CDPL.Chem.setUnpairedElectronCount	(	Atom	atom,
		int	count
	)

Parameters

atom
count

clear3DCoordinatesArray()

None CDPL.Chem.clear3DCoordinatesArray

(

Atom

atom

)

Parameters

atom

has3DCoordinatesArray()

bool CDPL.Chem.has3DCoordinatesArray

(

Atom

atom

)

Parameters

atom

Returns

get3DCoordinatesArray()

Math.Vector3DArray CDPL.Chem.get3DCoordinatesArray

(

Atom

atom

)

Parameters

atom

Returns

set3DCoordinatesArray()

None CDPL.Chem.set3DCoordinatesArray	(	Atom	atom,
		Math.Vector3DArray	coords_array
	)

Parameters

atom
coords_array

calcMDLParity()

int CDPL.Chem.calcMDLParity	(	Atom	atom,
		MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

calcStereoDescriptorFromMDLParity()

StereoDescriptor CDPL.Chem.calcStereoDescriptorFromMDLParity	(	Atom	atom,
		MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

clearMDLParity()

None CDPL.Chem.clearMDLParity

(

Atom

atom

)

Parameters

atom

hasMDLParity()

bool CDPL.Chem.hasMDLParity

(

Atom

atom

)

Parameters

atom

Returns

getMDLParity()

int CDPL.Chem.getMDLParity

(

Atom

atom

)

Parameters

atom

Returns

setMDLParity()

None CDPL.Chem.setMDLParity	(	Atom	atom,
		int	parity
	)

Parameters

atom
parity

clearCIPPriority()

None CDPL.Chem.clearCIPPriority

(

Atom

atom

)

Parameters

atom

hasCIPPriority()

bool CDPL.Chem.hasCIPPriority

(

Atom

atom

)

Parameters

atom

Returns

getCIPPriority()

int CDPL.Chem.getCIPPriority

(

Atom

atom

)

Parameters

atom

Returns

setCIPPriority()

None CDPL.Chem.setCIPPriority	(	Atom	atom,
		int	priority
	)

Parameters

atom
priority

perceiveSybylType() [2/2]

int CDPL.Chem.perceiveSybylType	(	Bond	bond,
		MolecularGraph	molgraph
	)

Parameters

bond
molgraph

Returns

clearSybylType() [2/2]

None CDPL.Chem.clearSybylType

(

Bond

bond

)

Parameters

bond

hasSybylType() [2/2]

bool CDPL.Chem.hasSybylType

(

Bond

bond

)

Parameters

bond

Returns

getSybylType() [2/2]

int CDPL.Chem.getSybylType

(

Bond

bond

)

Parameters

bond

Returns

setSybylType() [2/2]

None CDPL.Chem.setSybylType	(	Bond	bond,
		int	type
	)

Parameters

bond
type

isInFragmentOfSize() [2/2]

bool CDPL.Chem.isInFragmentOfSize	(	Bond	bond,
		FragmentList	frag_list,
		int	size
	)

Parameters

bond
frag_list
size

Returns

clearRingFlag() [2/2]

None CDPL.Chem.clearRingFlag

(

Bond

bond

)

Parameters

bond

hasRingFlag() [2/2]

bool CDPL.Chem.hasRingFlag

(

Bond

bond

)

Parameters

bond

Returns

getRingFlag() [2/2]

bool CDPL.Chem.getRingFlag

(

Bond

bond

)

Parameters

bond

Returns

setRingFlag() [2/2]

None CDPL.Chem.setRingFlag	(	Bond	bond,
		bool	in_ring
	)

Parameters

bond
in_ring

clear2DStereoFlag()

None CDPL.Chem.clear2DStereoFlag

(

Bond

bond

)

Parameters

bond

has2DStereoFlag()

bool CDPL.Chem.has2DStereoFlag

(

Bond

bond

)

Parameters

bond

Returns

get2DStereoFlag()

int CDPL.Chem.get2DStereoFlag

(

Bond

bond

)

Parameters

bond

Returns

set2DStereoFlag()

None CDPL.Chem.set2DStereoFlag	(	Bond	bond,
		int	flag
	)

Parameters

bond
flag

clearStereoCenterFlag() [2/2]

None CDPL.Chem.clearStereoCenterFlag

(

Bond

bond

)

Parameters

bond

hasStereoCenterFlag() [2/2]

bool CDPL.Chem.hasStereoCenterFlag

(

Bond

bond

)

Parameters

bond

Returns

getStereoCenterFlag() [2/2]

bool CDPL.Chem.getStereoCenterFlag

(

Bond

bond

)

Parameters

bond

Returns

setStereoCenterFlag() [2/2]

None CDPL.Chem.setStereoCenterFlag	(	Bond	bond,
		bool	is_center
	)

Parameters

bond
is_center

clearAromaticityFlag() [2/2]

None CDPL.Chem.clearAromaticityFlag

(

Bond

bond

)

Parameters

bond

hasAromaticityFlag() [2/2]

bool CDPL.Chem.hasAromaticityFlag

(

Bond

bond

)

Parameters

bond

Returns

getAromaticityFlag() [2/2]

bool CDPL.Chem.getAromaticityFlag

(

Bond

bond

)

Parameters

bond

Returns

setAromaticityFlag() [2/2]

None CDPL.Chem.setAromaticityFlag	(	Bond	bond,
		bool	aromatic
	)

Parameters

bond
aromatic

generateMatchExpressionString() [2/2]

str CDPL.Chem.generateMatchExpressionString	(	Bond	bond,
		MolecularGraph	molgraph
	)

Parameters

bond
molgraph

Returns

clearMatchExpressionString() [2/2]

None CDPL.Chem.clearMatchExpressionString

(

Bond

bond

)

Parameters

bond

hasMatchExpressionString() [2/2]

bool CDPL.Chem.hasMatchExpressionString

(

Bond

bond

)

Parameters

bond

Returns

getMatchExpressionString() [2/2]

str CDPL.Chem.getMatchExpressionString

(

Bond

bond

)

Parameters

bond

Returns

setMatchExpressionString() [2/2]

None CDPL.Chem.setMatchExpressionString	(	Bond	bond,
		str	expr_str
	)

Parameters

bond
expr_str

generateMatchExpression() [2/6]

BondMatchExpression CDPL.Chem.generateMatchExpression	(	Bond	bond,
		MolecularGraph	molgraph
	)

Parameters

bond
molgraph

Returns

clearMatchExpression() [2/4]

None CDPL.Chem.clearMatchExpression

(

Bond

bond

)

Parameters

bond

hasMatchExpression() [2/4]

bool CDPL.Chem.hasMatchExpression

(

Bond

bond

)

Parameters

bond

Returns

getMatchExpression() [2/4]

BondMatchExpression CDPL.Chem.getMatchExpression

(

Bond

bond

)

Parameters

bond

Returns

setMatchExpression() [2/4]

None CDPL.Chem.setMatchExpression	(	Bond	bond,
		BondMatchExpression	expr
	)

Parameters

bond
expr

clearCIPConfiguration() [2/2]

None CDPL.Chem.clearCIPConfiguration

(

Bond

bond

)

Parameters

bond

hasCIPConfiguration() [2/2]

bool CDPL.Chem.hasCIPConfiguration

(

Bond

bond

)

Parameters

bond

Returns

getCIPConfiguration() [2/2]

int CDPL.Chem.getCIPConfiguration

(

Bond

bond

)

Parameters

bond

Returns

setCIPConfiguration() [2/2]

None CDPL.Chem.setCIPConfiguration	(	Bond	bond,
		int	config
	)

Parameters

bond
config

calcConfiguration() [2/2]

int CDPL.Chem.calcConfiguration	(	Bond	bond,
		MolecularGraph	molgraph,
		StereoDescriptor	descr,
		Math.Vector3DArray	coords
	)

Parameters

bond
molgraph
descr
coords

Returns

clearDirection()

None CDPL.Chem.clearDirection

(

Bond

bond

)

Parameters

bond

hasDirection()

bool CDPL.Chem.hasDirection

(

Bond

bond

)

Parameters

bond

Returns

getDirection()

int CDPL.Chem.getDirection

(

Bond

bond

)

Parameters

bond

Returns

setDirection()

None CDPL.Chem.setDirection	(	Bond	bond,
		int	dir
	)

Parameters

bond
dir

clearOrder()

None CDPL.Chem.clearOrder

(

Bond

bond

)

Parameters

bond

hasOrder()

bool CDPL.Chem.hasOrder

(

Bond

bond

)

Parameters

bond

Returns

getOrder()

int CDPL.Chem.getOrder

(

Bond

bond

)

Parameters

bond

Returns

setOrder()

None CDPL.Chem.setOrder	(	Bond	bond,
		int	order
	)

Parameters

bond
order

isStereoCenter() [2/2]

bool CDPL.Chem.isStereoCenter	(	Bond	bond,
		MolecularGraph	molgraph,
		bool	check_asym = True,
		bool	check_term_n = True,
		bool	check_order = True,
		int	min_ring_size = 8
	)

Parameters

bond
molgraph
check_asym
check_term_n
check_order
min_ring_size

Returns

calcStereoDescriptor() [2/2]

StereoDescriptor CDPL.Chem.calcStereoDescriptor	(	Bond	bond,
		MolecularGraph	molgraph,
		int	dim = 1
	)

Parameters

bond
molgraph
dim

Returns

clearStereoDescriptor() [2/2]

None CDPL.Chem.clearStereoDescriptor

(

Bond

bond

)

Parameters

bond

hasStereoDescriptor() [2/2]

bool CDPL.Chem.hasStereoDescriptor

(

Bond

bond

)

Parameters

bond

Returns

getStereoDescriptor() [2/2]

StereoDescriptor CDPL.Chem.getStereoDescriptor

(

Bond

bond

)

Parameters

bond

Returns

setStereoDescriptor() [2/2]

None CDPL.Chem.setStereoDescriptor	(	Bond	bond,
		StereoDescriptor	descr
	)

Parameters

bond
descr

getNumContainingFragments() [2/2]

int CDPL.Chem.getNumContainingFragments	(	Bond	bond,
		FragmentList	frag_list
	)

Parameters

bond
frag_list

Returns

getContainingFragments() [2/3]

None CDPL.Chem.getContainingFragments	(	Bond	bond,
		FragmentList	frag_list,
		FragmentList	cont_frag_list
	)

