CDPL.Chem Package Reference

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

Classes
class	ANDAtomMatchExpressionList
	Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND). More...
class	ANDBondMatchExpressionList
	Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND). More...
class	ANDMolecularGraphMatchExpressionList
	Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND). More...
class	ANDReactionMatchExpressionList
	Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND). 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
	Abstract base class representing a chemical atom and its bonded neighborhood. More...
class	Atom2DCoordinatesCalculator
	Generates 2D coordinates for the atoms of a molecular graph using a layout algorithm that combines ring-system templates, chain extension, and substituent placement. More...
class	Atom3DCoordinatesFunction
	Generic wrapper class used to store a user-defined Chem.Atom 3D-coordinates function. More...
class	Atom3DCoordinatesFunctor
	Helper-functor for retrieving the 3D coordinates of an atom (via the Chem.AtomProperty.COORDINATES_3D property). More...
class	AtomArray3DCoordinatesFunctor
	Helper-functor for retrieving the 3D coordinates of an atom from a separately-stored coordinates array, indexed by the atom's position in the underlying molecular graph. More...
class	AtomBondMapping
	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 configuration of stereogenic atoms. More...
class	AtomConfigurationMatchExpression
	Chem.MatchExpression that constrains target atoms by their stereo configuration relative to a query atom. More...
class	AtomConformer3DCoordinatesFunctor
	Helper-functor for retrieving the 3D coordinates of an atom for a specific conformer (via the Chem.AtomProperty.CONFORMER_COORDINATES_3D conformer-array property). More...
class	AtomContainer
	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
	Chem.MatchExpression that constrains target atoms by the structural environment encoded as a SMARTS substructure pattern. More...
class	AtomMapping
	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
	Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	AtomMatchExpressionList
	Container for the storage and evaluation of logical match expression lists. More...
class	AtomMatchExpressionPtrAtomFunctor
class	AtomPredicate
	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
	Enumerates the atom/bond automorphisms of a molecular graph. More...
class	BRICSAtomLabel
	Provides constants for the labeling of atoms in bonds matched by a BRICS fragmentation rule. More...
class	BRICSFragmentGenerator
	Chem.FragmentGenerator preconfigured with the 16 BRICS bond-cleavage rules and the associated exclude patterns for combinatorial fragmentation of organic molecules. More...
class	BRICSRuleID
	Provides constants for the identification of BRICS fragmentation rules. More...
class	BasicAtom
	Concrete Chem.Atom implementation used as the atom type of Chem.BasicMolecule. More...
class	BasicBond
	Default implementation of the Chem.Bond interface. More...
class	BasicMolecule
	Concrete Chem.Molecule implementation that owns Chem.BasicAtom and Chem.BasicBond instances. More...
class	BasicReaction
	Default concrete implementation of the Chem.Reaction abstract interface. More...
class	BemisMurckoAnalyzer
	Decomposes a molecular graph into its Bemis-Murcko framework, ring systems, linkers and side chains. More...
class	Bond
	Abstract base class representing a chemical bond between two Chem.Atom instances. More...
class	BondConfiguration
	Provides constants that are used to specify the cis/trans configuration of bonds. More...
class	BondConfigurationMatchExpression
	Chem.MatchExpression that constrains target bonds by their stereo configuration relative to a query bond. More...
class	BondContainer
	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
	Chem.MatchExpression that constrains target bonds by their SMILES/SMARTS bond direction. More...
class	BondMapping
	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
	Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	BondMatchExpressionList
	Container for the storage and evaluation of logical match expression lists. More...
class	BondMatchExpressionPtrBondFunctor
class	BondOrderCalculator
	Perceives bond orders of a molecular graph from its 3D structure and atom connectivity. More...
class	BondPredicate
	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
	Chem.MatchExpression that constrains target bonds by their reaction-center status (see Chem.ReactionCenterStatus). 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
	Chem.MatchExpression that constrains target double bond geometry via the per-substituent bond-direction annotations carried by the query (in the style of Daylight SMARTS [SMARTS] cis/trans patterns). 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
	Handler for the output of bzip2-compressed molecular graph data in the native I/O format of the CDPL. More...
class	CDFBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed native I/O format of the CDPL. More...
class	CDFBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL. More...
class	CDFBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed native I/O format of the CDPL. More...
class	CDFBZ2ReactionInputHandler
	Handler for the input of bzip2-compressed reaction data in the native I/O format of the CDPL. More...
class	CDFBZ2ReactionOutputHandler
	Handler for the output of bzip2-compressed reaction data in the native I/O format of the CDPL. More...
class	CDFBZ2ReactionReader
	Reader for reaction data in the bzip2-compressed native I/O format of the CDPL. More...
class	CDFBZ2ReactionWriter
	Writer for reaction data in the bzip2-compressed native I/O format of the CDPL. More...
class	CDFGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More...
class	CDFGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed native I/O format of the CDPL. More...
class	CDFGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL. More...
class	CDFGZMoleculeReader
	Reader for molecule data in the gzip-compressed native I/O format of the CDPL. More...
class	CDFGZReactionInputHandler
	Handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More...
class	CDFGZReactionOutputHandler
	Handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More...
class	CDFGZReactionReader
	Reader for reaction data in the gzip-compressed native I/O format of the CDPL. More...
class	CDFGZReactionWriter
	Writer for reaction data in the gzip-compressed native I/O format of the CDPL. More...
class	CDFMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the native I/O format of the CDPL. More...
class	CDFMolecularGraphWriter
	Writer for molecular graph data in the native I/O format of the CDPL. More...
class	CDFMoleculeInputHandler
	Handler for the input of molecule data in the native I/O format of the CDPL. More...
class	CDFMoleculeReader
	Reader for molecule data in the native I/O format of the CDPL. More...
class	CDFReactionInputHandler
	Handler for the input of reaction data in the native I/O format of the CDPL. More...
class	CDFReactionOutputHandler
	Handler for the output of reaction data in the native I/O format of the CDPL. More...
class	CDFReactionReader
	Reader for reaction data in the native I/O format of the CDPL. More...
class	CDFReactionWriter
	Writer for reaction data in the native I/O format of the CDPL. More...
class	CIPConfigurationLabeler
	Assigns Cahn-Ingold-Prelog (CIP) configuration labels to stereogenic atoms and bonds of a molecular graph. More...
class	CIPDescriptor
	Provides constants for the specification of stereogenic atom/bond configurations determined by the Cahn-Ingold-Prelog (CIP) sequence rules. More...
class	CIPPriorityCalculator
	Computes a topological approximation of CIP (Cahn-Ingold-Prelog) priorities for the atoms of a molecular graph. More...
class	CMLBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the Chemical Markup Language [CML] format. More...
class	CMLBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Chemical Markup Language [CML] format. More...
class	CMLBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Chemical Markup Language [CML] format. More...
class	CMLBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Chemical Markup Language [CML] format. More...
class	CMLGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the Chemical Markup Language [CML] format. More...
class	CMLGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Chemical Markup Language [CML] format. More...
class	CMLGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the Chemical Markup Language [CML] format. More...
class	CMLGZMoleculeReader
	Reader for molecule data in the gzip-compressed Chemical Markup Language [CML] format. More...
class	CMLMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Chemical Markup Language [CML] format. More...
class	CMLMolecularGraphWriter
	Writer for molecular graph data in the Chemical Markup Language [CML] format. More...
class	CMLMoleculeInputHandler
	Handler for the input of molecule data in the Chemical Markup Language [CML] format. More...
class	CMLMoleculeReader
	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. More...
class	ChEMBLStandardizer
	Implementation of the ChEMBL structure preprocessing pipeline. More...
class	CommonConnectedSubstructureSearch
	Enumerates all maximal common connected substructures shared between a query and a target molecular graph. 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
	Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream. More...
class	CompoundReactionReader
	Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream. More...
class	ConjugatedRingBondPatternSwitching
	Chem.TautomerizationRule implementation that enumerates tautomers obtained by switching the single/double bond pattern of conjugated rings (e.g. More...
class	ConnectedSubstructureSet
	Enumerates the connected substructures of a molecular graph of a specified bond count. 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
	Default Chem.MultiConfMoleculeInputProcessor implementation that detects multi-conformer input by comparing atom and bond properties (and optionally molecule names) between successive input molecules. More...
class	DefaultTautomerGenerator
	Chem.TautomerGenerator preconfigured with the standard CDPKit tautomerization rules. 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
	Data type for the storage of Chem.ElectronSystem objects. More...
class	Entity3D
	Base class for objects that have a position in 3D space (e.g. More...
class	Entity3DContainer
	Common interface for data structures that support a random access to stored Chem.Entity3D instances. More...
class	Entity3DMapping
	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
	Concrete Chem.MolecularGraph implementation that stores references to a selectable subset of atoms and bonds (typically of a parent Chem.Molecule). More...
class	FragmentGenerator
	Generic rule-based molecule fragmentation engine that splits a molecular graph along bonds matching user-defined fragmentation rules. More...
class	FragmentList
	Data type for the storage of Chem.Fragment objects. More...
class	GenericHydrogen13ShiftTautomerization
	Chem.TautomerizationRule implementation that enumerates tautomers obtained by a generic 1,3-hydrogen shift (a proton migrates between atoms separated by two bonds, with the corresponding single/double bond pattern flipping). More...
class	GenericHydrogen15ShiftTautomerization
	Chem.TautomerizationRule implementation that enumerates tautomers obtained by a generic 1,5-hydrogen shift (a proton migrates between atoms separated by four bonds along a conjugated path, with the corresponding single/double bond pattern flipping). More...
class	HashCodeCalculator
	Computes a 64-bit hash code that identifies a molecular graph up to a configurable set of atom and bond properties. More...
class	HybridizationState
	Provides constants for the specification of atom hybridization states. More...
class	Hydrogen3DCoordinatesCalculator
	Generates 3D coordinates for the hydrogen atoms of a molecular graph from the existing positions of their heavy atom neighbors. More...
class	INCHIMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	INCHIMolecularGraphWriter
	Writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	INCHIMoleculeInputHandler
	Handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	INCHIMoleculeReader
	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
	Chem.TautomerizationRule implementation that enumerates the imine/enamine tautomers of an \( R_2C=N{-}CHR_2 \rightleftharpoons R_2CH{-}N=CR_2 \) system. More...
class	JMEMolecularGraphOutputHandler
	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
	Writer for molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEMoleculeInputHandler
	Handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEMoleculeReader
	Reader for molecule data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionInputHandler
	Handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionOutputHandler
	Handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionReader
	Reader for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionWriter
	Writer for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	KekuleStructureCalculator
	Assigns an alternating single/double bond pattern (Kekulé structure) to the previously undefined bonds of a molecular graph (typically used to convert aromatic-bond annotations into explicit single/double bonds). More...
class	KeteneYnolTautomerization
	Chem.PatternBasedTautomerizationRule implementation that enumerates ketene/ynol tautomers (Chem.TautomerizationType.KETENE_YNOL). More...
class	KetoEnolTautomerization
	Chem.TautomerizationRule implementation that enumerates the keto/enol tautomers of an \( R_2C{-}C(=O)R' \rightleftharpoons RC=C(OH)R' \) system. More...
class	LactamLactimTautomerization
	Chem.TautomerizationRule implementation that enumerates the lactam/lactim tautomers of a cyclic amide \( {-}NH{-}C(=O){-} \rightleftharpoons {-}N=C(OH){-} \) system. 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
	Handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format. More...
class	MOL2BZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Sybyl MOL2 format. More...
class	MOL2BZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format. More...
class	MOL2BZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Sybyl MOL2 format. More...
class	MOL2ChargeType
	Provides constants for the specification of the atom charge type in Sybyl MOL2 files. More...
class	MOL2GZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format. More...
class	MOL2GZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Sybyl MOL2 format. More...
class	MOL2GZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format. More...
class	MOL2GZMoleculeReader
	Reader for molecule data in the gzip-compressed Sybyl MOL2 format. More...
class	MOL2MolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Sybyl MOL2 format. More...
class	MOL2MolecularGraphWriter
	Writer for molecular graph data in the Sybyl MOL2 format. More...
class	MOL2MoleculeInputHandler
	Handler for the input of molecule data in the Sybyl MOL2 format. More...
class	MOL2MoleculeReader
	Reader for molecule data in the Sybyl MOL2 format. More...
class	MOL2MoleculeType
	Provides constants for the specification of the molecule type in Sybyl MOL2 files. More...
class	MOLMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format. More...
class	MOLMolecularGraphWriter
	Writer for molecular graph data in the MDL Mol-File [CTFILE] format. More...
class	MOLMoleculeInputHandler
	Handler for the input of molecule data in the MDL Mol-File [CTFILE] format. More...
class	MOLMoleculeReader
	Reader for molecule data in the MDL Mol-File [CTFILE] format. More...
class	MatchConstraint
	Describes a single attribute-comparison constraint between a query and a target object used by molecular graph matching algorithms. More...
class	MatchConstraintList
	List of Chem.MatchConstraint instances combined with a logical Type (AND_LIST, NOT_AND_LIST, OR_LIST, or NOT_OR_LIST) that controls how the contained constraints are aggregated during query/target evaluation. More...
class	MaxCommonAtomSubstructureSearch
	Computes the maximum common atom substructure between a query and a target molecular graph by reducing the problem to maximum-clique enumeration on an association (modular product) graph. More...
class	MaxCommonBondSubstructureSearch
	Computes the maximum common bond substructure between a query and a target molecular graph by reducing the problem to maximum-clique enumeration on a bond-based association graph. More...
class	MolGraphMatchExpressionPtrMolGraphFunctor
class	MolecularGraph
	Abstract base class for representations of a chemical structure as a graph of bonded atoms. More...
class	MolecularGraphComponentGroupingMatchExpression
	Chem.MatchExpression that constrains the substructure mapping by the query's component-level groupings (typically derived from the parenthesization of a Daylight SMARTS [SMARTS] pattern). More...
class	MolecularGraphIOManager
	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
	Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	MolecularGraphMatchExpressionList
class	MolecularGraphOutputHandler
	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
	Interface for writing data objects of type Chem.MolecularGraph to an arbitrary data sink. More...
class	Molecule
	Abstract base class representing a mutable molecular graph that owns its atoms and bonds. More...
class	MoleculeIOManager
	Singleton class that serves as a global registry for Chem.MoleculeInputHandler and Chem.MoleculeOutputHandler implementation instances. More...
class	MoleculeInputHandler
	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
	Interface for reading data objects of type Chem.Molecule from an arbitrary data source. More...
class	MorganNumberingCalculator
	Computes a canonical atom numbering of a molecular graph using a modified Morgan algorithm. More...
class	MultiConfMoleculeInputProcessor
	Abstract base interface for processors that detect and assemble multi-conformer molecules from a stream of successive single-conformer input molecules. More...
class	MultiSubstructureSearch
	Evaluates a boolean expression over multiple substructure queries against a target molecular graph. More...
class	NOTAtomMatchExpression
	Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance. More...
class	NOTBondMatchExpression
	Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance. More...
class	NOTMolecularGraphMatchExpression
	Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance. More...
class	NOTReactionMatchExpression
	Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance. More...
class	NitroAciTautomerization
	Implementation of the nitro ↔ aci-nitro tautomerization rule. More...
class	NitrosoOximeTautomerization
	Chem.PatternBasedTautomerizationRule implementation that enumerates nitroso/oxime tautomers (Chem.TautomerizationType.NITROSO_OXIME). More...
class	ORAtomMatchExpressionList
	Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR). More...
class	ORBondMatchExpressionList
	Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR). More...
class	ORMolecularGraphMatchExpressionList
	Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR). More...
class	ORReactionMatchExpressionList
	Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR). More...
class	PatternAtomTyper
	Assigns numeric labels to specific atoms of a molecular graph that are described by substructure patterns. More...
class	PatternBasedTautomerizationRule
	Match pattern-based implementation of the Chem.TautomerizationRule interface. More...
class	PhosphinicAcidTautomerization
	Chem.PatternBasedTautomerizationRule implementation that enumerates phosphinic-acid tautomers (Chem.TautomerizationType.PHOSPHINIC_ACID). More...
class	PiElectronSystemList
	Implements the perception of all pi electron systems present in a molecule. More...
class	ProtonationStateStandardizer
	Adjusts the protonation state of a molecule (atom formal charges and bonded hydrogen counts) according to one of several pre-defined objectives. More...
class	RDFBZ2ReactionInputHandler
	Handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFBZ2ReactionOutputHandler
	Handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFBZ2ReactionReader
	Reader for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format. More...
class	RDFBZ2ReactionWriter
class	RDFGZReactionInputHandler
	Handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFGZReactionOutputHandler
	Handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFGZReactionReader
class	RDFGZReactionWriter
class	RDFReactionInputHandler
	Handler for the input of reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFReactionOutputHandler
	Handler for the output of reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFReactionReader
	Reader for reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFReactionWriter
	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
	Chem.FragmentGenerator implementation applying the RECAP [RECAP] cleavage rules (see Chem.RECAPRuleID) to produce a set of fragment building blocks from a molecular graph. More...
class	RECAPRuleID
	Provides constants for the identification of RECAP fragmentation rules. More...
class	RXNReactionInputHandler
	Handler for the input of reaction data in the MDL Rxn-File [CTFILE] format. More...
class	RXNReactionOutputHandler
	Handler for the output of reaction data in the MDL Rxn-File [CTFILE] format. More...
class	RXNReactionReader
	Reader for reaction data in the MDL Rxn-File [CTFILE] format. More...
class	RXNReactionWriter
	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
	Abstract base class for chemical reactions composed of role-tagged Chem.Molecule components. More...
class	ReactionAtomMappingMatchExpression
	Chem.MatchExpression that constrains reaction substructure matches by a required reactant-to-product atom mapping. More...
class	ReactionCenterStatus
	Provides flags that are used to describe state changes of atoms and bonds in a reaction center. More...
class	ReactionComponentGroupingMatchExpression
	Chem.MatchExpression that constrains reaction substructure matches by the query's component-level groupings (typically derived from the parenthesization of a Daylight SMARTS [SMARTS] pattern). More...
class	ReactionIOManager
	Singleton class that serves as a global registry for Chem.ReactionInputHandler and Chem.ReactionOutputHandler implementation instances. More...
class	ReactionInputHandler
	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
	Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	ReactionMatchExpressionList
class	ReactionOutputHandler
	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
	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
	Reaction-level analogue of Chem.SubstructureSearch that locates atom/bond mappings of a query reaction pattern in a target reaction. More...
class	ReactionWriter
	Writer for reaction data in any supported format. More...
class	ReactionWriterBase
	Interface for writing data objects of type Chem.Reaction to an arbitrary data sink. More...
class	Reactor
	Applies a Chem.Reaction template to the reactant components of a target Chem.Reaction to generate the corresponding product molecules. More...
class	ResonanceStructureGenerator
	Enumerates the resonance structures of a molecular graph by redistributing π-electrons across the resonance-active bonds. More...
class	SDFBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
class	SDFBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed MDL SD-File [CTFILE] format. More...
class	SDFBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format. More...
class	SDFBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed MDL SD-File [CTFILE] format. More...
class	SDFGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
class	SDFGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed MDL SD-File [CTFILE] format. More...
class	SDFGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format. More...
class	SDFGZMoleculeReader
	Reader for molecule data in the gzip-compressed MDL SD-File [CTFILE] format. More...
class	SDFMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the MDL SD-File [CTFILE] format. More...
class	SDFMolecularGraphWriter
	Writer for molecular graph data in the MDL SD-File [CTFILE] format. More...
class	SDFMoleculeInputHandler
	Handler for the input of molecule data in the MDL SD-File [CTFILE] format. More...
class	SDFMoleculeReader
	Reader for molecule data in the MDL SD-File [CTFILE] format. More...
class	SMARTSMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSMolecularGraphWriter
	Writer for molecular graph data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSMoleculeInputHandler
	Handler for the input of molecule data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSMoleculeReader
	Reader for molecule data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionInputHandler
	Handler for the input of reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionOutputHandler
	Handler for the output of reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionReader
	Reader for reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionWriter
	Writer for reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMILESBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Daylight SMILES [SMILES] format. More...
class	SMILESBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format. More...
class	SMILESBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Daylight SMILES [SMILES] format. More...
class	SMILESBZ2ReactionInputHandler
	Handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESBZ2ReactionOutputHandler
	Handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESBZ2ReactionReader
	Reader for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format. More...
class	SMILESBZ2ReactionWriter
	Writer for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format. More...
class	SMILESGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Daylight SMILES [SMILES] format. More...
class	SMILESGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format. More...
class	SMILESGZMoleculeReader
	Reader for molecule data in the gzip-compressed Daylight SMILES [SMILES] format. More...
class	SMILESGZReactionInputHandler
	Handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESGZReactionOutputHandler
	Handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESGZReactionReader
	Reader for reaction data in the gzip-compressed Daylight SMILES [SMILES] format. More...
class	SMILESGZReactionWriter
	Writer for reaction data in the gzip-compressed Daylight SMILES [SMILES] format. More...
class	SMILESMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESMolecularGraphWriter
	Writer for molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESMoleculeInputHandler
	Handler for the input of molecule data in the Daylight SMILES [SMILES] format. More...
class	SMILESMoleculeReader
	Reader for molecule data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionInputHandler
	Handler for the input of reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionOutputHandler
	Handler for the output of reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionReader
	Reader for reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionWriter
	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
	Data structure for the storage and retrieval of stereochemical information about atoms and bonds. More...
class	StereoisomerGenerator
	Enumerates the stereoisomers of a molecular graph by flipping the configurations of selected atom and bond stereocenters. More...
class	StringDataBlock
	Array of Chem.StringDataBlockEntry objects. More...
class	StringDataBlockEntry
	Represents a data item consisting of a header and a data payload. More...
class	SubstructureEditor
	Pattern-driven editor that rewrites matched substructures of a Chem.Molecule using a result template, with optional exclude patterns guarding sites that must not be touched. More...
class	SubstructureHistogramCalculator
	Counts occurrences of registered substructure patterns in a molecular graph, emitting the per-pattern hit counts into a user-supplied histogram container. More...
class	SubstructureSearch
	Subgraph-isomorphism search of a query molecular graph against a target molecular graph, implemented after the VF2 algorithm. More...
class	SulfenicAcidTautomerization
	Chem.TautomerizationRule implementation that enumerates the sulfenic-acid tautomers of an \( R{-}S{-}OH \rightleftharpoons R{-}S(=O)H \) system. More...
class	SurfaceAtomExtractor
	Extracts the solvent-accessible surface atoms of a set of atoms. 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
	Perceives topological-symmetry classes of the atoms in a molecular graph. More...
class	TautomerGenerator
	Enumerates the tautomers of a molecular graph by iteratively applying a configurable set of Chem.TautomerizationRule instances and reporting each accepted tautomer to a user-supplied callback. More...
class	TautomerScore
	Functor for the calculation of a heuristic stability score of a tautomeric form represented as a molecular graph. More...
class	TautomerizationRule
	Abstract base class for all tautomerization rule implementations used by the Chem.TautomerGenerator. 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
	Handler for the output of bzip2-compressed molecular graph data in the XYZ format. More...
class	XYZBZ2MolecularGraphWriter
class	XYZBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the XYZ format. More...
class	XYZBZ2MoleculeReader
class	XYZGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the XYZ format. More...
class	XYZGZMolecularGraphWriter
class	XYZGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the XYZ format. More...
class	XYZGZMoleculeReader
class	XYZMolecularGraphOutputHandler
	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
	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)
	Sets the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom to coords. More...
bool	has2DCoordinates (Atom atom)
	Tells whether the Chem.AtomProperty.COORDINATES_2D property of the atom atom is set. More...
Math.Vector2D	get2DCoordinates (Atom atom)
	Returns the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom. More...
None	clear2DCoordinates (Atom atom)
	Clears the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom. More...
None	set2DCoordinates (AtomContainer cntnr, Math.Vector2DArray coords)
	Writes the 2D coordinates in coords back to the corresponding atoms of cntnr. More...
None	get2DCoordinates (AtomContainer cntnr, Math.Vector2DArray coords, bool append=False)
	Extracts the 2D coordinates of all atoms in cntnr into coords. More...
None	set2DStereoFlag (Bond bond, int flag)
	Sets the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond to flag (see namespace Chem.BondStereoFlag). More...
bool	has2DStereoFlag (Bond bond)
	Tells whether the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond is set. More...
int	get2DStereoFlag (Bond bond)
	Returns the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond (see namespace Chem.BondStereoFlag). More...
None	clear2DStereoFlag (Bond bond)
	Clears the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond. More...
None	set3DCoordinatesArray (Atom atom, Math.Vector3DArray coords_array)
	Sets the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom to coords_array. More...
bool	has3DCoordinatesArray (Atom atom)
	Tells whether the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom is set. More...
Math.Vector3DArray	get3DCoordinatesArray (Atom atom)
	Returns the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom. More...
None	clear3DCoordinatesArray (Atom atom)
	Clears the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom. More...
None	get3DCoordinates (AtomContainer cntnr, Math.Vector3DArray coords, Atom3DCoordinatesFunction coords_func, bool append=False)
	Extracts the 3D coordinates of all atoms in cntnr into coords using the per-atom coordinate lookup function coords_func. More...
None	set3DCoordinates (Entity3D entity, Math.Vector3D coords)
	Sets the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity to coords. More...
bool	has3DCoordinates (Entity3D entity)
	Tells whether the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity is set. More...
Math.Vector3D	get3DCoordinates (Entity3D entity)
	Returns the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity. More...
None	clear3DCoordinates (Entity3D entity)
	Clears the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity. More...
None	set3DCoordinates (Entity3DContainer cntnr, Math.Vector3DArray coords)
	Sets the 3D coordinates of the entities of cntnr from coords. More...
None	get3DCoordinates (Entity3DContainer cntnr, Math.Vector3DArray coords, bool append=False)
	Stores the 3D coordinates of the entities of cntnr in coords. More...
FragmentList	getAromaticRings (MolecularGraph molgraph)
	Returns the subset of the aromatic rings of the molecular graph molgraph. More...
FragmentList	getAromaticSSSRSubset (MolecularGraph molgraph)
	Returns the subset of the SSSR of the molecular graph molgraph that contains only aromatic rings,. More...
None	setAromaticSubstructure (MolecularGraph molgraph, Fragment substruct)
	Sets the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct. More...
bool	hasAromaticSubstructure (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph is set. More...
Fragment	getAromaticSubstructure (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph. More...
None	clearAromaticSubstructure (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph. More...
None	setAromaticityFlag (Atom atom, bool aromatic)
	Sets the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom to aromatic. More...
bool	hasAromaticityFlag (Atom atom)
	Tells whether the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom is set. More...
bool	getAromaticityFlag (Atom atom)
	Returns the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom. More...
None	clearAromaticityFlag (Atom atom)
	Clears the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom. More...
None	setAromaticityFlag (Bond bond, bool aromatic)
	Sets the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond to aromatic. More...
bool	hasAromaticityFlag (Bond bond)
	Tells whether the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond is set. More...
bool	getAromaticityFlag (Bond bond)
	Returns the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond. More...
None	clearAromaticityFlag (Bond bond)
	Clears the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond. More...
None	setAromaticityFlags (MolecularGraph molgraph, bool overwrite)
	Perceives aromaticity and sets the corresponding atom/bond aromaticity flags on the molecular graph molgraph. More...
None	setAtomMappingID (Atom atom, int id)
	Sets the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom to id. More...
bool	hasAtomMappingID (Atom atom)
	Tells whether the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom is set. More...
int	getAtomMappingID (Atom atom)
	Returns the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom. More...
None	clearAtomMappingID (Atom atom)
	Clears the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom. More...
None	setAtomMapping (Reaction rxn, AtomMapping mapping)
	Sets the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn to mapping. More...
bool	hasAtomMapping (Reaction rxn)
	Tells whether the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn is set. More...
AtomMapping	getAtomMapping (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn. More...
None	clearAtomMapping (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn. More...
None	setAtomMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr, bool overwrite)
	Sets the atom-level match-constraint list constr on every atom of the molecular graph molgraph. More...
None	setAtomMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite)
	Sets the atom-level match-constraint list constr on every atom of every component of the reaction rxn. More...
None	setAtomSymbolsFromTypes (MolecularGraph molgraph, bool overwrite)
	Sets the atom symbols of the molecular graph molgraph from their atom types. More...
None	setAtomTypesFromSymbols (MolecularGraph molgraph, bool overwrite)
	Sets the atom types of the molecular graph molgraph from their element symbols. More...
None	setBondMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr, bool overwrite)
	Sets the bond-level match-constraint list constr on every bond of the molecular graph molgraph. More...
None	setBondMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite)
	Sets the bond-level match-constraint list constr on every bond of every component of the reaction rxn. More...
None	setCIPConfiguration (Atom atom, int config)
	Sets the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom to config (see namespace Chem.CIPDescriptor). More...
bool	hasCIPConfiguration (Atom atom)
	Tells whether the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom is set. More...
int	getCIPConfiguration (Atom atom)
	Returns the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom (see namespace Chem.CIPDescriptor). More...
None	clearCIPConfiguration (Atom atom)
	Clears the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom. More...
None	setCIPConfiguration (Bond bond, int config)
	Sets the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond to config (see namespace Chem.CIPDescriptor). More...
bool	hasCIPConfiguration (Bond bond)
	Tells whether the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond is set. More...
int	getCIPConfiguration (Bond bond)
	Returns the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond (see namespace Chem.CIPDescriptor). More...
None	clearCIPConfiguration (Bond bond)
	Clears the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond. More...
None	setCIPPriority (Atom atom, int priority)
	Sets the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom to priority. More...
bool	hasCIPPriority (Atom atom)
	Tells whether the Chem.AtomProperty.CIP_PRIORITY property of the atom atom is set. More...
int	getCIPPriority (Atom atom)
	Returns the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom. More...
None	clearCIPPriority (Atom atom)
	Clears the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom. More...
None	setCanonicalNumber (Atom atom, int num)
	Sets the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom to num. More...
bool	hasCanonicalNumber (Atom atom)
	Tells whether the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom is set. More...
int	getCanonicalNumber (Atom atom)
	Returns the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom. More...
None	clearCanonicalNumber (Atom atom)
	Clears the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom. More...
None	setComment (MolecularGraph molgraph, str comment)
	Sets the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph to comment. More...
bool	hasComment (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph is set. More...
str	getComment (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph. More...
None	clearComment (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph. More...
None	setComment (Reaction rxn, str comment)
	Sets the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn to comment. More...
bool	hasComment (Reaction rxn)
	Tells whether the Chem.ReactionProperty.COMMENT property of the reaction rxn is set. More...
str	getComment (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn. More...
None	clearComment (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn. More...
int	getCompleteBondCount (MolecularGraph molgraph)
	Returns the number of bonds of the molecular graph molgraph whose connected atoms are likewise contained in molgraph. More...
None	setComponentGroupID (Atom atom, int id)
	Sets the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom to id. More...
bool	hasComponentGroupID (Atom atom)
	Tells whether the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom is set. More...
int	getComponentGroupID (Atom atom)
	Returns the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom. More...
None	clearComponentGroupID (Atom atom)
	Clears the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom. More...
None	setComponentGroups (MolecularGraph molgraph, FragmentList comp_groups)
	Sets the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph to comp_groups. More...
bool	hasComponentGroups (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph is set. More...
FragmentList	getComponentGroups (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph. More...
None	clearComponentGroups (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph. More...
None	setComponentGroups (Reaction rxn, FragmentList comp_groups)
	Sets the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn to comp_groups. More...
bool	hasComponentGroups (Reaction rxn)
	Tells whether the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn is set. More...
FragmentList	getComponentGroups (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn. More...
None	clearComponentGroups (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn. More...
None	setComponentMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite)
	Sets the molecular graph-level match-constraint list constr on every component of the reaction rxn. More...
None	setComponents (MolecularGraph molgraph, FragmentList comps)
	Sets the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph to comps. More...
bool	hasComponents (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph is set. More...
FragmentList	getComponents (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph. More...
None	clearComponents (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph. More...
None	getConformation (AtomContainer cntnr, int conf_idx, Math.Vector3DArray coords, bool append=False)
	Extracts the conformation at index conf_idx into coords. More...
float	getConformationEnergy (MolecularGraph molgraph, int conf_idx)
	Returns the energy of the conformation at index conf_idx. More...
None	setConformationIndex (MolecularGraph molgraph, int index)
	Sets the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph to index. More...
bool	hasConformationIndex (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph is set. More...
int	getConformationIndex (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph. More...
None	clearConformationIndex (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph. More...
None	setConformation (MolecularGraph molgraph, int conf_idx, Math.Vector3DArray coords, float energy)
	Overwrites the conformation at index conf_idx with the supplied coordinates and energy. More...
None	clearConformations (AtomContainer cntnr)
	Removes all stored conformations from the atoms of cntnr. More...
Math.Vector3D	getConformer3DCoordinates (Atom atom, int conf_idx)
	Returns the 3D coordinates of the atom atom for conformer conf_idx (from the Chem.AtomProperty.COORDINATES_3D_ARRAY property). More...
None	setConformerEnergies (MolecularGraph molgraph, Util.DArray energies)
	Sets the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph to energies. More...
bool	hasConformerEnergies (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph is set. More...
Util.DArray	getConformerEnergies (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph. More...
None	clearConformerEnergies (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph. More...
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)
	Collects the fragments in frag_list that are fully contained in the molecular graph molgraph into cont_frag_list. More...
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)
	Collects the fragments in frag_list that contain the molecular graph molgraph into cont_frag_list. More...
bool	hasCoordinates (AtomContainer cntnr, int dim)
	Tells whether all atoms of cntnr carry coordinates of the given dimensionality. More...
None	setCyclicSubstructure (MolecularGraph molgraph, Fragment substruct)
	Sets the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct. More...
bool	hasCyclicSubstructure (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph is set. More...
Fragment	getCyclicSubstructure (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph. More...
None	clearCyclicSubstructure (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph. More...
None	setDirection (Bond bond, int dir)
	Sets the value of the Chem.BondProperty.DIRECTION property of the bond bond to dir. More...
bool	hasDirection (Bond bond)
	Tells whether the Chem.BondProperty.DIRECTION property of the bond bond is set. More...
int	getDirection (Bond bond)
	Returns the value of the Chem.BondProperty.DIRECTION property of the bond bond. More...
None	clearDirection (Bond bond)
