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
	Implementation of the amide imidic-acid tautomerization rule. 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
	MatchExpression that checks the atom type of a target atom against a query atom type. 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
	Default concrete implementation of the Chem.Reaction abstract interface. 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
	Calculator that derives 2D wedge/hash bond stereo flags from atom 2D coordinates and stereochemical descriptors of a molecular graph. 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
	Calculation of canonical atom numberings for molecular graphs using McKay's algorithm for practical graph isomorphism. 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	ConjugatedRingBondPatternSwitching
	ConjugatedRingBondPatternSwitching. 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
	Abstract base class for representations of a chemical structure as a graph of bonded atoms. 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
	Implementation of the nitro aci-nitro tautomerization rule. 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 an MDL SD- or RD-File data record (see [CTFILE]). More...
class	StringDataBlockEntry
	Represents a data item in the structure or reaction data block of an MDL SD- or RD-File data record (see [CTFILE]). More...
class	SubstructureEditor
	SubstructureEditor. 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
	Functor for the calculation of a heuristic stability score of a tautomeric form represented as a molecular graph. 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
	Writer for molecular graph data in XYZ format to an output stream. More...
class	XYZMoleculeInputHandler
	A handler for the input of molecule data in the XYZ format. More...
class	XYZMoleculeReader
	Reader for molecule data in XYZ format from an input stream. More...