Parameters

bond
frag_list
cont_frag_list

clearMatchConstraints() [2/4]

None CDPL.Chem.clearMatchConstraints

(

Bond

bond

)

Parameters

bond

hasMatchConstraints() [2/4]

bool CDPL.Chem.hasMatchConstraints

(

Bond

bond

)

Parameters

bond

Returns

getMatchConstraints() [2/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

Bond

bond

)

Parameters

bond

Returns

setMatchConstraints() [2/4]

None CDPL.Chem.setMatchConstraints	(	Bond	bond,
		MatchConstraintList	constr
	)

Parameters

bond
constr

clearReactionCenterStatus() [2/2]

None CDPL.Chem.clearReactionCenterStatus

(

Bond

bond

)

Parameters

bond

hasReactionCenterStatus() [2/2]

bool CDPL.Chem.hasReactionCenterStatus

(

Bond

bond

)

Parameters

bond

Returns

getReactionCenterStatus() [2/2]

int CDPL.Chem.getReactionCenterStatus

(

Bond

bond

)

Parameters

bond

Returns

setReactionCenterStatus() [2/2]

None CDPL.Chem.setReactionCenterStatus	(	Bond	bond,
		int	status
	)

Parameters

bond
status

getSizeOfLargestContainingFragment() [2/2]

int CDPL.Chem.getSizeOfLargestContainingFragment	(	Bond	bond,
		FragmentList	frag_list
	)

Parameters

bond
frag_list

Returns

getSizeOfSmallestContainingFragment() [2/2]

int CDPL.Chem.getSizeOfSmallestContainingFragment	(	Bond	bond,
		FragmentList	frag_list
	)

Parameters

bond
frag_list

Returns

clearSMILESMolWriteAtomMappingIDParameter()

None CDPL.Chem.clearSMILESMolWriteAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESMolWriteAtomMappingIDParameter()

bool CDPL.Chem.hasSMILESMolWriteAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESMolWriteAtomMappingIDParameter()

bool CDPL.Chem.getSMILESMolWriteAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESMolWriteAtomMappingIDParameter()

None CDPL.Chem.setSMILESMolWriteAtomMappingIDParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearSMILESRxnWriteAtomMappingIDParameter()

None CDPL.Chem.clearSMILESRxnWriteAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESRxnWriteAtomMappingIDParameter()

bool CDPL.Chem.hasSMILESRxnWriteAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESRxnWriteAtomMappingIDParameter()

bool CDPL.Chem.getSMILESRxnWriteAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESRxnWriteAtomMappingIDParameter()

None CDPL.Chem.setSMILESRxnWriteAtomMappingIDParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearMDLOutputConfEnergyToEnergyFieldParameter()

None CDPL.Chem.clearMDLOutputConfEnergyToEnergyFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLOutputConfEnergyToEnergyFieldParameter()

bool CDPL.Chem.hasMDLOutputConfEnergyToEnergyFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLOutputConfEnergyToEnergyFieldParameter()

bool CDPL.Chem.getMDLOutputConfEnergyToEnergyFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLOutputConfEnergyToEnergyFieldParameter()

None CDPL.Chem.setMDLOutputConfEnergyToEnergyFieldParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

Parameters

cntnr
output

clearXYZCommentIsNameParameter()

None CDPL.Chem.clearXYZCommentIsNameParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasXYZCommentIsNameParameter()

bool CDPL.Chem.hasXYZCommentIsNameParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getXYZCommentIsNameParameter()

bool CDPL.Chem.getXYZCommentIsNameParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setXYZCommentIsNameParameter()

None CDPL.Chem.setXYZCommentIsNameParameter	(	Base.ControlParameterContainer	cntnr,
		bool	is_name
	)

Parameters

cntnr
is_name

clearSMILESWriteIsotopeParameter()

None CDPL.Chem.clearSMILESWriteIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESWriteIsotopeParameter()

bool CDPL.Chem.hasSMILESWriteIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESWriteIsotopeParameter()

bool CDPL.Chem.getSMILESWriteIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESWriteIsotopeParameter()

None CDPL.Chem.setSMILESWriteIsotopeParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearMOL2ChargeTypeParameter()

None CDPL.Chem.clearMOL2ChargeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMOL2ChargeTypeParameter()

bool CDPL.Chem.hasMOL2ChargeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2ChargeTypeParameter()

int CDPL.Chem.getMOL2ChargeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMOL2ChargeTypeParameter()

None CDPL.Chem.setMOL2ChargeTypeParameter	(	Base.ControlParameterContainer	cntnr,
		int	type
	)

Parameters

cntnr
type

clearMOL2MoleculeTypeParameter()

None CDPL.Chem.clearMOL2MoleculeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMOL2MoleculeTypeParameter()

bool CDPL.Chem.hasMOL2MoleculeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2MoleculeTypeParameter()

int CDPL.Chem.getMOL2MoleculeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMOL2MoleculeTypeParameter()

None CDPL.Chem.setMOL2MoleculeTypeParameter	(	Base.ControlParameterContainer	cntnr,
		int	type
	)

Parameters

cntnr
type

clearOrdinaryHydrogenDepleteParameter()

None CDPL.Chem.clearOrdinaryHydrogenDepleteParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasOrdinaryHydrogenDepleteParameter()

bool CDPL.Chem.hasOrdinaryHydrogenDepleteParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getOrdinaryHydrogenDepleteParameter()

bool CDPL.Chem.getOrdinaryHydrogenDepleteParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setOrdinaryHydrogenDepleteParameter()

None CDPL.Chem.setOrdinaryHydrogenDepleteParameter	(	Base.ControlParameterContainer	cntnr,
		bool	deplete
	)

Parameters

cntnr
deplete

clearSMILESMinStereoBondRingSizeParameter()

None CDPL.Chem.clearSMILESMinStereoBondRingSizeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESMinStereoBondRingSizeParameter()

bool CDPL.Chem.hasSMILESMinStereoBondRingSizeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESMinStereoBondRingSizeParameter()

int CDPL.Chem.getSMILESMinStereoBondRingSizeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESMinStereoBondRingSizeParameter()

None CDPL.Chem.setSMILESMinStereoBondRingSizeParameter	(	Base.ControlParameterContainer	cntnr,
		int	min_size
	)

Parameters

cntnr
min_size

clearMDLConfEnergySDTagParameter()

None CDPL.Chem.clearMDLConfEnergySDTagParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLConfEnergySDTagParameter()

bool CDPL.Chem.hasMDLConfEnergySDTagParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLConfEnergySDTagParameter()

str CDPL.Chem.getMDLConfEnergySDTagParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLConfEnergySDTagParameter()

None CDPL.Chem.setMDLConfEnergySDTagParameter	(	Base.ControlParameterContainer	cntnr,
		str	tag
	)

Parameters

cntnr
tag

clearStrictErrorCheckingParameter()

None CDPL.Chem.clearStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasStrictErrorCheckingParameter()

bool CDPL.Chem.hasStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getStrictErrorCheckingParameter()

bool CDPL.Chem.getStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setStrictErrorCheckingParameter()

None CDPL.Chem.setStrictErrorCheckingParameter	(	Base.ControlParameterContainer	cntnr,
		bool	strict
	)

Parameters

cntnr
strict

clearCheckLineLengthParameter()

None CDPL.Chem.clearCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasCheckLineLengthParameter()

bool CDPL.Chem.hasCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCheckLineLengthParameter()

bool CDPL.Chem.getCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setCheckLineLengthParameter()

None CDPL.Chem.setCheckLineLengthParameter	(	Base.ControlParameterContainer	cntnr,
		bool	check
	)

Parameters

cntnr
check

clearSMILESWriteKekuleFormParameter()

None CDPL.Chem.clearSMILESWriteKekuleFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESWriteKekuleFormParameter()

bool CDPL.Chem.hasSMILESWriteKekuleFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESWriteKekuleFormParameter()

bool CDPL.Chem.getSMILESWriteKekuleFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESWriteKekuleFormParameter()

None CDPL.Chem.setSMILESWriteKekuleFormParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearSMILESWriteCanonicalFormParameter()

None CDPL.Chem.clearSMILESWriteCanonicalFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESWriteCanonicalFormParameter()

bool CDPL.Chem.hasSMILESWriteCanonicalFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESWriteCanonicalFormParameter()

bool CDPL.Chem.getSMILESWriteCanonicalFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESWriteCanonicalFormParameter()

None CDPL.Chem.setSMILESWriteCanonicalFormParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearCoordinatesDimensionParameter()

None CDPL.Chem.clearCoordinatesDimensionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasCoordinatesDimensionParameter()

bool CDPL.Chem.hasCoordinatesDimensionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCoordinatesDimensionParameter()

int CDPL.Chem.getCoordinatesDimensionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setCoordinatesDimensionParameter()

None CDPL.Chem.setCoordinatesDimensionParameter	(	Base.ControlParameterContainer	cntnr,
		int	dim
	)

Parameters

cntnr
dim

clearMDLCTABVersionParameter()

None CDPL.Chem.clearMDLCTABVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLCTABVersionParameter()

bool CDPL.Chem.hasMDLCTABVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLCTABVersionParameter()

int CDPL.Chem.getMDLCTABVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLCTABVersionParameter()

None CDPL.Chem.setMDLCTABVersionParameter	(	Base.ControlParameterContainer	cntnr,
		int	version
	)

Parameters

cntnr
version

clearMDLRXNFileVersionParameter()

None CDPL.Chem.clearMDLRXNFileVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLRXNFileVersionParameter()

bool CDPL.Chem.hasMDLRXNFileVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLRXNFileVersionParameter()

int CDPL.Chem.getMDLRXNFileVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLRXNFileVersionParameter()

None CDPL.Chem.setMDLRXNFileVersionParameter	(	Base.ControlParameterContainer	cntnr,
		int	version
	)

Parameters

cntnr
version

clearConfIndexNameSuffixPatternParameter()

None CDPL.Chem.clearConfIndexNameSuffixPatternParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasConfIndexNameSuffixPatternParameter()

bool CDPL.Chem.hasConfIndexNameSuffixPatternParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getConfIndexNameSuffixPatternParameter()

str CDPL.Chem.getConfIndexNameSuffixPatternParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setConfIndexNameSuffixPatternParameter()

None CDPL.Chem.setConfIndexNameSuffixPatternParameter	(	Base.ControlParameterContainer	cntnr,
		str	pattern
	)