	Clears the value of the Chem.BondProperty.DIRECTION property of the bond bond. More...
int	getEnvironment (Atom atom, MolecularGraph molgraph, int max_dist, Fragment env, bool append=False)
	Collects every atom of the molecular graph molgraph that is within max_dist bonds of the atom atom into the fragment env. More...
None	setFormalCharge (Atom atom, int charge)
	Sets the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom to charge. More...
bool	hasFormalCharge (Atom atom)
	Tells whether the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom is set. More...
int	getFormalCharge (Atom atom)
	Returns the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom. More...
None	clearFormalCharge (Atom atom)
	Clears the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom. More...
int	getGenericType (Atom atom)
	Returns the generic atom type that the atom's Chem.AtomProperty.TYPE property value belongs to. More...
None	setGeometricalDistanceMatrix (MolecularGraph molgraph, Math.DMatrix mtx)
	Sets the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx. More...
bool	hasGeometricalDistanceMatrix (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set. More...
Math.DMatrix	getGeometricalDistanceMatrix (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More...
None	clearGeometricalDistanceMatrix (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More...
None	setHashCode (MolecularGraph molgraph, int hash_code)
	Sets the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph to hash_code. More...
bool	hasHashCode (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph is set. More...
int	getHashCode (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph. More...
None	clearHashCode (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph. More...
None	setHybridizationState (Atom atom, int state)
	Sets the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom to state (see namespace Chem.HybridizationState). More...
bool	hasHybridizationState (Atom atom)
	Tells whether the Chem.AtomProperty.HYBRIDIZATION property of the atom atom is set. More...
int	getHybridizationState (Atom atom)
	Returns the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom (see namespace Chem.HybridizationState). More...
None	clearHybridizationState (Atom atom)
	Clears the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom. More...
None	setImplicitHydrogenCount (Atom atom, int count)
	Sets the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom to count. More...
bool	hasImplicitHydrogenCount (Atom atom)
	Tells whether the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom is set. More...
int	getImplicitHydrogenCount (Atom atom)
	Returns the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom. More...
None	clearImplicitHydrogenCount (Atom atom)
	Clears the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom. More...
int	getIncidentBonds (Atom atom, MolecularGraph molgraph, list bonds, Atom excl_atom)
None	setIsotope (Atom atom, int isotope)
	Sets the value of the Chem.AtomProperty.ISOTOPE property of the atom atom to isotope. More...
bool	hasIsotope (Atom atom)
	Tells whether the Chem.AtomProperty.ISOTOPE property of the atom atom is set. More...
int	getIsotope (Atom atom)
	Returns the value of the Chem.AtomProperty.ISOTOPE property of the atom atom. More...
None	clearIsotope (Atom atom)
	Clears the value of the Chem.AtomProperty.ISOTOPE property of the atom atom. More...
None	setMDLCTABVersion (MolecularGraph molgraph, int version)
	Sets the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph to version (see namespace Chem.MDLDataFormatVersion). More...
bool	hasMDLCTABVersion (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph is set. More...
int	getMDLCTABVersion (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph (see namespace Chem.MDLDataFormatVersion). More...
None	clearMDLCTABVersion (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph. More...
None	setMDLChiralFlag (MolecularGraph molgraph, bool flag)
	Sets the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph to flag. More...
bool	hasMDLChiralFlag (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph is set. More...
bool	getMDLChiralFlag (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph. More...
None	clearMDLChiralFlag (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph. More...
None	setMDLDimensionality (MolecularGraph molgraph, int dim)
	Sets the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph to dim. More...
bool	hasMDLDimensionality (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph is set. More...
int	getMDLDimensionality (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph. More...
None	clearMDLDimensionality (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph. More...
None	setMDLEnergy (MolecularGraph molgraph, float energy)
	Sets the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph to energy. More...
bool	hasMDLEnergy (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph is set. More...
float	getMDLEnergy (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph. More...
None	clearMDLEnergy (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph. More...
None	setMDLExternalRegistryNumber (Reaction rxn, str reg_no)
	Sets the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no. More...
bool	hasMDLExternalRegistryNumber (Reaction rxn)
	Tells whether the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn is set. More...
str	getMDLExternalRegistryNumber (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn. More...
None	clearMDLExternalRegistryNumber (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn. More...
None	setMDLInternalRegistryNumber (Reaction rxn, str reg_no)
	Sets the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no. More...
bool	hasMDLInternalRegistryNumber (Reaction rxn)
	Tells whether the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn is set. More...
str	getMDLInternalRegistryNumber (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn. More...
None	clearMDLInternalRegistryNumber (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn. More...
None	setMDLMoleculeRecord (Reaction rxn, Molecule mol_rec)
	Sets the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn to mol_rec. More...
bool	hasMDLMoleculeRecord (Reaction rxn)
	Tells whether the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn is set. More...
Molecule	getMDLMoleculeRecord (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn. More...
None	clearMDLMoleculeRecord (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn. More...
None	setMDLParity (Atom atom, int parity)
	Sets the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom to parity (see namespace Chem.MDLParity). More...
bool	hasMDLParity (Atom atom)
	Tells whether the Chem.AtomProperty.MDL_PARITY property of the atom atom is set. More...
int	getMDLParity (Atom atom)
	Returns the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom (see namespace Chem.MDLParity). More...
None	clearMDLParity (Atom atom)
	Clears the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom. More...
None	setMDLProgramName (MolecularGraph molgraph, str name)
	Sets the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph to name. More...
bool	hasMDLProgramName (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph is set. More...
str	getMDLProgramName (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph. More...
None	clearMDLProgramName (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph. More...
None	setMDLProgramName (Reaction rxn, str name)
	Sets the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn to name. More...
bool	hasMDLProgramName (Reaction rxn)
	Tells whether the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn is set. More...
str	getMDLProgramName (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn. More...
None	clearMDLProgramName (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn. More...
None	setMDLRXNFileVersion (Reaction rxn, int version)
	Sets the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn to version. More...
bool	hasMDLRXNFileVersion (Reaction rxn)
	Tells whether the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn is set. More...
int	getMDLRXNFileVersion (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn. More...
None	clearMDLRXNFileVersion (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn. More...
None	setMDLRegistryNumber (MolecularGraph molgraph, int reg_no)
	Sets the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph to reg_no. More...
bool	hasMDLRegistryNumber (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph is set. More...
int	getMDLRegistryNumber (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph. More...
None	clearMDLRegistryNumber (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph. More...
None	setMDLRegistryNumber (Reaction rxn, int reg_no)
	Sets the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn to reg_no. More...
bool	hasMDLRegistryNumber (Reaction rxn)
	Tells whether the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn is set. More...
int	getMDLRegistryNumber (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn. More...
None	clearMDLRegistryNumber (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn. More...
None	setMDLScalingFactor1 (MolecularGraph molgraph, int factor)
	Sets the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph to factor. More...
bool	hasMDLScalingFactor1 (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph is set. More...
int	getMDLScalingFactor1 (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph. More...
None	clearMDLScalingFactor1 (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph. More...
None	setMDLScalingFactor2 (MolecularGraph molgraph, float factor)
	Sets the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph to factor. More...
bool	hasMDLScalingFactor2 (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph is set. More...
float	getMDLScalingFactor2 (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph. More...
None	clearMDLScalingFactor2 (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph. More...
None	setMDLStereoCareFlag (Atom atom, bool flag)
	Sets the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom to flag. More...
bool	hasMDLStereoCareFlag (Atom atom)
	Tells whether the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom is set. More...
bool	getMDLStereoCareFlag (Atom atom)
	Returns the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom. More...
None	clearMDLStereoCareFlag (Atom atom)
	Clears the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom. More...
None	setMDLUserInitials (MolecularGraph molgraph, str initials)
	Sets the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph to initials. More...
bool	hasMDLUserInitials (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph is set. More...
str	getMDLUserInitials (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph. More...
None	clearMDLUserInitials (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph. More...
None	setMDLUserInitials (Reaction rxn, str initials)
	Sets the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn to initials. More...
bool	hasMDLUserInitials (Reaction rxn)
	Tells whether the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn is set. More...
str	getMDLUserInitials (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn. More...
None	clearMDLUserInitials (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn. More...
None	setMOL2Charge (Atom atom, float charge)
	Sets the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom to charge. More...
bool	hasMOL2Charge (Atom atom)
	Tells whether the Chem.AtomProperty.MOL2_CHARGE property of the atom atom is set. More...
float	getMOL2Charge (Atom atom)
	Returns the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom. More...
None	clearMOL2Charge (Atom atom)
	Clears the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom. More...
None	setMOL2ChargeType (MolecularGraph molgraph, int type)
	Sets the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph to type (see namespace Chem.MOL2ChargeType). More...
bool	hasMOL2ChargeType (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph is set. More...
int	getMOL2ChargeType (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph (see namespace Chem.MOL2ChargeType). More...
None	clearMOL2ChargeType (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph. More...
None	setMOL2MoleculeType (MolecularGraph molgraph, int type)
	Sets the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph to type (see namespace Chem.MOL2MoleculeType). More...
bool	hasMOL2MoleculeType (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph is set. More...
int	getMOL2MoleculeType (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph (see namespace Chem.MOL2MoleculeType). More...
None	clearMOL2MoleculeType (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph. More...
None	setMOL2Name (Atom atom, str name)
	Sets the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom to name. More...
bool	hasMOL2Name (Atom atom)
	Tells whether the Chem.AtomProperty.MOL2_NAME property of the atom atom is set. More...
str	getMOL2Name (Atom atom)
	Returns the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom. More...
None	clearMOL2Name (Atom atom)
	Clears the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom. More...
None	setMOL2SubstructureChain (Atom atom, str chain)
	Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom to chain. More...
bool	hasMOL2SubstructureChain (Atom atom)
	Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom is set. More...
str	getMOL2SubstructureChain (Atom atom)
	Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom. More...
None	clearMOL2SubstructureChain (Atom atom)
	Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom. More...
None	setMOL2SubstructureID (Atom atom, int id)
	Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom to id. More...
bool	hasMOL2SubstructureID (Atom atom)
	Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom is set. More...
int	getMOL2SubstructureID (Atom atom)
	Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom. More...
None	clearMOL2SubstructureID (Atom atom)
	Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom. More...
None	setMOL2SubstructureName (Atom atom, str name)
bool	hasMOL2SubstructureName (Atom atom)
	Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom is set. More...
str	getMOL2SubstructureName (Atom atom)
	Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom. More...
None	clearMOL2SubstructureName (Atom atom)
	Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom. More...
None	setMOL2SubstructureSubtype (Atom atom, str subtype)
	Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom to subtype. More...
bool	hasMOL2SubstructureSubtype (Atom atom)
	Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom is set. More...
str	getMOL2SubstructureSubtype (Atom atom)
	Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom. More...
None	clearMOL2SubstructureSubtype (Atom atom)
	Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom. More...
None	setMatchConstraints (Atom atom, MatchConstraintList constr)
	Sets the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom to constr. More...
bool	hasMatchConstraints (Atom atom)
	Tells whether the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom is set. More...
MatchConstraintList	getMatchConstraints (Atom atom)
	Returns the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom. More...
None	clearMatchConstraints (Atom atom)
	Clears the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom. More...
None	setMatchConstraints (Bond bond, MatchConstraintList constr)
	Sets the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond to constr. More...
bool	hasMatchConstraints (Bond bond)
	Tells whether the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond is set. More...
MatchConstraintList	getMatchConstraints (Bond bond)
	Returns the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond. More...
None	clearMatchConstraints (Bond bond)
	Clears the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond. More...
None	setMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr)
	Sets the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph to constr. More...
bool	hasMatchConstraints (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph is set. More...
MatchConstraintList	getMatchConstraints (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph. More...
None	clearMatchConstraints (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph. More...
None	setMatchConstraints (Reaction rxn, MatchConstraintList constr)
	Sets the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn to constr. More...
bool	hasMatchConstraints (Reaction rxn)
	Tells whether the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn is set. More...
MatchConstraintList	getMatchConstraints (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn. More...
None	clearMatchConstraints (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn. More...
None	setMatchExpression (Atom atom, AtomMatchExpression expr)
	Sets the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom to expr. More...
bool	hasMatchExpression (Atom atom)
	Tells whether the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom is set. More...
AtomMatchExpression	getMatchExpression (Atom atom)
	Returns the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom. More...
None	clearMatchExpression (Atom atom)
	Clears the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom. More...
None	setMatchExpression (Bond bond, BondMatchExpression expr)
	Sets the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond to expr. More...
bool	hasMatchExpression (Bond bond)
	Tells whether the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond is set. More...
BondMatchExpression	getMatchExpression (Bond bond)
	Returns the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond. More...
None	clearMatchExpression (Bond bond)
	Clears the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond. More...
None	setMatchExpression (MolecularGraph molgraph, MolecularGraphMatchExpression expr)
	Sets the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph to expr. More...
bool	hasMatchExpression (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph is set. More...
MolecularGraphMatchExpression	getMatchExpression (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph. More...
None	clearMatchExpression (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph. More...
None	setMatchExpression (Reaction rxn, ReactionMatchExpression expr)
	Sets the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn to expr. More...
bool	hasMatchExpression (Reaction rxn)
	Tells whether the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn is set. More...
ReactionMatchExpression	getMatchExpression (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn. More...
None	clearMatchExpression (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn. More...
None	setMatchExpressionString (Atom atom, str expr_str)
	Sets the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom to expr_str. More...
bool	hasMatchExpressionString (Atom atom)
	Tells whether the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom is set. More...
str	getMatchExpressionString (Atom atom)
	Returns the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom. More...
None	clearMatchExpressionString (Atom atom)
	Clears the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom. More...
None	setMatchExpressionString (Bond bond, str expr_str)
	Sets the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond to expr_str. More...
bool	hasMatchExpressionString (Bond bond)
	Tells whether the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond is set. More...
str	getMatchExpressionString (Bond bond)
	Returns the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond. More...
None	clearMatchExpressionString (Bond bond)
	Clears the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond. More...
int	getMaxAtomMappingID (AtomContainer cntnr)
	Returns the largest atom-mapping ID assigned to any atom of cntnr. More...
int	getMaxAtomMappingID (Reaction rxn)
	Returns the largest atom-mapping ID found on any of the atoms in rxn. More...
int	getMaxComponentGroupID (AtomContainer cntnr)
	Returns the largest component-group ID assigned to any atom of cntnr. More...
int	getMaxComponentGroupID (Reaction rxn)
	Returns the largest component-group ID found on any of the components of the reaction rxn. More...
None	setMorganNumber (Atom atom, int num)
	Sets the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom to num. More...
bool	hasMorganNumber (Atom atom)
	Tells whether the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom is set. More...
int	getMorganNumber (Atom atom)
	Returns the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom. More...
None	clearMorganNumber (Atom atom)
	Clears the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom. More...
None	setName (Atom atom, str name)
	Sets the value of the Chem.AtomProperty.NAME property of the atom atom to name. More...
bool	hasName (Atom atom)
	Tells whether the Chem.AtomProperty.NAME property of the atom atom is set. More...
str	getName (Atom atom)
	Returns the value of the Chem.AtomProperty.NAME property of the atom atom. More...
None	clearName (Atom atom)
	Clears the value of the Chem.AtomProperty.NAME property of the atom atom. More...
None	setName (MolecularGraph molgraph, str name)
	Sets the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph to name. More...
bool	hasName (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph is set. More...
str	getName (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph. More...
None	clearName (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph. More...
None	setName (Reaction rxn, str name)
	Sets the value of the Chem.ReactionProperty.NAME property of the reaction rxn to name. More...
bool	hasName (Reaction rxn)
	Tells whether the Chem.ReactionProperty.NAME property of the reaction rxn is set. More...
str	getName (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.NAME property of the reaction rxn. More...
None	clearName (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.NAME property of the reaction rxn. More...
int	getNumConformations (AtomContainer cntnr)
	Returns the number of conformations stored on the atoms of cntnr. More...
int	getNumContainingFragments (Atom atom, FragmentList frag_list)
	Returns the number of fragments in frag_list that contain the atom atom. More...
int	getNumContainingFragments (Bond bond, FragmentList frag_list)
	Returns the number of fragments in frag_list that contain the bond bond. More...
None	setOrder (Bond bond, int order)
	Sets the value of the Chem.BondProperty.ORDER property of the bond bond to order. More...
bool	hasOrder (Bond bond)
	Tells whether the Chem.BondProperty.ORDER property of the bond bond is set. More...
int	getOrder (Bond bond)
	Returns the value of the Chem.BondProperty.ORDER property of the bond bond. More...
None	clearOrder (Bond bond)
	Clears the value of the Chem.BondProperty.ORDER property of the bond bond. More...
None	setPiElectronSystems (MolecularGraph molgraph, ElectronSystemList pi_systems)
	Sets the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph to pi_systems. More...
bool	hasPiElectronSystems (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph is set. More...
ElectronSystemList	getPiElectronSystems (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph. More...
None	clearPiElectronSystems (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph. More...
None	setRadicalType (Atom atom, int type)
	Sets the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom to type (see namespace Chem.RadicalType). More...
bool	hasRadicalType (Atom atom)
	Tells whether the Chem.AtomProperty.RADICAL_TYPE property of the atom atom is set. More...
int	getRadicalType (Atom atom)
	Returns the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom (see namespace Chem.RadicalType). More...
None	clearRadicalType (Atom atom)
	Clears the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom. More...
None	setReactionCenterStatus (Atom atom, int status)
	Sets the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom to status. More...
bool	hasReactionCenterStatus (Atom atom)
	Tells whether the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom is set. More...
int	getReactionCenterStatus (Atom atom)
	Returns the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom (see namespace Chem.ReactionCenterStatus). More...
None	clearReactionCenterStatus (Atom atom)
	Clears the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom. More...
None	setReactionCenterStatus (Bond bond, int status)
	Sets the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond to status. More...
bool	hasReactionCenterStatus (Bond bond)
	Tells whether the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond is set. More...
int	getReactionCenterStatus (Bond bond)
	Returns the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond. More...
None	clearReactionCenterStatus (Bond bond)
	Clears the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond. More...
None	setReactionData (Reaction rxn, StringDataBlock data)
	Sets the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn to data. More...
bool	hasReactionData (Reaction rxn)
	Tells whether the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn is set. More...
StringDataBlock	getReactionData (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn. More...
None	clearReactionData (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn. More...
None	setRingFlag (Atom atom, bool in_ring)
	Sets the value of the Chem.AtomProperty.RING_FLAG property of the atom atom to in_ring. More...
bool	hasRingFlag (Atom atom)
	Tells whether the Chem.AtomProperty.RING_FLAG property of the atom atom is set. More...
bool	getRingFlag (Atom atom)
	Returns the value of the Chem.AtomProperty.RING_FLAG property of the atom atom. More...
None	clearRingFlag (Atom atom)
	Clears the value of the Chem.AtomProperty.RING_FLAG property of the atom atom. More...
None	setRingFlag (Bond bond, bool in_ring)
	Sets the value of the Chem.BondProperty.RING_FLAG property of the bond bond to in_ring. More...
bool	hasRingFlag (Bond bond)
	Tells whether the Chem.BondProperty.RING_FLAG property of the bond bond is set. More...
bool	getRingFlag (Bond bond)
	Returns the value of the Chem.BondProperty.RING_FLAG property of the bond bond. More...
None	clearRingFlag (Bond bond)
	Clears the value of the Chem.BondProperty.RING_FLAG property of the bond bond. More...
None	setRingFlags (MolecularGraph molgraph, bool overwrite)
	Perceives ring membership and sets the corresponding atom/bond ring flags on the molecular graph molgraph. More...
None	setRings (MolecularGraph molgraph, FragmentList rings)
	Sets the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph to rings. More...
bool	hasRings (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph is set. More...
FragmentList	getRings (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph. More...
None	clearRings (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph. More...
None	setSSSR (MolecularGraph molgraph, FragmentList sssr)
	Sets the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph to sssr. More...
bool	hasSSSR (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph is set. More...
FragmentList	getSSSR (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph. More...
None	clearSSSR (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph. More...
int	getSizeOfLargestContainingFragment (Atom atom, FragmentList frag_list)
	Returns the size (in atoms) of the largest fragment in frag_list that contains the atom atom. More...
int	getSizeOfLargestContainingFragment (Bond bond, FragmentList frag_list)
	Returns the size (in atoms) of the largest fragment in frag_list that contains the bond bond. More...
int	getSizeOfSmallestContainingFragment (Atom atom, FragmentList frag_list)
	Returns the size (in atoms) of the smallest fragment in frag_list that contains the atom atom. More...
int	getSizeOfSmallestContainingFragment (Bond bond, FragmentList frag_list)
	Returns the size (in atoms) of the smallest fragment in frag_list that contains the bond bond. More...
None	setStereoCenterFlag (Atom atom, bool is_center)
	Sets the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom to is_center. More...
bool	hasStereoCenterFlag (Atom atom)
	Tells whether the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom is set. More...
bool	getStereoCenterFlag (Atom atom)
	Returns the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom. More...
None	clearStereoCenterFlag (Atom atom)
	Clears the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom. More...
None	setStereoCenterFlag (Bond bond, bool is_center)
	Sets the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond to is_center. More...
bool	hasStereoCenterFlag (Bond bond)
	Tells whether the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond is set. More...
bool	getStereoCenterFlag (Bond bond)
	Returns the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond. More...
None	clearStereoCenterFlag (Bond bond)
	Clears the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond. More...
None	setStereoDescriptor (Atom atom, StereoDescriptor descr)
	Sets the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom to descr. More...
bool	hasStereoDescriptor (Atom atom)
	Tells whether the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom is set. More...
StereoDescriptor	getStereoDescriptor (Atom atom)
	Returns the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom. More...
None	clearStereoDescriptor (Atom atom)
	Clears the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom. More...
None	setStereoDescriptor (Bond bond, StereoDescriptor descr)
	Sets the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond to descr. More...
bool	hasStereoDescriptor (Bond bond)
	Tells whether the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond is set. More...
StereoDescriptor	getStereoDescriptor (Bond bond)
	Returns the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond. More...
None	clearStereoDescriptor (Bond bond)
	Clears the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond. More...
None	setStoichiometricNumber (MolecularGraph molgraph, float num)
	Sets the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph to num. More...
bool	hasStoichiometricNumber (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph is set. More...
float	getStoichiometricNumber (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph. More...
None	clearStoichiometricNumber (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph. More...
None	setStructureData (MolecularGraph molgraph, StringDataBlock data)
	Sets the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph to data. More...
bool	hasStructureData (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph is set. More...
StringDataBlock	getStructureData (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph. More...
None	clearStructureData (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph. More...
str	getSybylAtomTypeString (int sybyl_type)
	Returns the canonical textual representation of the Sybyl atom type sybyl_type. More...
str	getSybylBondTypeString (int sybyl_type)
	Returns the canonical textual representation of the Sybyl bond type sybyl_type. More...
None	setSybylType (Atom atom, int type)
	Sets the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom to type. More...
bool	hasSybylType (Atom atom)
	Tells whether the Chem.AtomProperty.SYBYL_TYPE property of the atom atom is set. More...
int	getSybylType (Atom atom)
	Returns the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom. More...
None	clearSybylType (Atom atom)
	Clears the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom. More...
None	setSybylType (Bond bond, int type)
	Sets the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond to type. More...
bool	hasSybylType (Bond bond)
	Tells whether the Chem.BondProperty.SYBYL_TYPE property of the bond bond is set. More...
int	getSybylType (Bond bond)
	Returns the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond. More...
None	clearSybylType (Bond bond)
	Clears the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond. More...
None	setSymbol (Atom atom, str symbol)
	Sets the value of the Chem.AtomProperty.SYMBOL property of the atom atom to symbol. More...
bool	hasSymbol (Atom atom)
	Tells whether the Chem.AtomProperty.SYMBOL property of the atom atom is set. More...
str	getSymbol (Atom atom)
	Returns the value of the Chem.AtomProperty.SYMBOL property of the atom atom. More...
None	clearSymbol (Atom atom)
	Clears the value of the Chem.AtomProperty.SYMBOL property of the atom atom. More...
str	getSymbolForType (Atom atom)
	Returns the element symbol that corresponds to the Chem.AtomProperty.TYPE property of the atom atom. More...
None	setSymmetryClass (Atom atom, int class_id)
	Sets the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom to class_id. More...
bool	hasSymmetryClass (Atom atom)
	Tells whether the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom is set. More...
int	getSymmetryClass (Atom atom)
	Returns the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom. More...
None	clearSymmetryClass (Atom atom)
	Clears the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom. More...
None	setTimestamp (MolecularGraph molgraph, int time)
	Sets the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph to time. More...
bool	hasTimestamp (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph is set. More...
int	getTimestamp (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph. More...
None	clearTimestamp (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph. More...
None	setTimestamp (Reaction rxn, int time)
	Sets the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn to time. More...
bool	hasTimestamp (Reaction rxn)
	Tells whether the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn is set. More...
int	getTimestamp (Reaction rxn)
	Returns the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn. More...
None	clearTimestamp (Reaction rxn)
	Clears the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn. More...
int	getTopologicalDistance (Atom atom1, Atom atom2, MolecularGraph molgraph)
	Returns the topological distance between two atoms of the molecular graph molgraph. More...
None	setTopologicalDistanceMatrix (MolecularGraph molgraph, Math.ULMatrix mtx)
	Sets the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx. More...
bool	hasTopologicalDistanceMatrix (MolecularGraph molgraph)
	Tells whether the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set. More...
Math.ULMatrix	getTopologicalDistanceMatrix (MolecularGraph molgraph)
	Returns the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More...
None	clearTopologicalDistanceMatrix (MolecularGraph molgraph)
	Clears the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More...
None	setType (Atom atom, int type)
	Sets the value of the Chem.AtomProperty.TYPE property of the atom atom to type (see namespace Chem.AtomType). More...
bool	hasType (Atom atom)
	Tells whether the Chem.AtomProperty.TYPE property of the atom atom is set. More...
int	getType (Atom atom)
	Returns the value of the Chem.AtomProperty.TYPE property of the atom atom (see namespace Chem.AtomType). More...
None	clearType (Atom atom)
	Clears the value of the Chem.AtomProperty.TYPE property of the atom atom. More...
int	getTypeForSymbol (Atom atom)
	Returns the atom type that corresponds to the Chem.AtomProperty.SYMBOL property of the atom atom. More...
None	setUnpairedElectronCount (Atom atom, int count)
	Sets the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom to count. More...
bool	hasUnpairedElectronCount (Atom atom)
	Tells whether the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom is set. More...
int	getUnpairedElectronCount (Atom atom)
	Returns the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom. More...
None	clearUnpairedElectronCount (Atom atom)
	Clears the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom. More...
None	addConformation (AtomContainer cntnr, Math.Vector3DArray coords)
	Appends a new conformation built from the supplied 3D coordinates to the atoms of cntnr. More...
None	addConformation (MolecularGraph molgraph, Math.Vector3DArray coords, float energy)
	Appends a new conformation built from the supplied coordinates and energy. More...
bool	align2DCoordinates (MolecularGraph molgraph, AtomContainer atoms, Math.Vector2DArray ref_coords, bool fix_bond_stereo=True)
	Aligns molgraph's 2D coordinates so that the atoms of atoms come to lie at the reference coordinates ref_coords. More...
bool	align2DCoordinates (MolecularGraph molgraph, AtomMapping ref_atom_mpg, bool fix_bond_stereo=True)
	Aligns molgraph's 2D coordinates onto a reference atom mapping. More...
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)
	Aligns molgraph's 2D coordinates onto those of ref_molgraph, using substr_ptn as the explicit substructure pattern. More...
bool	align3DCoordinates (Entity3DContainer cntnr, Entity3DContainer ref_entities, Math.Vector3DArray ref_coords)
	Rigid-body aligns the 3D coordinates of cntnr to the reference geometry defined by the entity-coordinate pair (ref_entities, ref_coords). More...
bool	alignConformations (AtomContainer cntnr, Util.BitSet ref_atoms, Math.Vector3DArray ref_coords)
	Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms of ref_atoms as alignment anchors. More...
bool	alignConformations (AtomContainer cntnr, AtomContainer ref_atoms, Math.Vector3DArray ref_coords)
	Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms of ref_atoms as alignment anchors. More...
bool	alignConformations (AtomContainer cntnr, Util.BitSet ref_atoms)
	Aligns each stored conformation of cntnr to the first conformation using the atoms of ref_atoms as alignment anchors. More...
bool	alignConformations (AtomContainer cntnr, AtomContainer ref_atoms)
	Aligns each stored conformation of cntnr to the first conformation using the atoms of ref_atoms as alignment anchors. More...
None	applyConformation (AtomContainer cntnr, int conf_idx)
	Promotes the stored conformation at index conf_idx to the active per-atom 3D coordinates. More...
bool	atomTypesMatch (int qry_type, int tgt_type)
	Tells whether the target atom type tgt_type matches the query atom type qry_type (taking generic atom type classes like Chem.AtomType.HET into account). More...
None	calc2DCoordinates (MolecularGraph molgraph, bool overwrite)
	Computes 2D atom coordinates for molgraph and stores them as Chem.AtomProperty.COORDINATES_2D. More...
None	calcAtomCIPConfigurations (MolecularGraph molgraph, bool overwrite)
	Computes and stores CIP configuration labels for the atoms of the molecular graph molgraph. More...
None	calcAtomStereoDescriptorsFromMDLParities (MolecularGraph molgraph, bool overwrite)
	Derives atom stereo descriptors of the molecular graph molgraph from previously-assigned MDL parities. More...
None	calcAtomStereoDescriptors (MolecularGraph molgraph, bool overwrite, int dim=1, bool check_stc_flag=True)
	Computes and stores stereo descriptors for the atoms of the molecular graph molgraph from their geometric layout. More...
None	calcBasicProperties (MolecularGraph molgraph, bool overwrite)
	Computes the basic per-atom/per-bond properties (aromaticity, ring info, etc.) of the molecular graph molgraph. More...
None	calcBasicProperties (Reaction rxn, bool overwrite)
	Computes the basic per-component properties (aromaticity, ring info, etc.) of every component of the reaction rxn. More...
None	calcBond2DStereoFlags (MolecularGraph molgraph, bool overwrite)
	Derives 2D wedge/hash bond stereo flags for the bonds of the molecular graph molgraph from the atoms' stereo descriptors and 2D layout. More...
None	calcBondCIPConfigurations (MolecularGraph molgraph, bool overwrite)
	Computes and stores CIP configuration labels for the bonds of the molecular graph molgraph. More...
None	calcBondStereoDescriptors (MolecularGraph molgraph, bool overwrite, int dim=1, bool check_stc_flag=True)
	Computes and stores stereo descriptors for the bonds of the molecular graph molgraph from their geometric layout. More...
None	calcBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func, bool reset=True)
	Computes the axis-aligned bounding box enclosing the atoms of cntnr. More...
None	calcBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max, bool reset=True)
	Calculates the axis-aligned bounding box of the 3D coordinates of cntnr. More...
None	calcCIPPriorities (MolecularGraph molgraph, bool overwrite)
	Computes and stores CIP priorities for the atoms of the molecular graph molgraph. More...
None	calcCanonicalNumbering (MolecularGraph molgraph, bool overwrite, int atom_flags=2147483648, int bond_flags=2147483648)
	Computes and stores canonical atom numbers for the atoms of the molecular graph molgraph. More...
bool	calcCenterOfMass (AtomContainer cntnr, Atom3DCoordinatesFunction coords_func, Math.Vector3D ctr)
	Computes the mass-weighted center of mass of the atoms in cntnr. More...
bool	calcCentroid (AtomContainer cntnr, Atom3DCoordinatesFunction coords_func, Math.Vector3D ctr)
	Computes the unweighted centroid (arithmetic mean of atom coordinates) of cntnr. More...
bool	calcCentroid (Entity3DContainer cntnr, Math.Vector3D ctr)
	Calculates the geometric centroid of the entities of cntnr. More...
int	calcConfiguration (Atom atom, MolecularGraph molgraph, StereoDescriptor descr, Math.Vector3DArray coords)
	Derives the atom configuration label from the supplied descriptor and 3D coordinates. More...
int	calcConfiguration (Bond bond, MolecularGraph molgraph, StereoDescriptor descr, Math.Vector3DArray coords)
	Derives the bond configuration label from the supplied descriptor and 3D coordinates. More...
int	calcFormalCharge (Atom atom, MolecularGraph molgraph)
	Computes the formal charge of the atom atom from its valence environment in the molecular graph molgraph. More...
None	calcFormalCharges (MolecularGraph molgraph, bool overwrite)
	Computes and stores formal charges for the atoms of the molecular graph molgraph from their valence environment. More...
None	calcGeometricalDistanceMatrix (Entity3DContainer cntnr, Math.DMatrix mtx)
	Calculates the inter-entity geometric distance matrix for the entities of cntnr. More...
Math.DMatrix	calcGeometricalDistanceMatrix (MolecularGraph molgraph, bool overwrite)
	Computes and (optionally) stores the geometrical-distance matrix of the molecular graph molgraph from its 3D coordinates. More...
int	calcHashCode (MolecularGraph molgraph, int atom_flags=2147483648, int bond_flags=2147483648, bool ord_h_deplete=True)
	Computes a 64-bit hash code for molgraph taking into account the specified atom and bond properties. More...
int	calcHashCode (Reaction rxn, int role_mask=7, int atom_flags=2147483648, int bond_flags=2147483648, bool ord_h_deplete=True)
	Computes a 64-bit hash code for the reaction rxn taking into account the specified reaction roles and atom/bond properties. More...
None	calcHydrogen3DCoordinates (MolecularGraph molgraph, bool undef_only=True)
	Computes 3D coordinates for the hydrogen atoms of the molecular graph molgraph from the geometry of their non-hydrogen neighbors. More...
int	calcImplicitHydrogenCount (Atom atom, MolecularGraph molgraph)
	Computes the implicit hydrogen count of the atom atom from its valence environment in the molecular graph molgraph. More...
None	calcImplicitHydrogenCounts (MolecularGraph molgraph, bool overwrite)
	Computes and stores implicit-hydrogen counts for the atoms of the molecular graph molgraph. More...
None	calcMDLParities (MolecularGraph molgraph, bool overwrite)
	Computes and stores MDL parities for the atoms of the molecular graph molgraph. More...
int	calcMDLParity (Atom atom, MolecularGraph molgraph)
	Computes the MDL parity of the atom atom from its 2D layout and stereo flags in the molecular graph molgraph. More...
None	calcMorganNumbering (MolecularGraph molgraph, bool overwrite)
	Computes and stores Morgan numbers for the atoms of the molecular graph molgraph. More...
StereoDescriptor	calcStereoDescriptor (Atom atom, MolecularGraph molgraph, int dim=1)
	Computes the stereo descriptor for the atom atom based on the geometry of the molecular graph molgraph. More...
StereoDescriptor	calcStereoDescriptor (Bond bond, MolecularGraph molgraph, int dim=1)
	Computes the stereo descriptor for the bond bond based on the geometry of the molecular graph molgraph. More...
StereoDescriptor	calcStereoDescriptorFromMDLParity (Atom atom, MolecularGraph molgraph)
	Derives the stereo descriptor of the atom atom from its MDL parity in the molecular graph molgraph. More...
Math.ULMatrix	calcTopologicalDistanceMatrix (MolecularGraph molgraph, bool overwrite)