Functions
None	set2DCoordinates (Atom atom, Math.Vector2D coords)
bool	has2DCoordinates (Atom atom)
Math.Vector2D	get2DCoordinates (Atom atom)
None	clear2DCoordinates (Atom atom)
None	set2DCoordinates (AtomContainer cntnr, Math.Vector2DArray coords)
None	get2DCoordinates (AtomContainer cntnr, Math.Vector2DArray coords, bool append=False)
None	set2DStereoFlag (Bond bond, int flag)
bool	has2DStereoFlag (Bond bond)
int	get2DStereoFlag (Bond bond)
None	clear2DStereoFlag (Bond bond)
None	set3DCoordinatesArray (Atom atom, Math.Vector3DArray coords_array)
bool	has3DCoordinatesArray (Atom atom)
Math.Vector3DArray	get3DCoordinatesArray (Atom atom)
None	clear3DCoordinatesArray (Atom atom)
None	get3DCoordinates (AtomContainer cntnr, Math.Vector3DArray coords, Atom3DCoordinatesFunction coords_func, bool append=False)
None	set3DCoordinates (Entity3D entity, Math.Vector3D coords)
bool	has3DCoordinates (Entity3D entity)
Math.Vector3D	get3DCoordinates (Entity3D entity)
None	clear3DCoordinates (Entity3D entity)
None	set3DCoordinates (Entity3DContainer cntnr, Math.Vector3DArray coords)
None	get3DCoordinates (Entity3DContainer cntnr, Math.Vector3DArray coords, bool append=False)
FragmentList	getAromaticRings (MolecularGraph molgraph)
FragmentList	getAromaticSSSRSubset (MolecularGraph molgraph)
None	setAromaticSubstructure (MolecularGraph molgraph, Fragment substruct)
bool	hasAromaticSubstructure (MolecularGraph molgraph)
Fragment	getAromaticSubstructure (MolecularGraph molgraph)
None	clearAromaticSubstructure (MolecularGraph molgraph)
None	setAromaticityFlag (Atom atom, bool aromatic)
bool	hasAromaticityFlag (Atom atom)
bool	getAromaticityFlag (Atom atom)
None	clearAromaticityFlag (Atom atom)
None	setAromaticityFlag (Bond bond, bool aromatic)
bool	hasAromaticityFlag (Bond bond)
bool	getAromaticityFlag (Bond bond)
None	clearAromaticityFlag (Bond bond)
None	setAromaticityFlags (MolecularGraph molgraph, bool overwrite)
None	setAtomMappingID (Atom atom, int id)
bool	hasAtomMappingID (Atom atom)
int	getAtomMappingID (Atom atom)
None	clearAtomMappingID (Atom atom)
None	setAtomMapping (Reaction rxn, AtomMapping mapping)
bool	hasAtomMapping (Reaction rxn)
AtomMapping	getAtomMapping (Reaction rxn)
None	clearAtomMapping (Reaction rxn)
None	setAtomMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr, bool overwrite)
None	setAtomMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite)
None	setAtomSymbolsFromTypes (MolecularGraph molgraph, bool overwrite)
None	setAtomTypesFromSymbols (MolecularGraph molgraph, bool overwrite)
None	setBondMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr, bool overwrite)
None	setBondMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite)
None	setCIPConfiguration (Atom atom, int config)
bool	hasCIPConfiguration (Atom atom)
int	getCIPConfiguration (Atom atom)
None	clearCIPConfiguration (Atom atom)
None	setCIPConfiguration (Bond bond, int config)
bool	hasCIPConfiguration (Bond bond)
int	getCIPConfiguration (Bond bond)
None	clearCIPConfiguration (Bond bond)
None	setCIPPriority (Atom atom, int priority)
bool	hasCIPPriority (Atom atom)
int	getCIPPriority (Atom atom)
None	clearCIPPriority (Atom atom)
None	setCanonicalNumber (Atom atom, int num)
bool	hasCanonicalNumber (Atom atom)
int	getCanonicalNumber (Atom atom)
None	clearCanonicalNumber (Atom atom)
None	setComment (MolecularGraph molgraph, str comment)
bool	hasComment (MolecularGraph molgraph)
str	getComment (MolecularGraph molgraph)
None	clearComment (MolecularGraph molgraph)
None	setComment (Reaction rxn, str comment)
bool	hasComment (Reaction rxn)
str	getComment (Reaction rxn)
None	clearComment (Reaction rxn)
int	getCompleteBondCount (MolecularGraph molgraph)
None	setComponentGroupID (Atom atom, int id)
bool	hasComponentGroupID (Atom atom)
int	getComponentGroupID (Atom atom)
None	clearComponentGroupID (Atom atom)
None	setComponentGroups (MolecularGraph molgraph, FragmentList comp_groups)
bool	hasComponentGroups (MolecularGraph molgraph)
FragmentList	getComponentGroups (MolecularGraph molgraph)
None	clearComponentGroups (MolecularGraph molgraph)
None	setComponentGroups (Reaction rxn, FragmentList comp_groups)
bool	hasComponentGroups (Reaction rxn)
FragmentList	getComponentGroups (Reaction rxn)
None	clearComponentGroups (Reaction rxn)
None	setComponentMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite)
None	setComponents (MolecularGraph molgraph, FragmentList comps)
bool	hasComponents (MolecularGraph molgraph)
FragmentList	getComponents (MolecularGraph molgraph)
None	clearComponents (MolecularGraph molgraph)
None	getConformation (AtomContainer cntnr, int conf_idx, Math.Vector3DArray coords, bool append=False)
float	getConformationEnergy (MolecularGraph molgraph, int conf_idx)
None	setConformationIndex (MolecularGraph molgraph, int index)
bool	hasConformationIndex (MolecularGraph molgraph)
int	getConformationIndex (MolecularGraph molgraph)
None	clearConformationIndex (MolecularGraph molgraph)
None	setConformation (MolecularGraph molgraph, int conf_idx, Math.Vector3DArray coords, float energy)
None	clearConformations (AtomContainer cntnr)
Math.Vector3D	getConformer3DCoordinates (Atom atom, int conf_idx)
None	setConformerEnergies (MolecularGraph molgraph, Util.DArray energies)
bool	hasConformerEnergies (MolecularGraph molgraph)
Util.DArray	getConformerEnergies (MolecularGraph molgraph)
None	clearConformerEnergies (MolecularGraph molgraph)
int	getConnectedAtomsAndBonds (Atom atom, MolecularGraph molgraph, list atoms, list bonds, Atom excl_atom)
int	getConnectedAtoms (Atom atom, MolecularGraph molgraph, list atoms, Atom excl_atom)
None	getContainedFragments (MolecularGraph molgraph, FragmentList frag_list, FragmentList cont_frag_list, bool append=False, bool atoms=True, bool bonds=True)
None	getContainingFragments (Atom atom, FragmentList frag_list, FragmentList cont_frag_list)
None	getContainingFragments (Bond bond, FragmentList frag_list, FragmentList cont_frag_list)
None	getContainingFragments (MolecularGraph molgraph, FragmentList frag_list, FragmentList cont_frag_list, bool append=False, bool atoms=True, bool bonds=True)
bool	hasCoordinates (AtomContainer cntnr, int dim)
None	setCyclicSubstructure (MolecularGraph molgraph, Fragment substruct)
bool	hasCyclicSubstructure (MolecularGraph molgraph)
Fragment	getCyclicSubstructure (MolecularGraph molgraph)
None	clearCyclicSubstructure (MolecularGraph molgraph)
None	setDirection (Bond bond, int dir)
bool	hasDirection (Bond bond)
int	getDirection (Bond bond)
None	clearDirection (Bond bond)
int	getEnvironment (Atom atom, MolecularGraph molgraph, int max_dist, Fragment env, bool append=False)
None	setFormalCharge (Atom atom, int charge)
bool	hasFormalCharge (Atom atom)
int	getFormalCharge (Atom atom)
None	clearFormalCharge (Atom atom)
int	getGenericType (Atom atom)
None	setGeometricalDistanceMatrix (MolecularGraph molgraph, Math.DMatrix mtx)
bool	hasGeometricalDistanceMatrix (MolecularGraph molgraph)
Math.DMatrix	getGeometricalDistanceMatrix (MolecularGraph molgraph)
None	clearGeometricalDistanceMatrix (MolecularGraph molgraph)
None	setHashCode (MolecularGraph molgraph, int hash_code)
bool	hasHashCode (MolecularGraph molgraph)
int	getHashCode (MolecularGraph molgraph)
None	clearHashCode (MolecularGraph molgraph)
None	setHybridizationState (Atom atom, int state)
bool	hasHybridizationState (Atom atom)
int	getHybridizationState (Atom atom)
None	clearHybridizationState (Atom atom)
None	setImplicitHydrogenCount (Atom atom, int count)
bool	hasImplicitHydrogenCount (Atom atom)
int	getImplicitHydrogenCount (Atom atom)
None	clearImplicitHydrogenCount (Atom atom)
int	getIncidentBonds (Atom atom, MolecularGraph molgraph, list bonds, Atom excl_atom)
None	setIsotope (Atom atom, int isotope)
bool	hasIsotope (Atom atom)
int	getIsotope (Atom atom)
None	clearIsotope (Atom atom)
None	setMDLCTABVersion (MolecularGraph molgraph, int version)
bool	hasMDLCTABVersion (MolecularGraph molgraph)
int	getMDLCTABVersion (MolecularGraph molgraph)
None	clearMDLCTABVersion (MolecularGraph molgraph)
None	setMDLChiralFlag (MolecularGraph molgraph, bool flag)
bool	hasMDLChiralFlag (MolecularGraph molgraph)
bool	getMDLChiralFlag (MolecularGraph molgraph)
None	clearMDLChiralFlag (MolecularGraph molgraph)
None	setMDLDimensionality (MolecularGraph molgraph, int dim)
bool	hasMDLDimensionality (MolecularGraph molgraph)
int	getMDLDimensionality (MolecularGraph molgraph)
None	clearMDLDimensionality (MolecularGraph molgraph)
None	setMDLEnergy (MolecularGraph molgraph, float energy)
bool	hasMDLEnergy (MolecularGraph molgraph)
float	getMDLEnergy (MolecularGraph molgraph)
None	clearMDLEnergy (MolecularGraph molgraph)
None	setMDLExternalRegistryNumber (Reaction rxn, str reg_no)
bool	hasMDLExternalRegistryNumber (Reaction rxn)
str	getMDLExternalRegistryNumber (Reaction rxn)
None	clearMDLExternalRegistryNumber (Reaction rxn)
None	setMDLInternalRegistryNumber (Reaction rxn, str reg_no)
bool	hasMDLInternalRegistryNumber (Reaction rxn)
str	getMDLInternalRegistryNumber (Reaction rxn)
None	clearMDLInternalRegistryNumber (Reaction rxn)
None	setMDLMoleculeRecord (Reaction rxn, Molecule mol_rec)
bool	hasMDLMoleculeRecord (Reaction rxn)
Molecule	getMDLMoleculeRecord (Reaction rxn)
None	clearMDLMoleculeRecord (Reaction rxn)
None	setMDLParity (Atom atom, int parity)
bool	hasMDLParity (Atom atom)
int	getMDLParity (Atom atom)
None	clearMDLParity (Atom atom)
None	setMDLProgramName (MolecularGraph molgraph, str name)
bool	hasMDLProgramName (MolecularGraph molgraph)
str	getMDLProgramName (MolecularGraph molgraph)
None	clearMDLProgramName (MolecularGraph molgraph)
None	setMDLProgramName (Reaction rxn, str name)
bool	hasMDLProgramName (Reaction rxn)
str	getMDLProgramName (Reaction rxn)
None	clearMDLProgramName (Reaction rxn)
None	setMDLRXNFileVersion (Reaction rxn, int version)
bool	hasMDLRXNFileVersion (Reaction rxn)
int	getMDLRXNFileVersion (Reaction rxn)
None	clearMDLRXNFileVersion (Reaction rxn)
None	setMDLRegistryNumber (MolecularGraph molgraph, int reg_no)
bool	hasMDLRegistryNumber (MolecularGraph molgraph)
int	getMDLRegistryNumber (MolecularGraph molgraph)
None	clearMDLRegistryNumber (MolecularGraph molgraph)
None	setMDLRegistryNumber (Reaction rxn, int reg_no)
bool	hasMDLRegistryNumber (Reaction rxn)
int	getMDLRegistryNumber (Reaction rxn)
None	clearMDLRegistryNumber (Reaction rxn)
None	setMDLScalingFactor1 (MolecularGraph molgraph, int factor)
bool	hasMDLScalingFactor1 (MolecularGraph molgraph)
int	getMDLScalingFactor1 (MolecularGraph molgraph)
None	clearMDLScalingFactor1 (MolecularGraph molgraph)
None	setMDLScalingFactor2 (MolecularGraph molgraph, float factor)
bool	hasMDLScalingFactor2 (MolecularGraph molgraph)
float	getMDLScalingFactor2 (MolecularGraph molgraph)
None	clearMDLScalingFactor2 (MolecularGraph molgraph)
None	setMDLStereoCareFlag (Atom atom, bool flag)
bool	hasMDLStereoCareFlag (Atom atom)
bool	getMDLStereoCareFlag (Atom atom)
None	clearMDLStereoCareFlag (Atom atom)
None	setMDLUserInitials (MolecularGraph molgraph, str initials)
bool	hasMDLUserInitials (MolecularGraph molgraph)
str	getMDLUserInitials (MolecularGraph molgraph)
None	clearMDLUserInitials (MolecularGraph molgraph)
None	setMDLUserInitials (Reaction rxn, str initials)
bool	hasMDLUserInitials (Reaction rxn)
str	getMDLUserInitials (Reaction rxn)
None	clearMDLUserInitials (Reaction rxn)
None	setMOL2Charge (Atom atom, float charge)
bool	hasMOL2Charge (Atom atom)
float	getMOL2Charge (Atom atom)
None	clearMOL2Charge (Atom atom)
None	setMOL2ChargeType (MolecularGraph molgraph, int type)
bool	hasMOL2ChargeType (MolecularGraph molgraph)
int	getMOL2ChargeType (MolecularGraph molgraph)
None	clearMOL2ChargeType (MolecularGraph molgraph)
None	setMOL2MoleculeType (MolecularGraph molgraph, int type)
bool	hasMOL2MoleculeType (MolecularGraph molgraph)
int	getMOL2MoleculeType (MolecularGraph molgraph)
None	clearMOL2MoleculeType (MolecularGraph molgraph)
None	setMOL2Name (Atom atom, str name)
bool	hasMOL2Name (Atom atom)
str	getMOL2Name (Atom atom)
None	clearMOL2Name (Atom atom)
None	setMOL2SubstructureChain (Atom atom, str chain)
bool	hasMOL2SubstructureChain (Atom atom)
str	getMOL2SubstructureChain (Atom atom)
None	clearMOL2SubstructureChain (Atom atom)
None	setMOL2SubstructureID (Atom atom, int id)
bool	hasMOL2SubstructureID (Atom atom)
int	getMOL2SubstructureID (Atom atom)
None	clearMOL2SubstructureID (Atom atom)
None	setMOL2SubstructureName (Atom atom, str name)
bool	hasMOL2SubstructureName (Atom atom)
str	getMOL2SubstructureName (Atom atom)
None	clearMOL2SubstructureName (Atom atom)
None	setMOL2SubstructureSubtype (Atom atom, str subtype)
bool	hasMOL2SubstructureSubtype (Atom atom)
str	getMOL2SubstructureSubtype (Atom atom)
None	clearMOL2SubstructureSubtype (Atom atom)
None	setMatchConstraints (Atom atom, MatchConstraintList constr)
bool	hasMatchConstraints (Atom atom)
MatchConstraintList	getMatchConstraints (Atom atom)
None	clearMatchConstraints (Atom atom)
None	setMatchConstraints (Bond bond, MatchConstraintList constr)
bool	hasMatchConstraints (Bond bond)
MatchConstraintList	getMatchConstraints (Bond bond)
None	clearMatchConstraints (Bond bond)
None	setMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr)
bool	hasMatchConstraints (MolecularGraph molgraph)
MatchConstraintList	getMatchConstraints (MolecularGraph molgraph)
None	clearMatchConstraints (MolecularGraph molgraph)
None	setMatchConstraints (Reaction rxn, MatchConstraintList constr)
bool	hasMatchConstraints (Reaction rxn)
MatchConstraintList	getMatchConstraints (Reaction rxn)
None	clearMatchConstraints (Reaction rxn)
None	setMatchExpression (Atom atom, AtomMatchExpression expr)
bool	hasMatchExpression (Atom atom)
AtomMatchExpression	getMatchExpression (Atom atom)
None	clearMatchExpression (Atom atom)
None	setMatchExpression (Bond bond, BondMatchExpression expr)
bool	hasMatchExpression (Bond bond)
BondMatchExpression	getMatchExpression (Bond bond)
None	clearMatchExpression (Bond bond)
None	setMatchExpression (MolecularGraph molgraph, MolecularGraphMatchExpression expr)
bool	hasMatchExpression (MolecularGraph molgraph)
MolecularGraphMatchExpression	getMatchExpression (MolecularGraph molgraph)
None	clearMatchExpression (MolecularGraph molgraph)
None	setMatchExpression (Reaction rxn, ReactionMatchExpression expr)
bool	hasMatchExpression (Reaction rxn)
ReactionMatchExpression	getMatchExpression (Reaction rxn)
None	clearMatchExpression (Reaction rxn)
None	setMatchExpressionString (Atom atom, str expr_str)
bool	hasMatchExpressionString (Atom atom)
str	getMatchExpressionString (Atom atom)
None	clearMatchExpressionString (Atom atom)
None	setMatchExpressionString (Bond bond, str expr_str)
bool	hasMatchExpressionString (Bond bond)
str	getMatchExpressionString (Bond bond)
None	clearMatchExpressionString (Bond bond)
int	getMaxAtomMappingID (AtomContainer cntnr)
int	getMaxAtomMappingID (Reaction rxn)
int	getMaxComponentGroupID (AtomContainer cntnr)
int	getMaxComponentGroupID (Reaction rxn)
None	setMorganNumber (Atom atom, int num)
bool	hasMorganNumber (Atom atom)
int	getMorganNumber (Atom atom)
None	clearMorganNumber (Atom atom)
None	setName (Atom atom, str name)
bool	hasName (Atom atom)
str	getName (Atom atom)
None	clearName (Atom atom)
None	setName (MolecularGraph molgraph, str name)
bool	hasName (MolecularGraph molgraph)
str	getName (MolecularGraph molgraph)
None	clearName (MolecularGraph molgraph)
None	setName (Reaction rxn, str name)
bool	hasName (Reaction rxn)
str	getName (Reaction rxn)
None	clearName (Reaction rxn)
int	getNumConformations (AtomContainer cntnr)
int	getNumContainingFragments (Atom atom, FragmentList frag_list)
int	getNumContainingFragments (Bond bond, FragmentList frag_list)
None	setOrder (Bond bond, int order)
bool	hasOrder (Bond bond)
int	getOrder (Bond bond)
None	clearOrder (Bond bond)
None	setPiElectronSystems (MolecularGraph molgraph, ElectronSystemList pi_systems)
bool	hasPiElectronSystems (MolecularGraph molgraph)
ElectronSystemList	getPiElectronSystems (MolecularGraph molgraph)
None	clearPiElectronSystems (MolecularGraph molgraph)
None	setRadicalType (Atom atom, int type)
bool	hasRadicalType (Atom atom)
int	getRadicalType (Atom atom)
None	clearRadicalType (Atom atom)
None	setReactionCenterStatus (Atom atom, int status)
bool	hasReactionCenterStatus (Atom atom)
int	getReactionCenterStatus (Atom atom)
None	clearReactionCenterStatus (Atom atom)
None	setReactionCenterStatus (Bond bond, int status)
bool	hasReactionCenterStatus (Bond bond)
int	getReactionCenterStatus (Bond bond)
None	clearReactionCenterStatus (Bond bond)
None	setReactionData (Reaction rxn, StringDataBlock data)
bool	hasReactionData (Reaction rxn)
StringDataBlock	getReactionData (Reaction rxn)
None	clearReactionData (Reaction rxn)
None	setRingFlag (Atom atom, bool in_ring)
bool	hasRingFlag (Atom atom)
bool	getRingFlag (Atom atom)
None	clearRingFlag (Atom atom)
None	setRingFlag (Bond bond, bool in_ring)
bool	hasRingFlag (Bond bond)
bool	getRingFlag (Bond bond)
None	clearRingFlag (Bond bond)
None	setRingFlags (MolecularGraph molgraph, bool overwrite)
None	setRings (MolecularGraph molgraph, FragmentList rings)
bool	hasRings (MolecularGraph molgraph)
FragmentList	getRings (MolecularGraph molgraph)
None	clearRings (MolecularGraph molgraph)
None	setSSSR (MolecularGraph molgraph, FragmentList sssr)
bool	hasSSSR (MolecularGraph molgraph)
FragmentList	getSSSR (MolecularGraph molgraph)
None	clearSSSR (MolecularGraph molgraph)
int	getSizeOfLargestContainingFragment (Atom atom, FragmentList frag_list)
int	getSizeOfLargestContainingFragment (Bond bond, FragmentList frag_list)
int	getSizeOfSmallestContainingFragment (Atom atom, FragmentList frag_list)
int	getSizeOfSmallestContainingFragment (Bond bond, FragmentList frag_list)
None	setStereoCenterFlag (Atom atom, bool is_center)
bool	hasStereoCenterFlag (Atom atom)
bool	getStereoCenterFlag (Atom atom)
None	clearStereoCenterFlag (Atom atom)
None	setStereoCenterFlag (Bond bond, bool is_center)
bool	hasStereoCenterFlag (Bond bond)
bool	getStereoCenterFlag (Bond bond)
None	clearStereoCenterFlag (Bond bond)
None	setStereoDescriptor (Atom atom, StereoDescriptor descr)
bool	hasStereoDescriptor (Atom atom)
StereoDescriptor	getStereoDescriptor (Atom atom)
None	clearStereoDescriptor (Atom atom)
None	setStereoDescriptor (Bond bond, StereoDescriptor descr)
bool	hasStereoDescriptor (Bond bond)
StereoDescriptor	getStereoDescriptor (Bond bond)
None	clearStereoDescriptor (Bond bond)
None	setStoichiometricNumber (MolecularGraph molgraph, float num)
bool	hasStoichiometricNumber (MolecularGraph molgraph)
float	getStoichiometricNumber (MolecularGraph molgraph)
None	clearStoichiometricNumber (MolecularGraph molgraph)
None	setStructureData (MolecularGraph molgraph, StringDataBlock data)
bool	hasStructureData (MolecularGraph molgraph)
StringDataBlock	getStructureData (MolecularGraph molgraph)
None	clearStructureData (MolecularGraph molgraph)
str	getSybylAtomTypeString (int sybyl_type)
str	getSybylBondTypeString (int sybyl_type)
None	setSybylType (Atom atom, int type)
bool	hasSybylType (Atom atom)
int	getSybylType (Atom atom)
None	clearSybylType (Atom atom)
None	setSybylType (Bond bond, int type)
bool	hasSybylType (Bond bond)
int	getSybylType (Bond bond)
None	clearSybylType (Bond bond)
None	setSymbol (Atom atom, str symbol)
bool	hasSymbol (Atom atom)
str	getSymbol (Atom atom)
None	clearSymbol (Atom atom)
str	getSymbolForType (Atom atom)
None	setSymmetryClass (Atom atom, int class_id)
bool	hasSymmetryClass (Atom atom)
int	getSymmetryClass (Atom atom)
None	clearSymmetryClass (Atom atom)
None	setTimestamp (MolecularGraph molgraph, int time)
bool	hasTimestamp (MolecularGraph molgraph)
int	getTimestamp (MolecularGraph molgraph)
None	clearTimestamp (MolecularGraph molgraph)
None	setTimestamp (Reaction rxn, int time)
bool	hasTimestamp (Reaction rxn)
int	getTimestamp (Reaction rxn)
None	clearTimestamp (Reaction rxn)
int	getTopologicalDistance (Atom atom1, Atom atom2, MolecularGraph molgraph)
None	setTopologicalDistanceMatrix (MolecularGraph molgraph, Math.ULMatrix mtx)
bool	hasTopologicalDistanceMatrix (MolecularGraph molgraph)
Math.ULMatrix	getTopologicalDistanceMatrix (MolecularGraph molgraph)
None	clearTopologicalDistanceMatrix (MolecularGraph molgraph)
None	setType (Atom atom, int type)
bool	hasType (Atom atom)
int	getType (Atom atom)
None	clearType (Atom atom)
int	getTypeForSymbol (Atom atom)
None	setUnpairedElectronCount (Atom atom, int count)
bool	hasUnpairedElectronCount (Atom atom)
int	getUnpairedElectronCount (Atom atom)
None	clearUnpairedElectronCount (Atom atom)
None	addConformation (AtomContainer cntnr, Math.Vector3DArray coords)
None	addConformation (MolecularGraph molgraph, Math.Vector3DArray coords, float energy)
bool	align2DCoordinates (MolecularGraph molgraph, AtomContainer atoms, Math.Vector2DArray ref_coords, bool fix_bond_stereo=True)
bool	align2DCoordinates (MolecularGraph molgraph, AtomMapping ref_atom_mpg, bool fix_bond_stereo=True)
bool	align2DCoordinates (MolecularGraph molgraph, MolecularGraph ref_molgraph, bool use_mcs, bool fix_bond_stereo=True)
bool	align2DCoordinates (MolecularGraph molgraph, MolecularGraph ref_molgraph, MolecularGraph substr_ptn, bool fix_bond_stereo=True)
bool	align3DCoordinates (Entity3DContainer cntnr, Entity3DContainer ref_entities, Math.Vector3DArray ref_coords)
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	applyConformation (AtomContainer cntnr, int conf_idx)
bool	atomTypesMatch (int qry_type, int tgt_type)
None	calc2DCoordinates (MolecularGraph molgraph, bool overwrite)
None	calcAtomCIPConfigurations (MolecularGraph molgraph, bool overwrite)
None	calcAtomStereoDescriptorsFromMDLParities (MolecularGraph molgraph, bool overwrite)
None	calcAtomStereoDescriptors (MolecularGraph molgraph, bool overwrite, int dim=1, bool check_stc_flag=True)
None	calcBasicProperties (MolecularGraph molgraph, bool overwrite)
None	calcBasicProperties (Reaction rxn, bool overwrite)
None	calcBond2DStereoFlags (MolecularGraph molgraph, bool overwrite)
None	calcBondCIPConfigurations (MolecularGraph molgraph, bool overwrite)
None	calcBondStereoDescriptors (MolecularGraph molgraph, bool overwrite, int dim=1, bool check_stc_flag=True)
None	calcBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func, bool reset=True)
None	calcBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max, bool reset=True)
None	calcCIPPriorities (MolecularGraph molgraph, bool overwrite)
None	calcCanonicalNumbering (MolecularGraph molgraph, bool overwrite, int atom_flags=2147483648, int bond_flags=2147483648)