Parameters

cntnr
pattern

clearSMILESWriteBondStereoParameter()

None CDPL.Chem.clearSMILESWriteBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESWriteBondStereoParameter()

bool CDPL.Chem.hasSMILESWriteBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESWriteBondStereoParameter()

bool CDPL.Chem.getSMILESWriteBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESWriteBondStereoParameter()

None CDPL.Chem.setSMILESWriteBondStereoParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearSMILESWriteRingBondStereoParameter()

None CDPL.Chem.clearSMILESWriteRingBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESWriteRingBondStereoParameter()

bool CDPL.Chem.hasSMILESWriteRingBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESWriteRingBondStereoParameter()

bool CDPL.Chem.getSMILESWriteRingBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESWriteRingBondStereoParameter()

None CDPL.Chem.setSMILESWriteRingBondStereoParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearSMILESWriteAtomStereoParameter()

None CDPL.Chem.clearSMILESWriteAtomStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESWriteAtomStereoParameter()

bool CDPL.Chem.hasSMILESWriteAtomStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESWriteAtomStereoParameter()

bool CDPL.Chem.getSMILESWriteAtomStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESWriteAtomStereoParameter()

None CDPL.Chem.setSMILESWriteAtomStereoParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearMDLUpdateTimestampParameter()

None CDPL.Chem.clearMDLUpdateTimestampParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLUpdateTimestampParameter()

bool CDPL.Chem.hasMDLUpdateTimestampParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLUpdateTimestampParameter()

bool CDPL.Chem.getMDLUpdateTimestampParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLUpdateTimestampParameter()

None CDPL.Chem.setMDLUpdateTimestampParameter	(	Base.ControlParameterContainer	cntnr,
		bool	update
	)

Parameters

cntnr
update

clearMultiConfInputProcessorParameter()

None CDPL.Chem.clearMultiConfInputProcessorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMultiConfInputProcessorParameter()

bool CDPL.Chem.hasMultiConfInputProcessorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMultiConfInputProcessorParameter()

MultiConfMoleculeInputProcessor CDPL.Chem.getMultiConfInputProcessorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMultiConfInputProcessorParameter()

None CDPL.Chem.setMultiConfInputProcessorParameter	(	Base.ControlParameterContainer	cntnr,
		MultiConfMoleculeInputProcessor	proc
	)

Parameters

cntnr
proc

clearRecordSeparatorParameter()

None CDPL.Chem.clearRecordSeparatorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasRecordSeparatorParameter()

bool CDPL.Chem.hasRecordSeparatorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getRecordSeparatorParameter()

str CDPL.Chem.getRecordSeparatorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setRecordSeparatorParameter()

None CDPL.Chem.setRecordSeparatorParameter	(	Base.ControlParameterContainer	cntnr,
		str	sep
	)

Parameters

cntnr
sep

clearSMILESWriteAromaticBondsParameter()

None CDPL.Chem.clearSMILESWriteAromaticBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESWriteAromaticBondsParameter()

bool CDPL.Chem.hasSMILESWriteAromaticBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESWriteAromaticBondsParameter()

bool CDPL.Chem.getSMILESWriteAromaticBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESWriteAromaticBondsParameter()

None CDPL.Chem.setSMILESWriteAromaticBondsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearSMILESWriteSingleBondsParameter()

None CDPL.Chem.clearSMILESWriteSingleBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESWriteSingleBondsParameter()

bool CDPL.Chem.hasSMILESWriteSingleBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESWriteSingleBondsParameter()

bool CDPL.Chem.getSMILESWriteSingleBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESWriteSingleBondsParameter()

None CDPL.Chem.setSMILESWriteSingleBondsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	write
	)

Parameters

cntnr
write

clearMOL2CalcFormalChargesParameter()

None CDPL.Chem.clearMOL2CalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMOL2CalcFormalChargesParameter()

bool CDPL.Chem.hasMOL2CalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2CalcFormalChargesParameter()

bool CDPL.Chem.getMOL2CalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMOL2CalcFormalChargesParameter()

None CDPL.Chem.setMOL2CalcFormalChargesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	calc
	)

Parameters

cntnr
calc

clearXYZCalcFormalChargesParameter()

None CDPL.Chem.clearXYZCalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasXYZCalcFormalChargesParameter()

bool CDPL.Chem.hasXYZCalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getXYZCalcFormalChargesParameter()

bool CDPL.Chem.getXYZCalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setXYZCalcFormalChargesParameter()

None CDPL.Chem.setXYZCalcFormalChargesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	calc
	)

Parameters

cntnr
calc

clearMDLTruncateLinesParameter()

None CDPL.Chem.clearMDLTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLTruncateLinesParameter()

bool CDPL.Chem.hasMDLTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLTruncateLinesParameter()

bool CDPL.Chem.getMDLTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLTruncateLinesParameter()

None CDPL.Chem.setMDLTruncateLinesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	trunc
	)

Parameters

cntnr
trunc

clearMDLTrimLinesParameter()

None CDPL.Chem.clearMDLTrimLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLTrimLinesParameter()

bool CDPL.Chem.hasMDLTrimLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLTrimLinesParameter()

bool CDPL.Chem.getMDLTrimLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLTrimLinesParameter()

None CDPL.Chem.setMDLTrimLinesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	trim
	)

Parameters

cntnr
trim

clearMOL2EnableAromaticBondTypesParameter()

None CDPL.Chem.clearMOL2EnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMOL2EnableAromaticBondTypesParameter()

bool CDPL.Chem.hasMOL2EnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2EnableAromaticBondTypesParameter()

bool CDPL.Chem.getMOL2EnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMOL2EnableAromaticBondTypesParameter()

None CDPL.Chem.setMOL2EnableAromaticBondTypesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	enable
	)

Parameters

cntnr
enable

clearMOL2EnableExtendedAtomTypesParameter()

None CDPL.Chem.clearMOL2EnableExtendedAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMOL2EnableExtendedAtomTypesParameter()

bool CDPL.Chem.hasMOL2EnableExtendedAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2EnableExtendedAtomTypesParameter()

bool CDPL.Chem.getMOL2EnableExtendedAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMOL2EnableExtendedAtomTypesParameter()

None CDPL.Chem.setMOL2EnableExtendedAtomTypesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	enable
	)

Parameters

cntnr
enable

clearMOL2OutputSubstructuresParameter()

None CDPL.Chem.clearMOL2OutputSubstructuresParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMOL2OutputSubstructuresParameter()

bool CDPL.Chem.hasMOL2OutputSubstructuresParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2OutputSubstructuresParameter()

bool CDPL.Chem.getMOL2OutputSubstructuresParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMOL2OutputSubstructuresParameter()

None CDPL.Chem.setMOL2OutputSubstructuresParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

Parameters

cntnr
output

clearMDLTruncateStringsParameter()

None CDPL.Chem.clearMDLTruncateStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLTruncateStringsParameter()

bool CDPL.Chem.hasMDLTruncateStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLTruncateStringsParameter()

bool CDPL.Chem.getMDLTruncateStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLTruncateStringsParameter()

None CDPL.Chem.setMDLTruncateStringsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	trunc
	)

Parameters

cntnr
trunc

clearMDLTrimStringsParameter()

None CDPL.Chem.clearMDLTrimStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLTrimStringsParameter()

bool CDPL.Chem.hasMDLTrimStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLTrimStringsParameter()

bool CDPL.Chem.getMDLTrimStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLTrimStringsParameter()

None CDPL.Chem.setMDLTrimStringsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	trim
	)

Parameters

cntnr
trim

clearINCHIInputOptionsParameter()

None CDPL.Chem.clearINCHIInputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasINCHIInputOptionsParameter()

bool CDPL.Chem.hasINCHIInputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getINCHIInputOptionsParameter()

str CDPL.Chem.getINCHIInputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setINCHIInputOptionsParameter()

None CDPL.Chem.setINCHIInputOptionsParameter	(	Base.ControlParameterContainer	cntnr,
		str	opts
	)

Parameters

cntnr
opts

clearINCHIOutputOptionsParameter()

None CDPL.Chem.clearINCHIOutputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasINCHIOutputOptionsParameter()

bool CDPL.Chem.hasINCHIOutputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getINCHIOutputOptionsParameter()

str CDPL.Chem.getINCHIOutputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setINCHIOutputOptionsParameter()

None CDPL.Chem.setINCHIOutputOptionsParameter	(	Base.ControlParameterContainer	cntnr,
		str	opts
	)

Parameters

cntnr
opts

clearXYZPerceiveBondOrdersParameter()

None CDPL.Chem.clearXYZPerceiveBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasXYZPerceiveBondOrdersParameter()

bool CDPL.Chem.hasXYZPerceiveBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getXYZPerceiveBondOrdersParameter()

bool CDPL.Chem.getXYZPerceiveBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setXYZPerceiveBondOrdersParameter()

None CDPL.Chem.setXYZPerceiveBondOrdersParameter	(	Base.ControlParameterContainer	cntnr,
		bool	perceive
	)

Parameters

cntnr
perceive

clearCDFWriteSinglePrecisionFloatsParameter()

None CDPL.Chem.clearCDFWriteSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasCDFWriteSinglePrecisionFloatsParameter()

bool CDPL.Chem.hasCDFWriteSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCDFWriteSinglePrecisionFloatsParameter()

bool CDPL.Chem.getCDFWriteSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setCDFWriteSinglePrecisionFloatsParameter()

None CDPL.Chem.setCDFWriteSinglePrecisionFloatsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	single_prec
	)

Parameters

cntnr
single_prec

clearJMESeparateComponentsParameter()

None CDPL.Chem.clearJMESeparateComponentsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasJMESeparateComponentsParameter()

bool CDPL.Chem.hasJMESeparateComponentsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getJMESeparateComponentsParameter()

bool CDPL.Chem.getJMESeparateComponentsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setJMESeparateComponentsParameter()

None CDPL.Chem.setJMESeparateComponentsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	separate
	)

Parameters

cntnr
separate

clearSMILESRecordFormatParameter()

None CDPL.Chem.clearSMILESRecordFormatParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESRecordFormatParameter()

bool CDPL.Chem.hasSMILESRecordFormatParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESRecordFormatParameter()

str CDPL.Chem.getSMILESRecordFormatParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESRecordFormatParameter()