	Computes and (optionally) stores the topological-distance matrix of the molecular graph molgraph. More...
None	calcTopologicalDistanceMatrix (MolecularGraph molgraph, Math.ULMatrix mtx)
	Computes the topological-distance matrix of the molecular graph molgraph into the supplied mtx. More...
None	canonicalize (MolecularGraph molgraph, bool atoms=True, bool atom_nbrs=True, bool bonds=True, bool bond_atoms=False)
	Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to the canonical-numbering attached to its atoms. More...
None	canonicalize (MolecularGraph molgraph, BoolAtom2Functor func, bool atoms=True, bool atom_nbrs=True, bool bonds=True, bool bond_atoms=False)
	Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to a user-supplied comparator. More...
None	connectAtoms (Molecule mol, Atom3DCoordinatesFunction coords_func, float dist_tol=0.3, int atom_idx_offs=0)
	Adds bonds between atoms of the molecule mol whose 3D distance (obtained via coords_func) falls within the covalent-radii sum plus dist_tol. More...
None	connectAtoms (Molecule mol, float dist_tol=0.3, int atom_idx_offs=0)
	Adds bonds between atoms of the molecule mol whose 3D distance falls within the covalent-radii sum plus dist_tol. More...
bool	containsFragmentWithBond (FragmentList frag_list, Bond bond)
	Tells whether any fragment in frag_list contains the bond bond. More...
bool	containsFragmentWithMinSize (FragmentList frag_list, int min_size)
	Tells whether frag_list contains at least one fragment with at least min_size atoms. More...
bool	containsMolecularGraph (MolecularGraph molgraph, MolecularGraph sub_molgraph, bool atoms=True, bool bonds=True)
	Tells whether the molecular graph molgraph contains the atoms and/or bonds of sub_molgraph. More...
None	copyAtomsIf (AtomContainer cntnr, Molecule mol, AtomPredicate pred, bool append=False)
	Copies every atom of cntnr that satisfies pred into the molecule mol. More...
None	copyAtomsIf (AtomContainer cntnr, Fragment frag, AtomPredicate pred, bool append=False)
	Copies every atom of cntnr that satisfies pred into the fragment frag. More...
None	copyAtomsIfNot (AtomContainer cntnr, Molecule mol, AtomPredicate pred, bool append=False)
	Copies every atom of cntnr that does not satisfy pred into the molecule mol. More...
None	copyAtomsIfNot (AtomContainer cntnr, Fragment frag, AtomPredicate pred, bool append=False)
	Copies every atom of cntnr that does not satisfy pred into the fragment frag. More...
int	createAtomTypeMask (AtomContainer cntnr, Util.BitSet mask, int type, bool reset=True, bool strict=True)
	Sets bits in mask corresponding to atoms of cntnr whose atom type matches type. More...
int	editSubstructures (MolecularGraph molgraph, Molecule result_mol, str search_ptns, str result_ptn, str exclude_ptns='')
	Builds the molecule result_mol from the molecular graph molgraph by replacing all substructures matching the SMARTS patterns in search_ptns with result_ptn. More...
int	editSubstructures (Molecule mol, str search_ptns, str result_ptn, str exclude_ptns='')
	Edits the molecule mol by replacing all substructures matching the SMARTS search patterns in search_ptns with the SMARTS replacement pattern result_ptn, optionally skipping matches that also match exclude_ptns. More...
None	extendBoundingBox (Math.Vector3D min, Math.Vector3D max, Math.Vector3D coords, bool reset=False)
	Extends the axis-aligned bounding box defined by min and max so that it contains the point coords. More...
None	extractReactionCenter (MolecularGraph molgraph, Fragment rxn_center)
	Collects every atom and bond of the molecular graph molgraph that carries a reaction-center flag into the fragment rxn_center. More...
FragmentList	extractSSSRSubset (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph)
	Extracts the subset of the SSSR of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph. More...
FragmentList	extractSSSRSubset (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, bool overwrite)
	Extracts the SSSR subset of the molecular graph src_molgraph that fits within tgt_molgraph and (optionally) stores it on the latter. More...
Math.ULMatrix	extractTopologicalDistanceSubMatrix (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, bool overwrite)
	Extracts the topological-distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph and (optionally) stores it on the latter. More...
None	extractTopologicalDistanceSubMatrix (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, Math.ULMatrix mtx)
	Extracts the topological-distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph into the supplied mtx. More...
None	generateAdjacencyMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
	Builds the adjacency matrix of the molecular graph molgraph (entry (i,j) is the bond count between atoms i and j). More...
None	generateBondAtomTypeMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
	Builds a matrix combining bond order and atom type information of the endpoints of every bond in molgraph. More...
None	generateBondElectronMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
	Builds the bond-electron-count matrix of the molecular graph molgraph (entry (i,j) is the number of bonding electrons between atoms i and j). More...
None	generateBondMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
	Builds the bond-order matrix of the molecular graph molgraph (entry (i,j) is the order of the bond between atoms i and j). More...
object	generateINCHIKey (MolecularGraph molgraph)
object	generateINCHI (MolecularGraph molgraph, str options='/WarnOnEmptyStructure/AuxNone/NEWPSOFF', int dim=0)
None	generateIncidenceMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx)
	Builds the atom/bond incidence matrix of the molecular graph molgraph (entry (i,j) is 1 if atom i is an endpoint of bond j). More...
AtomMatchExpression	generateMatchExpression (Atom atom, MolecularGraph molgraph)
	Builds an atom-level match expression from the match-constraint list attached to the atom atom. More...
BondMatchExpression	generateMatchExpression (Bond bond, MolecularGraph molgraph)
	Builds a bond-level match expression from the match-constraint list attached to the bond bond. More...
MolecularGraphMatchExpression	generateMatchExpression (MolecularGraph molgraph)
	Builds a top-level match expression from the match-constraint list attached to molgraph. More...
MolecularGraphMatchExpression	generateMatchExpression (MolecularGraph molgraph, bool overwrite)
	Builds and (optionally) stores the top-level match expression of the molecular graph molgraph. More...
ReactionMatchExpression	generateMatchExpression (Reaction rxn)
	Builds a reaction-level match expression from the constraints currently attached to the reaction rxn. More...
ReactionMatchExpression	generateMatchExpression (Reaction rxn, bool overwrite)
	Builds and (optionally) stores the reaction-level match expression of the reaction rxn. More...
str	generateMatchExpressionString (Atom atom, MolecularGraph molgraph)
str	generateMatchExpressionString (Bond bond, MolecularGraph molgraph)
None	generateMatchExpressionStrings (MolecularGraph molgraph, bool overwrite)
	Generates and stores textual representations of the match expressions of the molecular graph molgraph. More...
None	generateMatchExpressions (MolecularGraph molgraph, bool overwrite)
	Generates and stores match expressions for every atom, bond and the molecular graph itself. More...
None	generateMatchExpressions (Reaction rxn, bool overwrite)
	Generates and stores match expressions for the atoms, bonds, components, and the reaction rxn itself. More...
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)
	Prepares the molecular graph molgraph for use as a substructure search query (precomputes match expressions and required cached properties). More...
None	initSubstructureSearchQuery (Reaction rxn, bool overwrite)
	Prepares the reaction rxn for use as a substructure search query (e.g. More...
None	initSubstructureSearchTarget (MolecularGraph molgraph, bool overwrite)
	Prepares the molecular graph molgraph for use as a substructure search target (precomputes required cached properties). More...
None	initSubstructureSearchTarget (Reaction rxn, bool overwrite)
	Prepares the reaction rxn for use as a substructure search target (e.g. More...
bool	insideBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func)
	Tells whether every atom of cntnr lies inside the axis-aligned bounding box defined by min and max. More...
bool	insideBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max)
	Tells whether all entities of cntnr lie within the axis-aligned box defined by min and max. More...
bool	insideBoundingBox (Math.Vector3D min, Math.Vector3D max, Math.Vector3D coords)
	Tells whether the point coords lies inside the axis-aligned bounding box defined by min and max. More...
bool	intersectsBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func)
	Tells whether at least one atom of cntnr lies inside the axis-aligned bounding box defined by min and max. More...
bool	intersectsBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max)
	Tells whether at least one entity of cntnr lies within the axis-aligned box defined by min and max. More...
bool	isAromatic (Fragment ring, MolecularGraph molgraph, Util.BitSet arom_bond_mask)
	Tells whether ring fulfills the Hückel (4n+2)π-electron criterion within molgraph. More...
bool	isInFragmentOfSize (Atom atom, FragmentList frag_list, int size)
	Tells whether the atom atom is a member of any fragment in frag_list whose size matches size. More...
bool	isInFragmentOfSize (Bond bond, FragmentList frag_list, int size)
	Tells whether the bond bond is a member of any fragment in frag_list whose size matches size. More...
bool	isNotAromatic (Fragment ring, MolecularGraph molgraph)
	Tells whether ring is guaranteed not to be aromatic (based on quick geometric/topological criteria). More...
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)
	Tells whether the atom atom qualifies as a stereo center in the context of the molecular graph molgraph. More...
bool	isStereoCenter (Bond bond, MolecularGraph molgraph, bool check_asym=True, bool check_term_n=True, bool check_order=True, int min_ring_size=8)
	Tells whether the bond bond qualifies as a stereo center in the context of the molecular graph molgraph. More...
None	kekulizeBonds (MolecularGraph molgraph)
	Assigns Kekulé bond orders to the aromatic bonds of the molecular graph molgraph. More...
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)
	Sets bits in atom_mask for every atom of the molecular graph molgraph that is reachable from the atom atom through the bonds of molgraph. More...
Molecule	parseSMARTS (str smarts, bool init_qry=True)
	Parses the SMARTS string smarts into a freshly allocated query Chem.Molecule. More...
bool	parseSMARTS (str smarts, Molecule mol, bool init_qry=True)
	Parses the SMARTS string smarts into the supplied molecule mol. More...
Molecule	parseSMILES (str smiles)
	Parses the SMILES string smiles into a freshly allocated Chem.Molecule. More...
bool	parseSMILES (str smiles, Molecule mol)
	Parses the SMILES string smiles into the supplied molecule mol. More...
Fragment	perceiveAromaticSubstructure (MolecularGraph molgraph)
	Perceives the aromatic substructure of the molecular graph molgraph. More...
Fragment	perceiveAromaticSubstructure (MolecularGraph molgraph, bool overwrite)
	Perceives and (optionally) stores the aromatic substructure of the molecular graph molgraph. More...
AtomMapping	perceiveAtomMapping (Reaction rxn)
	Derives the reactant-to-product atom mapping from the atom mapping IDs of the reaction rxn. More...
AtomMapping	perceiveAtomMapping (Reaction rxn, bool overwrite)
	Derives and (optionally) stores the reactant-to-product atom mapping of the reaction rxn. More...
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)
	Flags the atoms of the molecular graph molgraph that qualify as stereo centers under the supplied criteria. More...
None	perceiveBondOrders (MolecularGraph molgraph, bool overwrite)
	Perceives bond orders for the bonds of the molecular graph molgraph from atom geometry and ligand environment. More...
None	perceiveBondStereoCenters (MolecularGraph molgraph, bool overwrite, bool check_asym=True, bool check_term_n=True, bool check_order=True, int min_ring_size=8)
	Flags the bonds of the molecular graph molgraph that qualify as stereo centers under the supplied criteria. More...
FragmentList	perceiveComponentGroups (MolecularGraph molgraph)
	Perceives the component groups of the molecular graph molgraph (from atom-level Chem.AtomProperty.COMPONENT_GROUP_ID values). More...
FragmentList	perceiveComponentGroups (MolecularGraph molgraph, bool overwrite)
	Perceives and (optionally) stores the component groups of the molecular graph molgraph. More...
FragmentList	perceiveComponentGroups (Reaction rxn)
	Perceives the component groups of the reaction rxn. More...
FragmentList	perceiveComponentGroups (Reaction rxn, bool overwrite)
	Perceives and (optionally) stores the component groups of the reaction rxn. More...
FragmentList	perceiveComponents (MolecularGraph molgraph)
	Perceives the connected components of the molecular graph molgraph. More...
FragmentList	perceiveComponents (MolecularGraph molgraph, bool overwrite)
	Perceives and (optionally) stores the connected components of the molecular graph molgraph. More...
Fragment	perceiveCyclicSubstructure (MolecularGraph molgraph)
	Perceives the cyclic substructure (union of all rings) of the molecular graph molgraph. More...
Fragment	perceiveCyclicSubstructure (MolecularGraph molgraph, bool overwrite)
	Perceives and (optionally) stores the cyclic substructure of the molecular graph molgraph. More...
int	perceiveHybridizationState (Atom atom, MolecularGraph molgraph)
	Derives the hybridization state of the atom atom from its valence environment in the molecular graph molgraph. More...
None	perceiveHybridizationStates (MolecularGraph molgraph, bool overwrite)
	Computes and stores hybridization states for the atoms of the molecular graph molgraph from their valence environment. More...
ElectronSystemList	perceivePiElectronSystems (MolecularGraph molgraph)
	Perceives the pi-electron systems of the molecular graph molgraph. More...
ElectronSystemList	perceivePiElectronSystems (MolecularGraph molgraph, bool overwrite)
	Perceives and (optionally) stores the pi-electron systems of the molecular graph molgraph. More...
FragmentList	perceiveRings (MolecularGraph molgraph)
	Perceives the full set of rings of the molecular graph molgraph. More...
FragmentList	perceiveRings (MolecularGraph molgraph, bool overwrite)
	Perceives and (optionally) stores the full set of rings of the molecular graph molgraph. More...
FragmentList	perceiveSSSR (MolecularGraph molgraph)
	Perceives the Smallest Set of Smallest Rings of the molecular graph molgraph. More...
FragmentList	perceiveSSSR (MolecularGraph molgraph, bool overwrite)
	Perceives and (optionally) stores the Smallest Set of Smallest Rings of the molecular graph molgraph. More...
None	perceiveSybylAtomTypes (MolecularGraph molgraph, bool overwrite)
	Perceives Sybyl atom types for the atoms of the molecular graph molgraph. More...
int	perceiveSybylType (Atom atom, MolecularGraph molgraph)
	Derives the Sybyl atom type of the atom atom from its valence environment in the molecular graph molgraph. More...
int	perceiveSybylType (Bond bond, MolecularGraph molgraph)
	Derives the Sybyl MOL2 bond type of the bond bond from its bond order, aromaticity and ligand environment in the molecular graph molgraph. More...
None	perceiveSymmetryClasses (MolecularGraph molgraph, bool overwrite, int atom_flags=2147483648, int bond_flags=2147483648, bool inc_impl_h=True)
	Computes and stores topological-symmetry classes for the atoms of the molecular graph molgraph. More...
None	removeAtomsIf (Fragment frag, AtomPredicate pred)
	Removes all atoms of the fragment frag for which the predicate pred returns True. More...
None	removeAtomsIf (Molecule mol, AtomPredicate pred)
	Removes all atoms of the molecule mol for which the predicate pred returns True. More...
None	removeAtomsIfNot (Fragment frag, AtomPredicate pred)
	Removes all atoms of the fragment frag for which the predicate pred returns False. More...
None	removeAtomsIfNot (Molecule mol, AtomPredicate pred)
	Removes all atoms of the molecule mol for which the predicate pred returns False. More...
None	splitIntoFragments (MolecularGraph molgraph, FragmentList frag_list, Util.BitSet split_bond_mask, bool append=False)
	Splits the molecular graph molgraph into connected fragments by removing the bonds flagged in split_bond_mask. More...
int	sybylToAtomType (int sybyl_type)
	Translates a Sybyl atom type identifier to the corresponding generic Chem.AtomType value. More...
None	transform2DCoordinates (AtomContainer cntnr, Math.Matrix3D mtx)
	Transforms the 2D coordinates of all atoms in cntnr by the affine 3×3 matrix mtx. More...
None	transform3DCoordinates (Entity3DContainer cntnr, Math.Matrix4D mtx)
	Transforms the 3D coordinates of the entities of cntnr by the affine matrix mtx. More...
None	transformConformation (AtomContainer cntnr, int conf_idx, Math.Matrix4D mtx)
	Transforms the conformation at index conf_idx by the homogeneous 4×4 matrix mtx. More...
None	transformConformations (AtomContainer cntnr, Math.Matrix4D mtx)
	Transforms every stored conformation of the atoms in cntnr by the homogeneous 4×4 matrix mtx. More...
None	translateFragment (MolecularGraph src_molgraph, Fragment src_frag, MolecularGraph tgt_molgraph, Fragment tgt_frag, bool append=False)
	Translates the atoms/bonds of src_frag to the corresponding atoms/bonds of tgt_molgraph and stores them in tgt_frag. More...
None	translateFragments (MolecularGraph src_molgraph, FragmentList src_frag_list, MolecularGraph tgt_molgraph, FragmentList tgt_frag_list, bool append=False)
	Translates every fragment in src_frag_list to the corresponding fragments on tgt_molgraph. More...
None	setBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr, bool fix)
	Sets the value of the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr to fix. More...
bool	hasBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr is set. More...
bool	getBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter stored in cntnr. More...
None	clearBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter from cntnr. More...
None	setCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr, bool single_prec)
	Sets the value of the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr to single_prec. More...
bool	hasCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr is set. More...
bool	getCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter stored in cntnr. More...
None	clearCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter from cntnr. More...
None	setCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
	Sets the value of the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable. More...
bool	hasCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set. More...
bool	getCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr. More...
None	clearCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr. More...
None	setCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter of cntnr to output. More...
bool	hasCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter of cntnr is set. More...
bool	getCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter stored in cntnr. More...
None	clearCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter from cntnr. More...
None	setCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr to output. More...
bool	hasCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr is set. More...
bool	getCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter stored in cntnr. More...
None	clearCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter from cntnr. More...
None	setCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr to output. More...
bool	hasCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr is set. More...
bool	getCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter stored in cntnr. More...
None	clearCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter from cntnr. More...
None	setCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr to output. More...
bool	hasCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr is set. More...
bool	getCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter stored in cntnr. More...
None	clearCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter from cntnr. More...
None	setCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr, str ns)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr to ns. More...
bool	hasCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr is set. More...
str	getCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter stored in cntnr. More...
None	clearCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter from cntnr. More...
None	setCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter of cntnr to output. More...
bool	hasCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter of cntnr is set. More...
bool	getCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter stored in cntnr. More...
None	clearCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter from cntnr. More...
None	setCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter of cntnr to output. More...
bool	hasCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter of cntnr is set. More...
bool	getCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter stored in cntnr. More...
None	clearCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter from cntnr. More...
None	setCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr to output. More...
bool	hasCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr is set. More...
bool	getCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter stored in cntnr. More...
None	clearCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter from cntnr. More...
None	setCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr to output. More...
bool	hasCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr is set. More...
bool	getCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter stored in cntnr. More...
None	clearCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter from cntnr. More...
None	setCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter of cntnr to output. More...
bool	hasCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter of cntnr is set. More...
bool	getCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter stored in cntnr. More...
None	clearCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter from cntnr. More...
None	setCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter of cntnr to output. More...
bool	hasCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter of cntnr is set. More...
bool	getCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter stored in cntnr. More...
None	clearCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter from cntnr. More...
None	setCheckLineLengthParameter (Base.ControlParameterContainer cntnr, bool check)
	Sets the value of the Chem.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr to check. More...
bool	hasCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr is set. More...
bool	getCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CHECK_LINE_LENGTH parameter stored in cntnr. More...
None	clearCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CHECK_LINE_LENGTH parameter from cntnr. More...
None	setConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr, str pattern)
	Sets the value of the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr to pattern. More...
bool	hasConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr is set. More...
str	getConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter stored in cntnr. More...
None	clearConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter from cntnr. More...
None	setCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr, int dim)
	Sets the value of the Chem.ControlParameter.COORDINATES_DIMENSION parameter of cntnr to dim. More...
bool	hasCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.COORDINATES_DIMENSION parameter of cntnr is set. More...
int	getCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.COORDINATES_DIMENSION parameter stored in cntnr. More...
None	clearCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.COORDINATES_DIMENSION parameter from cntnr. More...
None	setINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr, str opts)
	Sets the value of the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter of cntnr to opts. More...
bool	hasINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter of cntnr is set. More...
str	getINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter stored in cntnr. More...
None	clearINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter from cntnr. More...
None	setINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr, str opts)
	Sets the value of the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter of cntnr to opts. More...
bool	hasINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter of cntnr is set. More...
str	getINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter stored in cntnr. More...
None	clearINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter from cntnr. More...
None	setJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr, bool separate)
	Sets the value of the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter of cntnr to separate. More...
bool	hasJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter of cntnr is set. More...
bool	getJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter stored in cntnr. More...
None	clearJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter from cntnr. More...
None	setMDLCTABVersionParameter (Base.ControlParameterContainer cntnr, int version)
	Sets the value of the Chem.ControlParameter.MDL_CTAB_VERSION parameter of cntnr to version. More...
bool	hasMDLCTABVersionParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_CTAB_VERSION parameter of cntnr is set. More...
int	getMDLCTABVersionParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_CTAB_VERSION parameter stored in cntnr. More...
None	clearMDLCTABVersionParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_CTAB_VERSION parameter from cntnr. More...
None	setMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr, str tag)
	Sets the value of the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter of cntnr to tag. More...
bool	hasMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter of cntnr is set. More...
str	getMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter stored in cntnr. More...
None	clearMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter from cntnr. More...
None	setMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
	Sets the value of the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable. More...
bool	hasMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set. More...
bool	getMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr. More...
None	clearMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr. More...
None	setMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr, bool ignore)
	Sets the value of the Chem.ControlParameter.MDL_IGNORE_PARITY parameter of cntnr to ignore. More...
bool	hasMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_IGNORE_PARITY parameter of cntnr is set. More...
bool	getMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_IGNORE_PARITY parameter stored in cntnr. More...
None	clearMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_IGNORE_PARITY parameter from cntnr. More...
None	setMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr to output. More...
bool	hasMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr is set. More...
bool	getMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter stored in cntnr. More...
None	clearMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter from cntnr. More...
None	setMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr to output. More...
bool	hasMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr is set. More...
bool	getMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter stored in cntnr. More...
None	clearMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter from cntnr. More...
None	setMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr, int version)
	Sets the value of the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter of cntnr to version. More...
bool	hasMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter of cntnr is set. More...
int	getMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter stored in cntnr. More...
None	clearMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter from cntnr. More...
None	setMDLTrimLinesParameter (Base.ControlParameterContainer cntnr, bool trim)
	Sets the value of the Chem.ControlParameter.MDL_TRIM_LINES parameter of cntnr to trim. More...
bool	hasMDLTrimLinesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_TRIM_LINES parameter of cntnr is set. More...
bool	getMDLTrimLinesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_TRIM_LINES parameter stored in cntnr. More...
None	clearMDLTrimLinesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_TRIM_LINES parameter from cntnr. More...
None	setMDLTrimStringsParameter (Base.ControlParameterContainer cntnr, bool trim)
	Sets the value of the Chem.ControlParameter.MDL_TRIM_STRINGS parameter of cntnr to trim. More...
bool	hasMDLTrimStringsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_TRIM_STRINGS parameter of cntnr is set. More...
bool	getMDLTrimStringsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_TRIM_STRINGS parameter stored in cntnr. More...
None	clearMDLTrimStringsParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_TRIM_STRINGS parameter from cntnr. More...
None	setMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr, bool trunc)
	Sets the value of the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter of cntnr to trunc. More...
bool	hasMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter of cntnr is set. More...
bool	getMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter stored in cntnr. More...
None	clearMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter from cntnr. More...
None	setMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr, bool trunc)
	Sets the value of the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter of cntnr to trunc. More...
bool	hasMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter of cntnr is set. More...
bool	getMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter stored in cntnr. More...
None	clearMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter from cntnr. More...
None	setMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr, bool update)
	Sets the value of the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter of cntnr to update. More...
bool	hasMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter of cntnr is set. More...
bool	getMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter stored in cntnr. More...
None	clearMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter from cntnr. More...
None	setMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)
	Sets the value of the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter of cntnr to calc. More...
bool	hasMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter of cntnr is set. More...
bool	getMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter stored in cntnr. More...
None	clearMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter from cntnr. More...
None	setMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr, int type)
	Sets the value of the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter of cntnr to type. More...
bool	hasMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter of cntnr is set. More...
int	getMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter stored in cntnr. More...
None	clearMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter from cntnr. More...
None	setMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
	Sets the value of the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable. More...
bool	hasMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set. More...
bool	getMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr. More...
None	clearMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr. More...
None	setMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr, bool enable)
	Sets the value of the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr to enable. More...
bool	hasMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr is set. More...
bool	getMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter stored in cntnr. More...
None	clearMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter from cntnr. More...
None	setMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr, int type)
	Sets the value of the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter of cntnr to type. More...
bool	hasMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter of cntnr is set. More...
int	getMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter stored in cntnr. More...
None	clearMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter from cntnr. More...
None	setMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr to output. More...
bool	hasMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr is set. More...
bool	getMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter stored in cntnr. More...
None	clearMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter from cntnr. More...
None	setMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr to output. More...
bool	hasMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr is set. More...
bool	getMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter stored in cntnr. More...
None	clearMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter from cntnr. More...
None	setMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr, bool read)
	Sets the value of the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr to read. More...
bool	hasMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr is set. More...
bool	getMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter stored in cntnr. More...
None	clearMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter from cntnr. More...
None	setMultiConfExportParameter (Base.ControlParameterContainer cntnr, bool multi_conf)
	Sets the value of the Chem.ControlParameter.MULTI_CONF_EXPORT parameter of cntnr to multi_conf. More...
bool	hasMultiConfExportParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MULTI_CONF_EXPORT parameter of cntnr is set. More...
bool	getMultiConfExportParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MULTI_CONF_EXPORT parameter stored in cntnr. More...
None	clearMultiConfExportParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MULTI_CONF_EXPORT parameter from cntnr. More...
None	setMultiConfImportParameter (Base.ControlParameterContainer cntnr, bool multi_conf)
	Sets the value of the Chem.ControlParameter.MULTI_CONF_IMPORT parameter of cntnr to multi_conf. More...
bool	hasMultiConfImportParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MULTI_CONF_IMPORT parameter of cntnr is set. More...
bool	getMultiConfImportParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MULTI_CONF_IMPORT parameter stored in cntnr. More...
None	clearMultiConfImportParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MULTI_CONF_IMPORT parameter from cntnr. More...
None	setMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr, MultiConfMoleculeInputProcessor proc)
	Sets the value of the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter of cntnr to proc. More...
bool	hasMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter of cntnr is set. More...
MultiConfMoleculeInputProcessor	getMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter stored in cntnr. More...
None	clearMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter from cntnr. More...
None	setOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr, bool deplete)
	Sets the value of the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter of cntnr to deplete. More...
bool	hasOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter of cntnr is set. More...
bool	getOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter stored in cntnr. More...
None	clearOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter from cntnr. More...
None	setOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr to output. More...
bool	hasOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr is set. More...
bool	getOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter stored in cntnr. More...
None	clearOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter from cntnr. More...
None	setRecordSeparatorParameter (Base.ControlParameterContainer cntnr, str sep)
	Sets the value of the Chem.ControlParameter.RECORD_SEPARATOR parameter of cntnr to sep. More...
bool	hasRecordSeparatorParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.RECORD_SEPARATOR parameter of cntnr is set. More...
str	getRecordSeparatorParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.RECORD_SEPARATOR parameter stored in cntnr. More...
None	clearRecordSeparatorParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.RECORD_SEPARATOR parameter from cntnr. More...
None	setSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr, int min_size)
	Sets the value of the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr to min_size. More...
bool	hasSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr is set. More...
int	getSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter stored in cntnr. More...
None	clearSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter from cntnr. More...
None	setSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output. More...
bool	hasSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set. More...
bool	getSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr. More...
None	clearSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter from cntnr. More...
None	setSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr, bool no_subset)
	Sets the value of the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter of cntnr to no_subset. More...
bool	hasSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter of cntnr is set. More...
bool	getSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter stored in cntnr. More...
None	clearSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter from cntnr. More...
None	setSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr to output. More...
bool	hasSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr is set. More...
bool	getSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter stored in cntnr. More...
None	clearSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter from cntnr. More...
None	setSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter of cntnr to output. More...
bool	hasSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter of cntnr is set. More...
bool	getSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter stored in cntnr. More...
None	clearSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter from cntnr. More...
None	setSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter of cntnr to output. More...
bool	hasSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter of cntnr is set. More...
bool	getSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter stored in cntnr. More...
None	clearSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter from cntnr. More...
None	setSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr to output. More...
bool	hasSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr is set. More...
bool	getSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter stored in cntnr. More...
None	clearSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter from cntnr. More...
None	setSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr to output. More...
bool	hasSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr is set. More...
bool	getSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter stored in cntnr. More...
None	clearSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter from cntnr. More...
None	setSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter of cntnr to output. More...
bool	hasSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter of cntnr is set. More...
bool	getSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter stored in cntnr. More...
None	clearSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter from cntnr. More...
None	setSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter of cntnr to output. More...
bool	hasSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter of cntnr is set. More...
bool	getSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter stored in cntnr. More...
None	clearSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter from cntnr. More...
None	setSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr to output. More...
bool	hasSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr is set. More...
bool	getSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter stored in cntnr. More...
None	clearSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter from cntnr. More...
None	setSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr to output. More...
bool	hasSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr is set. More...
bool	getSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter stored in cntnr. More...
None	clearSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter from cntnr. More...
None	setSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr, str format)
	Sets the value of the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter of cntnr to format. More...
bool	hasSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter of cntnr is set. More...
str	getSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter stored in cntnr. More...
None	clearSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter from cntnr. More...
None	setSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output. More...
bool	hasSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set. More...
bool	getSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr. More...
None	clearSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter from cntnr. More...
None	setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)
	Sets the value of the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr to strict. More...
bool	hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr is set. More...
bool	getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter stored in cntnr. More...
None	clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr. More...
None	setXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)
	Sets the value of the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter of cntnr to calc. More...
bool	hasXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter of cntnr is set. More...
bool	getXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter stored in cntnr. More...
None	clearXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter from cntnr. More...
None	setXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr, bool is_name)
	Sets the value of the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter of cntnr to is_name. More...
bool	hasXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter of cntnr is set. More...
bool	getXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter stored in cntnr. More...
None	clearXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter from cntnr. More...
None	setXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr, bool perceive)
	Sets the value of the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr to perceive. More...
bool	hasXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr is set. More...
bool	getXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter stored in cntnr. More...
None	clearXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter from cntnr. More...
None	setXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr, bool perceive)
	Sets the value of the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr to perceive. More...
bool	hasXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr is set. More...
bool	getXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter stored in cntnr. More...
None	clearXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr)
	Removes the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter from cntnr. More...