bool	calcCenterOfMass (AtomContainer cntnr, Atom3DCoordinatesFunction coords_func, Math.Vector3D ctr)
bool	calcCentroid (AtomContainer cntnr, Atom3DCoordinatesFunction coords_func, Math.Vector3D ctr)
bool	calcCentroid (Entity3DContainer cntnr, Math.Vector3D ctr)
int	calcConfiguration (Atom atom, MolecularGraph molgraph, StereoDescriptor descr, Math.Vector3DArray coords)
int	calcConfiguration (Bond bond, MolecularGraph molgraph, StereoDescriptor descr, Math.Vector3DArray coords)
int	calcFormalCharge (Atom atom, MolecularGraph molgraph)
None	calcFormalCharges (MolecularGraph molgraph, bool overwrite)
None	calcGeometricalDistanceMatrix (Entity3DContainer cntnr, Math.DMatrix mtx)
Math.DMatrix	calcGeometricalDistanceMatrix (MolecularGraph molgraph, bool overwrite)
int	calcHashCode (MolecularGraph molgraph, int atom_flags=2147483648, int bond_flags=2147483648, bool ord_h_deplete=True)
int	calcHashCode (Reaction rxn, int role_mask=7, int atom_flags=2147483648, int bond_flags=2147483648, bool ord_h_deplete=True)
None	calcHydrogen3DCoordinates (MolecularGraph molgraph, bool undef_only=True)
int	calcImplicitHydrogenCount (Atom atom, MolecularGraph molgraph)
None	calcImplicitHydrogenCounts (MolecularGraph molgraph, bool overwrite)
None	calcMDLParities (MolecularGraph molgraph, bool overwrite)
int	calcMDLParity (Atom atom, MolecularGraph molgraph)
None	calcMorganNumbering (MolecularGraph molgraph, bool overwrite)
StereoDescriptor	calcStereoDescriptor (Atom atom, MolecularGraph molgraph, int dim=1)
StereoDescriptor	calcStereoDescriptor (Bond bond, MolecularGraph molgraph, int dim=1)
StereoDescriptor	calcStereoDescriptorFromMDLParity (Atom atom, MolecularGraph molgraph)
Math.ULMatrix	calcTopologicalDistanceMatrix (MolecularGraph molgraph, bool overwrite)
None	calcTopologicalDistanceMatrix (MolecularGraph molgraph, Math.ULMatrix mtx)
None	canonicalize (MolecularGraph molgraph, bool atoms=True, bool atom_nbrs=True, bool bonds=True, bool bond_atoms=False)
None	canonicalize (MolecularGraph molgraph, BoolAtom2Functor func, bool atoms=True, bool atom_nbrs=True, bool bonds=True, bool bond_atoms=False)
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)
bool	containsFragmentWithBond (FragmentList frag_list, Bond bond)
bool	containsFragmentWithMinSize (FragmentList frag_list, int min_size)
bool	containsMolecularGraph (MolecularGraph molgraph, MolecularGraph sub_molgraph, bool atoms=True, bool bonds=True)
None	copyAtomsIf (AtomContainer cntnr, Molecule mol, AtomPredicate pred, bool append=False)
None	copyAtomsIf (AtomContainer cntnr, Fragment frag, AtomPredicate pred, bool append=False)
None	copyAtomsIfNot (AtomContainer cntnr, Molecule mol, AtomPredicate pred, bool append=False)
None	copyAtomsIfNot (AtomContainer cntnr, Fragment frag, AtomPredicate pred, bool append=False)
int	createAtomTypeMask (AtomContainer cntnr, Util.BitSet mask, int type, bool reset=True, bool strict=True)
int	editSubstructures (MolecularGraph molgraph, Molecule result_mol, str search_ptns, str result_ptn, str exclude_ptns='')
int	editSubstructures (Molecule mol, str search_ptns, str result_ptn, str exclude_ptns='')
None	extendBoundingBox (Math.Vector3D min, Math.Vector3D max, Math.Vector3D coords, bool reset=False)
None	extractReactionCenter (MolecularGraph molgraph, Fragment rxn_center)
FragmentList	extractSSSRSubset (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph)
FragmentList	extractSSSRSubset (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, bool overwrite)
Math.ULMatrix	extractTopologicalDistanceSubMatrix (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, bool overwrite)
None	extractTopologicalDistanceSubMatrix (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, Math.ULMatrix mtx)
None	generateAdjacencyMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
None	generateBondAtomTypeMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
None	generateBondElectronMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
None	generateBondMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
object	generateINCHIKey (MolecularGraph molgraph)
object	generateINCHI (MolecularGraph molgraph, str options='/WarnOnEmptyStructure/AuxNone/NEWPSOFF', int dim=0)
None	generateIncidenceMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
AtomMatchExpression	generateMatchExpression (Atom atom, MolecularGraph molgraph)
BondMatchExpression	generateMatchExpression (Bond bond, MolecularGraph molgraph)
MolecularGraphMatchExpression	generateMatchExpression (MolecularGraph molgraph)
MolecularGraphMatchExpression	generateMatchExpression (MolecularGraph molgraph, bool overwrite)
ReactionMatchExpression	generateMatchExpression (Reaction rxn)
ReactionMatchExpression	generateMatchExpression (Reaction rxn, bool overwrite)
str	generateMatchExpressionString (Atom atom, MolecularGraph molgraph)
str	generateMatchExpressionString (Bond bond, MolecularGraph molgraph)
None	generateMatchExpressionStrings (MolecularGraph molgraph, bool overwrite)
None	generateMatchExpressions (MolecularGraph molgraph, bool overwrite)
None	generateMatchExpressions (Reaction rxn, bool overwrite)
object	generateSMILES (MolecularGraph molgraph, bool canonical=False, bool ord_h_deplete=True, int atom_flags=2147483648, int bond_flags=2147483648)
object	generateSMILES (Reaction rxn, bool canonical=False, bool ord_h_deplete=True, int atom_flags=2147483648, int bond_flags=2147483648)
None	initSubstructureSearchQuery (MolecularGraph molgraph, bool overwrite)
None	initSubstructureSearchQuery (Reaction rxn, bool overwrite)
None	initSubstructureSearchTarget (MolecularGraph molgraph, bool overwrite)
None	initSubstructureSearchTarget (Reaction rxn, bool overwrite)
bool	insideBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func)
bool	insideBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max)
bool	insideBoundingBox (Math.Vector3D min, Math.Vector3D max, Math.Vector3D coords)
bool	intersectsBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func)
bool	intersectsBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max)
bool	isAromatic (Fragment ring, MolecularGraph molgraph, Util.BitSet arom_bond_mask)
bool	isInFragmentOfSize (Atom atom, FragmentList frag_list, int size)
bool	isInFragmentOfSize (Bond bond, FragmentList frag_list, int size)
bool	isNotAromatic (Fragment ring, MolecularGraph molgraph)
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)
bool	isStereoCenter (Bond bond, MolecularGraph molgraph, bool check_asym=True, bool check_term_n=True, bool check_order=True, int min_ring_size=8)
None	kekulizeBonds (MolecularGraph molgraph)
bool	makeHydrogenComplete (Molecule mol, bool corr_impl_h_count=True)
	Converts all implicit hydrogens of the molecule mol to explicit hydrogen atoms. More...
bool	makeHydrogenDeplete (Fragment frag)
	Removes all explicit hydrogen atoms from the fragment frag. More...
bool	makeHydrogenDeplete (Molecule mol, bool corr_impl_h_count=True)
	Removes all explicit hydrogen atoms from the molecule mol. More...
bool	makeOrdinaryHydrogenDeplete (Fragment frag, int flags)
	Removes all explicit ordinary hydrogen atoms from the fragment frag. More...
bool	makeOrdinaryHydrogenDeplete (Molecule mol, int flags, bool corr_impl_h_count=True)
	Removes all explicit ordinary hydrogen atoms from the molecule mol. More...
None	markReachableAtoms (Atom atom, MolecularGraph molgraph, Util.BitSet atom_mask, bool reset=True)
Molecule	parseSMARTS (str smarts, bool init_qry=True)
bool	parseSMARTS (str smarts, Molecule mol, bool init_qry=True)
Molecule	parseSMILES (str smiles)
bool	parseSMILES (str smiles, Molecule mol)
Fragment	perceiveAromaticSubstructure (MolecularGraph molgraph)
Fragment	perceiveAromaticSubstructure (MolecularGraph molgraph, bool overwrite)
AtomMapping	perceiveAtomMapping (Reaction rxn)
AtomMapping	perceiveAtomMapping (Reaction rxn, bool overwrite)
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	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)
FragmentList	perceiveComponentGroups (MolecularGraph molgraph)
FragmentList	perceiveComponentGroups (MolecularGraph molgraph, bool overwrite)
FragmentList	perceiveComponentGroups (Reaction rxn)
FragmentList	perceiveComponentGroups (Reaction rxn, bool overwrite)
FragmentList	perceiveComponents (MolecularGraph molgraph)
FragmentList	perceiveComponents (MolecularGraph molgraph, bool overwrite)
Fragment	perceiveCyclicSubstructure (MolecularGraph molgraph)
Fragment	perceiveCyclicSubstructure (MolecularGraph molgraph, bool overwrite)
int	perceiveHybridizationState (Atom atom, MolecularGraph molgraph)
None	perceiveHybridizationStates (MolecularGraph molgraph, bool overwrite)
ElectronSystemList	perceivePiElectronSystems (MolecularGraph molgraph)
ElectronSystemList	perceivePiElectronSystems (MolecularGraph molgraph, bool overwrite)
FragmentList	perceiveRings (MolecularGraph molgraph)
FragmentList	perceiveRings (MolecularGraph molgraph, bool overwrite)
FragmentList	perceiveSSSR (MolecularGraph molgraph)
FragmentList	perceiveSSSR (MolecularGraph molgraph, bool overwrite)
None	perceiveSybylAtomTypes (MolecularGraph molgraph, bool overwrite)
int	perceiveSybylType (Atom atom, MolecularGraph molgraph)
int	perceiveSybylType (Bond bond, MolecularGraph molgraph)
None	perceiveSymmetryClasses (MolecularGraph molgraph, bool overwrite, int atom_flags=2147483648, int bond_flags=2147483648, bool inc_impl_h=True)
None	removeAtomsIf (Fragment frag, AtomPredicate pred)
None	removeAtomsIf (Molecule mol, AtomPredicate pred)
None	removeAtomsIfNot (Fragment frag, AtomPredicate pred)
None	removeAtomsIfNot (Molecule mol, AtomPredicate pred)
None	splitIntoFragments (MolecularGraph molgraph, FragmentList frag_list, Util.BitSet split_bond_mask, bool append=False)
int	sybylToAtomType (int sybyl_type)
None	transform2DCoordinates (AtomContainer cntnr, Math.Matrix3D mtx)
None	transform3DCoordinates (Entity3DContainer cntnr, Math.Matrix4D mtx)
None	transformConformation (AtomContainer cntnr, int conf_idx, Math.Matrix4D mtx)
None	transformConformations (AtomContainer cntnr, Math.Matrix4D mtx)
None	translateFragment (MolecularGraph src_molgraph, Fragment src_frag, MolecularGraph tgt_molgraph, Fragment tgt_frag, bool append=False)
None	translateFragments (MolecularGraph src_molgraph, FragmentList src_frag_list, MolecularGraph tgt_molgraph, FragmentList tgt_frag_list, bool append=False)
None	setBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr, bool fix)
bool	hasBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr)
bool	getBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr)
None	clearBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr)
None	setCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr, bool single_prec)
bool	hasCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
bool	getCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
None	clearCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
None	setCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
bool	hasCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
bool	getCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
None	clearCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr, str ns)
bool	hasCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr)
str	getCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr)
None	setCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr)
bool	getCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr)
None	clearCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr)
None	setCheckLineLengthParameter (Base.ControlParameterContainer cntnr, bool check)
bool	hasCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
bool	getCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
None	clearCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
None	setConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr, str pattern)
bool	hasConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr)
str	getConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr)
None	clearConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr)
None	setCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr, int dim)
bool	hasCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr)
int	getCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr)
None	clearCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr)
None	setINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr, str opts)
bool	hasINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr)
str	getINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr)
None	clearINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr)
None	setINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr, str opts)
bool	hasINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr)
str	getINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr)
None	clearINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr)
None	setJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr, bool separate)
bool	hasJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr)
bool	getJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr)
None	clearJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr)
None	setMDLCTABVersionParameter (Base.ControlParameterContainer cntnr, int version)
bool	hasMDLCTABVersionParameter (Base.ControlParameterContainer cntnr)
int	getMDLCTABVersionParameter (Base.ControlParameterContainer cntnr)
None	clearMDLCTABVersionParameter (Base.ControlParameterContainer cntnr)
None	setMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr, str tag)
bool	hasMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr)
str	getMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr)
None	clearMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr)
None	setMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
bool	hasMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
bool	getMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
None	clearMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
None	setMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr, bool ignore)
bool	hasMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr)
bool	getMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr)
None	clearMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr)
None	setMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr)
bool	getMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr)
None	clearMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr)
None	setMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr)
bool	getMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr)
None	clearMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr)
None	setMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr, int version)
bool	hasMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr)
int	getMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr)
None	clearMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr)
None	setMDLTrimLinesParameter (Base.ControlParameterContainer cntnr, bool trim)
bool	hasMDLTrimLinesParameter (Base.ControlParameterContainer cntnr)
bool	getMDLTrimLinesParameter (Base.ControlParameterContainer cntnr)
None	clearMDLTrimLinesParameter (Base.ControlParameterContainer cntnr)
None	setMDLTrimStringsParameter (Base.ControlParameterContainer cntnr, bool trim)
bool	hasMDLTrimStringsParameter (Base.ControlParameterContainer cntnr)
bool	getMDLTrimStringsParameter (Base.ControlParameterContainer cntnr)
None	clearMDLTrimStringsParameter (Base.ControlParameterContainer cntnr)
None	setMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr, bool trunc)
bool	hasMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr)
bool	getMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr)
None	clearMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr)
None	setMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr, bool trunc)
bool	hasMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr)
bool	getMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr)
None	clearMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr)
None	setMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr, bool update)
bool	hasMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr)
bool	getMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr)
None	clearMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr)
None	setMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)
bool	hasMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	clearMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	setMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr, int type)
bool	hasMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr)
int	getMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr)
None	clearMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr)
None	setMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
bool	hasMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
None	clearMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
None	setMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
bool	hasMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr)
None	clearMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr)
None	setMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr, int type)
bool	hasMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr)
int	getMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr)
None	clearMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr)
None	setMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	clearMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	setMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr)
None	clearMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr)
None	setMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr, bool read)
bool	hasMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr)
bool	getMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	clearMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	setMultiConfExportParameter (Base.ControlParameterContainer cntnr, bool multi_conf)
bool	hasMultiConfExportParameter (Base.ControlParameterContainer cntnr)
bool	getMultiConfExportParameter (Base.ControlParameterContainer cntnr)
None	clearMultiConfExportParameter (Base.ControlParameterContainer cntnr)
None	setMultiConfImportParameter (Base.ControlParameterContainer cntnr, bool multi_conf)
bool	hasMultiConfImportParameter (Base.ControlParameterContainer cntnr)
bool	getMultiConfImportParameter (Base.ControlParameterContainer cntnr)
None	clearMultiConfImportParameter (Base.ControlParameterContainer cntnr)
None	setMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr, MultiConfMoleculeInputProcessor proc)
bool	hasMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr)
MultiConfMoleculeInputProcessor	getMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr)
None	clearMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr)
None	setOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr, bool deplete)
bool	hasOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr)
bool	getOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr)
None	clearOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr)
None	setOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr)
bool	getOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr)
None	clearOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr)
None	setRecordSeparatorParameter (Base.ControlParameterContainer cntnr, str sep)
bool	hasRecordSeparatorParameter (Base.ControlParameterContainer cntnr)
str	getRecordSeparatorParameter (Base.ControlParameterContainer cntnr)
None	clearRecordSeparatorParameter (Base.ControlParameterContainer cntnr)
None	setSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr, int min_size)
bool	hasSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr)
int	getSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr)
None	setSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
None	setSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr, bool no_subset)
bool	hasSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr)
None	setSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr)
None	setSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr)
None	setSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr)
None	setSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr)
None	setSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr)
None	setSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
None	setSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr)
None	setSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr)
None	setSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr)
None	setSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr, str format)
bool	hasSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr)
str	getSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr)
None	setSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr, bool output)
bool	hasSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
bool	getSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
None	clearSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
None	setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)
bool	hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
bool	getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
None	clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
None	setXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)
bool	hasXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
bool	getXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	clearXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
None	setXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr, bool is_name)
bool	hasXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr)
bool	getXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr)
None	clearXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr)
None	setXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr, bool perceive)
bool	hasXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr)
bool	getXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr)
None	clearXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr)
None	setXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr, bool perceive)
bool	hasXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr)
bool	getXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr)
None	clearXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr)