None CDPL.Chem.setSMILESRecordFormatParameter	(	Base.ControlParameterContainer	cntnr,
		str	format
	)

Parameters

cntnr
format

clearSMILESNoOrganicSubsetParameter()

None CDPL.Chem.clearSMILESNoOrganicSubsetParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasSMILESNoOrganicSubsetParameter()

bool CDPL.Chem.hasSMILESNoOrganicSubsetParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESNoOrganicSubsetParameter()

bool CDPL.Chem.getSMILESNoOrganicSubsetParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setSMILESNoOrganicSubsetParameter()

None CDPL.Chem.setSMILESNoOrganicSubsetParameter	(	Base.ControlParameterContainer	cntnr,
		bool	no_subset
	)

Parameters

cntnr
no_subset

clearOutputConfEnergyAsCommentParameter()

None CDPL.Chem.clearOutputConfEnergyAsCommentParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasOutputConfEnergyAsCommentParameter()

bool CDPL.Chem.hasOutputConfEnergyAsCommentParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getOutputConfEnergyAsCommentParameter()

bool CDPL.Chem.getOutputConfEnergyAsCommentParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setOutputConfEnergyAsCommentParameter()

None CDPL.Chem.setOutputConfEnergyAsCommentParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

Parameters

cntnr
output

clearMultiConfImportParameter()

None CDPL.Chem.clearMultiConfImportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMultiConfImportParameter()

bool CDPL.Chem.hasMultiConfImportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMultiConfImportParameter()

bool CDPL.Chem.getMultiConfImportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMultiConfImportParameter()

None CDPL.Chem.setMultiConfImportParameter	(	Base.ControlParameterContainer	cntnr,
		bool	multi_conf
	)

Parameters

cntnr
multi_conf

clearMultiConfExportParameter()

None CDPL.Chem.clearMultiConfExportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMultiConfExportParameter()

bool CDPL.Chem.hasMultiConfExportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMultiConfExportParameter()

bool CDPL.Chem.getMultiConfExportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMultiConfExportParameter()

None CDPL.Chem.setMultiConfExportParameter	(	Base.ControlParameterContainer	cntnr,
		bool	multi_conf
	)

Parameters

cntnr
multi_conf

clearBondMemberSwapStereoFixParameter()

None CDPL.Chem.clearBondMemberSwapStereoFixParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasBondMemberSwapStereoFixParameter()

bool CDPL.Chem.hasBondMemberSwapStereoFixParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getBondMemberSwapStereoFixParameter()

bool CDPL.Chem.getBondMemberSwapStereoFixParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setBondMemberSwapStereoFixParameter()

None CDPL.Chem.setBondMemberSwapStereoFixParameter	(	Base.ControlParameterContainer	cntnr,
		bool	fix
	)

Parameters

cntnr
fix

clearMDLOutputConfEnergyAsSDEntryParameter()

None CDPL.Chem.clearMDLOutputConfEnergyAsSDEntryParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLOutputConfEnergyAsSDEntryParameter()

bool CDPL.Chem.hasMDLOutputConfEnergyAsSDEntryParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLOutputConfEnergyAsSDEntryParameter()

bool CDPL.Chem.getMDLOutputConfEnergyAsSDEntryParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLOutputConfEnergyAsSDEntryParameter()

None CDPL.Chem.setMDLOutputConfEnergyAsSDEntryParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

Parameters

cntnr
output

clearMDLIgnoreParityParameter()

None CDPL.Chem.clearMDLIgnoreParityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasMDLIgnoreParityParameter()

bool CDPL.Chem.hasMDLIgnoreParityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLIgnoreParityParameter()

bool CDPL.Chem.getMDLIgnoreParityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setMDLIgnoreParityParameter()

None CDPL.Chem.setMDLIgnoreParityParameter	(	Base.ControlParameterContainer	cntnr,
		bool	ignore
	)

Parameters

cntnr
ignore

clearXYZPerceiveConnectivityParameter()

None CDPL.Chem.clearXYZPerceiveConnectivityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

hasXYZPerceiveConnectivityParameter()

bool CDPL.Chem.hasXYZPerceiveConnectivityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getXYZPerceiveConnectivityParameter()

bool CDPL.Chem.getXYZPerceiveConnectivityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

setXYZPerceiveConnectivityParameter()

None CDPL.Chem.setXYZPerceiveConnectivityParameter	(	Base.ControlParameterContainer	cntnr,
		bool	perceive
	)

Parameters

cntnr
perceive

calcCentroid() [2/2]

bool CDPL.Chem.calcCentroid	(	Entity3DContainer	cntnr,
		Math.Vector3D	ctr
	)

Parameters

cntnr
ctr

Returns

transform3DCoordinates()

None CDPL.Chem.transform3DCoordinates	(	Entity3DContainer	cntnr,
		Math.Matrix4D	mtx
	)

Parameters

cntnr
mtx

align3DCoordinates()

bool CDPL.Chem.align3DCoordinates	(	Entity3DContainer	cntnr,
		Entity3DContainer	ref_entities,
		Math.Vector3DArray	ref_coords
	)

Parameters

cntnr
ref_entities
ref_coords

Returns

get3DCoordinates() [2/3]

None CDPL.Chem.get3DCoordinates	(	Entity3DContainer	cntnr,
		Math.Vector3DArray	coords,
		bool	append = False
	)

Parameters

cntnr
coords
append

set3DCoordinates() [1/2]

None CDPL.Chem.set3DCoordinates	(	Entity3DContainer	cntnr,
		Math.Vector3DArray	coords
	)

Parameters

cntnr
coords

calcGeometricalDistanceMatrix() [1/2]

None CDPL.Chem.calcGeometricalDistanceMatrix	(	Entity3DContainer	cntnr,
		Math.DMatrix	mtx
	)

Parameters

cntnr
mtx

calcBoundingBox() [2/2]

None CDPL.Chem.calcBoundingBox	(	Entity3DContainer	cntnr,
		Math.Vector3D	min,
		Math.Vector3D	max,
		bool	reset = True
	)

Parameters

cntnr
min
max
reset

insideBoundingBox() [2/3]

bool CDPL.Chem.insideBoundingBox	(	Entity3DContainer	cntnr,
		Math.Vector3D	min,
		Math.Vector3D	max
	)

Parameters

cntnr
min
max

Returns

intersectsBoundingBox() [2/2]

bool CDPL.Chem.intersectsBoundingBox	(	Entity3DContainer	cntnr,
		Math.Vector3D	min,
		Math.Vector3D	max
	)

Parameters

cntnr
min
max

Returns

clear3DCoordinates()

None CDPL.Chem.clear3DCoordinates

(

Entity3D

entity

)

Parameters

entity

has3DCoordinates()

bool CDPL.Chem.has3DCoordinates

(

Entity3D

entity

)

Parameters

entity

Returns

get3DCoordinates() [3/3]

Math.Vector3D CDPL.Chem.get3DCoordinates

(

Entity3D

entity

)

Parameters

entity

Returns

set3DCoordinates() [2/2]

None CDPL.Chem.set3DCoordinates	(	Entity3D	entity,
		Math.Vector3D	coords
	)

Parameters

entity
coords

containsFragmentWithBond()

bool CDPL.Chem.containsFragmentWithBond	(	FragmentList	frag_list,
		Bond	bond
	)

Parameters

frag_list
bond

Returns

containsFragmentWithMinSize()

bool CDPL.Chem.containsFragmentWithMinSize	(	FragmentList	frag_list,
		int	min_size
	)

Parameters

frag_list
min_size

Returns

isAromatic()

bool CDPL.Chem.isAromatic	(	Fragment	ring,
		MolecularGraph	molgraph,
		Util.BitSet	arom_bond_mask
	)

Parameters

ring
molgraph
arom_bond_mask

Returns

isNotAromatic()

bool CDPL.Chem.isNotAromatic	(	Fragment	ring,
		MolecularGraph	molgraph
	)

Parameters

ring
molgraph

Returns

makeHydrogenDeplete() [1/2]

bool CDPL.Chem.makeHydrogenDeplete

(

Fragment

frag

)

Removes all explicit hydrogen atoms from the fragment frag.

Parameters

frag	The fragment for which to remove all explicit hydrogen atoms.

Returns

False if frag was not altered, True otherwise.

makeOrdinaryHydrogenDeplete() [1/2]

bool CDPL.Chem.makeOrdinaryHydrogenDeplete	(	Fragment	frag,
		int	flags
	)

Removes all explicit ordinary hydrogen atoms from the fragment frag.

Parameters

frag	The fragment for which to remove all explicit ordinary hydrogen atoms.
flags	Specifies the set of atom properties to check (see namespace Chem.AtomPropertyFlag).

Returns

False if frag was not altered, True otherwise.

See also

Chem.isOrdinaryHydrogen

removeAtomsIf() [1/2]

None CDPL.Chem.removeAtomsIf	(	Fragment	frag,
		AtomPredicate	pred
	)

Parameters

frag
pred

removeAtomsIfNot() [1/2]

None CDPL.Chem.removeAtomsIfNot	(	Fragment	frag,
		AtomPredicate	pred
	)

Parameters

frag
pred

clearMDLScalingFactor1()

None CDPL.Chem.clearMDLScalingFactor1

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMDLScalingFactor1()

bool CDPL.Chem.hasMDLScalingFactor1

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLScalingFactor1()

int CDPL.Chem.getMDLScalingFactor1

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMDLScalingFactor1()

None CDPL.Chem.setMDLScalingFactor1	(	MolecularGraph	molgraph,
		int	factor
	)

Parameters

molgraph
factor

clearMDLScalingFactor2()

None CDPL.Chem.clearMDLScalingFactor2

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMDLScalingFactor2()

bool CDPL.Chem.hasMDLScalingFactor2

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLScalingFactor2()

float CDPL.Chem.getMDLScalingFactor2

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMDLScalingFactor2()

None CDPL.Chem.setMDLScalingFactor2	(	MolecularGraph	molgraph,
		float	factor
	)

Parameters

molgraph
factor

generateINCHI()

object CDPL.Chem.generateINCHI	(	MolecularGraph	molgraph,
		str	options = '/WarnOnEmptyStructure /AuxNone /NEWPSOFF',
		int	dim = 0
	)

Parameters

molgraph
options
dim

Returns

perceiveSSSR() [1/2]

FragmentList CDPL.Chem.perceiveSSSR

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

perceiveSSSR() [2/2]