Detailed Description

Contains classes and functions related to chemistry.

Function Documentation

set2DCoordinates() [1/2]

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

Sets the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom to coords.

Parameters

atom	The atom for which to set the property value.
coords	The new 2D coordinates.

has2DCoordinates()

bool CDPL.Chem.has2DCoordinates

(

Atom

atom

)

Tells whether the Chem.AtomProperty.COORDINATES_2D property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

get2DCoordinates() [1/2]

Math.Vector2D CDPL.Chem.get2DCoordinates

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored 2D coordinates.

clear2DCoordinates()

None CDPL.Chem.clear2DCoordinates

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

set2DCoordinates() [2/2]

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

Writes the 2D coordinates in coords back to the corresponding atoms of cntnr.

Parameters

cntnr	The atom container.
coords	The 2D coordinates to assign (must contain at least one entry per atom).

get2DCoordinates() [2/2]

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

Extracts the 2D coordinates of all atoms in cntnr into coords.

Parameters

cntnr	The atom container.
coords	The output 2D-coordinate array.
append	If True, the coordinates are appended to coords. Otherwise, coords is cleared first.

set2DStereoFlag()

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

Sets the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond to flag (see namespace Chem.BondStereoFlag).

Parameters

bond	The bond for which to set the property value.
flag	The new 2D stereo flag value.

has2DStereoFlag()

bool CDPL.Chem.has2DStereoFlag

(

Bond

bond

)

Tells whether the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

get2DStereoFlag()

int CDPL.Chem.get2DStereoFlag

(

Bond

bond

)

Returns the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond (see namespace Chem.BondStereoFlag).

Parameters

bond	The bond for which to return the property value.

Returns

The stored 2D stereo flag.

clear2DStereoFlag()

None CDPL.Chem.clear2DStereoFlag

(

Bond

bond

)

Clears the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

set3DCoordinatesArray()

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

Sets the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom to coords_array.

Parameters

atom	The atom for which to set the property value.
coords_array	The new 3D conformer-coordinates array.

has3DCoordinatesArray()

bool CDPL.Chem.has3DCoordinatesArray

(

Atom

atom

)

Tells whether the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

get3DCoordinatesArray()

Math.Vector3DArray CDPL.Chem.get3DCoordinatesArray

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored 3D conformer-coordinates array.

clear3DCoordinatesArray()

None CDPL.Chem.clear3DCoordinatesArray

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

get3DCoordinates() [1/3]

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

Extracts the 3D coordinates of all atoms in cntnr into coords using the per-atom coordinate lookup function coords_func.

Parameters

cntnr	The atom container.
coords	The output 3D-coordinate array.
coords_func	The function returning the 3D coordinates of an atom.
append	If True, the coordinates are appended to coords. Otherwise, coords is cleared first.

set3DCoordinates() [1/2]

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

Sets the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity to coords.

Parameters

entity	The 3D entity for which to set the property value.
coords	The new 3D coordinates.

has3DCoordinates()

bool CDPL.Chem.has3DCoordinates

(

Entity3D

entity

)

Tells whether the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity is set.

Parameters

entity

The 3D entity for which to query the property value.

Returns

True if the property is set, and False otherwise.

get3DCoordinates() [2/3]

Math.Vector3D CDPL.Chem.get3DCoordinates

(

Entity3D

entity

)

Returns the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity.

Parameters

entity

The 3D entity for which to return the property value.

Returns

The stored 3D coordinates.

Exceptions

Base.ItemNotFound

if the property has not been set.

clear3DCoordinates()

None CDPL.Chem.clear3DCoordinates

(

Entity3D

entity

)

Clears the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity.

Parameters

entity

The 3D entity for which to clear the property value.

set3DCoordinates() [2/2]

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

Sets the 3D coordinates of the entities of cntnr from coords.

Parameters

cntnr	The entity 3D container whose coordinates are to be updated.
coords	The input coordinates array (must contain at least one position per entity in cntnr).

get3DCoordinates() [3/3]

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

Stores the 3D coordinates of the entities of cntnr in coords.

Parameters

cntnr	The entity 3D container providing the source coordinates.
coords	The output coordinates array.
append	If True, the entity coordinates are appended to coords. If False, coords is cleared first.

getAromaticRings()

FragmentList CDPL.Chem.getAromaticRings

(

MolecularGraph

molgraph

)

Returns the subset of the aromatic rings of the molecular graph molgraph.

Parameters

molgraph

The molecular graph to inspect.

Returns

The aromatic rings.

getAromaticSSSRSubset()

FragmentList CDPL.Chem.getAromaticSSSRSubset

(

MolecularGraph

molgraph

)

Returns the subset of the SSSR of the molecular graph molgraph that contains only aromatic rings,.

Parameters

molgraph

The molecular graph to inspect.

Returns

The aromatic-SSSR subset.

setAromaticSubstructure()

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

Sets the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct.

Parameters

molgraph	The molecular graph for which to set the property value.
substruct	The new aromatic substructure.

hasAromaticSubstructure()

bool CDPL.Chem.hasAromaticSubstructure

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getAromaticSubstructure()

Fragment CDPL.Chem.getAromaticSubstructure

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored aromatic substructure.

clearAromaticSubstructure()

None CDPL.Chem.clearAromaticSubstructure

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setAromaticityFlag() [1/2]

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

Sets the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom to aromatic.

Parameters

atom	The atom for which to set the property value.
aromatic	True to flag the atom as aromatic, and False to flag it as non-aromatic.

hasAromaticityFlag() [1/2]

bool CDPL.Chem.hasAromaticityFlag

(

Atom

atom

)

Tells whether the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getAromaticityFlag() [1/2]

bool CDPL.Chem.getAromaticityFlag

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

True if the atom is flagged as aromatic, and False otherwise.

clearAromaticityFlag() [1/2]

None CDPL.Chem.clearAromaticityFlag

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setAromaticityFlag() [2/2]

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

Sets the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond to aromatic.

Parameters

bond	The bond for which to set the property value.
aromatic	True to flag the bond as aromatic, and False to flag it as non-aromatic.

hasAromaticityFlag() [2/2]

bool CDPL.Chem.hasAromaticityFlag

(

Bond

bond

)

Tells whether the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getAromaticityFlag() [2/2]

bool CDPL.Chem.getAromaticityFlag

(

Bond

bond

)

Returns the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

True if the bond is flagged as aromatic, and False otherwise.

clearAromaticityFlag() [2/2]

None CDPL.Chem.clearAromaticityFlag

(

Bond

bond

)

Clears the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setAromaticityFlags()

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

Perceives aromaticity and sets the corresponding atom/bond aromaticity flags on the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing aromaticity flags.

setAtomMappingID()

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

Sets the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom to id.

Parameters

atom	The atom for which to set the property value.
id	The new reactant-to-product atom-mapping ID.

hasAtomMappingID()

bool CDPL.Chem.hasAtomMappingID

(

Atom

atom

)

Tells whether the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getAtomMappingID()

int CDPL.Chem.getAtomMappingID

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored reactant-to-product atom-mapping ID.

clearAtomMappingID()

None CDPL.Chem.clearAtomMappingID

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setAtomMapping()

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

Sets the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn to mapping.

Parameters

rxn	The reaction for which to set the property value.
mapping	The new reactant-to-product atom mapping.

hasAtomMapping()

bool CDPL.Chem.hasAtomMapping

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getAtomMapping()

AtomMapping CDPL.Chem.getAtomMapping

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored reactant-to-product atom mapping.

clearAtomMapping()

None CDPL.Chem.clearAtomMapping

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setAtomMatchConstraints() [1/2]

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

Sets the atom-level match-constraint list constr on every atom of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
constr	The match-constraint list to assign.
overwrite	If True, replaces any existing per-atom constraints. If False, leaves atoms that already carry a list unchanged.

setAtomMatchConstraints() [2/2]

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

Sets the atom-level match-constraint list constr on every atom of every component of the reaction rxn.

Parameters

rxn	The reaction to modify.
constr	The match-constraint list to assign.
overwrite	If True, replaces any existing per-atom constraints. If False, leaves atoms that already carry a list unchanged.

setAtomSymbolsFromTypes()

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

Sets the atom symbols of the molecular graph molgraph from their atom types.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing atom symbols.

setAtomTypesFromSymbols()

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

Sets the atom types of the molecular graph molgraph from their element symbols.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing atom types.

setBondMatchConstraints() [1/2]

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

Sets the bond-level match-constraint list constr on every bond of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
constr	The match-constraint list to assign.
overwrite	If True, replaces any existing per-bond constraints. If False, leaves bonds that already carry a list unchanged.

setBondMatchConstraints() [2/2]

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

Sets the bond-level match-constraint list constr on every bond of every component of the reaction rxn.

Parameters

rxn	The reaction to modify.
constr	The match-constraint list to assign.
overwrite	If True, replaces any existing per-bond constraints. If False, leaves bonds that already carry a list unchanged.

setCIPConfiguration() [1/2]

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

Sets the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom to config (see namespace Chem.CIPDescriptor).

Parameters

atom	The atom for which to set the property value.
config	The new CIP configuration label.

hasCIPConfiguration() [1/2]

bool CDPL.Chem.hasCIPConfiguration

(

Atom

atom

)

Tells whether the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getCIPConfiguration() [1/2]

int CDPL.Chem.getCIPConfiguration

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom (see namespace Chem.CIPDescriptor).

Parameters

atom	The atom for which to return the property value.

Returns

The stored CIP configuration label.

clearCIPConfiguration() [1/2]

None CDPL.Chem.clearCIPConfiguration

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setCIPConfiguration() [2/2]

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

Sets the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond to config (see namespace Chem.CIPDescriptor).

Parameters

bond	The bond for which to set the property value.
config	The new CIP configuration label.

hasCIPConfiguration() [2/2]

bool CDPL.Chem.hasCIPConfiguration

(

Bond

bond

)

Tells whether the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getCIPConfiguration() [2/2]

int CDPL.Chem.getCIPConfiguration

(

Bond

bond

)

Returns the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond (see namespace Chem.CIPDescriptor).

Parameters

bond	The bond for which to return the property value.

Returns

The stored CIP configuration label.

clearCIPConfiguration() [2/2]

None CDPL.Chem.clearCIPConfiguration

(

Bond

bond

)

Clears the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setCIPPriority()

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

Sets the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom to priority.

Parameters

atom	The atom for which to set the property value.
priority	The new CIP priority.

hasCIPPriority()

bool CDPL.Chem.hasCIPPriority

(

Atom

atom

)

Tells whether the Chem.AtomProperty.CIP_PRIORITY property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getCIPPriority()

int CDPL.Chem.getCIPPriority

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored CIP priority.

clearCIPPriority()

None CDPL.Chem.clearCIPPriority

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setCanonicalNumber()

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

Sets the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom to num.

Parameters

atom	The atom for which to set the property value.
num	The new canonical number.

hasCanonicalNumber()

bool CDPL.Chem.hasCanonicalNumber

(

Atom

atom

)

Tells whether the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getCanonicalNumber()

int CDPL.Chem.getCanonicalNumber

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored canonical number.

clearCanonicalNumber()

None CDPL.Chem.clearCanonicalNumber

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setComment() [1/2]

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

Sets the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph to comment.

Parameters

molgraph	The molecular graph for which to set the property value.
comment	The new comment string.

hasComment() [1/2]

bool CDPL.Chem.hasComment

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getComment() [1/2]

str CDPL.Chem.getComment

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored comment.

clearComment() [1/2]

None CDPL.Chem.clearComment

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setComment() [2/2]

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

Sets the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn to comment.

Parameters

rxn	The reaction for which to set the property value.
comment	The new comment string.

hasComment() [2/2]

bool CDPL.Chem.hasComment

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.COMMENT property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getComment() [2/2]

str CDPL.Chem.getComment

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored comment.

clearComment() [2/2]

None CDPL.Chem.clearComment

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

getCompleteBondCount()

int CDPL.Chem.getCompleteBondCount

(

MolecularGraph

molgraph

)

Returns the number of bonds of the molecular graph molgraph whose connected atoms are likewise contained in molgraph.

Parameters

molgraph

The molecular graph to inspect.

Returns

The count of non-dangling bonds.

setComponentGroupID()

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

Sets the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom to id.

Parameters

atom	The atom for which to set the property value.
id	The new component-group ID.

hasComponentGroupID()

bool CDPL.Chem.hasComponentGroupID

(

Atom

atom

)

Tells whether the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getComponentGroupID()

int CDPL.Chem.getComponentGroupID

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored component-group ID.

clearComponentGroupID()

None CDPL.Chem.clearComponentGroupID

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setComponentGroups() [1/2]

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

Sets the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph to comp_groups.

Parameters

molgraph	The molecular graph for which to set the property value.
comp_groups	The new component-group fragment list.

hasComponentGroups() [1/2]

bool CDPL.Chem.hasComponentGroups

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getComponentGroups() [1/2]

FragmentList CDPL.Chem.getComponentGroups

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored component-group fragment list.

clearComponentGroups() [1/2]

None CDPL.Chem.clearComponentGroups

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setComponentGroups() [2/2]

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

Sets the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn to comp_groups.

Parameters

rxn	The reaction for which to set the property value.
comp_groups	The new component-group fragment list.

hasComponentGroups() [2/2]

bool CDPL.Chem.hasComponentGroups

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getComponentGroups() [2/2]

FragmentList CDPL.Chem.getComponentGroups

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored component-group fragment list.

clearComponentGroups() [2/2]

None CDPL.Chem.clearComponentGroups

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setComponentMatchConstraints()

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

Sets the molecular graph-level match-constraint list constr on every component of the reaction rxn.

Parameters

rxn	The reaction to modify.
constr	The match-constraint list to assign.
overwrite	If True, replaces any existing per-component constraints. If False, leaves components that already carry a list unchanged.

setComponents()

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

Sets the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph to comps.

Parameters

molgraph	The molecular graph for which to set the property value.
comps	The new connected-component list.

hasComponents()

bool CDPL.Chem.hasComponents

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getComponents()

FragmentList CDPL.Chem.getComponents

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored connected-component list.

clearComponents()

None CDPL.Chem.clearComponents

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

getConformation()

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

Extracts the conformation at index conf_idx into coords.

Parameters

cntnr	The atom container.
conf_idx	The zero-based conformation index.
coords	The output 3D-coordinate array.
append	If True, the coordinates are appended to coords. Otherwise, coords is cleared first.

getConformationEnergy()

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

Returns the energy of the conformation at index conf_idx.

Parameters

molgraph	The molecular graph to query.
conf_idx	The zero-based conformation index.

Returns

The energy of the requested conformation.

setConformationIndex()

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

Sets the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph to index.

Parameters

molgraph	The molecular graph for which to set the property value.
index	The new zero-based conformation index.

hasConformationIndex()

bool CDPL.Chem.hasConformationIndex

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getConformationIndex()

int CDPL.Chem.getConformationIndex

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored zero-based conformation index.

clearConformationIndex()

None CDPL.Chem.clearConformationIndex

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setConformation()

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

Overwrites the conformation at index conf_idx with the supplied coordinates and energy.