Detailed Description

Contains classes and functions related to chemistry.

Function Documentation

set2DCoordinates() [1/2]

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

Parameters

atom
coords

has2DCoordinates()

bool CDPL.Chem.has2DCoordinates

(

Atom

atom

)

Parameters

atom

Returns

get2DCoordinates() [1/2]

Math.Vector2D CDPL.Chem.get2DCoordinates

(

Atom

atom

)

Parameters

atom

Returns

clear2DCoordinates()

None CDPL.Chem.clear2DCoordinates

(

Atom

atom

)

Parameters

atom

set2DCoordinates() [2/2]

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

Parameters

cntnr
coords

get2DCoordinates() [2/2]

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

Parameters

cntnr
coords
append

set2DStereoFlag()

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

Parameters

bond
flag

has2DStereoFlag()

bool CDPL.Chem.has2DStereoFlag

(

Bond

bond

)

Parameters

bond

Returns

get2DStereoFlag()

int CDPL.Chem.get2DStereoFlag

(

Bond

bond

)

Parameters

bond

Returns

clear2DStereoFlag()

None CDPL.Chem.clear2DStereoFlag

(

Bond

bond

)

Parameters

bond

set3DCoordinatesArray()

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

Parameters

atom
coords_array

has3DCoordinatesArray()

bool CDPL.Chem.has3DCoordinatesArray

(

Atom

atom

)

Parameters

atom

Returns

get3DCoordinatesArray()

Math.Vector3DArray CDPL.Chem.get3DCoordinatesArray

(

Atom

atom

)

Parameters

atom

Returns

clear3DCoordinatesArray()

None CDPL.Chem.clear3DCoordinatesArray

(

Atom

atom

)

Parameters

atom

get3DCoordinates() [1/3]

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

Parameters

cntnr
coords
coords_func
append

set3DCoordinates() [1/2]

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

Parameters

entity
coords

has3DCoordinates()

bool CDPL.Chem.has3DCoordinates

(

Entity3D

entity

)

Parameters

entity

Returns

get3DCoordinates() [2/3]

Math.Vector3D CDPL.Chem.get3DCoordinates

(

Entity3D

entity

)

Parameters

entity

Returns

clear3DCoordinates()

None CDPL.Chem.clear3DCoordinates

(

Entity3D

entity

)

Parameters

entity

set3DCoordinates() [2/2]

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

Parameters

cntnr
coords

get3DCoordinates() [3/3]

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

Parameters

cntnr
coords
append

getAromaticRings()

FragmentList CDPL.Chem.getAromaticRings

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getAromaticSSSRSubset()

FragmentList CDPL.Chem.getAromaticSSSRSubset

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setAromaticSubstructure()

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

Parameters

molgraph
substruct

hasAromaticSubstructure()

bool CDPL.Chem.hasAromaticSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getAromaticSubstructure()

Fragment CDPL.Chem.getAromaticSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearAromaticSubstructure()

None CDPL.Chem.clearAromaticSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

setAromaticityFlag() [1/2]

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

Parameters

atom
aromatic

hasAromaticityFlag() [1/2]

bool CDPL.Chem.hasAromaticityFlag

(

Atom

atom

)

Parameters

atom

Returns

getAromaticityFlag() [1/2]

bool CDPL.Chem.getAromaticityFlag

(

Atom

atom

)

Parameters

atom

Returns

clearAromaticityFlag() [1/2]

None CDPL.Chem.clearAromaticityFlag

(

Atom

atom

)

Parameters

atom

setAromaticityFlag() [2/2]

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

Parameters

bond
aromatic

hasAromaticityFlag() [2/2]

bool CDPL.Chem.hasAromaticityFlag

(

Bond

bond

)

Parameters

bond

Returns

getAromaticityFlag() [2/2]

bool CDPL.Chem.getAromaticityFlag

(

Bond

bond

)

Parameters

bond

Returns

clearAromaticityFlag() [2/2]

None CDPL.Chem.clearAromaticityFlag

(

Bond

bond

)

Parameters

bond

setAromaticityFlags()

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

Parameters

molgraph
overwrite

setAtomMappingID()

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

Parameters

atom
id

hasAtomMappingID()

bool CDPL.Chem.hasAtomMappingID

(

Atom

atom

)

Parameters

atom

Returns

getAtomMappingID()

int CDPL.Chem.getAtomMappingID

(

Atom

atom

)

Parameters

atom

Returns

clearAtomMappingID()

None CDPL.Chem.clearAtomMappingID

(

Atom

atom

)

Parameters

atom

setAtomMapping()

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

Parameters

rxn
mapping

hasAtomMapping()

bool CDPL.Chem.hasAtomMapping

(

Reaction

rxn

)

Parameters

rxn

Returns

getAtomMapping()

AtomMapping CDPL.Chem.getAtomMapping

(

Reaction

rxn

)

Parameters

rxn

Returns

clearAtomMapping()

None CDPL.Chem.clearAtomMapping

(

Reaction

rxn

)

Parameters

rxn

setAtomMatchConstraints() [1/2]

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

Parameters

molgraph
constr
overwrite

setAtomMatchConstraints() [2/2]

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

Parameters

rxn
constr
overwrite

setAtomSymbolsFromTypes()

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

Parameters

molgraph
overwrite

setAtomTypesFromSymbols()

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

Parameters

molgraph
overwrite

setBondMatchConstraints() [1/2]

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

Parameters

molgraph
constr
overwrite

setBondMatchConstraints() [2/2]

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

Parameters

rxn
constr
overwrite

setCIPConfiguration() [1/2]

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

Parameters

atom
config

hasCIPConfiguration() [1/2]

bool CDPL.Chem.hasCIPConfiguration

(

Atom

atom

)

Parameters

atom

Returns

getCIPConfiguration() [1/2]

int CDPL.Chem.getCIPConfiguration

(

Atom

atom

)

Parameters

atom

Returns

clearCIPConfiguration() [1/2]

None CDPL.Chem.clearCIPConfiguration

(

Atom

atom

)

Parameters

atom

setCIPConfiguration() [2/2]

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

Parameters

bond
config

hasCIPConfiguration() [2/2]

bool CDPL.Chem.hasCIPConfiguration

(

Bond

bond

)

Parameters

bond

Returns

getCIPConfiguration() [2/2]

int CDPL.Chem.getCIPConfiguration

(

Bond

bond

)

Parameters

bond

Returns

clearCIPConfiguration() [2/2]

None CDPL.Chem.clearCIPConfiguration

(

Bond

bond

)

Parameters

bond

setCIPPriority()

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

Parameters

atom
priority

hasCIPPriority()

bool CDPL.Chem.hasCIPPriority

(

Atom

atom

)

Parameters

atom

Returns

getCIPPriority()

int CDPL.Chem.getCIPPriority

(

Atom

atom

)

Parameters

atom

Returns

clearCIPPriority()

None CDPL.Chem.clearCIPPriority

(

Atom

atom

)

Parameters

atom

setCanonicalNumber()

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

Parameters

atom
num

hasCanonicalNumber()

bool CDPL.Chem.hasCanonicalNumber

(

Atom

atom

)

Parameters

atom

Returns

getCanonicalNumber()

int CDPL.Chem.getCanonicalNumber

(

Atom

atom

)

Parameters

atom

Returns

clearCanonicalNumber()

None CDPL.Chem.clearCanonicalNumber

(

Atom

atom

)

Parameters

atom

setComment() [1/2]

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

Parameters

molgraph
comment

hasComment() [1/2]

bool CDPL.Chem.hasComment

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getComment() [1/2]

str CDPL.Chem.getComment

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearComment() [1/2]

None CDPL.Chem.clearComment

(

MolecularGraph

molgraph

)

Parameters

molgraph

setComment() [2/2]

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

Parameters

rxn
comment

hasComment() [2/2]

bool CDPL.Chem.hasComment

(

Reaction

rxn

)

Parameters

rxn

Returns

getComment() [2/2]

str CDPL.Chem.getComment

(

Reaction

rxn

)

Parameters

rxn

Returns

clearComment() [2/2]

None CDPL.Chem.clearComment

(

Reaction

rxn

)

Parameters

rxn

getCompleteBondCount()

int CDPL.Chem.getCompleteBondCount

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

setComponentGroupID()

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

Parameters

atom
id

hasComponentGroupID()

bool CDPL.Chem.hasComponentGroupID

(

Atom

atom

)

Parameters

atom

Returns

getComponentGroupID()

int CDPL.Chem.getComponentGroupID

(

Atom

atom

)

Parameters

atom

Returns

clearComponentGroupID()

None CDPL.Chem.clearComponentGroupID

(

Atom

atom

)

Parameters

atom

setComponentGroups() [1/2]

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

Parameters

molgraph
comp_groups

hasComponentGroups() [1/2]

bool CDPL.Chem.hasComponentGroups

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getComponentGroups() [1/2]

FragmentList CDPL.Chem.getComponentGroups

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearComponentGroups() [1/2]

None CDPL.Chem.clearComponentGroups

(

MolecularGraph

molgraph

)

Parameters

molgraph

setComponentGroups() [2/2]

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

Parameters

rxn
comp_groups

hasComponentGroups() [2/2]

bool CDPL.Chem.hasComponentGroups

(

Reaction

rxn

)

Parameters

rxn

Returns

getComponentGroups() [2/2]

FragmentList CDPL.Chem.getComponentGroups

(

Reaction

rxn

)

Parameters

rxn

Returns

clearComponentGroups() [2/2]

None CDPL.Chem.clearComponentGroups

(

Reaction

rxn

)

Parameters

rxn

setComponentMatchConstraints()

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

Parameters

rxn
constr
overwrite

setComponents()

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

Parameters

molgraph
comps

hasComponents()

bool CDPL.Chem.hasComponents

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getComponents()

FragmentList CDPL.Chem.getComponents

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearComponents()

None CDPL.Chem.clearComponents

(

MolecularGraph

molgraph

)

Parameters

molgraph

getConformation()

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

Parameters

cntnr
conf_idx
coords
append

getConformationEnergy()

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

Parameters

molgraph
conf_idx

Returns

setConformationIndex()

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

Parameters

molgraph
index

hasConformationIndex()

bool CDPL.Chem.hasConformationIndex

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getConformationIndex()

int CDPL.Chem.getConformationIndex

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearConformationIndex()

None CDPL.Chem.clearConformationIndex

(

MolecularGraph

molgraph

)

Parameters

molgraph

setConformation()

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

Parameters

molgraph
conf_idx
coords
energy

clearConformations()

None CDPL.Chem.clearConformations

(

AtomContainer

cntnr

)

Parameters

cntnr

getConformer3DCoordinates()

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

Parameters

atom
conf_idx

Returns

setConformerEnergies()

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

Parameters

molgraph
energies

hasConformerEnergies()

bool CDPL.Chem.hasConformerEnergies

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getConformerEnergies()

Util.DArray CDPL.Chem.getConformerEnergies

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearConformerEnergies()

None CDPL.Chem.clearConformerEnergies

(

MolecularGraph

molgraph

)

Parameters

molgraph

getConnectedAtomsAndBonds()

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

Parameters

atom
molgraph
atoms
bonds
excl_atom

Returns

getConnectedAtoms()

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

Parameters

atom
molgraph
atoms
excl_atom

Returns

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

getContainingFragments() [1/3]

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

Parameters

atom
frag_list
cont_frag_list

getContainingFragments() [2/3]

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

Parameters

bond
frag_list
cont_frag_list

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

hasCoordinates()

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

Parameters

cntnr
dim

Returns

setCyclicSubstructure()

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

Parameters

molgraph
substruct

hasCyclicSubstructure()

bool CDPL.Chem.hasCyclicSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getCyclicSubstructure()

Fragment CDPL.Chem.getCyclicSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearCyclicSubstructure()

None CDPL.Chem.clearCyclicSubstructure

(

MolecularGraph

molgraph

)

Parameters

molgraph

setDirection()

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

Parameters

bond
dir

hasDirection()

bool CDPL.Chem.hasDirection

(

Bond

bond

)

Parameters

bond

Returns

getDirection()

int CDPL.Chem.getDirection

(

Bond

bond

)

Parameters

bond

Returns

clearDirection()

None CDPL.Chem.clearDirection

(

Bond

bond

)

Parameters

bond

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

setFormalCharge()

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

Parameters

atom
charge

hasFormalCharge()

bool CDPL.Chem.hasFormalCharge

(

Atom

atom

)

Parameters

atom

Returns

getFormalCharge()

int CDPL.Chem.getFormalCharge

(

Atom

atom

)

Parameters

atom

Returns

clearFormalCharge()

None CDPL.Chem.clearFormalCharge

(

Atom

atom

)

Parameters

atom

getGenericType()

int CDPL.Chem.getGenericType

(

Atom

atom

)

Parameters

atom

Returns

setGeometricalDistanceMatrix()

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

Parameters

molgraph
mtx

hasGeometricalDistanceMatrix()

bool CDPL.Chem.hasGeometricalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getGeometricalDistanceMatrix()

Math.DMatrix CDPL.Chem.getGeometricalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearGeometricalDistanceMatrix()

None CDPL.Chem.clearGeometricalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

setHashCode()

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

Parameters

molgraph
hash_code

hasHashCode()

bool CDPL.Chem.hasHashCode

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getHashCode()

int CDPL.Chem.getHashCode

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearHashCode()

None CDPL.Chem.clearHashCode

(

MolecularGraph

molgraph

)

Parameters

molgraph

setHybridizationState()

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

Parameters

atom
state

hasHybridizationState()

bool CDPL.Chem.hasHybridizationState

(

Atom

atom

)

Parameters

atom

Returns

getHybridizationState()

int CDPL.Chem.getHybridizationState

(

Atom

atom

)

Parameters

atom

Returns

clearHybridizationState()

None CDPL.Chem.clearHybridizationState

(

Atom

atom

)

Parameters

atom

setImplicitHydrogenCount()

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

Parameters

atom
count

hasImplicitHydrogenCount()

bool CDPL.Chem.hasImplicitHydrogenCount

(

Atom

atom

)

Parameters

atom

Returns

getImplicitHydrogenCount()

int CDPL.Chem.getImplicitHydrogenCount

(

Atom

atom

)

Parameters

atom

Returns

clearImplicitHydrogenCount()

None CDPL.Chem.clearImplicitHydrogenCount

(

Atom

atom

)

Parameters

atom

getIncidentBonds()

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

Parameters

atom
molgraph
bonds
excl_atom

Returns

setIsotope()

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

Parameters

atom
isotope

hasIsotope()

bool CDPL.Chem.hasIsotope

(

Atom

atom

)

Parameters

atom

Returns

getIsotope()

int CDPL.Chem.getIsotope

(

Atom

atom

)

Parameters

atom

Returns

clearIsotope()

None CDPL.Chem.clearIsotope

(

Atom

atom

)

Parameters

atom

setMDLCTABVersion()

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

Parameters

molgraph
version

hasMDLCTABVersion()

bool CDPL.Chem.hasMDLCTABVersion

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLCTABVersion()

int CDPL.Chem.getMDLCTABVersion

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLCTABVersion()

None CDPL.Chem.clearMDLCTABVersion

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMDLChiralFlag()

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

Parameters

molgraph
flag

hasMDLChiralFlag()

bool CDPL.Chem.hasMDLChiralFlag

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLChiralFlag()

bool CDPL.Chem.getMDLChiralFlag

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLChiralFlag()

None CDPL.Chem.clearMDLChiralFlag

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMDLDimensionality()

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

Parameters

molgraph
dim

hasMDLDimensionality()

bool CDPL.Chem.hasMDLDimensionality

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLDimensionality()

int CDPL.Chem.getMDLDimensionality

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLDimensionality()

None CDPL.Chem.clearMDLDimensionality

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMDLEnergy()

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

Parameters

molgraph
energy

hasMDLEnergy()

bool CDPL.Chem.hasMDLEnergy

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLEnergy()

float CDPL.Chem.getMDLEnergy

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLEnergy()

None CDPL.Chem.clearMDLEnergy

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMDLExternalRegistryNumber()

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

Parameters

rxn
reg_no

hasMDLExternalRegistryNumber()

bool CDPL.Chem.hasMDLExternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLExternalRegistryNumber()

str CDPL.Chem.getMDLExternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

clearMDLExternalRegistryNumber()

None CDPL.Chem.clearMDLExternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

setMDLInternalRegistryNumber()

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

Parameters

rxn
reg_no

hasMDLInternalRegistryNumber()

bool CDPL.Chem.hasMDLInternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLInternalRegistryNumber()

str CDPL.Chem.getMDLInternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

clearMDLInternalRegistryNumber()

None CDPL.Chem.clearMDLInternalRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

setMDLMoleculeRecord()

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

Parameters

rxn
mol_rec

hasMDLMoleculeRecord()

bool CDPL.Chem.hasMDLMoleculeRecord

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLMoleculeRecord()

Molecule CDPL.Chem.getMDLMoleculeRecord

(

Reaction

rxn

)

Parameters

rxn

Returns

clearMDLMoleculeRecord()

None CDPL.Chem.clearMDLMoleculeRecord

(

Reaction

rxn

)

Parameters

rxn

setMDLParity()

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

Parameters

atom
parity

hasMDLParity()

bool CDPL.Chem.hasMDLParity

(

Atom

atom

)

Parameters

atom

Returns

getMDLParity()

int CDPL.Chem.getMDLParity

(

Atom

atom

)

Parameters

atom

Returns

clearMDLParity()

None CDPL.Chem.clearMDLParity

(

Atom

atom

)

Parameters

atom

setMDLProgramName() [1/2]

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

Parameters

molgraph
name

hasMDLProgramName() [1/2]

bool CDPL.Chem.hasMDLProgramName

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLProgramName() [1/2]

str CDPL.Chem.getMDLProgramName

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLProgramName() [1/2]

None CDPL.Chem.clearMDLProgramName

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMDLProgramName() [2/2]

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

Parameters

rxn
name

hasMDLProgramName() [2/2]

bool CDPL.Chem.hasMDLProgramName

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLProgramName() [2/2]

str CDPL.Chem.getMDLProgramName

(

Reaction

rxn

)

Parameters

rxn

Returns

clearMDLProgramName() [2/2]

None CDPL.Chem.clearMDLProgramName

(

Reaction

rxn

)

Parameters

rxn

setMDLRXNFileVersion()

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

Parameters

rxn
version

hasMDLRXNFileVersion()

bool CDPL.Chem.hasMDLRXNFileVersion

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLRXNFileVersion()

int CDPL.Chem.getMDLRXNFileVersion

(

Reaction

rxn

)

Parameters

rxn

Returns

clearMDLRXNFileVersion()

None CDPL.Chem.clearMDLRXNFileVersion

(

Reaction

rxn

)

Parameters

rxn

setMDLRegistryNumber() [1/2]

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

Parameters

molgraph
reg_no

hasMDLRegistryNumber() [1/2]

bool CDPL.Chem.hasMDLRegistryNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLRegistryNumber() [1/2]

int CDPL.Chem.getMDLRegistryNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLRegistryNumber() [1/2]

None CDPL.Chem.clearMDLRegistryNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMDLRegistryNumber() [2/2]

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

Parameters

rxn
reg_no

hasMDLRegistryNumber() [2/2]

bool CDPL.Chem.hasMDLRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLRegistryNumber() [2/2]

int CDPL.Chem.getMDLRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

Returns

clearMDLRegistryNumber() [2/2]

None CDPL.Chem.clearMDLRegistryNumber

(

Reaction

rxn

)

Parameters

rxn

setMDLScalingFactor1()

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

Parameters

molgraph
factor

hasMDLScalingFactor1()

bool CDPL.Chem.hasMDLScalingFactor1

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLScalingFactor1()

int CDPL.Chem.getMDLScalingFactor1

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLScalingFactor1()

None CDPL.Chem.clearMDLScalingFactor1

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMDLScalingFactor2()

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

Parameters

molgraph
factor

hasMDLScalingFactor2()

bool CDPL.Chem.hasMDLScalingFactor2

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLScalingFactor2()

float CDPL.Chem.getMDLScalingFactor2

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLScalingFactor2()

None CDPL.Chem.clearMDLScalingFactor2

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMDLStereoCareFlag()

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

Parameters

atom
flag

hasMDLStereoCareFlag()

bool CDPL.Chem.hasMDLStereoCareFlag

(

Atom

atom

)

Parameters

atom

Returns

getMDLStereoCareFlag()

bool CDPL.Chem.getMDLStereoCareFlag

(

Atom

atom

)

Parameters

atom

Returns

clearMDLStereoCareFlag()

None CDPL.Chem.clearMDLStereoCareFlag

(

Atom

atom

)

Parameters

atom

setMDLUserInitials() [1/2]

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

Parameters

molgraph
initials

hasMDLUserInitials() [1/2]

bool CDPL.Chem.hasMDLUserInitials

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMDLUserInitials() [1/2]

str CDPL.Chem.getMDLUserInitials

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMDLUserInitials() [1/2]

None CDPL.Chem.clearMDLUserInitials

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMDLUserInitials() [2/2]

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

Parameters

rxn
initials

hasMDLUserInitials() [2/2]

bool CDPL.Chem.hasMDLUserInitials

(

Reaction

rxn

)

Parameters

rxn

Returns

getMDLUserInitials() [2/2]

str CDPL.Chem.getMDLUserInitials

(

Reaction

rxn

)

Parameters

rxn

Returns

clearMDLUserInitials() [2/2]

None CDPL.Chem.clearMDLUserInitials

(

Reaction

rxn

)

Parameters

rxn

setMOL2Charge()

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

Parameters

atom
charge

hasMOL2Charge()

bool CDPL.Chem.hasMOL2Charge

(

Atom

atom

)

Parameters

atom

Returns

getMOL2Charge()

float CDPL.Chem.getMOL2Charge

(

Atom

atom

)

Parameters

atom

Returns

clearMOL2Charge()

None CDPL.Chem.clearMOL2Charge

(

Atom

atom

)

Parameters

atom

setMOL2ChargeType()

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

Parameters

molgraph
type

hasMOL2ChargeType()

bool CDPL.Chem.hasMOL2ChargeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMOL2ChargeType()

int CDPL.Chem.getMOL2ChargeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMOL2ChargeType()

None CDPL.Chem.clearMOL2ChargeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMOL2MoleculeType()

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

Parameters

molgraph
type

hasMOL2MoleculeType()

bool CDPL.Chem.hasMOL2MoleculeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMOL2MoleculeType()

int CDPL.Chem.getMOL2MoleculeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMOL2MoleculeType()

None CDPL.Chem.clearMOL2MoleculeType

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMOL2Name()

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

Parameters

atom
name

hasMOL2Name()

bool CDPL.Chem.hasMOL2Name

(

Atom

atom

)

Parameters

atom

Returns

getMOL2Name()

str CDPL.Chem.getMOL2Name

(

Atom

atom

)

Parameters

atom

Returns

clearMOL2Name()

None CDPL.Chem.clearMOL2Name

(

Atom

atom

)

Parameters

atom

setMOL2SubstructureChain()

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

Parameters

atom
chain

hasMOL2SubstructureChain()

bool CDPL.Chem.hasMOL2SubstructureChain

(

Atom

atom

)

Parameters

atom

Returns

getMOL2SubstructureChain()

str CDPL.Chem.getMOL2SubstructureChain

(

Atom

atom

)

Parameters

atom

Returns

clearMOL2SubstructureChain()

None CDPL.Chem.clearMOL2SubstructureChain

(

Atom

atom

)

Parameters

atom

setMOL2SubstructureID()

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

Parameters

atom
id

hasMOL2SubstructureID()

bool CDPL.Chem.hasMOL2SubstructureID

(

Atom

atom

)

Parameters

atom

Returns

getMOL2SubstructureID()

int CDPL.Chem.getMOL2SubstructureID

(

Atom

atom

)

Parameters

atom

Returns

clearMOL2SubstructureID()

None CDPL.Chem.clearMOL2SubstructureID

(

Atom

atom

)

Parameters

atom

setMOL2SubstructureName()

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

Parameters

atom
name

hasMOL2SubstructureName()

bool CDPL.Chem.hasMOL2SubstructureName

(

Atom

atom

)

Parameters

atom

Returns

getMOL2SubstructureName()

str CDPL.Chem.getMOL2SubstructureName

(

Atom

atom

)

Parameters

atom

Returns

clearMOL2SubstructureName()

None CDPL.Chem.clearMOL2SubstructureName

(

Atom

atom

)

Parameters

atom

setMOL2SubstructureSubtype()

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

Parameters

atom
subtype

hasMOL2SubstructureSubtype()

bool CDPL.Chem.hasMOL2SubstructureSubtype

(

Atom

atom

)

Parameters

atom

Returns

getMOL2SubstructureSubtype()

str CDPL.Chem.getMOL2SubstructureSubtype

(

Atom

atom

)

Parameters

atom

Returns

clearMOL2SubstructureSubtype()

None CDPL.Chem.clearMOL2SubstructureSubtype

(

Atom

atom

)

Parameters

atom

setMatchConstraints() [1/4]

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

Parameters

atom
constr

hasMatchConstraints() [1/4]

bool CDPL.Chem.hasMatchConstraints

(

Atom

atom

)

Parameters

atom

Returns

getMatchConstraints() [1/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

Atom

atom

)

Parameters

atom

Returns

clearMatchConstraints() [1/4]

None CDPL.Chem.clearMatchConstraints

(

Atom

atom

)

Parameters

atom

setMatchConstraints() [2/4]

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

Parameters

bond
constr

hasMatchConstraints() [2/4]

bool CDPL.Chem.hasMatchConstraints

(

Bond

bond

)

Parameters

bond

Returns

getMatchConstraints() [2/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

Bond

bond

)

Parameters

bond

Returns

clearMatchConstraints() [2/4]

None CDPL.Chem.clearMatchConstraints

(

Bond

bond

)

Parameters

bond

setMatchConstraints() [3/4]

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

Parameters

molgraph
constr

hasMatchConstraints() [3/4]

bool CDPL.Chem.hasMatchConstraints

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMatchConstraints() [3/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMatchConstraints() [3/4]

None CDPL.Chem.clearMatchConstraints

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMatchConstraints() [4/4]

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

Parameters

rxn
constr

hasMatchConstraints() [4/4]

bool CDPL.Chem.hasMatchConstraints

(

Reaction

rxn

)

Parameters

rxn

Returns

getMatchConstraints() [4/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

Reaction

rxn

)

Parameters

rxn

Returns

clearMatchConstraints() [4/4]

None CDPL.Chem.clearMatchConstraints

(

Reaction

rxn

)

Parameters

rxn

setMatchExpression() [1/4]

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

Parameters

atom
expr

hasMatchExpression() [1/4]

bool CDPL.Chem.hasMatchExpression

(

Atom

atom

)

Parameters

atom

Returns

getMatchExpression() [1/4]

AtomMatchExpression CDPL.Chem.getMatchExpression

(

Atom

atom

)

Parameters

atom

Returns

clearMatchExpression() [1/4]

None CDPL.Chem.clearMatchExpression

(

Atom

atom

)

Parameters

atom

setMatchExpression() [2/4]

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

Parameters

bond
expr

hasMatchExpression() [2/4]

bool CDPL.Chem.hasMatchExpression

(

Bond

bond

)

Parameters

bond

Returns

getMatchExpression() [2/4]

BondMatchExpression CDPL.Chem.getMatchExpression

(

Bond

bond

)

Parameters

bond

Returns

clearMatchExpression() [2/4]

None CDPL.Chem.clearMatchExpression

(

Bond

bond

)

Parameters

bond

setMatchExpression() [3/4]

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

Parameters

molgraph
expr

hasMatchExpression() [3/4]

bool CDPL.Chem.hasMatchExpression

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getMatchExpression() [3/4]

MolecularGraphMatchExpression CDPL.Chem.getMatchExpression

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearMatchExpression() [3/4]

None CDPL.Chem.clearMatchExpression

(

MolecularGraph

molgraph

)

Parameters

molgraph

setMatchExpression() [4/4]

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

Parameters

rxn
expr

hasMatchExpression() [4/4]

bool CDPL.Chem.hasMatchExpression

(

Reaction

rxn

)

Parameters

rxn

Returns

getMatchExpression() [4/4]

ReactionMatchExpression CDPL.Chem.getMatchExpression

(

Reaction

rxn

)

Parameters

rxn

Returns

clearMatchExpression() [4/4]

None CDPL.Chem.clearMatchExpression

(

Reaction

rxn

)

Parameters

rxn

setMatchExpressionString() [1/2]

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

Parameters

atom
expr_str

hasMatchExpressionString() [1/2]

bool CDPL.Chem.hasMatchExpressionString

(

Atom

atom

)

Parameters

atom

Returns

getMatchExpressionString() [1/2]

str CDPL.Chem.getMatchExpressionString

(

Atom

atom

)

Parameters

atom

Returns

clearMatchExpressionString() [1/2]

None CDPL.Chem.clearMatchExpressionString

(

Atom

atom

)

Parameters

atom

setMatchExpressionString() [2/2]

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

Parameters

bond
expr_str

hasMatchExpressionString() [2/2]

bool CDPL.Chem.hasMatchExpressionString

(

Bond

bond

)

Parameters

bond

Returns

getMatchExpressionString() [2/2]

str CDPL.Chem.getMatchExpressionString

(

Bond

bond

)

Parameters

bond

Returns

clearMatchExpressionString() [2/2]

None CDPL.Chem.clearMatchExpressionString

(

Bond

bond

)

Parameters

bond

getMaxAtomMappingID() [1/2]

int CDPL.Chem.getMaxAtomMappingID

(

AtomContainer

cntnr

)

Parameters

cntnr

Returns

getMaxAtomMappingID() [2/2]

int CDPL.Chem.getMaxAtomMappingID

(

Reaction

rxn

)

Parameters

rxn

Returns

getMaxComponentGroupID() [1/2]

int CDPL.Chem.getMaxComponentGroupID

(

AtomContainer

cntnr

)

Parameters

cntnr

Returns

getMaxComponentGroupID() [2/2]

int CDPL.Chem.getMaxComponentGroupID

(

Reaction

rxn

)

Parameters

rxn

Returns

setMorganNumber()

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

Parameters

atom
num

hasMorganNumber()

bool CDPL.Chem.hasMorganNumber

(

Atom

atom

)

Parameters

atom

Returns

getMorganNumber()

int CDPL.Chem.getMorganNumber

(

Atom

atom

)

Parameters

atom

Returns

clearMorganNumber()

None CDPL.Chem.clearMorganNumber

(

Atom

atom

)

Parameters

atom

setName() [1/3]

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

Parameters

atom
name

hasName() [1/3]

bool CDPL.Chem.hasName

(

Atom

atom

)

Parameters

atom

Returns

getName() [1/3]

str CDPL.Chem.getName

(

Atom

atom

)

Parameters

atom

Returns

clearName() [1/3]

None CDPL.Chem.clearName

(

Atom

atom

)

Parameters

atom

setName() [2/3]

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

Parameters

molgraph
name

hasName() [2/3]

bool CDPL.Chem.hasName

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getName() [2/3]

str CDPL.Chem.getName

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearName() [2/3]

None CDPL.Chem.clearName

(

MolecularGraph

molgraph

)