FragmentList CDPL.Chem.perceiveSSSR	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

clearSSSR()

None CDPL.Chem.clearSSSR

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasSSSR()

bool CDPL.Chem.hasSSSR

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getSSSR()

FragmentList CDPL.Chem.getSSSR

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setSSSR()

None CDPL.Chem.setSSSR	(	MolecularGraph	molgraph,
		FragmentList	sssr
	)

Parameters

molgraph
sssr

generateSMILES() [1/2]

object CDPL.Chem.generateSMILES	(	MolecularGraph	molgraph,
		bool	canonical = False,
		bool	ord_h_deplete = True,
		int	atom_flags = 2147483648,
		int	bond_flags = 2147483648
	)

Parameters

molgraph
canonical
ord_h_deplete
atom_flags
bond_flags

Returns

clearStructureData()

None CDPL.Chem.clearStructureData

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasStructureData()

bool CDPL.Chem.hasStructureData

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getStructureData()

StringDataBlock CDPL.Chem.getStructureData

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setStructureData()

None CDPL.Chem.setStructureData	(	MolecularGraph	molgraph,
		StringDataBlock	data
	)

Parameters

molgraph
data

calcHashCode() [1/2]

int CDPL.Chem.calcHashCode	(	MolecularGraph	molgraph,
		int	atom_flags = 2147483648,
		int	bond_flags = 2147483648,
		bool	ord_h_deplete = True
	)

Parameters

molgraph
atom_flags
bond_flags
ord_h_deplete

Returns

clearHashCode()

None CDPL.Chem.clearHashCode

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasHashCode()

bool CDPL.Chem.hasHashCode

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getHashCode()

int CDPL.Chem.getHashCode

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setHashCode()

None CDPL.Chem.setHashCode	(	MolecularGraph	molgraph,
		int	hash_code
	)

Parameters

molgraph
hash_code

clearMDLProgramName() [1/2]

None CDPL.Chem.clearMDLProgramName

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMDLProgramName() [1/2]

bool CDPL.Chem.hasMDLProgramName

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLProgramName() [1/2]

str CDPL.Chem.getMDLProgramName

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMDLProgramName() [1/2]

None CDPL.Chem.setMDLProgramName	(	MolecularGraph	molgraph,
		str	name
	)

Parameters

molgraph
name

clearName() [2/3]

None CDPL.Chem.clearName

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasName() [2/3]

bool CDPL.Chem.hasName

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getName() [2/3]

str CDPL.Chem.getName

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setName() [2/3]

None CDPL.Chem.setName	(	MolecularGraph	molgraph,
		str	name
	)

Parameters

molgraph
name

clearMOL2ChargeType()

None CDPL.Chem.clearMOL2ChargeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMOL2ChargeType()

bool CDPL.Chem.hasMOL2ChargeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMOL2ChargeType()

int CDPL.Chem.getMOL2ChargeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMOL2ChargeType()

None CDPL.Chem.setMOL2ChargeType	(	MolecularGraph	molgraph,
		int	type
	)

Parameters

molgraph
type

clearMOL2MoleculeType()

None CDPL.Chem.clearMOL2MoleculeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMOL2MoleculeType()

bool CDPL.Chem.hasMOL2MoleculeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMOL2MoleculeType()

int CDPL.Chem.getMOL2MoleculeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMOL2MoleculeType()

None CDPL.Chem.setMOL2MoleculeType	(	MolecularGraph	molgraph,
		int	type
	)

Parameters

molgraph
type

perceiveCyclicSubstructure() [1/2]

Fragment CDPL.Chem.perceiveCyclicSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

perceiveCyclicSubstructure() [2/2]

Fragment CDPL.Chem.perceiveCyclicSubstructure	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

clearCyclicSubstructure()

None CDPL.Chem.clearCyclicSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasCyclicSubstructure()

bool CDPL.Chem.hasCyclicSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getCyclicSubstructure()

Fragment CDPL.Chem.getCyclicSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setCyclicSubstructure()

None CDPL.Chem.setCyclicSubstructure	(	MolecularGraph	molgraph,
		Fragment	substruct
	)

Parameters

molgraph
substruct

perceiveAromaticSubstructure() [1/2]

Fragment CDPL.Chem.perceiveAromaticSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

perceiveAromaticSubstructure() [2/2]

Fragment CDPL.Chem.perceiveAromaticSubstructure	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

clearAromaticSubstructure()

None CDPL.Chem.clearAromaticSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasAromaticSubstructure()

bool CDPL.Chem.hasAromaticSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getAromaticSubstructure()

Fragment CDPL.Chem.getAromaticSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setAromaticSubstructure()

None CDPL.Chem.setAromaticSubstructure	(	MolecularGraph	molgraph,
		Fragment	substruct
	)

Parameters

molgraph
substruct

canonicalize() [1/2]

None CDPL.Chem.canonicalize	(	MolecularGraph	molgraph,
		bool	atoms = True,
		bool	atom_nbrs = True,
		bool	bonds = True,
		bool	bond_atoms = False
	)

Parameters

molgraph
atoms
atom_nbrs
bonds
bond_atoms

canonicalize() [2/2]

None CDPL.Chem.canonicalize	(	MolecularGraph	molgraph,
		ForceField.InteractionFilterFunction2	func,
		bool	atoms = True,
		bool	atom_nbrs = True,
		bool	bonds = True,
		bool	bond_atoms = False
	)

Parameters

molgraph
func
atoms
atom_nbrs
bonds
bond_atoms

clearMDLChiralFlag()

None CDPL.Chem.clearMDLChiralFlag

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMDLChiralFlag()

bool CDPL.Chem.hasMDLChiralFlag

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLChiralFlag()

bool CDPL.Chem.getMDLChiralFlag

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMDLChiralFlag()

None CDPL.Chem.setMDLChiralFlag	(	MolecularGraph	molgraph,
		bool	flag
	)

Parameters

molgraph
flag

calcCanonicalNumbering()

None CDPL.Chem.calcCanonicalNumbering	(	MolecularGraph	molgraph,
		bool	overwrite,
		int	atom_flags = 2147483648,
		int	bond_flags = 2147483648
	)

Parameters

molgraph
overwrite
atom_flags
bond_flags

calcMorganNumbering()

None CDPL.Chem.calcMorganNumbering	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

containsMolecularGraph()

bool CDPL.Chem.containsMolecularGraph	(	MolecularGraph	molgraph,
		MolecularGraph	sub_molgraph,
		bool	atoms = True,
		bool	bonds = True
	)

Parameters

molgraph
sub_molgraph
atoms
bonds

Returns

clearMDLCTABVersion()

None CDPL.Chem.clearMDLCTABVersion

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMDLCTABVersion()

bool CDPL.Chem.hasMDLCTABVersion

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLCTABVersion()

int CDPL.Chem.getMDLCTABVersion

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMDLCTABVersion()

None CDPL.Chem.setMDLCTABVersion	(	MolecularGraph	molgraph,
		int	version
	)

Parameters

molgraph
version

generateMatchExpression() [3/6]

MolecularGraphMatchExpression CDPL.Chem.generateMatchExpression

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

generateMatchExpression() [4/6]

MolecularGraphMatchExpression CDPL.Chem.generateMatchExpression	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

clearMatchExpression() [3/4]

None CDPL.Chem.clearMatchExpression

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMatchExpression() [3/4]

bool CDPL.Chem.hasMatchExpression

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMatchExpression() [3/4]

MolecularGraphMatchExpression CDPL.Chem.getMatchExpression

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMatchExpression() [3/4]

None CDPL.Chem.setMatchExpression	(	MolecularGraph	molgraph,
		MolecularGraphMatchExpression	expr
	)

Parameters

molgraph
expr

addConformation() [2/2]

None CDPL.Chem.addConformation	(	MolecularGraph	molgraph,
		Math.Vector3DArray	coords,
		float	energy
	)

Parameters

molgraph
coords
energy

setConformation()

None CDPL.Chem.setConformation	(	MolecularGraph	molgraph,
		int	conf_idx,
		Math.Vector3DArray	coords,
		float	energy
	)

Parameters

molgraph
conf_idx
coords
energy

clearTimestamp() [1/2]

None CDPL.Chem.clearTimestamp

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasTimestamp() [1/2]

bool CDPL.Chem.hasTimestamp

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getTimestamp() [1/2]

int CDPL.Chem.getTimestamp

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setTimestamp() [1/2]

None CDPL.Chem.setTimestamp	(	MolecularGraph	molgraph,
		int	time
	)

Parameters

molgraph
time

clearStoichiometricNumber()

None CDPL.Chem.clearStoichiometricNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasStoichiometricNumber()

bool CDPL.Chem.hasStoichiometricNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getStoichiometricNumber()

float CDPL.Chem.getStoichiometricNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setStoichiometricNumber()

None CDPL.Chem.setStoichiometricNumber	(	MolecularGraph	molgraph,
		float	num
	)

Parameters

molgraph
num

clearMDLRegistryNumber() [1/2]

None CDPL.Chem.clearMDLRegistryNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMDLRegistryNumber() [1/2]

bool CDPL.Chem.hasMDLRegistryNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLRegistryNumber() [1/2]

int CDPL.Chem.getMDLRegistryNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMDLRegistryNumber() [1/2]

None CDPL.Chem.setMDLRegistryNumber	(	MolecularGraph	molgraph,
		int	reg_no
	)

Parameters

molgraph
reg_no

extractReactionCenter()

None CDPL.Chem.extractReactionCenter	(	MolecularGraph	molgraph,
		Fragment	rxn_center
	)

Parameters

molgraph
rxn_center

kekulizeBonds()

None CDPL.Chem.kekulizeBonds

(

MolecularGraph

molgraph

)

Parameters

molgraph

calcFormalCharges()

None CDPL.Chem.calcFormalCharges	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

clearConformerEnergies()

None CDPL.Chem.clearConformerEnergies

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasConformerEnergies()

bool CDPL.Chem.hasConformerEnergies

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getConformerEnergies()

Util.DArray CDPL.Chem.getConformerEnergies

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setConformerEnergies()

None CDPL.Chem.setConformerEnergies	(	MolecularGraph	molgraph,
		Util.DArray	energies
	)

Parameters

molgraph
energies

calcMDLParities()

None CDPL.Chem.calcMDLParities	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

calcAtomStereoDescriptorsFromMDLParities()

None CDPL.Chem.calcAtomStereoDescriptorsFromMDLParities	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

calcCIPPriorities()