Parameters

molgraph	The molecular graph to modify.
conf_idx	The zero-based conformation index.
coords	The 3D coordinates of the conformation.
energy	The energy associated with the conformation.

clearConformations()

None CDPL.Chem.clearConformations

(

AtomContainer

cntnr

)

Removes all stored conformations from the atoms of cntnr.

Parameters

cntnr

The atom container.

getConformer3DCoordinates()

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

Returns the 3D coordinates of the atom atom for conformer conf_idx (from the Chem.AtomProperty.COORDINATES_3D_ARRAY property).

Parameters

atom	The atom for which to return the conformer 3D coordinates.
conf_idx	The zero-based conformer index.

Returns

The 3D coordinates of the specified conformer.

setConformerEnergies()

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

Sets the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph to energies.

Parameters

molgraph	The molecular graph for which to set the property value.
energies	The new per-conformer energy array.

hasConformerEnergies()

bool CDPL.Chem.hasConformerEnergies

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getConformerEnergies()

Util.DArray CDPL.Chem.getConformerEnergies

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored per-conformer energy array.

clearConformerEnergies()

None CDPL.Chem.clearConformerEnergies

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

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
	)

Collects the fragments in frag_list that are fully contained in the molecular graph molgraph into cont_frag_list.

Parameters

molgraph	The host molecular graph.
frag_list	The candidate fragment list.
cont_frag_list	The output fragment list receiving the matches.
append	If True, matches are appended to cont_frag_list. Otherwise, it is cleared first.
atoms	If True, atom membership is required for a match.
bonds	If True, bond membership is required for a match.

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
	)

Collects the fragments in frag_list that contain the molecular graph molgraph into cont_frag_list.

Parameters

molgraph	The query molecular graph.
frag_list	The candidate fragment list.
cont_frag_list	The output fragment list receiving the matches.
append	If True, matches are appended to cont_frag_list. Otherwise, it is cleared first.
atoms	If True, atom membership is required for a match.
bonds	If True, bond membership is required for a match.

hasCoordinates()

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

Tells whether all atoms of cntnr carry coordinates of the given dimensionality.

Parameters

cntnr	The atom container.
dim	The coordinate dimensionality (2 or 3).

Returns

True if all atoms have the requested coordinates, and False otherwise.

setCyclicSubstructure()

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

Sets the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct.

Parameters

molgraph	The molecular graph for which to set the property value.
substruct	The new cyclic substructure.

hasCyclicSubstructure()

bool CDPL.Chem.hasCyclicSubstructure

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getCyclicSubstructure()

Fragment CDPL.Chem.getCyclicSubstructure

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored cyclic substructure.

clearCyclicSubstructure()

None CDPL.Chem.clearCyclicSubstructure

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setDirection()

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

Sets the value of the Chem.BondProperty.DIRECTION property of the bond bond to dir.

Parameters

bond	The bond for which to set the property value.
dir	The new bond direction descriptor (see namespace Chem.BondDirection).

hasDirection()

bool CDPL.Chem.hasDirection

(

Bond

bond

)

Tells whether the Chem.BondProperty.DIRECTION property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getDirection()

int CDPL.Chem.getDirection

(

Bond

bond

)

Returns the value of the Chem.BondProperty.DIRECTION property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored SMILES/SMARTS bond direction descriptor (see namespace Chem.BondDirection).

clearDirection()

None CDPL.Chem.clearDirection

(

Bond

bond

)

Clears the value of the Chem.BondProperty.DIRECTION property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

getEnvironment()

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

Collects every atom of the molecular graph molgraph that is within max_dist bonds of the atom atom into the fragment env.

Parameters

atom	The seed atom.
molgraph	The molecular graph providing the bonding context.
max_dist	The maximum topological distance.
env	The output fragment receiving the environment atoms and the bonds between them.
append	If True, atoms/bonds are appended to env. Otherwise, it is cleared first.

Returns

The number of atoms appended to env.

setFormalCharge()

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

Sets the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom to charge.

Parameters

atom	The atom for which to set the property value.
charge	The new formal charge.

hasFormalCharge()

bool CDPL.Chem.hasFormalCharge

(

Atom

atom

)

Tells whether the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getFormalCharge()

int CDPL.Chem.getFormalCharge

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored formal charge.

clearFormalCharge()

None CDPL.Chem.clearFormalCharge

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

getGenericType()

int CDPL.Chem.getGenericType

(

Atom

atom

)

Returns the generic atom type that the atom's Chem.AtomProperty.TYPE property value belongs to.

Parameters

atom	The atom to query.

Returns

The generic atom type.

setGeometricalDistanceMatrix()

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

Sets the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx.

Parameters

molgraph	The molecular graph for which to set the property value.
mtx	The new geometrical-distance matrix.

hasGeometricalDistanceMatrix()

bool CDPL.Chem.hasGeometricalDistanceMatrix

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getGeometricalDistanceMatrix()

Math.DMatrix CDPL.Chem.getGeometricalDistanceMatrix

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored geometrical-distance matrix.

clearGeometricalDistanceMatrix()

None CDPL.Chem.clearGeometricalDistanceMatrix

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setHashCode()

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

Sets the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph to hash_code.

Parameters

molgraph	The molecular graph for which to set the property value.
hash_code	The new 64-bit hash code.

hasHashCode()

bool CDPL.Chem.hasHashCode

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getHashCode()

int CDPL.Chem.getHashCode

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored 64-bit hash code.

clearHashCode()

None CDPL.Chem.clearHashCode

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setHybridizationState()

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

Sets the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom to state (see namespace Chem.HybridizationState).

Parameters

atom	The atom for which to set the property value.
state	The new hybridization state.

hasHybridizationState()

bool CDPL.Chem.hasHybridizationState

(

Atom

atom

)

Tells whether the Chem.AtomProperty.HYBRIDIZATION property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getHybridizationState()

int CDPL.Chem.getHybridizationState

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom (see namespace Chem.HybridizationState).

Parameters

atom	The atom for which to return the property value.

Returns

The stored hybridization state.

clearHybridizationState()

None CDPL.Chem.clearHybridizationState

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setImplicitHydrogenCount()

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

Sets the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom to count.

Parameters

atom	The atom for which to set the property value.
count	The new implicit-hydrogen count.

hasImplicitHydrogenCount()

bool CDPL.Chem.hasImplicitHydrogenCount

(

Atom

atom

)

Tells whether the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getImplicitHydrogenCount()

int CDPL.Chem.getImplicitHydrogenCount

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored implicit-hydrogen count.

clearImplicitHydrogenCount()

None CDPL.Chem.clearImplicitHydrogenCount

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

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
	)

Sets the value of the Chem.AtomProperty.ISOTOPE property of the atom atom to isotope.

Parameters

atom	The atom for which to set the property value.
isotope	The new mass number (zero for the natural isotope mixture).

hasIsotope()

bool CDPL.Chem.hasIsotope

(

Atom

atom

)

Tells whether the Chem.AtomProperty.ISOTOPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getIsotope()

int CDPL.Chem.getIsotope

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.ISOTOPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored mass number, or zero for the natural isotope mixture.

clearIsotope()

None CDPL.Chem.clearIsotope

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.ISOTOPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMDLCTABVersion()

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

Sets the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph to version (see namespace Chem.MDLDataFormatVersion).

Parameters

molgraph	The molecular graph for which to set the property value.
version	The new CTab version.

hasMDLCTABVersion()

bool CDPL.Chem.hasMDLCTABVersion

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLCTABVersion()

int CDPL.Chem.getMDLCTABVersion

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph (see namespace Chem.MDLDataFormatVersion).

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored CTab version.

clearMDLCTABVersion()

None CDPL.Chem.clearMDLCTABVersion

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMDLChiralFlag()

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

Sets the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph to flag.

Parameters

molgraph	The molecular graph for which to set the property value.
flag	The new MDL chiral flag.

hasMDLChiralFlag()

bool CDPL.Chem.hasMDLChiralFlag

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLChiralFlag()

bool CDPL.Chem.getMDLChiralFlag

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL chiral flag.

clearMDLChiralFlag()

None CDPL.Chem.clearMDLChiralFlag

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMDLDimensionality()

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

Sets the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph to dim.

Parameters

molgraph	The molecular graph for which to set the property value.
dim	The new MDL coordinate dimensionality.

hasMDLDimensionality()

bool CDPL.Chem.hasMDLDimensionality

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLDimensionality()

int CDPL.Chem.getMDLDimensionality

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL coordinate dimensionality.

clearMDLDimensionality()

None CDPL.Chem.clearMDLDimensionality

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMDLEnergy()

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

Sets the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph to energy.

Parameters

molgraph	The molecular graph for which to set the property value.
energy	The new MDL energy.

hasMDLEnergy()

bool CDPL.Chem.hasMDLEnergy

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLEnergy()

float CDPL.Chem.getMDLEnergy

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL energy.

clearMDLEnergy()

None CDPL.Chem.clearMDLEnergy

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMDLExternalRegistryNumber()

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

Sets the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no.

Parameters

rxn	The reaction for which to set the property value.
reg_no	The new MDL external registry number.

hasMDLExternalRegistryNumber()

bool CDPL.Chem.hasMDLExternalRegistryNumber

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLExternalRegistryNumber()

str CDPL.Chem.getMDLExternalRegistryNumber

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL external registry number.

clearMDLExternalRegistryNumber()

None CDPL.Chem.clearMDLExternalRegistryNumber

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setMDLInternalRegistryNumber()

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

Sets the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no.

Parameters

rxn	The reaction for which to set the property value.
reg_no	The new MDL internal registry number.

hasMDLInternalRegistryNumber()

bool CDPL.Chem.hasMDLInternalRegistryNumber

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLInternalRegistryNumber()

str CDPL.Chem.getMDLInternalRegistryNumber

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL internal registry number.

clearMDLInternalRegistryNumber()

None CDPL.Chem.clearMDLInternalRegistryNumber

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setMDLMoleculeRecord()

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

Sets the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn to mol_rec.

Parameters

rxn	The reaction for which to set the property value.
mol_rec	The new MDL molecule record.

hasMDLMoleculeRecord()

bool CDPL.Chem.hasMDLMoleculeRecord

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLMoleculeRecord()

Molecule CDPL.Chem.getMDLMoleculeRecord

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL molecule record (typically the structure component of an RD-file).

clearMDLMoleculeRecord()

None CDPL.Chem.clearMDLMoleculeRecord

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setMDLParity()

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

Sets the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom to parity (see namespace Chem.MDLParity).

Parameters

atom	The atom for which to set the property value.
parity	The new MDL stereo parity.

hasMDLParity()

bool CDPL.Chem.hasMDLParity

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MDL_PARITY property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLParity()

int CDPL.Chem.getMDLParity

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom (see namespace Chem.MDLParity).

Parameters

atom	The atom for which to return the property value.

Returns

The stored MDL stereo parity.

clearMDLParity()

None CDPL.Chem.clearMDLParity

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMDLProgramName() [1/2]

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

Sets the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph to name.

Parameters

molgraph	The molecular graph for which to set the property value.
name	The new MDL program name.

hasMDLProgramName() [1/2]

bool CDPL.Chem.hasMDLProgramName

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLProgramName() [1/2]

str CDPL.Chem.getMDLProgramName

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL program name.

clearMDLProgramName() [1/2]

None CDPL.Chem.clearMDLProgramName

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMDLProgramName() [2/2]

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

Sets the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn to name.

Parameters

rxn	The reaction for which to set the property value.
name	The new MDL program name.

hasMDLProgramName() [2/2]

bool CDPL.Chem.hasMDLProgramName

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLProgramName() [2/2]

str CDPL.Chem.getMDLProgramName

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL program name.

clearMDLProgramName() [2/2]

None CDPL.Chem.clearMDLProgramName

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setMDLRXNFileVersion()

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

Sets the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn to version.

Parameters

rxn	The reaction for which to set the property value.
version	The new RXN-file version (see Chem.MDLDataFormatVersion).

hasMDLRXNFileVersion()

bool CDPL.Chem.hasMDLRXNFileVersion

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLRXNFileVersion()

int CDPL.Chem.getMDLRXNFileVersion

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored RXN-file version (see Chem.MDLDataFormatVersion).

clearMDLRXNFileVersion()

None CDPL.Chem.clearMDLRXNFileVersion

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setMDLRegistryNumber() [1/2]

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

Sets the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph to reg_no.

Parameters

molgraph	The molecular graph for which to set the property value.
reg_no	The new MDL registry number.

hasMDLRegistryNumber() [1/2]

bool CDPL.Chem.hasMDLRegistryNumber

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLRegistryNumber() [1/2]

int CDPL.Chem.getMDLRegistryNumber

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL registry number.

clearMDLRegistryNumber() [1/2]

None CDPL.Chem.clearMDLRegistryNumber

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMDLRegistryNumber() [2/2]

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

Sets the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn to reg_no.

Parameters

rxn	The reaction for which to set the property value.
reg_no	The new MDL registry number.

hasMDLRegistryNumber() [2/2]

bool CDPL.Chem.hasMDLRegistryNumber

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLRegistryNumber() [2/2]

int CDPL.Chem.getMDLRegistryNumber

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL registry number.

clearMDLRegistryNumber() [2/2]

None CDPL.Chem.clearMDLRegistryNumber

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setMDLScalingFactor1()

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

Sets the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph to factor.

Parameters

molgraph	The molecular graph for which to set the property value.
factor	The new MDL scaling factor 1.

hasMDLScalingFactor1()

bool CDPL.Chem.hasMDLScalingFactor1

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLScalingFactor1()

int CDPL.Chem.getMDLScalingFactor1

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL scaling factor 1.

clearMDLScalingFactor1()

None CDPL.Chem.clearMDLScalingFactor1

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMDLScalingFactor2()

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

Sets the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph to factor.

Parameters

molgraph	The molecular graph for which to set the property value.
factor	The new MDL scaling factor 2.

hasMDLScalingFactor2()

bool CDPL.Chem.hasMDLScalingFactor2

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLScalingFactor2()

float CDPL.Chem.getMDLScalingFactor2

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL scaling factor 2.

clearMDLScalingFactor2()

None CDPL.Chem.clearMDLScalingFactor2

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMDLStereoCareFlag()

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

Sets the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom to flag.

Parameters

atom	The atom for which to set the property value.
flag	The new MDL stereo-care flag.

hasMDLStereoCareFlag()

bool CDPL.Chem.hasMDLStereoCareFlag

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLStereoCareFlag()

bool CDPL.Chem.getMDLStereoCareFlag

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored MDL stereo-care flag.

clearMDLStereoCareFlag()

None CDPL.Chem.clearMDLStereoCareFlag

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMDLUserInitials() [1/2]

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

Sets the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph to initials.

Parameters

molgraph	The molecular graph for which to set the property value.
initials	The new MDL user initials.

hasMDLUserInitials() [1/2]

bool CDPL.Chem.hasMDLUserInitials

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLUserInitials() [1/2]

str CDPL.Chem.getMDLUserInitials

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL user initials.

clearMDLUserInitials() [1/2]

None CDPL.Chem.clearMDLUserInitials

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMDLUserInitials() [2/2]

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

Sets the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn to initials.

Parameters

rxn	The reaction for which to set the property value.
initials	The new MDL user initials.

hasMDLUserInitials() [2/2]

bool CDPL.Chem.hasMDLUserInitials

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMDLUserInitials() [2/2]

str CDPL.Chem.getMDLUserInitials

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL user initials.

clearMDLUserInitials() [2/2]

None CDPL.Chem.clearMDLUserInitials

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setMOL2Charge()

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

Sets the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom to charge.

Parameters

atom	The atom for which to set the property value.
charge	The new Sybyl MOL2 partial charge.

hasMOL2Charge()

bool CDPL.Chem.hasMOL2Charge

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MOL2_CHARGE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMOL2Charge()

float CDPL.Chem.getMOL2Charge

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 partial charge.

clearMOL2Charge()

None CDPL.Chem.clearMOL2Charge

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMOL2ChargeType()

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

Sets the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph to type (see namespace Chem.MOL2ChargeType).

Parameters

molgraph	The molecular graph for which to set the property value.
type	The new MOL2 charge type.

hasMOL2ChargeType()

bool CDPL.Chem.hasMOL2ChargeType

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMOL2ChargeType()

int CDPL.Chem.getMOL2ChargeType

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph (see namespace Chem.MOL2ChargeType).

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MOL2 charge type.

clearMOL2ChargeType()

None CDPL.Chem.clearMOL2ChargeType

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMOL2MoleculeType()

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

Sets the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph to type (see namespace Chem.MOL2MoleculeType).

Parameters

molgraph	The molecular graph for which to set the property value.
type	The new MOL2 molecule type.

hasMOL2MoleculeType()

bool CDPL.Chem.hasMOL2MoleculeType

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMOL2MoleculeType()

int CDPL.Chem.getMOL2MoleculeType

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph (see namespace Chem.MOL2MoleculeType).

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MOL2 molecule type.

clearMOL2MoleculeType()

None CDPL.Chem.clearMOL2MoleculeType

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMOL2Name()

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

Sets the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom to name.

Parameters

atom	The atom for which to set the property value.
name	The new Sybyl MOL2 atom name.

hasMOL2Name()

bool CDPL.Chem.hasMOL2Name

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MOL2_NAME property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMOL2Name()

str CDPL.Chem.getMOL2Name

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 atom name.

clearMOL2Name()

None CDPL.Chem.clearMOL2Name

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMOL2SubstructureChain()

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

Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom to chain.

Parameters

atom	The atom for which to set the property value.
chain	The new Sybyl MOL2 substructure chain identifier.

hasMOL2SubstructureChain()

bool CDPL.Chem.hasMOL2SubstructureChain

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMOL2SubstructureChain()

str CDPL.Chem.getMOL2SubstructureChain

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 substructure chain identifier.

clearMOL2SubstructureChain()

None CDPL.Chem.clearMOL2SubstructureChain

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMOL2SubstructureID()

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

Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom to id.

Parameters

atom	The atom for which to set the property value.
id	The new Sybyl MOL2 substructure ID.

hasMOL2SubstructureID()

bool CDPL.Chem.hasMOL2SubstructureID

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMOL2SubstructureID()

int CDPL.Chem.getMOL2SubstructureID

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 substructure ID.

clearMOL2SubstructureID()

None CDPL.Chem.clearMOL2SubstructureID

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMOL2SubstructureName()

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

Parameters

atom
name

hasMOL2SubstructureName()

bool CDPL.Chem.hasMOL2SubstructureName

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMOL2SubstructureName()

str CDPL.Chem.getMOL2SubstructureName

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 substructure name.

clearMOL2SubstructureName()

None CDPL.Chem.clearMOL2SubstructureName

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMOL2SubstructureSubtype()

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

Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom to subtype.

Parameters

atom	The atom for which to set the property value.
subtype	The new Sybyl MOL2 substructure subtype string.

hasMOL2SubstructureSubtype()

bool CDPL.Chem.hasMOL2SubstructureSubtype

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMOL2SubstructureSubtype()

str CDPL.Chem.getMOL2SubstructureSubtype

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 substructure subtype string.

clearMOL2SubstructureSubtype()

None CDPL.Chem.clearMOL2SubstructureSubtype

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMatchConstraints() [1/4]

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

Sets the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom to constr.

Parameters

atom	The atom for which to set the property value.
constr	The new match-constraint list.

hasMatchConstraints() [1/4]

bool CDPL.Chem.hasMatchConstraints

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchConstraints() [1/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored match-constraint list.

clearMatchConstraints() [1/4]

None CDPL.Chem.clearMatchConstraints

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMatchConstraints() [2/4]

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

Sets the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond to constr.

Parameters

bond	The bond for which to set the property value.
constr	The new match-constraint list.

hasMatchConstraints() [2/4]

bool CDPL.Chem.hasMatchConstraints

(

Bond

bond

)

Tells whether the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchConstraints() [2/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

Bond

bond

)

Returns the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored match-constraint list.

clearMatchConstraints() [2/4]

None CDPL.Chem.clearMatchConstraints

(

Bond

bond

)

Clears the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setMatchConstraints() [3/4]

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

Sets the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph to constr.

Parameters

molgraph	The molecular graph for which to set the property value.
constr	The new top-level match-constraint list.

hasMatchConstraints() [3/4]

bool CDPL.Chem.hasMatchConstraints

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchConstraints() [3/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored top-level match-constraint list.

clearMatchConstraints() [3/4]

None CDPL.Chem.clearMatchConstraints

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMatchConstraints() [4/4]

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

Sets the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn to constr.

Parameters

rxn	The reaction for which to set the property value.
constr	The new match-constraint list to store.

hasMatchConstraints() [4/4]

bool CDPL.Chem.hasMatchConstraints

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchConstraints() [4/4]

MatchConstraintList CDPL.Chem.getMatchConstraints

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored top-level match-constraint list.

clearMatchConstraints() [4/4]

None CDPL.Chem.clearMatchConstraints

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setMatchExpression() [1/4]

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

Sets the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom to expr.

Parameters

atom	The atom for which to set the property value.
expr	The new atom-level match expression.

hasMatchExpression() [1/4]

bool CDPL.Chem.hasMatchExpression

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchExpression() [1/4]

AtomMatchExpression CDPL.Chem.getMatchExpression

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored atom-level match expression.

clearMatchExpression() [1/4]

None CDPL.Chem.clearMatchExpression

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMatchExpression() [2/4]

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

Sets the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond to expr.

Parameters

bond	The bond for which to set the property value.
expr	The new bond-level match expression.

hasMatchExpression() [2/4]

bool CDPL.Chem.hasMatchExpression

(

Bond

bond

)

Tells whether the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchExpression() [2/4]

BondMatchExpression CDPL.Chem.getMatchExpression

(

Bond

bond

)

Returns the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored bond-level match expression.

clearMatchExpression() [2/4]

None CDPL.Chem.clearMatchExpression

(

Bond

bond

)

Clears the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setMatchExpression() [3/4]

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

Sets the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph to expr.

Parameters

molgraph	The molecular graph for which to set the property value.
expr	The new top-level match expression.

hasMatchExpression() [3/4]

bool CDPL.Chem.hasMatchExpression

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchExpression() [3/4]

MolecularGraphMatchExpression CDPL.Chem.getMatchExpression

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored top-level match expression.

clearMatchExpression() [3/4]

None CDPL.Chem.clearMatchExpression

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setMatchExpression() [4/4]

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

Sets the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn to expr.

Parameters

rxn	The reaction for which to set the property value.
expr	The new match expression to store.

hasMatchExpression() [4/4]

bool CDPL.Chem.hasMatchExpression

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchExpression() [4/4]

ReactionMatchExpression CDPL.Chem.getMatchExpression

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored top-level reaction match expression.

clearMatchExpression() [4/4]

None CDPL.Chem.clearMatchExpression

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setMatchExpressionString() [1/2]

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

Sets the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom to expr_str.

Parameters

atom	The atom for which to set the property value.
expr_str	The new match-expression string.

hasMatchExpressionString() [1/2]

bool CDPL.Chem.hasMatchExpressionString

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchExpressionString() [1/2]

str CDPL.Chem.getMatchExpressionString

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored match-expression string.

clearMatchExpressionString() [1/2]

None CDPL.Chem.clearMatchExpressionString

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setMatchExpressionString() [2/2]

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

Sets the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond to expr_str.

Parameters

bond	The bond for which to set the property value.
expr_str	The new match-expression string.

hasMatchExpressionString() [2/2]

bool CDPL.Chem.hasMatchExpressionString

(

Bond

bond

)

Tells whether the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMatchExpressionString() [2/2]

str CDPL.Chem.getMatchExpressionString

(

Bond

bond

)

Returns the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored match-expression string.

clearMatchExpressionString() [2/2]

None CDPL.Chem.clearMatchExpressionString

(

Bond

bond

)

Clears the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

getMaxAtomMappingID() [1/2]

int CDPL.Chem.getMaxAtomMappingID

(

AtomContainer

cntnr

)

Returns the largest atom-mapping ID assigned to any atom of cntnr.

Parameters

cntnr

The atom container.

Returns

The largest atom-mapping ID (zero if no atom carries an atom-mapping ID).

getMaxAtomMappingID() [2/2]

int CDPL.Chem.getMaxAtomMappingID

(

Reaction

rxn

)

Returns the largest atom-mapping ID found on any of the atoms in rxn.

Parameters

rxn	The reaction to scan.

Returns

The largest atom-mapping ID, or zero if no IDs are assigned.

getMaxComponentGroupID() [1/2]

int CDPL.Chem.getMaxComponentGroupID

(

AtomContainer

cntnr

)

Returns the largest component-group ID assigned to any atom of cntnr.

Parameters

cntnr

The atom container.

Returns

The largest component-group ID (zero if no atom carries a component-group ID).

getMaxComponentGroupID() [2/2]

int CDPL.Chem.getMaxComponentGroupID

(

Reaction

rxn

)

Returns the largest component-group ID found on any of the components of the reaction rxn.

Parameters

rxn	The reaction to scan.

Returns

The largest component-group ID, or zero if no IDs are assigned.

setMorganNumber()

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

Sets the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom to num.

Parameters

atom	The atom for which to set the property value.
num	The new Morgan number.

hasMorganNumber()

bool CDPL.Chem.hasMorganNumber

(

Atom

atom

)

Tells whether the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getMorganNumber()

int CDPL.Chem.getMorganNumber

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored Morgan number.

clearMorganNumber()

None CDPL.Chem.clearMorganNumber

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setName() [1/3]

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

Sets the value of the Chem.AtomProperty.NAME property of the atom atom to name.

Parameters

atom	The atom for which to set the property value.
name	The new atom name.

hasName() [1/3]

bool CDPL.Chem.hasName

(

Atom

atom

)

Tells whether the Chem.AtomProperty.NAME property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getName() [1/3]

str CDPL.Chem.getName

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.NAME property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored atom name.

clearName() [1/3]

None CDPL.Chem.clearName

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.NAME property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setName() [2/3]

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

Sets the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph to name.

Parameters

molgraph	The molecular graph for which to set the property value.
name	The new name.

hasName() [2/3]

bool CDPL.Chem.hasName

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getName() [2/3]

str CDPL.Chem.getName

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored name.

clearName() [2/3]

None CDPL.Chem.clearName

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setName() [3/3]

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

Sets the value of the Chem.ReactionProperty.NAME property of the reaction rxn to name.

Parameters

rxn	The reaction for which to set the property value.
name	The new reaction name.

hasName() [3/3]

bool CDPL.Chem.hasName

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.NAME property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getName() [3/3]

str CDPL.Chem.getName

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.NAME property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored reaction name.

clearName() [3/3]

None CDPL.Chem.clearName

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.NAME property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

getNumConformations()

int CDPL.Chem.getNumConformations

(

AtomContainer

cntnr

)

Returns the number of conformations stored on the atoms of cntnr.

Parameters

cntnr

The atom container.

Returns

The conformation count.

getNumContainingFragments() [1/2]

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

Returns the number of fragments in frag_list that contain the atom atom.

Parameters

atom	The atom to query.
frag_list	The list of fragments to search.

Returns

The number of containing fragments.

getNumContainingFragments() [2/2]

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

Returns the number of fragments in frag_list that contain the bond bond.

Parameters

bond	The bond to query.
frag_list	The list of fragments to search.

Returns

The number of containing fragments.

setOrder()

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

Sets the value of the Chem.BondProperty.ORDER property of the bond bond to order.

Parameters

bond	The bond for which to set the property value.
order	The new bond order.

hasOrder()

bool CDPL.Chem.hasOrder

(

Bond

bond

)

Tells whether the Chem.BondProperty.ORDER property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getOrder()

int CDPL.Chem.getOrder

(

Bond

bond

)

Returns the value of the Chem.BondProperty.ORDER property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored bond order.

clearOrder()

None CDPL.Chem.clearOrder

(

Bond

bond

)

Clears the value of the Chem.BondProperty.ORDER property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setPiElectronSystems()

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

Sets the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph to pi_systems.

Parameters

molgraph	The molecular graph for which to set the property value.
pi_systems	The new pi-electron-system list.

hasPiElectronSystems()

bool CDPL.Chem.hasPiElectronSystems

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getPiElectronSystems()

ElectronSystemList CDPL.Chem.getPiElectronSystems

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored pi-electron-system list.

clearPiElectronSystems()

None CDPL.Chem.clearPiElectronSystems

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setRadicalType()

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

Sets the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom to type (see namespace Chem.RadicalType).

Parameters

atom	The atom for which to set the property value.
type	The new radical type.

hasRadicalType()

bool CDPL.Chem.hasRadicalType

(

Atom

atom

)

Tells whether the Chem.AtomProperty.RADICAL_TYPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getRadicalType()

int CDPL.Chem.getRadicalType

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom (see namespace Chem.RadicalType).

Parameters

atom	The atom for which to return the property value.

Returns

The stored radical type.

clearRadicalType()

None CDPL.Chem.clearRadicalType

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setReactionCenterStatus() [1/2]

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

Sets the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom to status.