Parameters

molgraph

setName() [3/3]

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

Parameters

rxn
name

hasName() [3/3]

bool CDPL.Chem.hasName

(

Reaction

rxn

)

Parameters

rxn

Returns

getName() [3/3]

str CDPL.Chem.getName

(

Reaction

rxn

)

Parameters

rxn

Returns

clearName() [3/3]

None CDPL.Chem.clearName

(

Reaction

rxn

)

Parameters

rxn

getNumConformations()

int CDPL.Chem.getNumConformations

(

AtomContainer

cntnr

)

Parameters

cntnr

Returns

getNumContainingFragments() [1/2]

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

Parameters

atom
frag_list

Returns

getNumContainingFragments() [2/2]

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

Parameters

bond
frag_list

Returns

setOrder()

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

Parameters

bond
order

hasOrder()

bool CDPL.Chem.hasOrder

(

Bond

bond

)

Parameters

bond

Returns

getOrder()

int CDPL.Chem.getOrder

(

Bond

bond

)

Parameters

bond

Returns

clearOrder()

None CDPL.Chem.clearOrder

(

Bond

bond

)

Parameters

bond

setPiElectronSystems()

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

Parameters

molgraph
pi_systems

hasPiElectronSystems()

bool CDPL.Chem.hasPiElectronSystems

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getPiElectronSystems()

ElectronSystemList CDPL.Chem.getPiElectronSystems

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearPiElectronSystems()

None CDPL.Chem.clearPiElectronSystems

(

MolecularGraph

molgraph

)

Parameters

molgraph

setRadicalType()

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

Parameters

atom
type

hasRadicalType()

bool CDPL.Chem.hasRadicalType

(

Atom

atom

)

Parameters

atom

Returns

getRadicalType()

int CDPL.Chem.getRadicalType

(

Atom

atom

)

Parameters

atom

Returns

clearRadicalType()

None CDPL.Chem.clearRadicalType

(

Atom

atom

)

Parameters

atom

setReactionCenterStatus() [1/2]

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

Parameters

atom
status

hasReactionCenterStatus() [1/2]

bool CDPL.Chem.hasReactionCenterStatus

(

Atom

atom

)

Parameters

atom

Returns

getReactionCenterStatus() [1/2]

int CDPL.Chem.getReactionCenterStatus

(

Atom

atom

)

Parameters

atom

Returns

clearReactionCenterStatus() [1/2]

None CDPL.Chem.clearReactionCenterStatus

(

Atom

atom

)

Parameters

atom

setReactionCenterStatus() [2/2]

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

Parameters

bond
status

hasReactionCenterStatus() [2/2]

bool CDPL.Chem.hasReactionCenterStatus

(

Bond

bond

)

Parameters

bond

Returns

getReactionCenterStatus() [2/2]

int CDPL.Chem.getReactionCenterStatus

(

Bond

bond

)

Parameters

bond

Returns

clearReactionCenterStatus() [2/2]

None CDPL.Chem.clearReactionCenterStatus

(

Bond

bond

)

Parameters

bond

setReactionData()

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

Parameters

rxn
data

hasReactionData()

bool CDPL.Chem.hasReactionData

(

Reaction

rxn

)

Parameters

rxn

Returns

getReactionData()

StringDataBlock CDPL.Chem.getReactionData

(

Reaction

rxn

)

Parameters

rxn

Returns

clearReactionData()

None CDPL.Chem.clearReactionData

(

Reaction

rxn

)

Parameters

rxn

setRingFlag() [1/2]

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

Parameters

atom
in_ring

hasRingFlag() [1/2]

bool CDPL.Chem.hasRingFlag

(

Atom

atom

)

Parameters

atom

Returns

getRingFlag() [1/2]

bool CDPL.Chem.getRingFlag

(

Atom

atom

)

Parameters

atom

Returns

clearRingFlag() [1/2]

None CDPL.Chem.clearRingFlag

(

Atom

atom

)

Parameters

atom

setRingFlag() [2/2]

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

Parameters

bond
in_ring

hasRingFlag() [2/2]

bool CDPL.Chem.hasRingFlag

(

Bond

bond

)

Parameters

bond

Returns

getRingFlag() [2/2]

bool CDPL.Chem.getRingFlag

(

Bond

bond

)

Parameters

bond

Returns

clearRingFlag() [2/2]

None CDPL.Chem.clearRingFlag

(

Bond

bond

)

Parameters

bond

setRingFlags()

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

Parameters

molgraph
overwrite

setRings()

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

Parameters

molgraph
rings

hasRings()

bool CDPL.Chem.hasRings

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getRings()

FragmentList CDPL.Chem.getRings

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearRings()

None CDPL.Chem.clearRings

(

MolecularGraph

molgraph

)

Parameters

molgraph

setSSSR()

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

Parameters

molgraph
sssr

hasSSSR()

bool CDPL.Chem.hasSSSR

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getSSSR()

FragmentList CDPL.Chem.getSSSR

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearSSSR()

None CDPL.Chem.clearSSSR

(

MolecularGraph

molgraph

)

Parameters

molgraph

getSizeOfLargestContainingFragment() [1/2]

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

Parameters

atom
frag_list

Returns

getSizeOfLargestContainingFragment() [2/2]

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

Parameters

bond
frag_list

Returns

getSizeOfSmallestContainingFragment() [1/2]

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

Parameters

atom
frag_list

Returns

getSizeOfSmallestContainingFragment() [2/2]

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

Parameters

bond
frag_list

Returns

setStereoCenterFlag() [1/2]

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

Parameters

atom
is_center

hasStereoCenterFlag() [1/2]

bool CDPL.Chem.hasStereoCenterFlag

(

Atom

atom

)

Parameters

atom

Returns

getStereoCenterFlag() [1/2]

bool CDPL.Chem.getStereoCenterFlag

(

Atom

atom

)

Parameters

atom

Returns

clearStereoCenterFlag() [1/2]

None CDPL.Chem.clearStereoCenterFlag

(

Atom

atom

)

Parameters

atom

setStereoCenterFlag() [2/2]

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

Parameters

bond
is_center

hasStereoCenterFlag() [2/2]

bool CDPL.Chem.hasStereoCenterFlag

(

Bond

bond

)

Parameters

bond

Returns

getStereoCenterFlag() [2/2]

bool CDPL.Chem.getStereoCenterFlag

(

Bond

bond

)

Parameters

bond

Returns

clearStereoCenterFlag() [2/2]

None CDPL.Chem.clearStereoCenterFlag

(

Bond

bond

)

Parameters

bond

setStereoDescriptor() [1/2]

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

Parameters

atom
descr

hasStereoDescriptor() [1/2]

bool CDPL.Chem.hasStereoDescriptor

(

Atom

atom

)

Parameters

atom

Returns

getStereoDescriptor() [1/2]

StereoDescriptor CDPL.Chem.getStereoDescriptor

(

Atom

atom

)

Parameters

atom

Returns

clearStereoDescriptor() [1/2]

None CDPL.Chem.clearStereoDescriptor

(

Atom

atom

)

Parameters

atom

setStereoDescriptor() [2/2]

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

Parameters

bond
descr

hasStereoDescriptor() [2/2]

bool CDPL.Chem.hasStereoDescriptor

(

Bond

bond

)

Parameters

bond

Returns

getStereoDescriptor() [2/2]

StereoDescriptor CDPL.Chem.getStereoDescriptor

(

Bond

bond

)

Parameters

bond

Returns

clearStereoDescriptor() [2/2]

None CDPL.Chem.clearStereoDescriptor

(

Bond

bond

)

Parameters

bond

setStoichiometricNumber()

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

Parameters

molgraph
num

hasStoichiometricNumber()

bool CDPL.Chem.hasStoichiometricNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getStoichiometricNumber()

float CDPL.Chem.getStoichiometricNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearStoichiometricNumber()

None CDPL.Chem.clearStoichiometricNumber

(

MolecularGraph

molgraph

)

Parameters

molgraph

setStructureData()

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

Parameters

molgraph
data

hasStructureData()

bool CDPL.Chem.hasStructureData

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getStructureData()

StringDataBlock CDPL.Chem.getStructureData

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearStructureData()

None CDPL.Chem.clearStructureData

(

MolecularGraph

molgraph

)

Parameters

molgraph

getSybylAtomTypeString()

str CDPL.Chem.getSybylAtomTypeString

(

int

sybyl_type

)

Parameters

sybyl_type

Returns

getSybylBondTypeString()

str CDPL.Chem.getSybylBondTypeString

(

int

sybyl_type

)

Parameters

sybyl_type

Returns

setSybylType() [1/2]

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

Parameters

atom
type

hasSybylType() [1/2]

bool CDPL.Chem.hasSybylType

(

Atom

atom

)

Parameters

atom

Returns

getSybylType() [1/2]

int CDPL.Chem.getSybylType

(

Atom

atom

)

Parameters

atom

Returns

clearSybylType() [1/2]

None CDPL.Chem.clearSybylType

(

Atom

atom

)

Parameters

atom

setSybylType() [2/2]

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

Parameters

bond
type

hasSybylType() [2/2]

bool CDPL.Chem.hasSybylType

(

Bond

bond

)

Parameters

bond

Returns

getSybylType() [2/2]

int CDPL.Chem.getSybylType

(

Bond

bond

)

Parameters

bond

Returns

clearSybylType() [2/2]

None CDPL.Chem.clearSybylType

(

Bond

bond

)

Parameters

bond

setSymbol()

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

Parameters

atom
symbol

hasSymbol()

bool CDPL.Chem.hasSymbol

(

Atom

atom

)

Parameters

atom

Returns

getSymbol()

str CDPL.Chem.getSymbol

(

Atom

atom

)

Parameters

atom

Returns

clearSymbol()

None CDPL.Chem.clearSymbol

(

Atom

atom

)

Parameters

atom

getSymbolForType()

str CDPL.Chem.getSymbolForType

(

Atom

atom

)

Parameters

atom

Returns

setSymmetryClass()

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

Parameters

atom
class_id

hasSymmetryClass()

bool CDPL.Chem.hasSymmetryClass

(

Atom

atom

)

Parameters

atom

Returns

getSymmetryClass()

int CDPL.Chem.getSymmetryClass

(

Atom

atom

)

Parameters

atom

Returns

clearSymmetryClass()

None CDPL.Chem.clearSymmetryClass

(

Atom

atom

)

Parameters

atom

setTimestamp() [1/2]

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

Parameters

molgraph
time

hasTimestamp() [1/2]

bool CDPL.Chem.hasTimestamp

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getTimestamp() [1/2]

int CDPL.Chem.getTimestamp

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearTimestamp() [1/2]

None CDPL.Chem.clearTimestamp

(

MolecularGraph

molgraph

)

Parameters

molgraph

setTimestamp() [2/2]

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

Parameters

rxn
time

hasTimestamp() [2/2]

bool CDPL.Chem.hasTimestamp

(

Reaction

rxn

)

Parameters

rxn

Returns

getTimestamp() [2/2]

int CDPL.Chem.getTimestamp

(

Reaction

rxn

)

Parameters

rxn

Returns

clearTimestamp() [2/2]

None CDPL.Chem.clearTimestamp

(

Reaction

rxn

)

Parameters

rxn

getTopologicalDistance()

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

Parameters

atom1
atom2
molgraph

Returns

setTopologicalDistanceMatrix()

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

Parameters

molgraph
mtx

hasTopologicalDistanceMatrix()

bool CDPL.Chem.hasTopologicalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

getTopologicalDistanceMatrix()

Math.ULMatrix CDPL.Chem.getTopologicalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

clearTopologicalDistanceMatrix()

None CDPL.Chem.clearTopologicalDistanceMatrix

(

MolecularGraph

molgraph

)

Parameters

molgraph

setType()

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

Parameters

atom
type

hasType()

bool CDPL.Chem.hasType

(

Atom

atom

)

Parameters

atom

Returns

getType()

int CDPL.Chem.getType

(

Atom

atom

)

Parameters

atom

Returns

clearType()

None CDPL.Chem.clearType

(

Atom

atom

)

Parameters

atom

getTypeForSymbol()

int CDPL.Chem.getTypeForSymbol

(

Atom

atom

)

Parameters

atom

Returns

setUnpairedElectronCount()

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

Parameters

atom
count

hasUnpairedElectronCount()

bool CDPL.Chem.hasUnpairedElectronCount

(

Atom

atom

)

Parameters

atom

Returns

getUnpairedElectronCount()

int CDPL.Chem.getUnpairedElectronCount

(

Atom

atom

)

Parameters

atom

Returns

clearUnpairedElectronCount()

None CDPL.Chem.clearUnpairedElectronCount

(

Atom

atom

)

Parameters

atom

addConformation() [1/2]

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

Parameters

cntnr
coords

addConformation() [2/2]

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

Parameters

molgraph
coords
energy

align2DCoordinates() [1/4]

bool CDPL.Chem.align2DCoordinates	(	MolecularGraph	molgraph,
		AtomContainer	atoms,
		Math.Vector2DArray	ref_coords,
		bool	fix_bond_stereo = True
	)

Parameters

molgraph
atoms
ref_coords
fix_bond_stereo

Returns

align2DCoordinates() [2/4]

bool CDPL.Chem.align2DCoordinates	(	MolecularGraph	molgraph,
		AtomMapping	ref_atom_mpg,
		bool	fix_bond_stereo = True
	)

Parameters

molgraph
ref_atom_mpg
fix_bond_stereo

Returns

align2DCoordinates() [3/4]

bool CDPL.Chem.align2DCoordinates	(	MolecularGraph	molgraph,
		MolecularGraph	ref_molgraph,
		bool	use_mcs,
		bool	fix_bond_stereo = True
	)

Parameters

molgraph
ref_molgraph
use_mcs
fix_bond_stereo

Returns

align2DCoordinates() [4/4]

bool CDPL.Chem.align2DCoordinates	(	MolecularGraph	molgraph,
		MolecularGraph	ref_molgraph,
		MolecularGraph	substr_ptn,
		bool	fix_bond_stereo = True
	)

Parameters

molgraph
ref_molgraph
substr_ptn
fix_bond_stereo

Returns

align3DCoordinates()

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

Parameters

cntnr
ref_entities
ref_coords

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

applyConformation()

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

Parameters

cntnr
conf_idx

atomTypesMatch()

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

Parameters

qry_type
tgt_type

Returns

calc2DCoordinates()

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

Parameters

molgraph
overwrite

calcAtomCIPConfigurations()

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

Parameters

molgraph
overwrite

calcAtomStereoDescriptorsFromMDLParities()

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

Parameters

molgraph
overwrite

calcAtomStereoDescriptors()

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

Parameters

molgraph
overwrite
dim
check_stc_flag

calcBasicProperties() [1/2]

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

Parameters

molgraph
overwrite

calcBasicProperties() [2/2]

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

Parameters

rxn
overwrite

calcBond2DStereoFlags()

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

Parameters

molgraph
overwrite

calcBondCIPConfigurations()

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

Parameters

molgraph
overwrite

calcBondStereoDescriptors()

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

Parameters

molgraph
overwrite
dim
check_stc_flag

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

calcBoundingBox() [2/2]

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

Parameters

cntnr
min
max
reset

calcCIPPriorities()

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

Parameters

molgraph
overwrite

calcCanonicalNumbering()

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

Parameters

molgraph
overwrite
atom_flags
bond_flags

calcCenterOfMass()

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

Parameters

cntnr
coords_func
ctr

Returns

calcCentroid() [1/2]