None CDPL.Chem.calcCIPPriorities	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

calcBasicProperties() [1/2]

None CDPL.Chem.calcBasicProperties	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

setAtomSymbolsFromTypes()

None CDPL.Chem.setAtomSymbolsFromTypes	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

perceiveSybylAtomTypes()

None CDPL.Chem.perceiveSybylAtomTypes	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

perceiveSymmetryClasses()

None CDPL.Chem.perceiveSymmetryClasses	(	MolecularGraph	molgraph,
		bool	overwrite,
		int	atom_flags = 2147483648,
		int	bond_flags = 2147483648,
		bool	inc_impl_h = True
	)

Parameters

molgraph
overwrite
atom_flags
bond_flags
inc_impl_h

calc2DCoordinates()

None CDPL.Chem.calc2DCoordinates	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

calcHydrogen3DCoordinates()

None CDPL.Chem.calcHydrogen3DCoordinates	(	MolecularGraph	molgraph,
		bool	undef_only = True
	)

Parameters

molgraph
undef_only

perceiveHybridizationStates()

None CDPL.Chem.perceiveHybridizationStates	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

setRingFlags()

None CDPL.Chem.setRingFlags	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

calcBond2DStereoFlags()

None CDPL.Chem.calcBond2DStereoFlags	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

setAromaticityFlags()

None CDPL.Chem.setAromaticityFlags	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

getAromaticRings()

FragmentList CDPL.Chem.getAromaticRings

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

perceiveRings() [1/2]

FragmentList CDPL.Chem.perceiveRings

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

perceiveRings() [2/2]

FragmentList CDPL.Chem.perceiveRings	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

clearRings()

None CDPL.Chem.clearRings

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasRings()

bool CDPL.Chem.hasRings

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getRings()

FragmentList CDPL.Chem.getRings

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setRings()

None CDPL.Chem.setRings	(	MolecularGraph	molgraph,
		FragmentList	rings
	)

Parameters

molgraph
rings

generateMatchExpressionStrings()

None CDPL.Chem.generateMatchExpressionStrings	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

clearMDLUserInitials() [1/2]

None CDPL.Chem.clearMDLUserInitials

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMDLUserInitials() [1/2]

bool CDPL.Chem.hasMDLUserInitials

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLUserInitials() [1/2]

str CDPL.Chem.getMDLUserInitials

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMDLUserInitials() [1/2]

None CDPL.Chem.setMDLUserInitials	(	MolecularGraph	molgraph,
		str	initials
	)

Parameters

molgraph
initials

setAtomTypesFromSymbols()

None CDPL.Chem.setAtomTypesFromSymbols	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

perceivePiElectronSystems() [1/2]

ElectronSystemList CDPL.Chem.perceivePiElectronSystems

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

perceivePiElectronSystems() [2/2]

ElectronSystemList CDPL.Chem.perceivePiElectronSystems	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

clearPiElectronSystems()

None CDPL.Chem.clearPiElectronSystems

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasPiElectronSystems()

bool CDPL.Chem.hasPiElectronSystems

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getPiElectronSystems()

ElectronSystemList CDPL.Chem.getPiElectronSystems

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setPiElectronSystems()

None CDPL.Chem.setPiElectronSystems	(	MolecularGraph	molgraph,
		ElectronSystemList	pi_systems
	)

Parameters

molgraph
pi_systems

generateMatchExpressions() [1/2]

None CDPL.Chem.generateMatchExpressions	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

calcBondCIPConfigurations()

None CDPL.Chem.calcBondCIPConfigurations	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

calcAtomCIPConfigurations()

None CDPL.Chem.calcAtomCIPConfigurations	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

perceiveComponentGroups() [1/4]

FragmentList CDPL.Chem.perceiveComponentGroups

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

perceiveComponentGroups() [2/4]

FragmentList CDPL.Chem.perceiveComponentGroups	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

clearComponentGroups() [1/2]

None CDPL.Chem.clearComponentGroups

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasComponentGroups() [1/2]

bool CDPL.Chem.hasComponentGroups

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getComponentGroups() [1/2]

FragmentList CDPL.Chem.getComponentGroups

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setComponentGroups() [1/2]

None CDPL.Chem.setComponentGroups	(	MolecularGraph	molgraph,
		FragmentList	comp_groups
	)

Parameters

molgraph
comp_groups

perceiveBondOrders()

None CDPL.Chem.perceiveBondOrders	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

perceiveBondStereoCenters()

None CDPL.Chem.perceiveBondStereoCenters	(	MolecularGraph	molgraph,
		bool	overwrite,
		bool	check_asym = True,
		bool	check_term_n = True,
		bool	check_order = True,
		int	min_ring_size = 8
	)

Parameters

molgraph
overwrite
check_asym
check_term_n
check_order
min_ring_size

perceiveAtomStereoCenters()

None CDPL.Chem.perceiveAtomStereoCenters	(	MolecularGraph	molgraph,
		bool	overwrite,
		bool	check_asym = True,
		bool	check_inv_n = True,
		bool	check_quart_n = True,
		bool	check_plan_n = True,
		bool	check_amide_n = True,
		bool	check_res_ctrs = True
	)

Parameters

molgraph
overwrite
check_asym
check_inv_n
check_quart_n
check_plan_n
check_amide_n
check_res_ctrs

calcBondStereoDescriptors()

None CDPL.Chem.calcBondStereoDescriptors	(	MolecularGraph	molgraph,
		bool	overwrite,
		int	dim = 1,
		bool	check_stc_flag = True
	)

Parameters

molgraph
overwrite
dim
check_stc_flag

calcAtomStereoDescriptors()

None CDPL.Chem.calcAtomStereoDescriptors	(	MolecularGraph	molgraph,
		bool	overwrite,
		int	dim = 1,
		bool	check_stc_flag = True
	)

Parameters

molgraph
overwrite
dim
check_stc_flag

getContainedFragments()

None CDPL.Chem.getContainedFragments	(	MolecularGraph	molgraph,
		FragmentList	frag_list,
		FragmentList	cont_frag_list,
		bool	append = False,
		bool	atoms = True,
		bool	bonds = True
	)

Parameters

molgraph
frag_list
cont_frag_list
append
atoms
bonds

translateFragments()

None CDPL.Chem.translateFragments	(	MolecularGraph	src_molgraph,
		FragmentList	src_frag_list,
		MolecularGraph	tgt_molgraph,
		FragmentList	tgt_frag_list,
		bool	append = False
	)

Parameters

src_molgraph
src_frag_list
tgt_molgraph
tgt_frag_list
append

getContainingFragments() [3/3]

None CDPL.Chem.getContainingFragments	(	MolecularGraph	molgraph,
		FragmentList	frag_list,
		FragmentList	cont_frag_list,
		bool	append = False,
		bool	atoms = True,
		bool	bonds = True
	)

Parameters

molgraph
frag_list
cont_frag_list
append
atoms
bonds

splitIntoFragments()

None CDPL.Chem.splitIntoFragments	(	MolecularGraph	molgraph,
		FragmentList	frag_list,
		Util.BitSet	split_bond_mask,
		bool	append = False
	)

Parameters

molgraph
frag_list
split_bond_mask
append

perceiveComponents() [1/2]

FragmentList CDPL.Chem.perceiveComponents

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

perceiveComponents() [2/2]

FragmentList CDPL.Chem.perceiveComponents	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

clearComponents()

None CDPL.Chem.clearComponents

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasComponents()

bool CDPL.Chem.hasComponents

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getComponents()

FragmentList CDPL.Chem.getComponents

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setComponents()

None CDPL.Chem.setComponents	(	MolecularGraph	molgraph,
		FragmentList	comps
	)

Parameters

molgraph
comps

setBondMatchConstraints() [1/2]

None CDPL.Chem.setBondMatchConstraints	(	MolecularGraph	molgraph,
		MatchConstraintList	constr,
		bool	overwrite
	)

Parameters

molgraph
constr
overwrite

setAtomMatchConstraints() [1/2]

None CDPL.Chem.setAtomMatchConstraints	(	MolecularGraph	molgraph,
		MatchConstraintList	constr,
		bool	overwrite
	)

Parameters

molgraph
constr
overwrite

clearMatchConstraints() [3/4]

None CDPL.Chem.clearMatchConstraints

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMatchConstraints() [3/4]

bool CDPL.Chem.hasMatchConstraints

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMatchConstraints() [3/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMatchConstraints() [3/4]

None CDPL.Chem.setMatchConstraints	(	MolecularGraph	molgraph,
		MatchConstraintList	constr
	)

Parameters

molgraph
constr

calcImplicitHydrogenCounts()

None CDPL.Chem.calcImplicitHydrogenCounts	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

initSubstructureSearchTarget() [1/2]

None CDPL.Chem.initSubstructureSearchTarget	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

getAromaticSSSRSubset()

FragmentList CDPL.Chem.getAromaticSSSRSubset

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

extractSSSRSubset() [1/2]

FragmentList CDPL.Chem.extractSSSRSubset	(	MolecularGraph	src_molgraph,
		MolecularGraph	tgt_molgraph
	)

Parameters

src_molgraph
tgt_molgraph

Returns

extractSSSRSubset() [2/2]

FragmentList CDPL.Chem.extractSSSRSubset	(	MolecularGraph	src_molgraph,
		MolecularGraph	tgt_molgraph,
		bool	overwrite
	)

Parameters

src_molgraph
tgt_molgraph
overwrite

Returns

translateFragment()

None CDPL.Chem.translateFragment	(	MolecularGraph	src_molgraph,
		Fragment	src_frag,
		MolecularGraph	tgt_molgraph,
		Fragment	tgt_frag,
		bool	append = False
	)

Parameters

src_molgraph
src_frag
tgt_molgraph
tgt_frag
append

clearComment() [1/2]

None CDPL.Chem.clearComment

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasComment() [1/2]

bool CDPL.Chem.hasComment

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getComment() [1/2]

str CDPL.Chem.getComment

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setComment() [1/2]

None CDPL.Chem.setComment	(	MolecularGraph	molgraph,
		str	comment
	)

Parameters

molgraph
comment

getCompleteBondCount()

int CDPL.Chem.getCompleteBondCount

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearConformationIndex()

None CDPL.Chem.clearConformationIndex

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasConformationIndex()

bool CDPL.Chem.hasConformationIndex

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getConformationIndex()

int CDPL.Chem.getConformationIndex

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setConformationIndex()