Parameters

atom	The atom for which to set the property value.
status	The new reaction-center status.

hasReactionCenterStatus() [1/2]

bool CDPL.Chem.hasReactionCenterStatus

(

Atom

atom

)

Tells whether the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getReactionCenterStatus() [1/2]

int CDPL.Chem.getReactionCenterStatus

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom (see namespace Chem.ReactionCenterStatus).

Parameters

atom	The atom for which to return the property value.

Returns

The stored reaction-center status.

clearReactionCenterStatus() [1/2]

None CDPL.Chem.clearReactionCenterStatus

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setReactionCenterStatus() [2/2]

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

Sets the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond to status.

Parameters

bond	The bond for which to set the property value.
status	The new reaction-center status (see namespace Chem.ReactionCenterStatus).

hasReactionCenterStatus() [2/2]

bool CDPL.Chem.hasReactionCenterStatus

(

Bond

bond

)

Tells whether the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getReactionCenterStatus() [2/2]

int CDPL.Chem.getReactionCenterStatus

(

Bond

bond

)

Returns the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored reaction-center status (see namespace Chem.ReactionCenterStatus).

clearReactionCenterStatus() [2/2]

None CDPL.Chem.clearReactionCenterStatus

(

Bond

bond

)

Clears the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setReactionData()

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

Sets the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn to data.

Parameters

rxn	The reaction for which to set the property value.
data	The new MDL reaction data block.

hasReactionData()

bool CDPL.Chem.hasReactionData

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getReactionData()

StringDataBlock CDPL.Chem.getReactionData

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL reaction data block.

clearReactionData()

None CDPL.Chem.clearReactionData

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

setRingFlag() [1/2]

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

Sets the value of the Chem.AtomProperty.RING_FLAG property of the atom atom to in_ring.

Parameters

atom	The atom for which to set the property value.
in_ring	True to flag the atom as part of a ring, and False to flag it as acyclic.

hasRingFlag() [1/2]

bool CDPL.Chem.hasRingFlag

(

Atom

atom

)

Tells whether the Chem.AtomProperty.RING_FLAG property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getRingFlag() [1/2]

bool CDPL.Chem.getRingFlag

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.RING_FLAG property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

True if the atom is flagged as part of any ring, and False otherwise.

clearRingFlag() [1/2]

None CDPL.Chem.clearRingFlag

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.RING_FLAG property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setRingFlag() [2/2]

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

Sets the value of the Chem.BondProperty.RING_FLAG property of the bond bond to in_ring.

Parameters

bond	The bond for which to set the property value.
in_ring	True to flag the bond as part of a ring, and False to flag it as acyclic.

hasRingFlag() [2/2]

bool CDPL.Chem.hasRingFlag

(

Bond

bond

)

Tells whether the Chem.BondProperty.RING_FLAG property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getRingFlag() [2/2]

bool CDPL.Chem.getRingFlag

(

Bond

bond

)

Returns the value of the Chem.BondProperty.RING_FLAG property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

True if the bond is flagged as part of any ring, and False otherwise.

clearRingFlag() [2/2]

None CDPL.Chem.clearRingFlag

(

Bond

bond

)

Clears the value of the Chem.BondProperty.RING_FLAG property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setRingFlags()

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

Perceives ring membership and sets the corresponding atom/bond ring flags on the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing ring flags.

setRings()

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

Sets the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph to rings.

Parameters

molgraph	The molecular graph for which to set the property value.
rings	The new full ring set.

hasRings()

bool CDPL.Chem.hasRings

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getRings()

FragmentList CDPL.Chem.getRings

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored full ring set.

clearRings()

None CDPL.Chem.clearRings

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setSSSR()

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

Sets the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph to sssr.

Parameters

molgraph	The molecular graph for which to set the property value.
sssr	The new Smallest Set of Smallest Rings.

hasSSSR()

bool CDPL.Chem.hasSSSR

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getSSSR()

FragmentList CDPL.Chem.getSSSR

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored Smallest Set of Smallest Rings.

clearSSSR()

None CDPL.Chem.clearSSSR

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

getSizeOfLargestContainingFragment() [1/2]

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

Returns the size (in atoms) of the largest fragment in frag_list that contains the atom atom.

Parameters

atom	The atom to query.
frag_list	The list of fragments to search.

Returns

The largest containing fragment's size, or zero if no fragment contains atom.

getSizeOfLargestContainingFragment() [2/2]

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

Returns the size (in atoms) of the largest fragment in frag_list that contains the bond bond.

Parameters

bond	The bond to query.
frag_list	The list of fragments to search.

Returns

The largest containing fragment's size, or zero if no fragment contains the bond bond.

getSizeOfSmallestContainingFragment() [1/2]

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

Returns the size (in atoms) of the smallest fragment in frag_list that contains the atom atom.

Parameters

atom	The atom to query.
frag_list	The list of fragments to search.

Returns

The smallest containing fragment's size, or zero if no fragment contains atom.

getSizeOfSmallestContainingFragment() [2/2]

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

Returns the size (in atoms) of the smallest fragment in frag_list that contains the bond bond.

Parameters

bond	The bond to query.
frag_list	The list of fragments to search.

Returns

The smallest containing fragment's size, or zero if no fragment contains the bond bond.

setStereoCenterFlag() [1/2]

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

Sets the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom to is_center.

Parameters

atom	The atom for which to set the property value.
is_center	True to flag the atom as a stereo center, and False otherwise.

hasStereoCenterFlag() [1/2]

bool CDPL.Chem.hasStereoCenterFlag

(

Atom

atom

)

Tells whether the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getStereoCenterFlag() [1/2]

bool CDPL.Chem.getStereoCenterFlag

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

True if the atom is flagged as a stereo center, and False otherwise.

clearStereoCenterFlag() [1/2]

None CDPL.Chem.clearStereoCenterFlag

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setStereoCenterFlag() [2/2]

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

Sets the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond to is_center.

Parameters

bond	The bond for which to set the property value.
is_center	True to flag the bond as a stereo center, and False otherwise.

hasStereoCenterFlag() [2/2]

bool CDPL.Chem.hasStereoCenterFlag

(

Bond

bond

)

Tells whether the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getStereoCenterFlag() [2/2]

bool CDPL.Chem.getStereoCenterFlag

(

Bond

bond

)

Returns the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

True if the bond is flagged as a stereo center, and False otherwise.

clearStereoCenterFlag() [2/2]

None CDPL.Chem.clearStereoCenterFlag

(

Bond

bond

)

Clears the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setStereoDescriptor() [1/2]

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

Sets the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom to descr.

Parameters

atom	The atom for which to set the property value.
descr	The new stereo descriptor.

hasStereoDescriptor() [1/2]

bool CDPL.Chem.hasStereoDescriptor

(

Atom

atom

)

Tells whether the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getStereoDescriptor() [1/2]

StereoDescriptor CDPL.Chem.getStereoDescriptor

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored stereo descriptor.

clearStereoDescriptor() [1/2]

None CDPL.Chem.clearStereoDescriptor

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setStereoDescriptor() [2/2]

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

Sets the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond to descr.

Parameters

bond	The bond for which to set the property value.
descr	The new stereo descriptor.

hasStereoDescriptor() [2/2]

bool CDPL.Chem.hasStereoDescriptor

(

Bond

bond

)

Tells whether the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getStereoDescriptor() [2/2]

StereoDescriptor CDPL.Chem.getStereoDescriptor

(

Bond

bond

)

Returns the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored stereo descriptor.

clearStereoDescriptor() [2/2]

None CDPL.Chem.clearStereoDescriptor

(

Bond

bond

)

Clears the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setStoichiometricNumber()

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

Sets the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph to num.

Parameters

molgraph	The molecular graph for which to set the property value.
num	The new stoichiometric number.

hasStoichiometricNumber()

bool CDPL.Chem.hasStoichiometricNumber

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getStoichiometricNumber()

float CDPL.Chem.getStoichiometricNumber

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored stoichiometric number.

clearStoichiometricNumber()

None CDPL.Chem.clearStoichiometricNumber

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setStructureData()

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

Sets the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph to data.

Parameters

molgraph	The molecular graph for which to set the property value.
data	The new MDL structure-data block.

hasStructureData()

bool CDPL.Chem.hasStructureData

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getStructureData()

StringDataBlock CDPL.Chem.getStructureData

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL structure-data block.

clearStructureData()

None CDPL.Chem.clearStructureData

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

getSybylAtomTypeString()

str CDPL.Chem.getSybylAtomTypeString

(

int

sybyl_type

)

Returns the canonical textual representation of the Sybyl atom type sybyl_type.

Parameters

sybyl_type

The Sybyl atom type identifier (Chem.SybylAtomType value).

Returns

A reference to the type-name string (empty for unknown types).

getSybylBondTypeString()

str CDPL.Chem.getSybylBondTypeString

(

int

sybyl_type

)

Returns the canonical textual representation of the Sybyl bond type sybyl_type.

Parameters

sybyl_type

The Sybyl bond-type identifier (Chem.SybylBondType value).

Returns

A reference to the type-name string (empty for unknown types).

setSybylType() [1/2]

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

Sets the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom to type.

Parameters

atom	The atom for which to set the property value.
type	The new Sybyl MOL2 atom type (see namespace Chem.SybylAtomType).

hasSybylType() [1/2]

bool CDPL.Chem.hasSybylType

(

Atom

atom

)

Tells whether the Chem.AtomProperty.SYBYL_TYPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getSybylType() [1/2]

int CDPL.Chem.getSybylType

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 atom type (see namespace Chem.SybylAtomType).

clearSybylType() [1/2]

None CDPL.Chem.clearSybylType

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setSybylType() [2/2]

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

Sets the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond to type.

Parameters

bond	The bond for which to set the property value.
type	The new Sybyl MOL2 bond type (see namespace Chem.SybylBondType).

hasSybylType() [2/2]

bool CDPL.Chem.hasSybylType

(

Bond

bond

)

Tells whether the Chem.BondProperty.SYBYL_TYPE property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns

True if the property is set, and False otherwise.

getSybylType() [2/2]

int CDPL.Chem.getSybylType

(

Bond

bond

)

Returns the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored Sybyl MOL2 bond type (see namespace Chem.SybylBondType).

clearSybylType() [2/2]

None CDPL.Chem.clearSybylType

(

Bond

bond

)

Clears the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

setSymbol()

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

Sets the value of the Chem.AtomProperty.SYMBOL property of the atom atom to symbol.

Parameters

atom	The atom for which to set the property value.
symbol	The new element symbol.

hasSymbol()

bool CDPL.Chem.hasSymbol

(

Atom

atom

)

Tells whether the Chem.AtomProperty.SYMBOL property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getSymbol()

str CDPL.Chem.getSymbol

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.SYMBOL property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored element symbol.

clearSymbol()

None CDPL.Chem.clearSymbol

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.SYMBOL property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

getSymbolForType()

str CDPL.Chem.getSymbolForType

(

Atom

atom

)

Returns the element symbol that corresponds to the Chem.AtomProperty.TYPE property of the atom atom.

Parameters

atom	The atom to query.

Returns

The element symbol mapped from the atom's type (see namespace Chem.AtomType).

setSymmetryClass()

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

Sets the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom to class_id.

Parameters

atom	The atom for which to set the property value.
class_id	The new topological-symmetry class ID.

hasSymmetryClass()

bool CDPL.Chem.hasSymmetryClass

(

Atom

atom

)

Tells whether the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getSymmetryClass()

int CDPL.Chem.getSymmetryClass

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored topological-symmetry class ID.

clearSymmetryClass()

None CDPL.Chem.clearSymmetryClass

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setTimestamp() [1/2]

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

Sets the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph to time.

Parameters

molgraph	The molecular graph for which to set the property value.
time	The new timestamp value.

hasTimestamp() [1/2]

bool CDPL.Chem.hasTimestamp

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getTimestamp() [1/2]

int CDPL.Chem.getTimestamp

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored timestamp.

clearTimestamp() [1/2]

None CDPL.Chem.clearTimestamp

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setTimestamp() [2/2]

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

Sets the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn to time.

Parameters

rxn	The reaction for which to set the property value.
time	The new timestamp value.

hasTimestamp() [2/2]

bool CDPL.Chem.hasTimestamp

(

Reaction

rxn

)

Tells whether the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

True if the property is set, and False otherwise.

getTimestamp() [2/2]

int CDPL.Chem.getTimestamp

(

Reaction

rxn

)

Returns the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored timestamp.

clearTimestamp() [2/2]

None CDPL.Chem.clearTimestamp

(

Reaction

rxn

)

Clears the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

getTopologicalDistance()

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

Returns the topological distance between two atoms of the molecular graph molgraph.

Parameters

atom1	The first atom.
atom2	The second atom.
molgraph	The molecular graph providing the bonding context.

Returns

The topological distance between atom1 and atom2.

setTopologicalDistanceMatrix()

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

Sets the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx.

Parameters

molgraph	The molecular graph for which to set the property value.
mtx	The new topological-distance matrix.

hasTopologicalDistanceMatrix()

bool CDPL.Chem.hasTopologicalDistanceMatrix

(

MolecularGraph

molgraph

)

Tells whether the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the property is set, and False otherwise.

getTopologicalDistanceMatrix()

Math.ULMatrix CDPL.Chem.getTopologicalDistanceMatrix

(

MolecularGraph

molgraph

)

Returns the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored topological-distance matrix.

clearTopologicalDistanceMatrix()

None CDPL.Chem.clearTopologicalDistanceMatrix

(

MolecularGraph

molgraph

)

Clears the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setType()

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

Sets the value of the Chem.AtomProperty.TYPE property of the atom atom to type (see namespace Chem.AtomType).

Parameters

atom	The atom for which to set the property value.
type	The new atom type.

hasType()

bool CDPL.Chem.hasType

(

Atom

atom

)

Tells whether the Chem.AtomProperty.TYPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getType()

int CDPL.Chem.getType

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.TYPE property of the atom atom (see namespace Chem.AtomType).

Parameters

atom	The atom for which to return the property value.

Returns

The stored atom type.

clearType()

None CDPL.Chem.clearType

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.TYPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

getTypeForSymbol()

int CDPL.Chem.getTypeForSymbol

(

Atom

atom

)

Returns the atom type that corresponds to the Chem.AtomProperty.SYMBOL property of the atom atom.

Parameters

atom	The atom to query.

Returns

The atom type mapped from the element symbol.

setUnpairedElectronCount()

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

Sets the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom to count.

Parameters

atom	The atom for which to set the property value.
count	The new unpaired electron count.

hasUnpairedElectronCount()

bool CDPL.Chem.hasUnpairedElectronCount

(

Atom

atom

)

Tells whether the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the property is set, and False otherwise.

getUnpairedElectronCount()

int CDPL.Chem.getUnpairedElectronCount

(

Atom

atom

)

Returns the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored unpaired electron count.

clearUnpairedElectronCount()

None CDPL.Chem.clearUnpairedElectronCount

(

Atom

atom

)

Clears the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

addConformation() [1/2]

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

Appends a new conformation built from the supplied 3D coordinates to the atoms of cntnr.

Parameters

cntnr	The atom container.
coords	The 3D coordinates of the new conformation.

addConformation() [2/2]

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

Appends a new conformation built from the supplied coordinates and energy.

Parameters

molgraph	The molecular graph to modify.
coords	The 3D coordinates of the new conformation.
energy	The energy associated with the new conformation.

align2DCoordinates() [1/4]

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

Aligns molgraph's 2D coordinates so that the atoms of atoms come to lie at the reference coordinates ref_coords.

Parameters

molgraph	The molecular graph to align.
atoms	The atoms used as alignment anchors.
ref_coords	Reference 2D coordinates of the alignment-anchor atoms.
fix_bond_stereo	If True, postprocess bond stereo flags so that they remain consistent with the aligned coordinates.

Returns

True if the alignment succeeded, and False otherwise.

Since

1.3

align2DCoordinates() [2/4]

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

Aligns molgraph's 2D coordinates onto a reference atom mapping.

Parameters

molgraph	The molecular graph to align.
ref_atom_mpg	The atom mapping providing the target atom→atom correspondence.
fix_bond_stereo	If True, postprocess bond stereo flags so that they remain consistent with the aligned coordinates.

Returns

True if the alignment succeeded, and False otherwise.

Since

1.3

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
	)

Aligns molgraph's 2D coordinates onto those of ref_molgraph, using substr_ptn as the explicit substructure pattern.

Parameters

molgraph	The molecular graph to align.
ref_molgraph	The reference molecular graph providing the target coordinates.
substr_ptn	The substructure pattern that defines the atom correspondence.
fix_bond_stereo	If True, postprocess bond stereo flags so that they remain consistent with the aligned coordinates.

Returns

True if the alignment succeeded, and False otherwise.

Since

1.3

align3DCoordinates()

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

Rigid-body aligns the 3D coordinates of cntnr to the reference geometry defined by the entity-coordinate pair (ref_entities, ref_coords).

Parameters

cntnr	The entity 3D container whose coordinates are to be aligned.
ref_entities	The reference entity 3D container.
ref_coords	The reference coordinates corresponding to the entities of ref_entities.

Returns

True if the alignment succeeded, and False otherwise.

Since

1.1

alignConformations() [1/4]

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

Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms of ref_atoms as alignment anchors.

Parameters

cntnr	The atom container holding the conformations to be aligned.
ref_atoms	The atoms used as alignment anchors (must all be members of cntnr).
ref_coords	Reference 3D coordinates of the alignment-anchor atoms.

Returns

True if the alignment succeeded for every conformation, and False otherwise.

Since

1.1

alignConformations() [2/4]

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

Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms of ref_atoms as alignment anchors.

Parameters

cntnr	The atom container holding the conformations to be aligned.
ref_atoms	The atoms used as alignment anchors (must all be members of cntnr).
ref_coords	Reference 3D coordinates of the alignment-anchor atoms.

Returns

True if the alignment succeeded for every conformation, and False otherwise.

Since

1.1

alignConformations() [3/4]

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

Aligns each stored conformation of cntnr to the first conformation using the atoms of ref_atoms as alignment anchors.

Parameters

cntnr	The atom container holding the conformations to be aligned.
ref_atoms	The atoms used as alignment anchors (must all be members of cntnr).

Returns

True if the alignment succeeded for every conformation, and False otherwise.

Since

1.1

alignConformations() [4/4]

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

Aligns each stored conformation of cntnr to the first conformation using the atoms of ref_atoms as alignment anchors.

Parameters

cntnr	The atom container holding the conformations to be aligned.
ref_atoms	The atoms used as alignment anchors (must all be members of cntnr).

Returns

True if the alignment succeeded for every conformation, and False otherwise.

Since

1.1

applyConformation()

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

Promotes the stored conformation at index conf_idx to the active per-atom 3D coordinates.

Parameters

cntnr	The atom container.
conf_idx	The zero-based conformation index.

atomTypesMatch()

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

Tells whether the target atom type tgt_type matches the query atom type qry_type (taking generic atom type classes like Chem.AtomType.HET into account).

Parameters

qry_type	The query atom type (Chem.AtomType value).
tgt_type	The target atom type (Chem.AtomType value).

Returns

True if the target matches the query, and False otherwise.

calc2DCoordinates()

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

Computes 2D atom coordinates for molgraph and stores them as Chem.AtomProperty.COORDINATES_2D.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing 2D coordinates. Otherwise, leaves atoms that already carry coordinates unchanged.

calcAtomCIPConfigurations()

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

Computes and stores CIP configuration labels for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing CIP configuration labels.

calcAtomStereoDescriptorsFromMDLParities()

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

Derives atom stereo descriptors of the molecular graph molgraph from previously-assigned MDL parities.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing stereo descriptors.

calcAtomStereoDescriptors()

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

Computes and stores stereo descriptors for the atoms of the molecular graph molgraph from their geometric layout.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing stereo descriptors.
dim	The dimensionality of the atomic coordinates to use (2 or 3).
check_stc_flag	If True, descriptors are only computed for atoms whose Chem.AtomProperty.STEREO_CENTER_FLAG is set.

calcBasicProperties() [1/2]

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

Computes the basic per-atom/per-bond properties (aromaticity, ring info, etc.) of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, recomputes derived data. If False, leaves up-to-date data unchanged.

Since

1.1

calcBasicProperties() [2/2]

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

Computes the basic per-component properties (aromaticity, ring info, etc.) of every component of the reaction rxn.

Parameters

rxn	The reaction to modify.
overwrite	If True, recomputes derived data. If False, leaves up-to-date data unchanged.

Since

1.1

calcBond2DStereoFlags()

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

Derives 2D wedge/hash bond stereo flags for the bonds of the molecular graph molgraph from the atoms' stereo descriptors and 2D layout.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing 2D stereo flags.

calcBondCIPConfigurations()

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

Computes and stores CIP configuration labels for the bonds of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing CIP configuration labels.

calcBondStereoDescriptors()

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

Computes and stores stereo descriptors for the bonds of the molecular graph molgraph from their geometric layout.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing stereo descriptors.
dim	The dimensionality of the atomic coordinates to use (2 or 3).
check_stc_flag	If True, descriptors are only computed for bonds whose Chem.BondProperty.STEREO_CENTER_FLAG is set.

calcBoundingBox() [1/2]

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

Computes the axis-aligned bounding box enclosing the atoms of cntnr.

Parameters

cntnr	The atom container.
min	The output lower-left corner of the bounding box.
max	The output upper-right corner of the bounding box.
coords_func	The function returning the 3D coordinates of an atom.
reset	If True, the bounding box is reset to the first atom. Otherwise, min and max are extended in place.

calcBoundingBox() [2/2]

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

Calculates the axis-aligned bounding box of the 3D coordinates of cntnr.

Parameters

cntnr	The entity 3D container.
min	The output vector receiving the per-axis minimum coordinates.
max	The output vector receiving the per-axis maximum coordinates.
reset	If True, min and max are reset before the calculation. If False, the box is extended to include the existing range.

calcCIPPriorities()

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

Computes and stores CIP priorities for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing CIP-priority values.

calcCanonicalNumbering()

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

Computes and stores canonical atom numbers for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing canonical numbers.
atom_flags	A bitmask of Chem.AtomPropertyFlag flags controlling which atomic properties enter the numbering.
bond_flags	A bitmask of Chem.BondPropertyFlag flags controlling which bond properties enter the numbering.

calcCenterOfMass()

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

Computes the mass-weighted center of mass of the atoms in cntnr.

Parameters

cntnr	The atom container.
coords_func	The function returning the 3D coordinates of an atom.
ctr	The output center-of-mass coordinates.

Returns

True if the center of mass could be computed (at least one atom with non-zero mass), and False otherwise.

calcCentroid() [1/2]

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

Computes the unweighted centroid (arithmetic mean of atom coordinates) of cntnr.

Parameters

cntnr	The atom container.
coords_func	The function returning the 3D coordinates of an atom.
ctr	The output centroid coordinates.

Returns

True if the centroid could be computed (cntnr is non-empty), and False otherwise.

calcCentroid() [2/2]

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

Calculates the geometric centroid of the entities of cntnr.

Parameters

cntnr	The entity 3D container.
ctr	The output centroid vector.

Returns

True if the centroid could be calculated (i.e. cntnr is non-empty), and False otherwise.

calcConfiguration() [1/2]

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

Derives the atom configuration label from the supplied descriptor and 3D coordinates.

Parameters

atom	The atom for which to calculate the configuration.
molgraph	The molecular graph providing the structural context.
descr	The stereo descriptor whose configuration is to be evaluated.
coords	The 3D atomic coordinates used by the evaluation.

Returns

The derived configuration label (see namespace Chem.AtomConfiguration).

calcConfiguration() [2/2]

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

Derives the bond configuration label from the supplied descriptor and 3D coordinates.

Parameters

bond	The bond to inspect.
molgraph	The molecular graph providing the structural context.
descr	The stereo descriptor whose configuration is to be evaluated.
coords	The 3D atomic coordinates used by the evaluation.

Returns

The derived configuration label (see namespace Chem.BondConfiguration).

calcFormalCharge()

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

Computes the formal charge of the atom atom from its valence environment in the molecular graph molgraph.

Parameters

atom	The atom for which to calculate the charge.
molgraph	The molecular graph providing the structural context.

Returns

The computed formal charge.

calcFormalCharges()

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

Computes and stores formal charges for the atoms of the molecular graph molgraph from their valence environment.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing formal charges.

calcGeometricalDistanceMatrix() [1/2]

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

Calculates the inter-entity geometric distance matrix for the entities of cntnr.

Parameters

cntnr	The entity 3D container providing the source coordinates.
mtx	The output matrix receiving the calculated pairwise distances.

calcGeometricalDistanceMatrix() [2/2]

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

Computes and (optionally) stores the geometrical-distance matrix of the molecular graph molgraph from its 3D coordinates.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing geometrical-distance matrix.

Returns

The computed (or pre-existing) matrix.

calcHashCode() [1/2]

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

Computes a 64-bit hash code for molgraph taking into account the specified atom and bond properties.

Parameters

molgraph	The molecular graph to hash.
atom_flags	A bitmask of Chem.AtomPropertyFlag flags controlling which atomic properties enter the hash.
bond_flags	A bitmask of Chem.BondPropertyFlag flags controlling which bond properties enter the hash.
ord_h_deplete	True to suppress ordinary hydrogens before hashing.

Returns

The computed hash code.

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
	)

Computes a 64-bit hash code for the reaction rxn taking into account the specified reaction roles and atom/bond properties.

Parameters

rxn	The reaction to hash.
role_mask	A bitmask of Chem.ReactionRole flags selecting the considered component sets.
atom_flags	A bitmask of Chem.AtomPropertyFlag flags controlling which atomic properties enter the hash.
bond_flags	A bitmask of Chem.BondPropertyFlag flags controlling which bond properties enter the hash.
ord_h_deplete	True to suppress ordinary hydrogens before hashing.

Returns

The computed hash code.

calcHydrogen3DCoordinates()

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

Computes 3D coordinates for the hydrogen atoms of the molecular graph molgraph from the geometry of their non-hydrogen neighbors.

Parameters

molgraph	The molecular graph to modify.
undef_only	If True, only hydrogens without prior 3D coordinates are placed. If False, all hydrogen coordinates are recomputed.

calcImplicitHydrogenCount()

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

Computes the implicit hydrogen count of the atom atom from its valence environment in the molecular graph molgraph.

Parameters

atom	The atom for which to calculate the hydrogen count.
molgraph	The molecular graph providing the structural context.

Returns

The computed implicit-hydrogen count.

calcImplicitHydrogenCounts()

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

Computes and stores implicit-hydrogen counts for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing implicit-hydrogen counts.

calcMDLParities()

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

Computes and stores MDL parities for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing MDL parities.

calcMDLParity()

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

Computes the MDL parity of the atom atom from its 2D layout and stereo flags in the molecular graph molgraph.

Parameters

atom	The atom for which to calculate the parity.
molgraph	The molecular graph providing the structural context.

Returns

The computed MDL parity (see namespace Chem.MDLParity).

calcMorganNumbering()

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

Computes and stores Morgan numbers for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing Morgan numbers.

calcStereoDescriptor() [1/2]

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

Computes the stereo descriptor for the atom atom based on the geometry of the molecular graph molgraph.

Parameters

atom	The atom for which to calculate the stereo descriptor.
molgraph	The molecular graph providing the structural context.
dim	The dimensionality of the atomic coordinates to use (2 or 3).

Returns

The computed stereo descriptor.

calcStereoDescriptor() [2/2]

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

Computes the stereo descriptor for the bond bond based on the geometry of the molecular graph molgraph.

Parameters

bond	The bond to inspect.
molgraph	The molecular graph providing the structural context.
dim	The dimensionality of the atomic coordinates to use (2 or 3).

Returns

The computed stereo descriptor.

calcStereoDescriptorFromMDLParity()

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

Derives the stereo descriptor of the atom atom from its MDL parity in the molecular graph molgraph.

Parameters

atom	The atom for which to calculate the stereo descriptor.
molgraph	The molecular graph providing the structural context.

Returns

The derived stereo descriptor.

calcTopologicalDistanceMatrix() [1/2]

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

Computes and (optionally) stores the topological-distance matrix of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing topological-distance matrix.

Returns

The computed (or pre-existing) matrix.

calcTopologicalDistanceMatrix() [2/2]

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

Computes the topological-distance matrix of the molecular graph molgraph into the supplied mtx.

Parameters

molgraph	The molecular graph to inspect.
mtx	The output dense matrix receiving the topological distances.

canonicalize() [1/2]

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

Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to the canonical-numbering attached to its atoms.

Parameters

molgraph	The molecular graph to canonicalize.
atoms	True to sort atoms.
atom_nbrs	True to sort each atom's neighbor list.
bonds	True to sort bonds.
bond_atoms	True to reorder the start/end atoms of each bond.

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
	)

Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to a user-supplied comparator.

Parameters

molgraph	The molecular graph to canonicalize.
func	The atom comparator that defines the canonical ordering.
atoms	True to sort atoms.
atom_nbrs	True to sort each atom's neighbor list.
bonds	True to sort bonds.
bond_atoms	True to reorder the start/end atoms of each bond according to the comparator.

connectAtoms() [1/2]

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

Adds bonds between atoms of the molecule mol whose 3D distance (obtained via coords_func) falls within the covalent-radii sum plus dist_tol.