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

Parameters

cntnr
coords_func
ctr

Returns

calcCentroid() [2/2]

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

Parameters

cntnr
ctr

Returns

calcConfiguration() [1/2]

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

Parameters

atom
molgraph
descr
coords

Returns

calcConfiguration() [2/2]

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

Parameters

bond
molgraph
descr
coords

Returns

calcFormalCharge()

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

Parameters

atom
molgraph

Returns

calcFormalCharges()

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

Parameters

molgraph
overwrite

calcGeometricalDistanceMatrix() [1/2]

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

Parameters

cntnr
mtx

calcGeometricalDistanceMatrix() [2/2]

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

Parameters

molgraph
overwrite

Returns

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

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

calcHydrogen3DCoordinates()

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

Parameters

molgraph
undef_only

calcImplicitHydrogenCount()

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

Parameters

atom
molgraph

Returns

calcImplicitHydrogenCounts()

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

Parameters

molgraph
overwrite

calcMDLParities()

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

Parameters

molgraph
overwrite

calcMDLParity()

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

Parameters

atom
molgraph

Returns

calcMorganNumbering()

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

Parameters

molgraph
overwrite

calcStereoDescriptor() [1/2]

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

Parameters

atom
molgraph
dim

Returns

calcStereoDescriptor() [2/2]

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

Parameters

bond
molgraph
dim

Returns

calcStereoDescriptorFromMDLParity()

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

Parameters

atom
molgraph

Returns

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

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,
		BoolAtom2Functor	func,
		bool	atoms = True,
		bool	atom_nbrs = True,
		bool	bonds = True,
		bool	bond_atoms = False
	)

Parameters

molgraph
func
atoms
atom_nbrs
bonds
bond_atoms

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

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

containsMolecularGraph()

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

Parameters

molgraph
sub_molgraph
atoms
bonds

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

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

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

editSubstructures() [1/2]

int CDPL.Chem.editSubstructures	(	MolecularGraph	molgraph,
		Molecule	result_mol,
		str	search_ptns,
		str	result_ptn,
		str	exclude_ptns = ''
	)

Parameters

molgraph
result_mol
search_ptns
result_ptn
exclude_ptns

Returns

editSubstructures() [2/2]

int CDPL.Chem.editSubstructures	(	Molecule	mol,
		str	search_ptns,
		str	result_ptn,
		str	exclude_ptns = ''
	)

Parameters

mol
search_ptns
result_ptn
exclude_ptns

Returns

extendBoundingBox()

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

Parameters

min
max
coords
reset

extractReactionCenter()

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

Parameters

molgraph
rxn_center

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

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

generateAdjacencyMatrix()

None CDPL.Chem.generateAdjacencyMatrix	(	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

generateBondMatrix()

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

Parameters

molgraph
mtx

generateINCHIKey()

object CDPL.Chem.generateINCHIKey

(

MolecularGraph

molgraph

)

Parameters

molgraph

Returns

generateINCHI()

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

Parameters

molgraph
options
dim

Returns

generateIncidenceMatrix()

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

Parameters

molgraph
mtx

generateMatchExpression() [1/6]

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

Parameters

atom
molgraph

Returns

generateMatchExpression() [2/6]

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

Parameters

bond
molgraph

Returns

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

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

generateMatchExpressionString() [1/2]

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

Parameters

atom
molgraph

Returns

generateMatchExpressionString() [2/2]

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

Parameters

bond
molgraph

Returns

generateMatchExpressionStrings()

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

Parameters

molgraph
overwrite

generateMatchExpressions() [1/2]

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

Parameters

molgraph
overwrite

generateMatchExpressions() [2/2]

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

Parameters

rxn
overwrite

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

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

initSubstructureSearchQuery() [1/2]

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

Parameters

molgraph
overwrite

initSubstructureSearchQuery() [2/2]

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

Parameters

rxn
overwrite

initSubstructureSearchTarget() [1/2]

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

Parameters

molgraph
overwrite

initSubstructureSearchTarget() [2/2]

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

Parameters

rxn
overwrite

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

insideBoundingBox() [2/3]

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

Parameters

cntnr
min
max

Returns

insideBoundingBox() [3/3]

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

Parameters

min
max
coords

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

intersectsBoundingBox() [2/2]

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

Parameters

cntnr
min
max

Returns

isAromatic()

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

Parameters

ring
molgraph
arom_bond_mask

Returns

isInFragmentOfSize() [1/2]

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

Parameters

atom
frag_list
size

Returns

isInFragmentOfSize() [2/2]

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

Parameters

bond
frag_list
size

Returns

isNotAromatic()

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

Parameters

ring
molgraph

Returns

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

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

kekulizeBonds()

None CDPL.Chem.kekulizeBonds

(

MolecularGraph

molgraph

)

Parameters

molgraph

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.

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.

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() [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

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

markReachableAtoms()

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

Parameters

atom
molgraph
atom_mask
reset

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

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

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

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

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

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

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

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

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

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

perceiveHybridizationState()

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

Parameters

atom
molgraph

Returns

perceiveHybridizationStates()

None CDPL.Chem.perceiveHybridizationStates	(	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

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

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

perceiveSybylAtomTypes()

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

Parameters

molgraph
overwrite

perceiveSybylType() [1/2]

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

Parameters

atom
molgraph

Returns

perceiveSybylType() [2/2]

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

Parameters

bond
molgraph

Returns

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

removeAtomsIf() [1/2]

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

Parameters

frag
pred

removeAtomsIf() [2/2]

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

Parameters

mol
pred

removeAtomsIfNot() [1/2]

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

Parameters

frag
pred

removeAtomsIfNot() [2/2]

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

Parameters

mol
pred

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

sybylToAtomType()

int CDPL.Chem.sybylToAtomType

(

int

sybyl_type

)

Parameters

sybyl_type

Returns

transform2DCoordinates()

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

Parameters

cntnr
mtx

transform3DCoordinates()

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

Parameters

cntnr
mtx

transformConformation()

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

Parameters

cntnr
conf_idx
mtx

transformConformations()

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

Parameters

cntnr
mtx

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

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

setBondMemberSwapStereoFixParameter()

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

Parameters

cntnr
fix

hasBondMemberSwapStereoFixParameter()

bool CDPL.Chem.hasBondMemberSwapStereoFixParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getBondMemberSwapStereoFixParameter()

bool CDPL.Chem.getBondMemberSwapStereoFixParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearBondMemberSwapStereoFixParameter()

None CDPL.Chem.clearBondMemberSwapStereoFixParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCDFOutputSinglePrecisionFloatsParameter()

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

Parameters

cntnr
single_prec

hasCDFOutputSinglePrecisionFloatsParameter()

bool CDPL.Chem.hasCDFOutputSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCDFOutputSinglePrecisionFloatsParameter()

bool CDPL.Chem.getCDFOutputSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCDFOutputSinglePrecisionFloatsParameter()

None CDPL.Chem.clearCDFOutputSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLEnableAromaticBondTypesParameter()

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

Parameters

cntnr
enable

hasCMLEnableAromaticBondTypesParameter()

bool CDPL.Chem.hasCMLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLEnableAromaticBondTypesParameter()

bool CDPL.Chem.getCMLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLEnableAromaticBondTypesParameter()

None CDPL.Chem.clearCMLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputAtomParityParameter()

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

Parameters

cntnr
output

hasCMLOutputAtomParityParameter()

bool CDPL.Chem.hasCMLOutputAtomParityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputAtomParityParameter()

bool CDPL.Chem.getCMLOutputAtomParityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputAtomParityParameter()

None CDPL.Chem.clearCMLOutputAtomParityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputCompactAtomDataParameter()

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

Parameters

cntnr
output

hasCMLOutputCompactAtomDataParameter()

bool CDPL.Chem.hasCMLOutputCompactAtomDataParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputCompactAtomDataParameter()

bool CDPL.Chem.getCMLOutputCompactAtomDataParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputCompactAtomDataParameter()

None CDPL.Chem.clearCMLOutputCompactAtomDataParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputCompactBondDataParameter()

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

Parameters

cntnr
output

hasCMLOutputCompactBondDataParameter()

bool CDPL.Chem.hasCMLOutputCompactBondDataParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputCompactBondDataParameter()

bool CDPL.Chem.getCMLOutputCompactBondDataParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputCompactBondDataParameter()

None CDPL.Chem.clearCMLOutputCompactBondDataParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputDoubleBondStereoParameter()

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

Parameters

cntnr
output

hasCMLOutputDoubleBondStereoParameter()

bool CDPL.Chem.hasCMLOutputDoubleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputDoubleBondStereoParameter()

bool CDPL.Chem.getCMLOutputDoubleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputDoubleBondStereoParameter()

None CDPL.Chem.clearCMLOutputDoubleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputElementPackageParameter()

None CDPL.Chem.setCMLOutputElementPackageParameter	(	Base.ControlParameterContainer	cntnr,
		str	ns
	)

Parameters

cntnr
ns

hasCMLOutputElementPackageParameter()

bool CDPL.Chem.hasCMLOutputElementPackageParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputElementPackageParameter()

str CDPL.Chem.getCMLOutputElementPackageParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputElementPackageParameter()

None CDPL.Chem.clearCMLOutputElementPackageParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputIsotopeParameter()

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

Parameters

cntnr
output

hasCMLOutputIsotopeParameter()

bool CDPL.Chem.hasCMLOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputIsotopeParameter()

bool CDPL.Chem.getCMLOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputIsotopeParameter()

None CDPL.Chem.clearCMLOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputMoleculeNameParameter()

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

Parameters

cntnr
output

hasCMLOutputMoleculeNameParameter()

bool CDPL.Chem.hasCMLOutputMoleculeNameParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputMoleculeNameParameter()

bool CDPL.Chem.getCMLOutputMoleculeNameParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputMoleculeNameParameter()

None CDPL.Chem.clearCMLOutputMoleculeNameParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputSingleBondStereoParameter()

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

Parameters

cntnr
output

hasCMLOutputSingleBondStereoParameter()

bool CDPL.Chem.hasCMLOutputSingleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputSingleBondStereoParameter()

bool CDPL.Chem.getCMLOutputSingleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputSingleBondStereoParameter()

None CDPL.Chem.clearCMLOutputSingleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputSpinMultiplicityParameter()

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

Parameters

cntnr
output

hasCMLOutputSpinMultiplicityParameter()

bool CDPL.Chem.hasCMLOutputSpinMultiplicityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputSpinMultiplicityParameter()

bool CDPL.Chem.getCMLOutputSpinMultiplicityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputSpinMultiplicityParameter()

None CDPL.Chem.clearCMLOutputSpinMultiplicityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputStructureDataParameter()

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

Parameters

cntnr
output

hasCMLOutputStructureDataParameter()

bool CDPL.Chem.hasCMLOutputStructureDataParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputStructureDataParameter()

bool CDPL.Chem.getCMLOutputStructureDataParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputStructureDataParameter()

None CDPL.Chem.clearCMLOutputStructureDataParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCMLOutputXMLDeclarationParameter()

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

Parameters

cntnr
output

hasCMLOutputXMLDeclarationParameter()

bool CDPL.Chem.hasCMLOutputXMLDeclarationParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCMLOutputXMLDeclarationParameter()

bool CDPL.Chem.getCMLOutputXMLDeclarationParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCMLOutputXMLDeclarationParameter()

None CDPL.Chem.clearCMLOutputXMLDeclarationParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCheckLineLengthParameter()

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

Parameters

cntnr
check

hasCheckLineLengthParameter()

bool CDPL.Chem.hasCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCheckLineLengthParameter()

bool CDPL.Chem.getCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCheckLineLengthParameter()

None CDPL.Chem.clearCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setConfIndexNameSuffixPatternParameter()

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

Parameters

cntnr
pattern

hasConfIndexNameSuffixPatternParameter()

bool CDPL.Chem.hasConfIndexNameSuffixPatternParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getConfIndexNameSuffixPatternParameter()

str CDPL.Chem.getConfIndexNameSuffixPatternParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearConfIndexNameSuffixPatternParameter()

None CDPL.Chem.clearConfIndexNameSuffixPatternParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setCoordinatesDimensionParameter()

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

Parameters

cntnr
dim

hasCoordinatesDimensionParameter()

bool CDPL.Chem.hasCoordinatesDimensionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCoordinatesDimensionParameter()

int CDPL.Chem.getCoordinatesDimensionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCoordinatesDimensionParameter()

None CDPL.Chem.clearCoordinatesDimensionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setINCHIInputOptionsParameter()

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

Parameters

cntnr
opts

hasINCHIInputOptionsParameter()

bool CDPL.Chem.hasINCHIInputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getINCHIInputOptionsParameter()

str CDPL.Chem.getINCHIInputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearINCHIInputOptionsParameter()

None CDPL.Chem.clearINCHIInputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setINCHIOutputOptionsParameter()

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

Parameters

cntnr
opts

hasINCHIOutputOptionsParameter()

bool CDPL.Chem.hasINCHIOutputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getINCHIOutputOptionsParameter()

str CDPL.Chem.getINCHIOutputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearINCHIOutputOptionsParameter()

None CDPL.Chem.clearINCHIOutputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setJMESeparateComponentsParameter()

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

Parameters

cntnr
separate

hasJMESeparateComponentsParameter()

bool CDPL.Chem.hasJMESeparateComponentsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getJMESeparateComponentsParameter()

bool CDPL.Chem.getJMESeparateComponentsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearJMESeparateComponentsParameter()

None CDPL.Chem.clearJMESeparateComponentsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLCTABVersionParameter()

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

Parameters

cntnr
version

hasMDLCTABVersionParameter()

bool CDPL.Chem.hasMDLCTABVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLCTABVersionParameter()

int CDPL.Chem.getMDLCTABVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLCTABVersionParameter()

None CDPL.Chem.clearMDLCTABVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLConfEnergySDTagParameter()

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

Parameters

cntnr
tag

hasMDLConfEnergySDTagParameter()

bool CDPL.Chem.hasMDLConfEnergySDTagParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLConfEnergySDTagParameter()

str CDPL.Chem.getMDLConfEnergySDTagParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLConfEnergySDTagParameter()

None CDPL.Chem.clearMDLConfEnergySDTagParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLEnableAromaticBondTypesParameter()

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

Parameters

cntnr
enable

hasMDLEnableAromaticBondTypesParameter()

bool CDPL.Chem.hasMDLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLEnableAromaticBondTypesParameter()

bool CDPL.Chem.getMDLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLEnableAromaticBondTypesParameter()

None CDPL.Chem.clearMDLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLIgnoreParityParameter()

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

Parameters

cntnr
ignore

hasMDLIgnoreParityParameter()

bool CDPL.Chem.hasMDLIgnoreParityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLIgnoreParityParameter()

bool CDPL.Chem.getMDLIgnoreParityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLIgnoreParityParameter()

None CDPL.Chem.clearMDLIgnoreParityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLOutputConfEnergyAsSDEntryParameter()

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

Parameters

cntnr
output

hasMDLOutputConfEnergyAsSDEntryParameter()

bool CDPL.Chem.hasMDLOutputConfEnergyAsSDEntryParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLOutputConfEnergyAsSDEntryParameter()

bool CDPL.Chem.getMDLOutputConfEnergyAsSDEntryParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLOutputConfEnergyAsSDEntryParameter()

None CDPL.Chem.clearMDLOutputConfEnergyAsSDEntryParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLOutputConfEnergyToEnergyFieldParameter()