None CDPL.Chem.setConformationIndex	(	MolecularGraph	molgraph,
		int	index
	)

Parameters

molgraph
index

extractTopologicalDistanceSubMatrix() [1/2]

Math.ULMatrix CDPL.Chem.extractTopologicalDistanceSubMatrix	(	MolecularGraph	src_molgraph,
		MolecularGraph	tgt_molgraph,
		bool	overwrite
	)

Parameters

src_molgraph
tgt_molgraph
overwrite

Returns

extractTopologicalDistanceSubMatrix() [2/2]

None CDPL.Chem.extractTopologicalDistanceSubMatrix	(	MolecularGraph	src_molgraph,
		MolecularGraph	tgt_molgraph,
		Math.ULMatrix	mtx
	)

Parameters

src_molgraph
tgt_molgraph
mtx

generateBondMatrix()

None CDPL.Chem.generateBondMatrix	(	MolecularGraph	molgraph,
		Math.SparseULMatrix	mtx
	)

Parameters

molgraph
mtx

calcTopologicalDistanceMatrix() [1/2]

Math.ULMatrix CDPL.Chem.calcTopologicalDistanceMatrix	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

calcTopologicalDistanceMatrix() [2/2]

None CDPL.Chem.calcTopologicalDistanceMatrix	(	MolecularGraph	molgraph,
		Math.ULMatrix	mtx
	)

Parameters

molgraph
mtx

clearTopologicalDistanceMatrix()

None CDPL.Chem.clearTopologicalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasTopologicalDistanceMatrix()

bool CDPL.Chem.hasTopologicalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getTopologicalDistanceMatrix()

Math.ULMatrix CDPL.Chem.getTopologicalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setTopologicalDistanceMatrix()

None CDPL.Chem.setTopologicalDistanceMatrix	(	MolecularGraph	molgraph,
		Math.ULMatrix	mtx
	)

Parameters

molgraph
mtx

calcGeometricalDistanceMatrix() [2/2]

Math.DMatrix CDPL.Chem.calcGeometricalDistanceMatrix	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

Returns

clearGeometricalDistanceMatrix()

None CDPL.Chem.clearGeometricalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasGeometricalDistanceMatrix()

bool CDPL.Chem.hasGeometricalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getGeometricalDistanceMatrix()

Math.DMatrix CDPL.Chem.getGeometricalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setGeometricalDistanceMatrix()

None CDPL.Chem.setGeometricalDistanceMatrix	(	MolecularGraph	molgraph,
		Math.DMatrix	mtx
	)

Parameters

molgraph
mtx

generateIncidenceMatrix()

None CDPL.Chem.generateIncidenceMatrix	(	MolecularGraph	molgraph,
		Math.SparseULMatrix	mtx
	)

Parameters

molgraph
mtx

generateBondAtomTypeMatrix()

None CDPL.Chem.generateBondAtomTypeMatrix	(	MolecularGraph	molgraph,
		Math.SparseULMatrix	mtx
	)

Parameters

molgraph
mtx

generateBondElectronMatrix()

None CDPL.Chem.generateBondElectronMatrix	(	MolecularGraph	molgraph,
		Math.SparseULMatrix	mtx
	)

Parameters

molgraph
mtx

generateAdjacencyMatrix()

None CDPL.Chem.generateAdjacencyMatrix	(	MolecularGraph	molgraph,
		Math.SparseULMatrix	mtx
	)

Parameters

molgraph
mtx

generateINCHIKey()

object CDPL.Chem.generateINCHIKey

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLEnergy()

None CDPL.Chem.clearMDLEnergy

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMDLEnergy()

bool CDPL.Chem.hasMDLEnergy

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLEnergy()

float CDPL.Chem.getMDLEnergy

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMDLEnergy()

None CDPL.Chem.setMDLEnergy	(	MolecularGraph	molgraph,
		float	energy
	)

Parameters

molgraph
energy

getConformationEnergy()

float CDPL.Chem.getConformationEnergy	(	MolecularGraph	molgraph,
		int	conf_idx
	)

Parameters

molgraph
conf_idx

Returns

initSubstructureSearchQuery() [1/2]

None CDPL.Chem.initSubstructureSearchQuery	(	MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

clearMDLDimensionality()

None CDPL.Chem.clearMDLDimensionality

(

MolecularGraph

molgraph

)

Parameters

molgraph

hasMDLDimensionality()

bool CDPL.Chem.hasMDLDimensionality

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLDimensionality()

int CDPL.Chem.getMDLDimensionality

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setMDLDimensionality()

None CDPL.Chem.setMDLDimensionality	(	MolecularGraph	molgraph,
		int	dim
	)

Parameters

molgraph
dim

makeHydrogenDeplete() [2/2]

bool CDPL.Chem.makeHydrogenDeplete	(	Molecule	mol,
		bool	corr_impl_h_count = True
	)

Removes all explicit hydrogen atoms from the molecule mol.

Parameters

mol	The molecule for which to remove all explicit hydrogen atoms.
corr_impl_h_count	True if the implicit hydrogen count property of the hydrogen completed atoms shall be corrected, False if the property shall be left unchanged.

Returns

False if mol was not altered, True otherwise.

makeOrdinaryHydrogenDeplete() [2/2]

bool CDPL.Chem.makeOrdinaryHydrogenDeplete	(	Molecule	mol,
		int	flags,
		bool	corr_impl_h_count = True
	)

Removes all explicit ordinary hydrogen atoms from the molecule mol.

Parameters

mol	The molecule for which to remove all explicit ordinary hydrogen atoms.
flags	Specifies the set of atom properties to check (see namespace Chem.AtomPropertyFlag).
corr_impl_h_count	True if the implicit hydrogen count property of the hydrogen completed atoms shall be corrected, False if the property shall be left unchanged.

Returns

False if mol was not altered, True otherwise.

See also

Chem.isOrdinaryHydrogen

makeHydrogenComplete()

bool CDPL.Chem.makeHydrogenComplete	(	Molecule	mol,
		bool	corr_impl_h_count = True
	)

Converts all implicit hydrogens of the molecule mol to explicit hydrogen atoms.

Parameters

mol	The molecule that has to be made hydrogen complete.
corr_impl_h_count	True if the implicit hydrogen count property of the hydrogen completed atoms shall be set to zero, False if the property shall be left unchanged.

Returns

False if mol was not altered, True otherwise.

removeAtomsIf() [2/2]

None CDPL.Chem.removeAtomsIf	(	Molecule	mol,
		AtomPredicate	pred
	)

Parameters

mol
pred

connectAtoms() [1/2]

None CDPL.Chem.connectAtoms	(	Molecule	mol,
		Atom3DCoordinatesFunction	coords_func,
		float	dist_tol = 0.3,
		int	atom_idx_offs = 0
	)

Parameters

mol
coords_func
dist_tol
atom_idx_offs

connectAtoms() [2/2]

None CDPL.Chem.connectAtoms	(	Molecule	mol,
		float	dist_tol = 0.3,
		int	atom_idx_offs = 0
	)

Parameters

mol
dist_tol
atom_idx_offs

removeAtomsIfNot() [2/2]

None CDPL.Chem.removeAtomsIfNot	(	Molecule	mol,
		AtomPredicate	pred
	)

Parameters

mol
pred

getMaxAtomMappingID() [2/2]

int CDPL.Chem.getMaxAtomMappingID

(

Reaction

rxn

)

Parameters

rxn

Returns

getMaxComponentGroupID() [2/2]

int CDPL.Chem.getMaxComponentGroupID

(

Reaction

rxn

)

Parameters

rxn

Returns

generateSMILES() [2/2]

object CDPL.Chem.generateSMILES	(	Reaction	rxn,
		bool	canonical = False,
		bool	ord_h_deplete = True,
		int	atom_flags = 2147483648,
		int	bond_flags = 2147483648
	)

Parameters

rxn
canonical
ord_h_deplete
atom_flags
bond_flags

Returns

clearReactionData()

None CDPL.Chem.clearReactionData

(

Reaction

rxn

)

Parameters

rxn

hasReactionData()

bool CDPL.Chem.hasReactionData

(

Reaction

rxn

)

Parameters

rxn

Returns

getReactionData()

StringDataBlock CDPL.Chem.getReactionData

(

Reaction

rxn

)

Parameters

rxn

Returns

setReactionData()

None CDPL.Chem.setReactionData	(	Reaction	rxn,
		StringDataBlock	data
	)

Parameters

rxn
data

clearMDLMoleculeRecord()

None CDPL.Chem.clearMDLMoleculeRecord

(

Reaction

rxn

)

Parameters

rxn

hasMDLMoleculeRecord()

bool CDPL.Chem.hasMDLMoleculeRecord

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLMoleculeRecord()

Molecule CDPL.Chem.getMDLMoleculeRecord

(

Reaction

rxn

)

Parameters

rxn

Returns

setMDLMoleculeRecord()

None CDPL.Chem.setMDLMoleculeRecord	(	Reaction	rxn,
		Molecule	mol_rec
	)

Parameters

rxn
mol_rec

calcHashCode() [2/2]

int CDPL.Chem.calcHashCode	(	Reaction	rxn,
		int	role_mask = 7,
		int	atom_flags = 2147483648,
		int	bond_flags = 2147483648,
		bool	ord_h_deplete = True
	)

Parameters

rxn
role_mask
atom_flags
bond_flags
ord_h_deplete

Returns

clearMDLProgramName() [2/2]

None CDPL.Chem.clearMDLProgramName

(

Reaction

rxn

)

Parameters

rxn

hasMDLProgramName() [2/2]

bool CDPL.Chem.hasMDLProgramName

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLProgramName() [2/2]

str CDPL.Chem.getMDLProgramName

(

Reaction

rxn

)

Parameters

rxn

Returns

setMDLProgramName() [2/2]

None CDPL.Chem.setMDLProgramName	(	Reaction	rxn,
		str	name
	)

Parameters

rxn
name

clearName() [3/3]

None CDPL.Chem.clearName

(

Reaction

rxn

)

Parameters

rxn

hasName() [3/3]

bool CDPL.Chem.hasName

(

Reaction

rxn

)

Parameters

rxn

Returns

getName() [3/3]

str CDPL.Chem.getName

(

Reaction

rxn

)

Parameters

rxn

Returns

setName() [3/3]

None CDPL.Chem.setName	(	Reaction	rxn,
		str	name
	)

Parameters

rxn
name

perceiveAtomMapping() [1/2]

AtomMapping CDPL.Chem.perceiveAtomMapping

(

Reaction

rxn

)

Parameters

rxn

Returns

perceiveAtomMapping() [2/2]

AtomMapping CDPL.Chem.perceiveAtomMapping	(	Reaction	rxn,
		bool	overwrite
	)

Parameters

rxn
overwrite

Returns

clearAtomMapping()

None CDPL.Chem.clearAtomMapping

(

Reaction

rxn

)

Parameters

rxn

hasAtomMapping()

bool CDPL.Chem.hasAtomMapping

(

Reaction

rxn

)

Parameters

rxn

Returns

getAtomMapping()

AtomMapping CDPL.Chem.getAtomMapping

(

Reaction

rxn

)

Parameters

rxn

Returns

setAtomMapping()

None CDPL.Chem.setAtomMapping	(	Reaction	rxn,
		AtomMapping	mapping
	)

Parameters

rxn
mapping

clearMDLRXNFileVersion()

None CDPL.Chem.clearMDLRXNFileVersion

(

Reaction

rxn

)

Parameters

rxn

hasMDLRXNFileVersion()

bool CDPL.Chem.hasMDLRXNFileVersion

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLRXNFileVersion()

int CDPL.Chem.getMDLRXNFileVersion

(

Reaction

rxn

)

Parameters

rxn

Returns

setMDLRXNFileVersion()

None CDPL.Chem.setMDLRXNFileVersion	(	Reaction	rxn,
		int	version
	)

Parameters

rxn
version

generateMatchExpression() [5/6]

ReactionMatchExpression CDPL.Chem.generateMatchExpression

(

Reaction

rxn

)

Parameters

rxn

Returns

generateMatchExpression() [6/6]

ReactionMatchExpression CDPL.Chem.generateMatchExpression	(	Reaction	rxn,
		bool	overwrite
	)

Parameters

rxn
overwrite

Returns

clearMatchExpression() [4/4]

None CDPL.Chem.clearMatchExpression

(

Reaction

rxn

)

Parameters

rxn

hasMatchExpression() [4/4]

bool CDPL.Chem.hasMatchExpression

(

Reaction

rxn

)

Parameters

rxn

Returns

getMatchExpression() [4/4]

ReactionMatchExpression CDPL.Chem.getMatchExpression

(

Reaction

rxn

)

Parameters

rxn

Returns

setMatchExpression() [4/4]

None CDPL.Chem.setMatchExpression	(	Reaction	rxn,
		ReactionMatchExpression	expr
	)

Parameters

rxn
expr

clearTimestamp() [2/2]

None CDPL.Chem.clearTimestamp

(

Reaction

rxn

)

Parameters

rxn

hasTimestamp() [2/2]

bool CDPL.Chem.hasTimestamp

(

Reaction

rxn

)

Parameters

rxn

Returns

getTimestamp() [2/2]

int CDPL.Chem.getTimestamp

(

Reaction

rxn

)

Parameters

rxn

Returns

setTimestamp() [2/2]

None CDPL.Chem.setTimestamp	(	Reaction	rxn,
		int	time
	)

Parameters

rxn
time

clearMDLRegistryNumber() [2/2]

None CDPL.Chem.clearMDLRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

hasMDLRegistryNumber() [2/2]

bool CDPL.Chem.hasMDLRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLRegistryNumber() [2/2]

int CDPL.Chem.getMDLRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

setMDLRegistryNumber() [2/2]

None CDPL.Chem.setMDLRegistryNumber	(	Reaction	rxn,
		int	reg_no
	)

Parameters

rxn
reg_no

clearMDLInternalRegistryNumber()

None CDPL.Chem.clearMDLInternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

hasMDLInternalRegistryNumber()

bool CDPL.Chem.hasMDLInternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLInternalRegistryNumber()

str CDPL.Chem.getMDLInternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

setMDLInternalRegistryNumber()

None CDPL.Chem.setMDLInternalRegistryNumber	(	Reaction	rxn,
		str	reg_no
	)

Parameters

rxn
reg_no

clearMDLExternalRegistryNumber()

None CDPL.Chem.clearMDLExternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

hasMDLExternalRegistryNumber()

bool CDPL.Chem.hasMDLExternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLExternalRegistryNumber()

str CDPL.Chem.getMDLExternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

setMDLExternalRegistryNumber()

None CDPL.Chem.setMDLExternalRegistryNumber	(	Reaction	rxn,
		str	reg_no
	)

Parameters

rxn
reg_no

calcBasicProperties() [2/2]

None CDPL.Chem.calcBasicProperties	(	Reaction	rxn,
		bool	overwrite
	)

Parameters

rxn
overwrite

clearMDLUserInitials() [2/2]

None CDPL.Chem.clearMDLUserInitials

(

Reaction

rxn

)

Parameters

rxn

hasMDLUserInitials() [2/2]

bool CDPL.Chem.hasMDLUserInitials

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLUserInitials() [2/2]

str CDPL.Chem.getMDLUserInitials

(

Reaction

rxn

)

Parameters

rxn

Returns

setMDLUserInitials() [2/2]

None CDPL.Chem.setMDLUserInitials	(	Reaction	rxn,
		str	initials
	)

Parameters

rxn
initials

generateMatchExpressions() [2/2]

None CDPL.Chem.generateMatchExpressions	(	Reaction	rxn,
		bool	overwrite
	)

Parameters

rxn
overwrite

perceiveComponentGroups() [3/4]

FragmentList CDPL.Chem.perceiveComponentGroups

(

Reaction

rxn

)

Parameters

rxn

Returns

perceiveComponentGroups() [4/4]

FragmentList CDPL.Chem.perceiveComponentGroups	(	Reaction	rxn,
		bool	overwrite
	)

Parameters

rxn
overwrite

Returns

clearComponentGroups() [2/2]

None CDPL.Chem.clearComponentGroups

(

Reaction

rxn

)

Parameters

rxn

hasComponentGroups() [2/2]

bool CDPL.Chem.hasComponentGroups

(

Reaction

rxn

)

Parameters

rxn

Returns

getComponentGroups() [2/2]

FragmentList CDPL.Chem.getComponentGroups

(

Reaction

rxn

)

Parameters

rxn

Returns

setComponentGroups() [2/2]

None CDPL.Chem.setComponentGroups	(	Reaction	rxn,
		FragmentList	comp_groups
	)

Parameters

rxn
comp_groups

setBondMatchConstraints() [2/2]

None CDPL.Chem.setBondMatchConstraints	(	Reaction	rxn,
		MatchConstraintList	constr,
		bool	overwrite
	)

Parameters

rxn
constr
overwrite

setAtomMatchConstraints() [2/2]

None CDPL.Chem.setAtomMatchConstraints	(	Reaction	rxn,
		MatchConstraintList	constr,
		bool	overwrite
	)

Parameters

rxn
constr
overwrite

clearMatchConstraints() [4/4]

None CDPL.Chem.clearMatchConstraints

(

Reaction

rxn

)

Parameters

rxn

hasMatchConstraints() [4/4]

bool CDPL.Chem.hasMatchConstraints

(

Reaction

rxn

)

Parameters

rxn

Returns

getMatchConstraints() [4/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

Reaction

rxn

)

Parameters

rxn

Returns

setMatchConstraints() [4/4]

None CDPL.Chem.setMatchConstraints	(	Reaction	rxn,
		MatchConstraintList	constr
	)

Parameters

rxn
constr

setComponentMatchConstraints()

None CDPL.Chem.setComponentMatchConstraints	(	Reaction	rxn,
		MatchConstraintList	constr,
		bool	overwrite
	)

Parameters

rxn
constr
overwrite

initSubstructureSearchTarget() [2/2]

None CDPL.Chem.initSubstructureSearchTarget	(	Reaction	rxn,
		bool	overwrite
	)

Parameters

rxn
overwrite

clearComment() [2/2]

None CDPL.Chem.clearComment

(

Reaction

rxn

)

Parameters

rxn

hasComment() [2/2]

bool CDPL.Chem.hasComment

(

Reaction

rxn

)

Parameters

rxn

Returns

getComment() [2/2]

str CDPL.Chem.getComment

(

Reaction

rxn

)

Parameters

rxn

Returns

setComment() [2/2]

None CDPL.Chem.setComment	(	Reaction	rxn,
		str	comment
	)

Parameters

rxn
comment

initSubstructureSearchQuery() [2/2]

None CDPL.Chem.initSubstructureSearchQuery	(	Reaction	rxn,
		bool	overwrite
	)

Parameters

rxn
overwrite

extendBoundingBox()

None CDPL.Chem.extendBoundingBox	(	Math.Vector3D	min,
		Math.Vector3D	max,
		Math.Vector3D	coords,
		bool	reset = False
	)

Parameters

min
max
coords
reset

insideBoundingBox() [3/3]

bool CDPL.Chem.insideBoundingBox	(	Math.Vector3D	min,
		Math.Vector3D	max,
		Math.Vector3D	coords
	)

Parameters

min
max
coords

Returns

sybylToAtomType()

int CDPL.Chem.sybylToAtomType

(

int

sybyl_type

)

Parameters

sybyl_type

Returns

getSybylBondTypeString()

str CDPL.Chem.getSybylBondTypeString

(

int

sybyl_type

)

Parameters

sybyl_type

Returns

getSybylAtomTypeString()

str CDPL.Chem.getSybylAtomTypeString

(

int

sybyl_type

)

Parameters

sybyl_type

Returns

atomTypesMatch()

bool CDPL.Chem.atomTypesMatch	(	int	qry_type,
		int	tgt_type
	)

Parameters

qry_type
tgt_type

Returns

parseSMILES() [1/2]

Molecule CDPL.Chem.parseSMILES

(

str

smiles

)

Parameters

smiles

Returns

parseSMILES() [2/2]

bool CDPL.Chem.parseSMILES	(	str	smiles,
		Molecule	mol
	)

Parameters

smiles
mol

Returns

parseSMARTS() [1/2]

Molecule CDPL.Chem.parseSMARTS	(	str	smarts,
		bool	init_qry = True
	)

Parameters

smarts
init_qry

Returns

parseSMARTS() [2/2]

bool CDPL.Chem.parseSMARTS	(	str	smarts,
		Molecule	mol,
		bool	init_qry = True
	)

Parameters

smarts
mol
init_qry

Returns