Parameters

mol	The molecule whose atoms are to be connected.
coords_func	The function used to retrieve the 3D coordinates of an atom.
dist_tol	The tolerance added to the sum of the two atoms' covalent radii.
atom_idx_offs	Bonds are only added when at least one of the two atom indices is greater than or equal to atom_idx_offs.

connectAtoms() [2/2]

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

Adds bonds between atoms of the molecule mol whose 3D distance falls within the covalent-radii sum plus dist_tol.

Parameters

mol	The molecule whose atoms are to be connected.
dist_tol	The tolerance added to the sum of the two atoms' covalent radii.
atom_idx_offs	Bonds are only added when at least one of the two atom indices is greater than or equal to atom_idx_offs (useful to extend an existing bonding network without re-evaluating already-connected atoms).

containsFragmentWithBond()

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

Tells whether any fragment in frag_list contains the bond bond.

Parameters

frag_list	The list of fragments to search.
bond	The queried bond.

Returns

True if at least one fragment contains bond, and False otherwise.

containsFragmentWithMinSize()

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

Tells whether frag_list contains at least one fragment with at least min_size atoms.

Parameters

frag_list	The list of fragments to search.
min_size	The minimum required atom count.

Returns

True if such a fragment exists, and False otherwise.

containsMolecularGraph()

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

Tells whether the molecular graph molgraph contains the atoms and/or bonds of sub_molgraph.

Parameters

molgraph	The host molecular graph.
sub_molgraph	The candidate sub-graph.
atoms	If True, every atom of sub_molgraph must be a member of the molecular graph molgraph.
bonds	If True, every bond of sub_molgraph must be a member of the molecular graph molgraph.

Returns

True if the requested containment relations all hold, and False otherwise.

copyAtomsIf() [1/2]

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

Copies every atom of cntnr that satisfies pred into the molecule mol.

Parameters

cntnr	The source atom container.
mol	The target molecule.
pred	The predicate evaluated for each atom; only atoms for which it returns True are copied.
append	If True, atoms are appended to mol. Otherwise, mol is cleared first.

copyAtomsIf() [2/2]

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

Copies every atom of cntnr that satisfies pred into the fragment frag.

Parameters

cntnr	The source atom container.
frag	The target fragment.
pred	The predicate evaluated for each atom; only atoms for which it returns True are copied.
append	If True, atoms are appended to frag. Otherwise, frag is cleared first.

copyAtomsIfNot() [1/2]

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

Copies every atom of cntnr that does not satisfy pred into the molecule mol.

Parameters

cntnr	The source atom container.
mol	The target molecule.
pred	The predicate evaluated for each atom; only atoms for which it returns False are copied.
append	If True, atoms are appended to mol. Otherwise, mol is cleared first.

copyAtomsIfNot() [2/2]

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

Copies every atom of cntnr that does not satisfy pred into the fragment frag.

Parameters

cntnr	The source atom container.
frag	The target fragment.
pred	The predicate evaluated for each atom; only atoms for which it returns False are copied.
append	If True, atoms are appended to frag. Otherwise, frag is cleared first.

createAtomTypeMask()

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

Sets bits in mask corresponding to atoms of cntnr whose atom type matches type.

Parameters

cntnr	The atom container.
mask	The output bit mask (bit i is set if atom i of cntnr has the requested type).
type	The query atom type (Chem.AtomType value, possibly a generic class such as Chem.AtomType.HET).
reset	If True, mask is reset before processing. Otherwise, existing bits are preserved.
strict	If True, only exact type matches are accepted. If False, generic-class matches also set the bit.

Returns

The number of atoms whose bit was set.

editSubstructures() [1/2]

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

Builds the molecule result_mol from the molecular graph molgraph by replacing all substructures matching the SMARTS patterns in search_ptns with result_ptn.

Parameters

molgraph	The source molecular graph.
result_mol	The molecule receiving the edited result.
search_ptns	A whitespace-separated list of SMARTS patterns matching the substructures to replace.
result_ptn	The SMARTS replacement pattern.
exclude_ptns	A whitespace-separated list of SMARTS patterns matching substructures that shall be retained even if they also match search_ptns.

Returns

The number of applied substructure replacements.

Since

1.3

editSubstructures() [2/2]

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

Edits the molecule mol by replacing all substructures matching the SMARTS search patterns in search_ptns with the SMARTS replacement pattern result_ptn, optionally skipping matches that also match exclude_ptns.

Parameters

mol	The molecule to edit in place.
search_ptns	A whitespace-separated list of SMARTS patterns matching the substructures to replace.
result_ptn	The SMARTS replacement pattern.
exclude_ptns	A whitespace-separated list of SMARTS patterns matching substructures that shall be retained even if they match search_ptns.

Returns

The number of replaced substructures.

Since

1.3

extendBoundingBox()

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

Extends the axis-aligned bounding box defined by min and max so that it contains the point coords.

Parameters

min	The lower-left corner of the bounding box (updated in place).
max	The upper-right corner of the bounding box (updated in place).
coords	The 3D point to include.
reset	If True, the bounding box is first reset to coords (degenerate point box) before extension.

extractReactionCenter()

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

Collects every atom and bond of the molecular graph molgraph that carries a reaction-center flag into the fragment rxn_center.

Parameters

molgraph	The molecular graph to inspect.
rxn_center	The output fragment receiving the reaction-center atoms and bonds.

extractSSSRSubset() [1/2]

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

Extracts the subset of the SSSR of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph.

Parameters

src_molgraph	The source molecular graph whose SSSR is to be projected.
tgt_molgraph	The target molecular graph providing the membership filter.

Returns

The extracted SSSR subset.

extractSSSRSubset() [2/2]

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

Extracts the SSSR subset of the molecular graph src_molgraph that fits within tgt_molgraph and (optionally) stores it on the latter.

Parameters

src_molgraph	The source molecular graph whose SSSR is to be projected.
tgt_molgraph	The target molecular graph that receives the projected SSSR.
overwrite	If True, replaces any existing SSSR on tgt_molgraph.

Returns

The extracted (or pre-existing) SSSR subset.

extractTopologicalDistanceSubMatrix() [1/2]

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

Extracts the topological-distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph and (optionally) stores it on the latter.

Parameters

src_molgraph	The source molecular graph providing the full matrix.
tgt_molgraph	The target molecular graph providing the atom subset and (optionally) receiving the sub-matrix.
overwrite	If True, replaces any existing matrix on tgt_molgraph.

Returns

The extracted (or pre-existing) sub-matrix.

extractTopologicalDistanceSubMatrix() [2/2]

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

Extracts the topological-distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph into the supplied mtx.

Parameters

src_molgraph	The source molecular graph providing the full matrix.
tgt_molgraph	The target molecular graph providing the atom subset.
mtx	The output dense matrix receiving the sub-matrix entries.

generateAdjacencyMatrix()

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

Builds the adjacency matrix of the molecular graph molgraph (entry (i,j) is the bond count between atoms i and j).

Parameters

molgraph	The molecular graph to inspect.
mtx	The output sparse matrix receiving the adjacency entries.

generateBondAtomTypeMatrix()

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

Builds a matrix combining bond order and atom type information of the endpoints of every bond in molgraph.

Parameters

molgraph	The molecular graph to inspect.
mtx	The output sparse matrix receiving the combined entries.

generateBondElectronMatrix()

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

Builds the bond-electron-count matrix of the molecular graph molgraph (entry (i,j) is the number of bonding electrons between atoms i and j).

Parameters

molgraph	The molecular graph to inspect.
mtx	The output sparse matrix receiving the bond-electron counts.

generateBondMatrix()

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

Builds the bond-order matrix of the molecular graph molgraph (entry (i,j) is the order of the bond between atoms i and j).

Parameters

molgraph	The molecular graph to inspect.
mtx	The output sparse matrix receiving the bond-order entries.

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
	)

Builds the atom/bond incidence matrix of the molecular graph molgraph (entry (i,j) is 1 if atom i is an endpoint of bond j).

Parameters

molgraph	The molecular graph to inspect.
mtx	The output sparse matrix receiving the incidence entries.

generateMatchExpression() [1/6]

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

Builds an atom-level match expression from the match-constraint list attached to the atom atom.

Parameters

atom	The atom for which to generate the expression.
molgraph	The molecular graph providing the structural context.

Returns

The generated match expression.

generateMatchExpression() [2/6]

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

Builds a bond-level match expression from the match-constraint list attached to the bond bond.

Parameters

bond	The bond to inspect.
molgraph	The molecular graph providing the structural context.

Returns

The generated match expression.

generateMatchExpression() [3/6]

MolecularGraphMatchExpression CDPL.Chem.generateMatchExpression

(

MolecularGraph

molgraph

)

Builds a top-level match expression from the match-constraint list attached to molgraph.

Parameters

molgraph

The molecular graph to inspect.

Returns

The generated match expression.

generateMatchExpression() [4/6]

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

Builds and (optionally) stores the top-level match expression of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing match expression. Otherwise, the existing one (if any) is returned unchanged.

Returns

The generated (or pre-existing) match expression.

generateMatchExpression() [5/6]

ReactionMatchExpression CDPL.Chem.generateMatchExpression

(

Reaction

rxn

)

Builds a reaction-level match expression from the constraints currently attached to the reaction rxn.

Parameters

rxn	The reaction to inspect.

Returns

The generated match expression.

generateMatchExpression() [6/6]

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

Builds and (optionally) stores the reaction-level match expression of the reaction rxn.

Parameters

rxn	The reaction to inspect/modify.
overwrite	If True, the generated expression replaces any existing Chem.ReactionProperty.MATCH_EXPRESSION. If False, the existing one (if any) is returned unchanged.

Returns

The generated (or pre-existing) match expression.

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
	)

Generates and stores textual representations of the match expressions of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing match-expression strings.

generateMatchExpressions() [1/2]

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

Generates and stores match expressions for every atom, bond and the molecular graph itself.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing match expressions. If False, leaves items that already carry a match expression unchanged.

generateMatchExpressions() [2/2]

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

Generates and stores match expressions for the atoms, bonds, components, and the reaction rxn itself.

Parameters

rxn	The reaction to modify.
overwrite	If True, replaces any existing match expressions. If False, leaves items that already carry a match expression unchanged.

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
	)

Prepares the molecular graph molgraph for use as a substructure search query (precomputes match expressions and required cached properties).

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, recomputes derived data. If False, leaves up-to-date data unchanged.

initSubstructureSearchQuery() [2/2]

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

Prepares the reaction rxn for use as a substructure search query (e.g.

by pre-computing match expressions and required cached properties).

Parameters

rxn	The reaction to modify.
overwrite	If True, recomputes derived data. If False, leaves up-to-date data unchanged.

initSubstructureSearchTarget() [1/2]

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

Prepares the molecular graph molgraph for use as a substructure search target (precomputes required cached properties).

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, recomputes derived data. If False, leaves up-to-date data unchanged.

initSubstructureSearchTarget() [2/2]

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

Prepares the reaction rxn for use as a substructure search target (e.g.

by pre-computing required cached properties).

Parameters

rxn	The reaction to modify.
overwrite	If True, recomputes derived data. If False, leaves up-to-date data unchanged.

insideBoundingBox() [1/3]

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

Tells whether every atom of cntnr lies inside the axis-aligned bounding box defined by min and max.

Parameters

cntnr	The atom container.
min	The lower-left corner of the bounding box.
max	The upper-right corner of the bounding box.
coords_func	The function returning the 3D coordinates of an atom.

Returns

True if all atoms are inside the box, and False otherwise.

insideBoundingBox() [2/3]

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

Tells whether all entities of cntnr lie within the axis-aligned box defined by min and max.

Parameters

cntnr	The entity 3D container.
min	The per-axis minimum coordinates of the box.
max	The per-axis maximum coordinates of the box.

Returns

True if every entity coordinate is inside the box, and False otherwise.

insideBoundingBox() [3/3]

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

Tells whether the point coords lies inside the axis-aligned bounding box defined by min and max.

Parameters

min	The lower-left corner of the bounding box.
max	The upper-right corner of the bounding box.
coords	The 3D point to test.

Returns

True if the point is inside (componentwise <= max and >= min), and False otherwise.

intersectsBoundingBox() [1/2]

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

Tells whether at least one atom of cntnr lies inside the axis-aligned bounding box defined by min and max.

Parameters

cntnr	The atom container.
min	The lower-left corner of the bounding box.
max	The upper-right corner of the bounding box.
coords_func	The function returning the 3D coordinates of an atom.

Returns

True if at least one atom is inside the box, and False otherwise.

intersectsBoundingBox() [2/2]

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

Tells whether at least one entity of cntnr lies within the axis-aligned box defined by min and max.

Parameters

cntnr	The entity 3D container.
min	The per-axis minimum coordinates of the box.
max	The per-axis maximum coordinates of the box.

Returns

True if any entity coordinate is inside the box, and False otherwise.

isAromatic()

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

Tells whether ring fulfills the Hückel (4n+2)π-electron criterion within molgraph.

Parameters

ring	The candidate aromatic ring.
molgraph	The parent molecular graph.
arom_bond_mask	A bond bit mask flagging bonds already known to be aromatic.

Returns

True if ring satisfies the Hückel rule, and False otherwise.

isInFragmentOfSize() [1/2]

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

Tells whether the atom atom is a member of any fragment in frag_list whose size matches size.

Parameters

atom	The atom to query.
frag_list	The list of fragments to search.
size	The required fragment size (in number of atoms).

Returns

True if at least one matching fragment contains atom, and False otherwise.

isInFragmentOfSize() [2/2]

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

Tells whether the bond bond is a member of any fragment in frag_list whose size matches size.

Parameters

bond	The bond to query.
frag_list	The list of fragments to search.
size	The required fragment size (in number of atoms).

Returns

True if at least one matching fragment contains the bond bond, and False otherwise.

isNotAromatic()

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

Tells whether ring is guaranteed not to be aromatic (based on quick geometric/topological criteria).

Parameters

ring	The ring to test.
molgraph	The parent molecular graph.

Returns

True if ring cannot be aromatic, and False if a more thorough test is required.

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
	)

Tells whether the atom atom qualifies as a stereo center in the context of the molecular graph molgraph.

Parameters

atom	The atom to evaluate.
molgraph	The molecular graph providing the structural context.
check_asym	True to enforce non-equivalent ligand environments.
check_inv_n	True to reject inversion-prone nitrogen centers (umbrella inversion).
check_quart_n	True to accept positively charged quaternary nitrogen centers.
check_plan_n	True to reject planar nitrogen centers.
check_amide_n	True to reject amide-nitrogen centers.
check_res_ctrs	True to reject centers participating in resonance.

Returns

True if the atom qualifies as a stereo center under the given conditions, and False otherwise.

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
	)

Tells whether the bond bond qualifies as a stereo center in the context of the molecular graph molgraph.

Parameters

bond	The bond to inspect.
molgraph	The molecular graph providing the structural context.
check_asym	True to enforce non-equivalent ligand environments.
check_term_n	True to reject bonds to terminal nitrogen atoms.
check_order	True to require that the bond order matches a stereogenic pattern.
min_ring_size	If the bond bond is a ring bond, the containing ring must have at least this size to qualify.

Returns

True if the bond qualifies as a stereo center under the given conditions, and False otherwise.

kekulizeBonds()

None CDPL.Chem.kekulizeBonds

(

MolecularGraph

molgraph

)

Assigns Kekulé bond orders to the aromatic bonds of the molecular graph molgraph.

Parameters

molgraph

The molecular graph to modify.

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

MolProp.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

MolProp.isOrdinaryHydrogen

markReachableAtoms()

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

Sets bits in atom_mask for every atom of the molecular graph molgraph that is reachable from the atom atom through the bonds of molgraph.

Parameters

atom	The seed atom.
molgraph	The molecular graph providing the bonding context.
atom_mask	The output bit mask.
reset	If True, atom_mask is cleared first. Otherwise, existing bits are preserved.

parseSMARTS() [1/2]

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

Parses the SMARTS string smarts into a freshly allocated query Chem.Molecule.

Parameters

smarts	The SMARTS string to parse.
init_qry	If True, query-specific perception (e.g. ring-membership, aromaticity) is run on the parsed molecule.

Returns

A smart reference to the parsed molecule, or an empty smart reference if parsing failed.

parseSMARTS() [2/2]

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

Parses the SMARTS string smarts into the supplied molecule mol.

Parameters

smarts	The SMARTS string to parse.
mol	The molecule to populate (cleared before parsing).
init_qry	If True, query-specific perception is run on the parsed molecule.

Returns

True if parsing succeeded, and False otherwise.

parseSMILES() [1/2]

Molecule CDPL.Chem.parseSMILES

(

str

smiles

)

Parses the SMILES string smiles into a freshly allocated Chem.Molecule.

Parameters

smiles

The SMILES string to parse.

Returns

A smart reference to the parsed molecule, or an empty smart reference if parsing failed.

parseSMILES() [2/2]

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

Parses the SMILES string smiles into the supplied molecule mol.

Parameters

smiles	The SMILES string to parse.
mol	The molecule to populate (cleared before parsing).

Returns

True if parsing succeeded, and False otherwise.

perceiveAromaticSubstructure() [1/2]

Fragment CDPL.Chem.perceiveAromaticSubstructure

(

MolecularGraph

molgraph

)

Perceives the aromatic substructure of the molecular graph molgraph.

Parameters

molgraph

The molecular graph to inspect.

Returns

The perceived aromatic substructure.

perceiveAromaticSubstructure() [2/2]

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

Perceives and (optionally) stores the aromatic substructure of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing aromatic substructure.

Returns

The perceived (or pre-existing) aromatic substructure.

perceiveAtomMapping() [1/2]

AtomMapping CDPL.Chem.perceiveAtomMapping

(

Reaction

rxn

)

Derives the reactant-to-product atom mapping from the atom mapping IDs of the reaction rxn.

Parameters

rxn	The reaction to inspect.

Returns

The perceived atom mapping.

perceiveAtomMapping() [2/2]

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

Derives and (optionally) stores the reactant-to-product atom mapping of the reaction rxn.

Parameters

rxn	The reaction to inspect/modify.
overwrite	If True, the perceived mapping replaces any existing Chem.ReactionProperty.ATOM_MAPPING property. If False, the existing one (if any) is returned unchanged.

Returns

The perceived (or pre-existing) atom mapping.

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
	)

Flags the atoms of the molecular graph molgraph that qualify as stereo centers under the supplied criteria.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing stereo-center flags.
check_asym	True to enforce non-equivalent ligand environments.
check_inv_n	True to reject inversion-prone nitrogen centers.
check_quart_n	True to accept positively charged quaternary nitrogen centers.
check_plan_n	True to reject planar nitrogen centers.
check_amide_n	True to reject amide-nitrogen centers.
check_res_ctrs	True to reject centers participating in resonance.

perceiveBondOrders()

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

Perceives bond orders for the bonds of the molecular graph molgraph from atom geometry and ligand environment.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing bond orders.

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
	)

Flags the bonds of the molecular graph molgraph that qualify as stereo centers under the supplied criteria.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing stereo-center flags.
check_asym	True to enforce non-equivalent ligand environments.
check_term_n	True to reject bonds to terminal nitrogen atoms.
check_order	True to require that the bond order matches a stereogenic pattern.
min_ring_size	The minimum ring size required for ring bonds to qualify.

perceiveComponentGroups() [1/4]

FragmentList CDPL.Chem.perceiveComponentGroups

(

MolecularGraph

molgraph

)

Perceives the component groups of the molecular graph molgraph (from atom-level Chem.AtomProperty.COMPONENT_GROUP_ID values).

Parameters

molgraph

The molecular graph to inspect.

Returns

The perceived component-group fragment list.

perceiveComponentGroups() [2/4]

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

Perceives and (optionally) stores the component groups of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing component-group list. Otherwise, the existing one (if any) is returned unchanged.

Returns

The perceived (or pre-existing) component-group list.

perceiveComponentGroups() [3/4]

FragmentList CDPL.Chem.perceiveComponentGroups

(

Reaction

rxn

)

Perceives the component groups of the reaction rxn.

Parameters

rxn	The reaction to inspect.

Returns

The perceived component-group fragment list.

perceiveComponentGroups() [4/4]

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

Perceives and (optionally) stores the component groups of the reaction rxn.

Parameters

rxn	The reaction to inspect/modify.
overwrite	If True, the perceived list replaces any existing Chem.ReactionProperty.COMPONENT_GROUPS. If False, the existing one (if any) is returned unchanged.

Returns

The perceived (or pre-existing) component-group fragment list.

perceiveComponents() [1/2]

FragmentList CDPL.Chem.perceiveComponents

(

MolecularGraph

molgraph

)

Perceives the connected components of the molecular graph molgraph.

Parameters

molgraph

The molecular graph to inspect.

Returns

The perceived connected-component list.

perceiveComponents() [2/2]

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

Perceives and (optionally) stores the connected components of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing component list. Otherwise, the existing one (if any) is returned unchanged.

Returns

The perceived (or pre-existing) component list.

perceiveCyclicSubstructure() [1/2]

Fragment CDPL.Chem.perceiveCyclicSubstructure

(

MolecularGraph

molgraph

)

Perceives the cyclic substructure (union of all rings) of the molecular graph molgraph.

Parameters

molgraph

The molecular graph to inspect.

Returns

The perceived cyclic substructure.

perceiveCyclicSubstructure() [2/2]

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

Perceives and (optionally) stores the cyclic substructure of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing cyclic substructure. Otherwise, the existing one (if any) is returned unchanged.

Returns

The perceived (or pre-existing) cyclic substructure.

perceiveHybridizationState()

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

Derives the hybridization state of the atom atom from its valence environment in the molecular graph molgraph.

Parameters

atom	The atom for which to perceive the hybridzation state.
molgraph	The molecular graph providing the structural context.

Returns

The perceived hybridization state (see namespace Chem.HybridizationState).

perceiveHybridizationStates()

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

Computes and stores hybridization states for the atoms of the molecular graph molgraph from their valence environment.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing hybridization states.

perceivePiElectronSystems() [1/2]

ElectronSystemList CDPL.Chem.perceivePiElectronSystems

(

MolecularGraph

molgraph

)

Perceives the pi-electron systems of the molecular graph molgraph.

Parameters

molgraph

The molecular graph to inspect.

Returns

The perceived pi-electron-system list.

perceivePiElectronSystems() [2/2]

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

Perceives and (optionally) stores the pi-electron systems of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing pi-electron-system list.

Returns

The perceived (or pre-existing) pi-electron-system list.

perceiveRings() [1/2]

FragmentList CDPL.Chem.perceiveRings

(

MolecularGraph

molgraph

)

Perceives the full set of rings of the molecular graph molgraph.

Parameters

molgraph

The molecular graph to inspect.

Returns

The perceived ring set.

perceiveRings() [2/2]

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

Perceives and (optionally) stores the full set of rings of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing ring set. Otherwise, the existing one (if any) is returned unchanged.

Returns

The perceived (or pre-existing) ring set.

perceiveSSSR() [1/2]

FragmentList CDPL.Chem.perceiveSSSR

(

MolecularGraph

molgraph

)

Perceives the Smallest Set of Smallest Rings of the molecular graph molgraph.

Parameters

molgraph

The molecular graph to inspect.

Returns

A shared reference to the perceived SSSR.

perceiveSSSR() [2/2]

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

Perceives and (optionally) stores the Smallest Set of Smallest Rings of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	If True, replaces any existing SSSR. Otherwise, the existing one (if any) is returned unchanged.

Returns

The perceived (or pre-existing) SSSR.

perceiveSybylAtomTypes()

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

Perceives Sybyl atom types for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing Sybyl atom types.

perceiveSybylType() [1/2]

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

Derives the Sybyl atom type of the atom atom from its valence environment in the molecular graph molgraph.

Parameters

atom	The atom for which to perceive the type.
molgraph	The molecular graph providing the structural context.

Returns

The perceived Sybyl MOL2 atom type (see namespace Chem.SybylAtomType).

perceiveSybylType() [2/2]

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

Derives the Sybyl MOL2 bond type of the bond bond from its bond order, aromaticity and ligand environment in the molecular graph molgraph.

Parameters

bond	The bond to inspect.
molgraph	The molecular graph providing the structural context.

Returns

The perceived Sybyl MOL2 bond type (see namespace Chem.SybylBondType).

perceiveSymmetryClasses()

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

Computes and stores topological-symmetry classes for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to modify.
overwrite	If True, replaces any existing symmetry-class IDs.
atom_flags	A bitmask of Chem.AtomPropertyFlag flags controlling which atomic properties enter the perception.
bond_flags	A bitmask of Chem.BondPropertyFlag flags controlling which bond properties enter the perception.
inc_impl_h	If True, implicit hydrogens are treated as if they were explicit. Otherwise, they are ignored.

removeAtomsIf() [1/2]

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

Removes all atoms of the fragment frag for which the predicate pred returns True.

Parameters

frag	The fragment to filter in place.
pred	The atom predicate to evaluate.

removeAtomsIf() [2/2]

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

Removes all atoms of the molecule mol for which the predicate pred returns True.

Parameters

mol	The molecule to filter in place.
pred	The atom predicate to evaluate.

removeAtomsIfNot() [1/2]

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

Removes all atoms of the fragment frag for which the predicate pred returns False.

Parameters

frag	The fragment to filter in place.
pred	The atom predicate to evaluate.

removeAtomsIfNot() [2/2]

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

Removes all atoms of the molecule mol for which the predicate pred returns False.

Parameters

mol	The molecule to filter in place.
pred	The atom predicate to evaluate.

splitIntoFragments()

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

Splits the molecular graph molgraph into connected fragments by removing the bonds flagged in split_bond_mask.

Parameters

molgraph	The molecular graph to split.
frag_list	The output fragment list receiving the resulting fragments.
split_bond_mask	Bit mask selecting the bonds to be virtually removed before fragmentation (bit i corresponds to the bond at index i in molgraph).
append	If True, fragments are appended to frag_list. Otherwise, it is cleared first.

sybylToAtomType()

int CDPL.Chem.sybylToAtomType

(

int

sybyl_type

)

Translates a Sybyl atom type identifier to the corresponding generic Chem.AtomType value.

Parameters

sybyl_type

The Sybyl atom type identifier (Chem.SybylAtomType value).

Returns

The corresponding Chem.AtomType value.

transform2DCoordinates()

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

Transforms the 2D coordinates of all atoms in cntnr by the affine 3×3 matrix mtx.

Parameters

cntnr	The atom container.
mtx	The 2D affine transformation matrix.

transform3DCoordinates()

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

Transforms the 3D coordinates of the entities of cntnr by the affine matrix mtx.

Parameters

cntnr	The entity 3D container whose coordinates are to be transformed.
mtx	The \( 4 \times 4 \) affine transformation matrix.

transformConformation()

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

Transforms the conformation at index conf_idx by the homogeneous 4×4 matrix mtx.

Parameters

cntnr	The atom container.
conf_idx	The zero-based conformation index.
mtx	The homogeneous 4×4 transformation matrix.

transformConformations()

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

Transforms every stored conformation of the atoms in cntnr by the homogeneous 4×4 matrix mtx.

Parameters

cntnr	The atom container.
mtx	The homogeneous 4×4 transformation matrix.

translateFragment()

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

Translates the atoms/bonds of src_frag to the corresponding atoms/bonds of tgt_molgraph and stores them in tgt_frag.

Parameters

src_molgraph	The source molecular graph providing the original atoms/bonds.
src_frag	The fragment defining the atom/bond subset to translate (a fragment of the molecular graph src_molgraph).
tgt_molgraph	The target molecular graph providing the translated atoms/bonds.
tgt_frag	The output fragment receiving the translated atoms/bonds.
append	If True, atoms/bonds are appended to tgt_frag. Otherwise, it is cleared first.

translateFragments()

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

Translates every fragment in src_frag_list to the corresponding fragments on tgt_molgraph.

Parameters

src_molgraph	The source molecular graph providing the original atoms/bonds.
src_frag_list	The fragments to translate (fragments of the molecular graph src_molgraph).
tgt_molgraph	The target molecular graph providing the translated atoms/bonds.
tgt_frag_list	The output fragment list receiving the translated fragments.
append	If True, fragments are appended to tgt_frag_list. Otherwise, it is cleared first.

setBondMemberSwapStereoFixParameter()

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

Sets the value of the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr to fix.

Parameters

cntnr	The control-parameter container.
fix	The new parameter value.

hasBondMemberSwapStereoFixParameter()

bool CDPL.Chem.hasBondMemberSwapStereoFixParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getBondMemberSwapStereoFixParameter()

bool CDPL.Chem.getBondMemberSwapStereoFixParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearBondMemberSwapStereoFixParameter()

None CDPL.Chem.clearBondMemberSwapStereoFixParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setCDFOutputSinglePrecisionFloatsParameter()

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

Sets the value of the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr to single_prec.

Parameters

cntnr	The control-parameter container.
single_prec	The new parameter value.

Since

1.2

hasCDFOutputSinglePrecisionFloatsParameter()

bool CDPL.Chem.hasCDFOutputSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCDFOutputSinglePrecisionFloatsParameter()

bool CDPL.Chem.getCDFOutputSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCDFOutputSinglePrecisionFloatsParameter()

None CDPL.Chem.clearCDFOutputSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLEnableAromaticBondTypesParameter()

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

Sets the value of the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable.

Parameters

cntnr	The control-parameter container.
enable	The new parameter value.

Since

1.3

hasCMLEnableAromaticBondTypesParameter()

bool CDPL.Chem.hasCMLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.3

getCMLEnableAromaticBondTypesParameter()

bool CDPL.Chem.getCMLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.3

clearCMLEnableAromaticBondTypesParameter()

None CDPL.Chem.clearCMLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.3

setCMLOutputAtomParityParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputAtomParityParameter()

bool CDPL.Chem.hasCMLOutputAtomParityParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputAtomParityParameter()

bool CDPL.Chem.getCMLOutputAtomParityParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputAtomParityParameter()

None CDPL.Chem.clearCMLOutputAtomParityParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputCompactAtomDataParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputCompactAtomDataParameter()

bool CDPL.Chem.hasCMLOutputCompactAtomDataParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputCompactAtomDataParameter()

bool CDPL.Chem.getCMLOutputCompactAtomDataParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputCompactAtomDataParameter()

None CDPL.Chem.clearCMLOutputCompactAtomDataParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputCompactBondDataParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputCompactBondDataParameter()

bool CDPL.Chem.hasCMLOutputCompactBondDataParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputCompactBondDataParameter()

bool CDPL.Chem.getCMLOutputCompactBondDataParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputCompactBondDataParameter()

None CDPL.Chem.clearCMLOutputCompactBondDataParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputDoubleBondStereoParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputDoubleBondStereoParameter()

bool CDPL.Chem.hasCMLOutputDoubleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputDoubleBondStereoParameter()

bool CDPL.Chem.getCMLOutputDoubleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputDoubleBondStereoParameter()

None CDPL.Chem.clearCMLOutputDoubleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputElementPackageParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr to ns.

Parameters

cntnr	The control-parameter container.
ns	The new XML-namespace string.

Since

1.2

hasCMLOutputElementPackageParameter()

bool CDPL.Chem.hasCMLOutputElementPackageParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputElementPackageParameter()

str CDPL.Chem.getCMLOutputElementPackageParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored XML-namespace string.

Since

1.2

clearCMLOutputElementPackageParameter()

None CDPL.Chem.clearCMLOutputElementPackageParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputIsotopeParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputIsotopeParameter()

bool CDPL.Chem.hasCMLOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputIsotopeParameter()

bool CDPL.Chem.getCMLOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputIsotopeParameter()

None CDPL.Chem.clearCMLOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputMoleculeNameParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputMoleculeNameParameter()

bool CDPL.Chem.hasCMLOutputMoleculeNameParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputMoleculeNameParameter()

bool CDPL.Chem.getCMLOutputMoleculeNameParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputMoleculeNameParameter()

None CDPL.Chem.clearCMLOutputMoleculeNameParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputSingleBondStereoParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputSingleBondStereoParameter()

bool CDPL.Chem.hasCMLOutputSingleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputSingleBondStereoParameter()

bool CDPL.Chem.getCMLOutputSingleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputSingleBondStereoParameter()

None CDPL.Chem.clearCMLOutputSingleBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputSpinMultiplicityParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputSpinMultiplicityParameter()

bool CDPL.Chem.hasCMLOutputSpinMultiplicityParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputSpinMultiplicityParameter()

bool CDPL.Chem.getCMLOutputSpinMultiplicityParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputSpinMultiplicityParameter()

None CDPL.Chem.clearCMLOutputSpinMultiplicityParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputStructureDataParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputStructureDataParameter()

bool CDPL.Chem.hasCMLOutputStructureDataParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputStructureDataParameter()

bool CDPL.Chem.getCMLOutputStructureDataParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputStructureDataParameter()

None CDPL.Chem.clearCMLOutputStructureDataParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCMLOutputXMLDeclarationParameter()

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

Sets the value of the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputXMLDeclarationParameter()

bool CDPL.Chem.hasCMLOutputXMLDeclarationParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCMLOutputXMLDeclarationParameter()

bool CDPL.Chem.getCMLOutputXMLDeclarationParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCMLOutputXMLDeclarationParameter()

None CDPL.Chem.clearCMLOutputXMLDeclarationParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCheckLineLengthParameter()

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

Sets the value of the Chem.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr to check.

Parameters

cntnr	The control-parameter container.
check	The new parameter value.

hasCheckLineLengthParameter()

bool CDPL.Chem.hasCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getCheckLineLengthParameter()

bool CDPL.Chem.getCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CHECK_LINE_LENGTH parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearCheckLineLengthParameter()

None CDPL.Chem.clearCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CHECK_LINE_LENGTH parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setConfIndexNameSuffixPatternParameter()

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

Sets the value of the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr to pattern.

Parameters

cntnr	The control-parameter container.
pattern	The new suffix pattern string.

hasConfIndexNameSuffixPatternParameter()

bool CDPL.Chem.hasConfIndexNameSuffixPatternParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getConfIndexNameSuffixPatternParameter()

str CDPL.Chem.getConfIndexNameSuffixPatternParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored suffix pattern string.

clearConfIndexNameSuffixPatternParameter()

None CDPL.Chem.clearConfIndexNameSuffixPatternParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setCoordinatesDimensionParameter()

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

Sets the value of the Chem.ControlParameter.COORDINATES_DIMENSION parameter of cntnr to dim.

Parameters

cntnr	The control-parameter container.
dim	The new coordinates dimensionality.

hasCoordinatesDimensionParameter()

bool CDPL.Chem.hasCoordinatesDimensionParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.COORDINATES_DIMENSION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getCoordinatesDimensionParameter()

int CDPL.Chem.getCoordinatesDimensionParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.COORDINATES_DIMENSION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored coordinates dimensionality.

clearCoordinatesDimensionParameter()

None CDPL.Chem.clearCoordinatesDimensionParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.COORDINATES_DIMENSION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setINCHIInputOptionsParameter()

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

Sets the value of the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter of cntnr to opts.

Parameters

cntnr	The control-parameter container.
opts	The new InChI input-options string.

hasINCHIInputOptionsParameter()

bool CDPL.Chem.hasINCHIInputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getINCHIInputOptionsParameter()

str CDPL.Chem.getINCHIInputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored InChI input-options string.

clearINCHIInputOptionsParameter()

None CDPL.Chem.clearINCHIInputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setINCHIOutputOptionsParameter()

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

Sets the value of the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter of cntnr to opts.

Parameters

cntnr	The control-parameter container.
opts	The new InChI output-options string.

hasINCHIOutputOptionsParameter()

bool CDPL.Chem.hasINCHIOutputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getINCHIOutputOptionsParameter()

str CDPL.Chem.getINCHIOutputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored InChI output-options string.

clearINCHIOutputOptionsParameter()

None CDPL.Chem.clearINCHIOutputOptionsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setJMESeparateComponentsParameter()

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

Sets the value of the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter of cntnr to separate.

Parameters

cntnr	The control-parameter container.
separate	The new parameter value.

hasJMESeparateComponentsParameter()

bool CDPL.Chem.hasJMESeparateComponentsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getJMESeparateComponentsParameter()

bool CDPL.Chem.getJMESeparateComponentsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearJMESeparateComponentsParameter()

None CDPL.Chem.clearJMESeparateComponentsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLCTABVersionParameter()

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

Sets the value of the Chem.ControlParameter.MDL_CTAB_VERSION parameter of cntnr to version.

Parameters

cntnr	The control-parameter container.
version	The new CTab version (see namespace Chem.MDLDataFormatVersion).

hasMDLCTABVersionParameter()

bool CDPL.Chem.hasMDLCTABVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_CTAB_VERSION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLCTABVersionParameter()

int CDPL.Chem.getMDLCTABVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_CTAB_VERSION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored CTab version (see namespace Chem.MDLDataFormatVersion).

clearMDLCTABVersionParameter()

None CDPL.Chem.clearMDLCTABVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_CTAB_VERSION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLConfEnergySDTagParameter()

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

Sets the value of the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter of cntnr to tag.

Parameters

cntnr	The control-parameter container.
tag	The new SD-tag string.

hasMDLConfEnergySDTagParameter()

bool CDPL.Chem.hasMDLConfEnergySDTagParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLConfEnergySDTagParameter()

str CDPL.Chem.getMDLConfEnergySDTagParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored SD-tag string.

clearMDLConfEnergySDTagParameter()

None CDPL.Chem.clearMDLConfEnergySDTagParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLEnableAromaticBondTypesParameter()

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

Sets the value of the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable.

Parameters

cntnr	The control-parameter container.
enable	The new parameter value.

Since

1.3

hasMDLEnableAromaticBondTypesParameter()

bool CDPL.Chem.hasMDLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.3

getMDLEnableAromaticBondTypesParameter()

bool CDPL.Chem.getMDLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.3

clearMDLEnableAromaticBondTypesParameter()

None CDPL.Chem.clearMDLEnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.3

setMDLIgnoreParityParameter()

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

Sets the value of the Chem.ControlParameter.MDL_IGNORE_PARITY parameter of cntnr to ignore.

Parameters

cntnr	The control-parameter container.
ignore	The new parameter value.

hasMDLIgnoreParityParameter()

bool CDPL.Chem.hasMDLIgnoreParityParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_IGNORE_PARITY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLIgnoreParityParameter()

bool CDPL.Chem.getMDLIgnoreParityParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_IGNORE_PARITY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMDLIgnoreParityParameter()

None CDPL.Chem.clearMDLIgnoreParityParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_IGNORE_PARITY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLOutputConfEnergyAsSDEntryParameter()

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

Sets the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

hasMDLOutputConfEnergyAsSDEntryParameter()

bool CDPL.Chem.hasMDLOutputConfEnergyAsSDEntryParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLOutputConfEnergyAsSDEntryParameter()

bool CDPL.Chem.getMDLOutputConfEnergyAsSDEntryParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMDLOutputConfEnergyAsSDEntryParameter()

None CDPL.Chem.clearMDLOutputConfEnergyAsSDEntryParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLOutputConfEnergyToEnergyFieldParameter()

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

Sets the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

hasMDLOutputConfEnergyToEnergyFieldParameter()

bool CDPL.Chem.hasMDLOutputConfEnergyToEnergyFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLOutputConfEnergyToEnergyFieldParameter()

bool CDPL.Chem.getMDLOutputConfEnergyToEnergyFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMDLOutputConfEnergyToEnergyFieldParameter()

None CDPL.Chem.clearMDLOutputConfEnergyToEnergyFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLRXNFileVersionParameter()

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

Sets the value of the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter of cntnr to version.

Parameters

cntnr	The control-parameter container.
version	The new RXN-file version (see namespace Chem.MDLDataFormatVersion).

hasMDLRXNFileVersionParameter()

bool CDPL.Chem.hasMDLRXNFileVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLRXNFileVersionParameter()

int CDPL.Chem.getMDLRXNFileVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored RXN-file version (see namespace Chem.MDLDataFormatVersion).

clearMDLRXNFileVersionParameter()

None CDPL.Chem.clearMDLRXNFileVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLTrimLinesParameter()

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

Sets the value of the Chem.ControlParameter.MDL_TRIM_LINES parameter of cntnr to trim.

Parameters

cntnr	The control-parameter container.
trim	The new parameter value.

hasMDLTrimLinesParameter()

bool CDPL.Chem.hasMDLTrimLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_TRIM_LINES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLTrimLinesParameter()

bool CDPL.Chem.getMDLTrimLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_TRIM_LINES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMDLTrimLinesParameter()

None CDPL.Chem.clearMDLTrimLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_TRIM_LINES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLTrimStringsParameter()

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

Sets the value of the Chem.ControlParameter.MDL_TRIM_STRINGS parameter of cntnr to trim.

Parameters

cntnr	The control-parameter container.
trim	The new parameter value.

hasMDLTrimStringsParameter()

bool CDPL.Chem.hasMDLTrimStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_TRIM_STRINGS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLTrimStringsParameter()

bool CDPL.Chem.getMDLTrimStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_TRIM_STRINGS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMDLTrimStringsParameter()

None CDPL.Chem.clearMDLTrimStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_TRIM_STRINGS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLTruncateLinesParameter()

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

Sets the value of the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter of cntnr to trunc.

Parameters

cntnr	The control-parameter container.
trunc	The new parameter value.

hasMDLTruncateLinesParameter()

bool CDPL.Chem.hasMDLTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLTruncateLinesParameter()

bool CDPL.Chem.getMDLTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMDLTruncateLinesParameter()

None CDPL.Chem.clearMDLTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLTruncateStringsParameter()

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

Sets the value of the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter of cntnr to trunc.

Parameters

cntnr	The control-parameter container.
trunc	The new parameter value.

hasMDLTruncateStringsParameter()

bool CDPL.Chem.hasMDLTruncateStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLTruncateStringsParameter()

bool CDPL.Chem.getMDLTruncateStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMDLTruncateStringsParameter()

None CDPL.Chem.clearMDLTruncateStringsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMDLUpdateTimestampParameter()

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

Sets the value of the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter of cntnr to update.

Parameters

cntnr	The control-parameter container.
update	The new parameter value.

hasMDLUpdateTimestampParameter()

bool CDPL.Chem.hasMDLUpdateTimestampParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMDLUpdateTimestampParameter()

bool CDPL.Chem.getMDLUpdateTimestampParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMDLUpdateTimestampParameter()

None CDPL.Chem.clearMDLUpdateTimestampParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMOL2CalcFormalChargesParameter()

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

Sets the value of the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter of cntnr to calc.

Parameters

cntnr	The control-parameter container.
calc	The new parameter value.

hasMOL2CalcFormalChargesParameter()

bool CDPL.Chem.hasMOL2CalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMOL2CalcFormalChargesParameter()

bool CDPL.Chem.getMOL2CalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMOL2CalcFormalChargesParameter()

None CDPL.Chem.clearMOL2CalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMOL2ChargeTypeParameter()

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

Sets the value of the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter of cntnr to type.

Parameters

cntnr	The control-parameter container.
type	The new Sybyl MOL2 charge type (see namespace Chem.MOL2ChargeType).

hasMOL2ChargeTypeParameter()

bool CDPL.Chem.hasMOL2ChargeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMOL2ChargeTypeParameter()

int CDPL.Chem.getMOL2ChargeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored Sybyl MOL2 charge type (see namespace Chem.MOL2ChargeType).

clearMOL2ChargeTypeParameter()

None CDPL.Chem.clearMOL2ChargeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMOL2EnableAromaticBondTypesParameter()

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

Sets the value of the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable.

Parameters

cntnr	The control-parameter container.
enable	The new parameter value.

hasMOL2EnableAromaticBondTypesParameter()

bool CDPL.Chem.hasMOL2EnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMOL2EnableAromaticBondTypesParameter()

bool CDPL.Chem.getMOL2EnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMOL2EnableAromaticBondTypesParameter()

None CDPL.Chem.clearMOL2EnableAromaticBondTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMOL2EnableExtendedAtomTypesParameter()

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

Sets the value of the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr to enable.

Parameters

cntnr	The control-parameter container.
enable	The new parameter value.

hasMOL2EnableExtendedAtomTypesParameter()

bool CDPL.Chem.hasMOL2EnableExtendedAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMOL2EnableExtendedAtomTypesParameter()

bool CDPL.Chem.getMOL2EnableExtendedAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMOL2EnableExtendedAtomTypesParameter()

None CDPL.Chem.clearMOL2EnableExtendedAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMOL2MoleculeTypeParameter()

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

Sets the value of the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter of cntnr to type.

Parameters

cntnr	The control-parameter container.
type	The new Sybyl MOL2 molecule type (see namespace Chem.MOL2MoleculeType).

hasMOL2MoleculeTypeParameter()

bool CDPL.Chem.hasMOL2MoleculeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMOL2MoleculeTypeParameter()

int CDPL.Chem.getMOL2MoleculeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored Sybyl MOL2 molecule type (see namespace Chem.MOL2MoleculeType).

clearMOL2MoleculeTypeParameter()

None CDPL.Chem.clearMOL2MoleculeTypeParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMOL2OutputFormalChargesParameter()

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

Sets the value of the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2.3

hasMOL2OutputFormalChargesParameter()

bool CDPL.Chem.hasMOL2OutputFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2.3

getMOL2OutputFormalChargesParameter()

bool CDPL.Chem.getMOL2OutputFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2.3

clearMOL2OutputFormalChargesParameter()

None CDPL.Chem.clearMOL2OutputFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2.3

setMOL2OutputSubstructuresParameter()

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

Sets the value of the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

hasMOL2OutputSubstructuresParameter()

bool CDPL.Chem.hasMOL2OutputSubstructuresParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMOL2OutputSubstructuresParameter()

bool CDPL.Chem.getMOL2OutputSubstructuresParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMOL2OutputSubstructuresParameter()

None CDPL.Chem.clearMOL2OutputSubstructuresParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMOL2ReadPartialAsFormalChargesParameter()

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

Sets the value of the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr to read.

Parameters

cntnr	The control-parameter container.
read	The new parameter value.

Since

1.2.3

hasMOL2ReadPartialAsFormalChargesParameter()

bool CDPL.Chem.hasMOL2ReadPartialAsFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2.3

getMOL2ReadPartialAsFormalChargesParameter()

bool CDPL.Chem.getMOL2ReadPartialAsFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2.3

clearMOL2ReadPartialAsFormalChargesParameter()

None CDPL.Chem.clearMOL2ReadPartialAsFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2.3

setMultiConfExportParameter()

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

Sets the value of the Chem.ControlParameter.MULTI_CONF_EXPORT parameter of cntnr to multi_conf.

Parameters

cntnr	The control-parameter container.
multi_conf	The new parameter value.

hasMultiConfExportParameter()

bool CDPL.Chem.hasMultiConfExportParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MULTI_CONF_EXPORT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMultiConfExportParameter()

bool CDPL.Chem.getMultiConfExportParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MULTI_CONF_EXPORT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMultiConfExportParameter()

None CDPL.Chem.clearMultiConfExportParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MULTI_CONF_EXPORT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMultiConfImportParameter()

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

Sets the value of the Chem.ControlParameter.MULTI_CONF_IMPORT parameter of cntnr to multi_conf.

Parameters

cntnr	The control-parameter container.
multi_conf	The new parameter value.

hasMultiConfImportParameter()

bool CDPL.Chem.hasMultiConfImportParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MULTI_CONF_IMPORT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMultiConfImportParameter()

bool CDPL.Chem.getMultiConfImportParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MULTI_CONF_IMPORT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearMultiConfImportParameter()

None CDPL.Chem.clearMultiConfImportParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MULTI_CONF_IMPORT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMultiConfInputProcessorParameter()

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

Sets the value of the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter of cntnr to proc.

Parameters

cntnr	The control-parameter container.
proc	The new Chem.MultiConfMoleculeInputProcessor implementation reference.

hasMultiConfInputProcessorParameter()

bool CDPL.Chem.hasMultiConfInputProcessorParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getMultiConfInputProcessorParameter()

MultiConfMoleculeInputProcessor CDPL.Chem.getMultiConfInputProcessorParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored Chem.MultiConfMoleculeInputProcessor implementation reference.

clearMultiConfInputProcessorParameter()

None CDPL.Chem.clearMultiConfInputProcessorParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setOrdinaryHydrogenDepleteParameter()

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

Sets the value of the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter of cntnr to deplete.

Parameters

cntnr	The control-parameter container.
deplete	The new parameter value.

hasOrdinaryHydrogenDepleteParameter()

bool CDPL.Chem.hasOrdinaryHydrogenDepleteParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getOrdinaryHydrogenDepleteParameter()

bool CDPL.Chem.getOrdinaryHydrogenDepleteParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearOrdinaryHydrogenDepleteParameter()

None CDPL.Chem.clearOrdinaryHydrogenDepleteParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setOutputConfEnergyAsCommentParameter()

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

Sets the value of the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

hasOutputConfEnergyAsCommentParameter()

bool CDPL.Chem.hasOutputConfEnergyAsCommentParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getOutputConfEnergyAsCommentParameter()

bool CDPL.Chem.getOutputConfEnergyAsCommentParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearOutputConfEnergyAsCommentParameter()

None CDPL.Chem.clearOutputConfEnergyAsCommentParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setRecordSeparatorParameter()

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

Sets the value of the Chem.ControlParameter.RECORD_SEPARATOR parameter of cntnr to sep.

Parameters

cntnr	The control-parameter container.
sep	The new record separator string.

hasRecordSeparatorParameter()

bool CDPL.Chem.hasRecordSeparatorParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.RECORD_SEPARATOR parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getRecordSeparatorParameter()

str CDPL.Chem.getRecordSeparatorParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.RECORD_SEPARATOR parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored record separator string.

clearRecordSeparatorParameter()

None CDPL.Chem.clearRecordSeparatorParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.RECORD_SEPARATOR parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setSMILESMinStereoBondRingSizeParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr to min_size.

Parameters

cntnr	The control-parameter container.
min_size	The new minimum ring size.

hasSMILESMinStereoBondRingSizeParameter()

bool CDPL.Chem.hasSMILESMinStereoBondRingSizeParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getSMILESMinStereoBondRingSizeParameter()

int CDPL.Chem.getSMILESMinStereoBondRingSizeParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored minimum ring size.

clearSMILESMinStereoBondRingSizeParameter()

None CDPL.Chem.clearSMILESMinStereoBondRingSizeParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setSMILESMolOutputAtomMappingIDParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESMolOutputAtomMappingIDParameter()

bool CDPL.Chem.hasSMILESMolOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESMolOutputAtomMappingIDParameter()

bool CDPL.Chem.getSMILESMolOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESMolOutputAtomMappingIDParameter()

None CDPL.Chem.clearSMILESMolOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setSMILESNoOrganicSubsetParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter of cntnr to no_subset.

Parameters

cntnr	The control-parameter container.
no_subset	The new parameter value.

hasSMILESNoOrganicSubsetParameter()

bool CDPL.Chem.hasSMILESNoOrganicSubsetParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getSMILESNoOrganicSubsetParameter()

bool CDPL.Chem.getSMILESNoOrganicSubsetParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearSMILESNoOrganicSubsetParameter()

None CDPL.Chem.clearSMILESNoOrganicSubsetParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setSMILESOutputAromaticBondsParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputAromaticBondsParameter()

bool CDPL.Chem.hasSMILESOutputAromaticBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESOutputAromaticBondsParameter()

bool CDPL.Chem.getSMILESOutputAromaticBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESOutputAromaticBondsParameter()

None CDPL.Chem.clearSMILESOutputAromaticBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setSMILESOutputAtomStereoParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputAtomStereoParameter()

bool CDPL.Chem.hasSMILESOutputAtomStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESOutputAtomStereoParameter()

bool CDPL.Chem.getSMILESOutputAtomStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESOutputAtomStereoParameter()

None CDPL.Chem.clearSMILESOutputAtomStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setSMILESOutputBondStereoParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputBondStereoParameter()

bool CDPL.Chem.hasSMILESOutputBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESOutputBondStereoParameter()

bool CDPL.Chem.getSMILESOutputBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESOutputBondStereoParameter()

None CDPL.Chem.clearSMILESOutputBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setSMILESOutputCanonicalFormParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputCanonicalFormParameter()

bool CDPL.Chem.hasSMILESOutputCanonicalFormParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESOutputCanonicalFormParameter()

bool CDPL.Chem.getSMILESOutputCanonicalFormParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESOutputCanonicalFormParameter()

None CDPL.Chem.clearSMILESOutputCanonicalFormParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setSMILESOutputHydrogenCountParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.3

hasSMILESOutputHydrogenCountParameter()

bool CDPL.Chem.hasSMILESOutputHydrogenCountParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.3

getSMILESOutputHydrogenCountParameter()

bool CDPL.Chem.getSMILESOutputHydrogenCountParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.3

clearSMILESOutputHydrogenCountParameter()

None CDPL.Chem.clearSMILESOutputHydrogenCountParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.3

setSMILESOutputIsotopeParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputIsotopeParameter()

bool CDPL.Chem.hasSMILESOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESOutputIsotopeParameter()

bool CDPL.Chem.getSMILESOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESOutputIsotopeParameter()

None CDPL.Chem.clearSMILESOutputIsotopeParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setSMILESOutputKekuleFormParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputKekuleFormParameter()

bool CDPL.Chem.hasSMILESOutputKekuleFormParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESOutputKekuleFormParameter()

bool CDPL.Chem.getSMILESOutputKekuleFormParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESOutputKekuleFormParameter()

None CDPL.Chem.clearSMILESOutputKekuleFormParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setSMILESOutputRingBondStereoParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputRingBondStereoParameter()

bool CDPL.Chem.hasSMILESOutputRingBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESOutputRingBondStereoParameter()

bool CDPL.Chem.getSMILESOutputRingBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESOutputRingBondStereoParameter()

None CDPL.Chem.clearSMILESOutputRingBondStereoParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setSMILESOutputSingleBondsParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputSingleBondsParameter()

bool CDPL.Chem.hasSMILESOutputSingleBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESOutputSingleBondsParameter()

bool CDPL.Chem.getSMILESOutputSingleBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESOutputSingleBondsParameter()

None CDPL.Chem.clearSMILESOutputSingleBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setSMILESRecordFormatParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter of cntnr to format.

Parameters

cntnr	The control-parameter container.
format	The new record-format string.

hasSMILESRecordFormatParameter()

bool CDPL.Chem.hasSMILESRecordFormatParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getSMILESRecordFormatParameter()

str CDPL.Chem.getSMILESRecordFormatParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored record-format string.

clearSMILESRecordFormatParameter()

None CDPL.Chem.clearSMILESRecordFormatParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setSMILESRxnOutputAtomMappingIDParameter()

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

Sets the value of the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESRxnOutputAtomMappingIDParameter()

bool CDPL.Chem.hasSMILESRxnOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getSMILESRxnOutputAtomMappingIDParameter()

bool CDPL.Chem.getSMILESRxnOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearSMILESRxnOutputAtomMappingIDParameter()

None CDPL.Chem.clearSMILESRxnOutputAtomMappingIDParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setStrictErrorCheckingParameter()

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

Sets the value of the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr to strict.

Parameters

cntnr	The control-parameter container.
strict	The new parameter value.

hasStrictErrorCheckingParameter()

bool CDPL.Chem.hasStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getStrictErrorCheckingParameter()

bool CDPL.Chem.getStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearStrictErrorCheckingParameter()

None CDPL.Chem.clearStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setXYZCalcFormalChargesParameter()

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

Sets the value of the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter of cntnr to calc.

Parameters

cntnr	The control-parameter container.
calc	The new parameter value.

Since

1.1

hasXYZCalcFormalChargesParameter()

bool CDPL.Chem.hasXYZCalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.1

getXYZCalcFormalChargesParameter()

bool CDPL.Chem.getXYZCalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.1

clearXYZCalcFormalChargesParameter()

None CDPL.Chem.clearXYZCalcFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.1

setXYZCommentIsNameParameter()

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

Sets the value of the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter of cntnr to is_name.

Parameters

cntnr	The control-parameter container.
is_name	The new parameter value.

Since

1.1

hasXYZCommentIsNameParameter()

bool CDPL.Chem.hasXYZCommentIsNameParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.1

getXYZCommentIsNameParameter()

bool CDPL.Chem.getXYZCommentIsNameParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.1

clearXYZCommentIsNameParameter()

None CDPL.Chem.clearXYZCommentIsNameParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.1

setXYZPerceiveBondOrdersParameter()

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

Sets the value of the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr to perceive.

Parameters

cntnr	The control-parameter container.
perceive	The new parameter value.

Since

1.1

hasXYZPerceiveBondOrdersParameter()

bool CDPL.Chem.hasXYZPerceiveBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.1

getXYZPerceiveBondOrdersParameter()

bool CDPL.Chem.getXYZPerceiveBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.1

clearXYZPerceiveBondOrdersParameter()

None CDPL.Chem.clearXYZPerceiveBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.1

setXYZPerceiveConnectivityParameter()

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

Sets the value of the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr to perceive.

Parameters

cntnr	The control-parameter container.
perceive	The new parameter value.

Since

1.1

hasXYZPerceiveConnectivityParameter()

bool CDPL.Chem.hasXYZPerceiveConnectivityParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.1

getXYZPerceiveConnectivityParameter()

bool CDPL.Chem.getXYZPerceiveConnectivityParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.1

clearXYZPerceiveConnectivityParameter()

None CDPL.Chem.clearXYZPerceiveConnectivityParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.1