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

Parameters

cntnr
output

hasMDLOutputConfEnergyToEnergyFieldParameter()

bool CDPL.Chem.hasMDLOutputConfEnergyToEnergyFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLOutputConfEnergyToEnergyFieldParameter()

bool CDPL.Chem.getMDLOutputConfEnergyToEnergyFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLOutputConfEnergyToEnergyFieldParameter()

None CDPL.Chem.clearMDLOutputConfEnergyToEnergyFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLRXNFileVersionParameter()

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

Parameters

cntnr
version

hasMDLRXNFileVersionParameter()

bool CDPL.Chem.hasMDLRXNFileVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLRXNFileVersionParameter()

int CDPL.Chem.getMDLRXNFileVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLRXNFileVersionParameter()

None CDPL.Chem.clearMDLRXNFileVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLTrimLinesParameter()

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

Parameters

cntnr
trim

hasMDLTrimLinesParameter()

bool CDPL.Chem.hasMDLTrimLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLTrimLinesParameter()

bool CDPL.Chem.getMDLTrimLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLTrimLinesParameter()

None CDPL.Chem.clearMDLTrimLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLTrimStringsParameter()

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

Parameters

cntnr
trim

hasMDLTrimStringsParameter()

bool CDPL.Chem.hasMDLTrimStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLTrimStringsParameter()

bool CDPL.Chem.getMDLTrimStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLTrimStringsParameter()

None CDPL.Chem.clearMDLTrimStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLTruncateLinesParameter()

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

Parameters

cntnr
trunc

hasMDLTruncateLinesParameter()

bool CDPL.Chem.hasMDLTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLTruncateLinesParameter()

bool CDPL.Chem.getMDLTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLTruncateLinesParameter()

None CDPL.Chem.clearMDLTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLTruncateStringsParameter()

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

Parameters

cntnr
trunc

hasMDLTruncateStringsParameter()

bool CDPL.Chem.hasMDLTruncateStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLTruncateStringsParameter()

bool CDPL.Chem.getMDLTruncateStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLTruncateStringsParameter()

None CDPL.Chem.clearMDLTruncateStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMDLUpdateTimestampParameter()

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

Parameters

cntnr
update

hasMDLUpdateTimestampParameter()

bool CDPL.Chem.hasMDLUpdateTimestampParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMDLUpdateTimestampParameter()

bool CDPL.Chem.getMDLUpdateTimestampParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMDLUpdateTimestampParameter()

None CDPL.Chem.clearMDLUpdateTimestampParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMOL2CalcFormalChargesParameter()

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

Parameters

cntnr
calc

hasMOL2CalcFormalChargesParameter()

bool CDPL.Chem.hasMOL2CalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2CalcFormalChargesParameter()

bool CDPL.Chem.getMOL2CalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMOL2CalcFormalChargesParameter()

None CDPL.Chem.clearMOL2CalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMOL2ChargeTypeParameter()

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

Parameters

cntnr
type

hasMOL2ChargeTypeParameter()

bool CDPL.Chem.hasMOL2ChargeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2ChargeTypeParameter()

int CDPL.Chem.getMOL2ChargeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMOL2ChargeTypeParameter()

None CDPL.Chem.clearMOL2ChargeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMOL2EnableAromaticBondTypesParameter()

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

Parameters

cntnr
enable

hasMOL2EnableAromaticBondTypesParameter()

bool CDPL.Chem.hasMOL2EnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2EnableAromaticBondTypesParameter()

bool CDPL.Chem.getMOL2EnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMOL2EnableAromaticBondTypesParameter()

None CDPL.Chem.clearMOL2EnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMOL2EnableExtendedAtomTypesParameter()

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

Parameters

cntnr
enable

hasMOL2EnableExtendedAtomTypesParameter()

bool CDPL.Chem.hasMOL2EnableExtendedAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2EnableExtendedAtomTypesParameter()

bool CDPL.Chem.getMOL2EnableExtendedAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMOL2EnableExtendedAtomTypesParameter()

None CDPL.Chem.clearMOL2EnableExtendedAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMOL2MoleculeTypeParameter()

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

Parameters

cntnr
type

hasMOL2MoleculeTypeParameter()

bool CDPL.Chem.hasMOL2MoleculeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2MoleculeTypeParameter()

int CDPL.Chem.getMOL2MoleculeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMOL2MoleculeTypeParameter()

None CDPL.Chem.clearMOL2MoleculeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMOL2OutputFormalChargesParameter()

None CDPL.Chem.setMOL2OutputFormalChargesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

Parameters

cntnr
output

hasMOL2OutputFormalChargesParameter()

bool CDPL.Chem.hasMOL2OutputFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2OutputFormalChargesParameter()

bool CDPL.Chem.getMOL2OutputFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMOL2OutputFormalChargesParameter()

None CDPL.Chem.clearMOL2OutputFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMOL2OutputSubstructuresParameter()

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

Parameters

cntnr
output

hasMOL2OutputSubstructuresParameter()

bool CDPL.Chem.hasMOL2OutputSubstructuresParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2OutputSubstructuresParameter()

bool CDPL.Chem.getMOL2OutputSubstructuresParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMOL2OutputSubstructuresParameter()

None CDPL.Chem.clearMOL2OutputSubstructuresParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMOL2ReadPartialAsFormalChargesParameter()

None CDPL.Chem.setMOL2ReadPartialAsFormalChargesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	read
	)

Parameters

cntnr
read

hasMOL2ReadPartialAsFormalChargesParameter()

bool CDPL.Chem.hasMOL2ReadPartialAsFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMOL2ReadPartialAsFormalChargesParameter()

bool CDPL.Chem.getMOL2ReadPartialAsFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMOL2ReadPartialAsFormalChargesParameter()

None CDPL.Chem.clearMOL2ReadPartialAsFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMultiConfExportParameter()

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

Parameters

cntnr
multi_conf

hasMultiConfExportParameter()

bool CDPL.Chem.hasMultiConfExportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMultiConfExportParameter()

bool CDPL.Chem.getMultiConfExportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMultiConfExportParameter()

None CDPL.Chem.clearMultiConfExportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMultiConfImportParameter()

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

Parameters

cntnr
multi_conf

hasMultiConfImportParameter()

bool CDPL.Chem.hasMultiConfImportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMultiConfImportParameter()

bool CDPL.Chem.getMultiConfImportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMultiConfImportParameter()

None CDPL.Chem.clearMultiConfImportParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setMultiConfInputProcessorParameter()

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

Parameters

cntnr
proc

hasMultiConfInputProcessorParameter()

bool CDPL.Chem.hasMultiConfInputProcessorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getMultiConfInputProcessorParameter()

MultiConfMoleculeInputProcessor CDPL.Chem.getMultiConfInputProcessorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearMultiConfInputProcessorParameter()

None CDPL.Chem.clearMultiConfInputProcessorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setOrdinaryHydrogenDepleteParameter()

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

Parameters

cntnr
deplete

hasOrdinaryHydrogenDepleteParameter()

bool CDPL.Chem.hasOrdinaryHydrogenDepleteParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getOrdinaryHydrogenDepleteParameter()

bool CDPL.Chem.getOrdinaryHydrogenDepleteParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearOrdinaryHydrogenDepleteParameter()

None CDPL.Chem.clearOrdinaryHydrogenDepleteParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setOutputConfEnergyAsCommentParameter()

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

Parameters

cntnr
output

hasOutputConfEnergyAsCommentParameter()

bool CDPL.Chem.hasOutputConfEnergyAsCommentParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getOutputConfEnergyAsCommentParameter()

bool CDPL.Chem.getOutputConfEnergyAsCommentParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearOutputConfEnergyAsCommentParameter()

None CDPL.Chem.clearOutputConfEnergyAsCommentParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setRecordSeparatorParameter()

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

Parameters

cntnr
sep

hasRecordSeparatorParameter()

bool CDPL.Chem.hasRecordSeparatorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getRecordSeparatorParameter()

str CDPL.Chem.getRecordSeparatorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearRecordSeparatorParameter()

None CDPL.Chem.clearRecordSeparatorParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESMinStereoBondRingSizeParameter()

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

Parameters

cntnr
min_size

hasSMILESMinStereoBondRingSizeParameter()

bool CDPL.Chem.hasSMILESMinStereoBondRingSizeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESMinStereoBondRingSizeParameter()

int CDPL.Chem.getSMILESMinStereoBondRingSizeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESMinStereoBondRingSizeParameter()

None CDPL.Chem.clearSMILESMinStereoBondRingSizeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESMolOutputAtomMappingIDParameter()

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

Parameters

cntnr
output

hasSMILESMolOutputAtomMappingIDParameter()

bool CDPL.Chem.hasSMILESMolOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESMolOutputAtomMappingIDParameter()

bool CDPL.Chem.getSMILESMolOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESMolOutputAtomMappingIDParameter()

None CDPL.Chem.clearSMILESMolOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESNoOrganicSubsetParameter()

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

Parameters

cntnr
no_subset

hasSMILESNoOrganicSubsetParameter()

bool CDPL.Chem.hasSMILESNoOrganicSubsetParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESNoOrganicSubsetParameter()

bool CDPL.Chem.getSMILESNoOrganicSubsetParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESNoOrganicSubsetParameter()

None CDPL.Chem.clearSMILESNoOrganicSubsetParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESOutputAromaticBondsParameter()

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

Parameters

cntnr
output

hasSMILESOutputAromaticBondsParameter()

bool CDPL.Chem.hasSMILESOutputAromaticBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESOutputAromaticBondsParameter()

bool CDPL.Chem.getSMILESOutputAromaticBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESOutputAromaticBondsParameter()

None CDPL.Chem.clearSMILESOutputAromaticBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESOutputAtomStereoParameter()

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

Parameters

cntnr
output

hasSMILESOutputAtomStereoParameter()

bool CDPL.Chem.hasSMILESOutputAtomStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESOutputAtomStereoParameter()

bool CDPL.Chem.getSMILESOutputAtomStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESOutputAtomStereoParameter()

None CDPL.Chem.clearSMILESOutputAtomStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESOutputBondStereoParameter()

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

Parameters

cntnr
output

hasSMILESOutputBondStereoParameter()

bool CDPL.Chem.hasSMILESOutputBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESOutputBondStereoParameter()

bool CDPL.Chem.getSMILESOutputBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESOutputBondStereoParameter()

None CDPL.Chem.clearSMILESOutputBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESOutputCanonicalFormParameter()

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

Parameters

cntnr
output

hasSMILESOutputCanonicalFormParameter()

bool CDPL.Chem.hasSMILESOutputCanonicalFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESOutputCanonicalFormParameter()

bool CDPL.Chem.getSMILESOutputCanonicalFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESOutputCanonicalFormParameter()

None CDPL.Chem.clearSMILESOutputCanonicalFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESOutputHydrogenCountParameter()

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

Parameters

cntnr
output

hasSMILESOutputHydrogenCountParameter()

bool CDPL.Chem.hasSMILESOutputHydrogenCountParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESOutputHydrogenCountParameter()

bool CDPL.Chem.getSMILESOutputHydrogenCountParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESOutputHydrogenCountParameter()

None CDPL.Chem.clearSMILESOutputHydrogenCountParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESOutputIsotopeParameter()

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

Parameters

cntnr
output

hasSMILESOutputIsotopeParameter()

bool CDPL.Chem.hasSMILESOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESOutputIsotopeParameter()

bool CDPL.Chem.getSMILESOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESOutputIsotopeParameter()

None CDPL.Chem.clearSMILESOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESOutputKekuleFormParameter()

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

Parameters

cntnr
output

hasSMILESOutputKekuleFormParameter()

bool CDPL.Chem.hasSMILESOutputKekuleFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESOutputKekuleFormParameter()

bool CDPL.Chem.getSMILESOutputKekuleFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESOutputKekuleFormParameter()

None CDPL.Chem.clearSMILESOutputKekuleFormParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESOutputRingBondStereoParameter()

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

Parameters

cntnr
output

hasSMILESOutputRingBondStereoParameter()

bool CDPL.Chem.hasSMILESOutputRingBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESOutputRingBondStereoParameter()

bool CDPL.Chem.getSMILESOutputRingBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESOutputRingBondStereoParameter()

None CDPL.Chem.clearSMILESOutputRingBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESOutputSingleBondsParameter()

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

Parameters

cntnr
output

hasSMILESOutputSingleBondsParameter()

bool CDPL.Chem.hasSMILESOutputSingleBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESOutputSingleBondsParameter()

bool CDPL.Chem.getSMILESOutputSingleBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESOutputSingleBondsParameter()

None CDPL.Chem.clearSMILESOutputSingleBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESRecordFormatParameter()

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

Parameters

cntnr
format

hasSMILESRecordFormatParameter()

bool CDPL.Chem.hasSMILESRecordFormatParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESRecordFormatParameter()

str CDPL.Chem.getSMILESRecordFormatParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESRecordFormatParameter()

None CDPL.Chem.clearSMILESRecordFormatParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setSMILESRxnOutputAtomMappingIDParameter()

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

Parameters

cntnr
output

hasSMILESRxnOutputAtomMappingIDParameter()

bool CDPL.Chem.hasSMILESRxnOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getSMILESRxnOutputAtomMappingIDParameter()

bool CDPL.Chem.getSMILESRxnOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearSMILESRxnOutputAtomMappingIDParameter()

None CDPL.Chem.clearSMILESRxnOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setStrictErrorCheckingParameter()

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

Parameters

cntnr
strict

hasStrictErrorCheckingParameter()

bool CDPL.Chem.hasStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getStrictErrorCheckingParameter()

bool CDPL.Chem.getStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearStrictErrorCheckingParameter()

None CDPL.Chem.clearStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setXYZCalcFormalChargesParameter()

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

Parameters

cntnr
calc

hasXYZCalcFormalChargesParameter()

bool CDPL.Chem.hasXYZCalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getXYZCalcFormalChargesParameter()

bool CDPL.Chem.getXYZCalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearXYZCalcFormalChargesParameter()

None CDPL.Chem.clearXYZCalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setXYZCommentIsNameParameter()

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

Parameters

cntnr
is_name

hasXYZCommentIsNameParameter()

bool CDPL.Chem.hasXYZCommentIsNameParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getXYZCommentIsNameParameter()

bool CDPL.Chem.getXYZCommentIsNameParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearXYZCommentIsNameParameter()

None CDPL.Chem.clearXYZCommentIsNameParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setXYZPerceiveBondOrdersParameter()

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

Parameters

cntnr
perceive

hasXYZPerceiveBondOrdersParameter()

bool CDPL.Chem.hasXYZPerceiveBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getXYZPerceiveBondOrdersParameter()

bool CDPL.Chem.getXYZPerceiveBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearXYZPerceiveBondOrdersParameter()

None CDPL.Chem.clearXYZPerceiveBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setXYZPerceiveConnectivityParameter()

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

Parameters

cntnr
perceive

hasXYZPerceiveConnectivityParameter()

bool CDPL.Chem.hasXYZPerceiveConnectivityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getXYZPerceiveConnectivityParameter()

bool CDPL.Chem.getXYZPerceiveConnectivityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearXYZPerceiveConnectivityParameter()

None CDPL.Chem.clearXYZPerceiveConnectivityParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr