CDPL::Chem Namespace Reference

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

Namespaces
	AtomConfiguration
	Provides constants that are used to specify the R/S configuration of atoms.
	AtomMatchConstraint
	Provides numerical identifiers for built-in Chem::Atom matching constraints.
	AtomProperty
	Provides keys for built-in Chem::Atom properties.
	AtomPropertyDefault
	Provides default values for built-in Chem::Atom properties.
	AtomPropertyFlag
	Provides flags for the specification of basic Chem::Atom properties.
	AtomType
	Provides constants for the specification of the chemical element or generic type of an atom.
	BondConfiguration
	Provides constants that are used to specify the cis/trans configuration of bonds.
	BondDirection
	Provides constants for the specification of directional bonds in Daylight SMILES and SMARTS strings.
	BondMatchConstraint
	Provides numerical identifiers for built-in Chem::Bond matching constraints and flags for the specification of bond orders.
	BondProperty
	Provides keys for built-in Chem::Bond properties.
	BondPropertyDefault
	Provides default values for built-in Chem::Bond properties.
	BondPropertyFlag
	Provides flags for the specification of basic Chem::Bond properties.
	BondStereoFlag
	Provides constants for the specification of stereo bonds in 2D depictions of chemical structures.
	BRICSAtomLabel
	Provides constants for the labeling of atoms in bonds matched by a BRICS fragmentation rule.
	BRICSRuleID
	Provides constants for the identification of BRICS fragmentation rules.
	CIPDescriptor
	Provides constants for the specification of stereogenic atom/bond configurations determined by the CIP sequence rules.
	ControlParameter
	Provides keys for built-in control-parameters.
	ControlParameterDefault
	Provides default values for built-in control-parameters.
	DataFormat
	Provides preinitialized Base::DataFormat objects for all supported chemical data formats.
	Entity3DProperty
	Provides keys for built-in Chem::Entity3D properties.
	HybridizationState
	Provides constants for the specification of atom hybridization states.
	INCHIReturnCode
	Provides constants that are used to describe the status of an InChI [INCHI] output or input operation.
	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].
	MDLParity
	Provides constants that are used to specify the MDL stereo parity of atoms.
	MOL2ChargeType
	Provides constants for the specification of the atom charge type in Tripos MOL2 files.
	MOL2MoleculeType
	Provides constants for the specification of the molecule type in Tripos MOL2 files.
	MolecularGraphMatchConstraint
	Provides numerical identifiers for built-in Chem::MolecularGraph matching constraints.
	MolecularGraphProperty
	Provides keys for built-in Chem::MolecularGraph properties.
	MolecularGraphPropertyDefault
	Provides default values for built-in Chem::MolecularGraph properties.
	RadicalType
	Provides constants that are used to specify the degeneracy of the electronic state of radical atoms.
	ReactionCenterStatus
	Provides flags that are used to describe state changes of atoms and bonds in a reaction center.
	ReactionMatchConstraint
	Provides numerical identifiers for built-in Chem::Reaction matching constraints.
	ReactionProperty
	Provides keys for built-in Chem::Reaction properties.
	ReactionPropertyDefault
	Provides default values for built-in Chem::Reaction properties.
	ReactionRole
	Provides constants that are used to specify the role of molecules (components) in a chemical reaction.
	RECAPAtomLabel
	Provides constants for the labeling of atoms in bonds matched by a RECAP fragmentation rule.
	RECAPRuleID
	Provides constants for the identification of RECAP fragmentation rules.
	SybylAtomType
	Provides constants for the specification of the Tripos Sybyl atom type.
	SybylBondType
	Provides constants for the specification of the Tripos Sybyl bond type.
	TautomerizationType
	Provides constants serving as identifiers for built-in Chem::TautomerizationRule implementations.

Classes
class	AmideImidicAcidTautomerization
	AmideImidicAcidTautomerizationRule. More...
class	ANDMatchExpressionList
	ANDMatchExpressionList. More...
class	ANDMatchExpressionList< ObjType, void >
	ANDMatchExpressionList. More...
class	AromaticRingSet
	Implements the perception of aromatic rings in a molecular graph. More...
class	AromaticSSSRSubset
	Implements the extraction of the aromatic rings in the SSSR of a molecular graph. More...
class	AromaticSubstructure
	Implements the perception of aromatic atoms and bonds in a molecular graph. More...
class	Atom
	Atom. More...
class	Atom2DCoordinatesCalculator
	Atom2DCoordinatesCalculator. More...
struct	Atom3DCoordinatesFunctor
	Atom3DCoordinatesFunctor. More...
class	AtomArray3DCoordinatesFunctor
	AtomArray3DCoordinatesFunctor. More...
class	AtomBondMapping
	A data structure for the common storage of related atom to atom and bond to bond mappings. More...
class	AtomConfigurationMatchExpression
	AtomConfigurationMatchExpression. More...
class	AtomConformer3DCoordinatesFunctor
	AtomConformer3DCoordinatesFunctor. More...
class	AtomContainer
	A common interface for data-structures that support a random access to stored Chem::Atom instances. More...
class	AtomDictionary
	A global dictionary for the lookup of data associated with the atom types defined in namespace Chem::AtomType. More...
class	AtomEnvironmentMatchExpression
	AtomEnvironmentMatchExpression. More...
class	AtomMapping
	A data type for the storage and lookup of arbitrary atom to atom mappings. More...
class	AtomSSSRRingSizeMatchExpression
	AtomSSSRRingSizeMatchExpression. More...
class	AtomTypeMatchExpression
	AtomTypeMatchExpression. More...
class	AutomorphismGroupSearch
	AutomorphismGroupSearch. More...
class	BasicAtom
	BasicAtom. More...
class	BasicBond
	BasicBond. More...
class	BasicMolecule
	BasicMolecule. More...
class	BasicReaction
	BasicReaction. More...
class	BemisMurckoAnalyzer
	BemisMurckoAnalyzer. More...
class	Bond
	Bond. More...
class	BondConfigurationMatchExpression
	BondConfigurationMatchExpression. More...
class	BondContainer
	A common interface for data-structures that support a random access to stored Chem::Bond instances. More...
class	BondDirectionMatchExpression
	BondDirectionMatchExpression. More...
class	BondMapping
	A data type for the storage and lookup of arbitrary bond to bond mappings. More...
class	BondOrderCalculator
	BondOrderCalculator. More...
class	BondReactionCenterStatusMatchExpression
	BondReactionCenterStatusMatchExpression. More...
class	BondStereoFlagCalculator
	BondStereoFlagCalculator. More...
class	BondSubstituentDirectionMatchExpression
	BondSubstituentDirectionMatchExpression. More...
class	BRICSFragmentGenerator
	BRICSFragmentGenerator. More...
class	CanonicalNumberingCalculator
	CanonicalNumberingCalculator. More...
class	CDFMolecularGraphWriter
	A writer for molecular graph data in the native I/O format of the CDPL. More...
class	CDFMoleculeReader
	A reader for molecule data in the native I/O format of the CDPL. More...
class	CDFReactionReader
	A reader for reaction data in the native I/O format of the CDPL. More...
class	CDFReactionWriter
	A writer for molecular graph data in the native I/O format of the CDPL. More...
class	ChEMBLStandardizer
	Implementation of the ChEMBL structure preprocessing pipeline. More...
class	CIPConfigurationLabeler
	CIPConfigurationLabeler. More...
class	CIPPriorityCalculator
	CIPPriorityCalculator. More...
class	CommonConnectedSubstructureSearch
	CommonConnectedSubstructureSearch. More...
class	CompleteRingSet
	Implements the exhaustive perception of rings in a molecular graph. More...
class	ComponentSet
	Implements the perception of molecular graph components. More...
class	ConnectedSubstructureSet
	ConnectedSubstructureSet. More...
class	CyclicSubstructure
	Implements the perception of ring atoms and bonds in a molecular graph. More...
class	DefaultMultiConfMoleculeInputProcessor
	MultiConfMoleculeInputProcessor. More...
class	DefaultTautomerGenerator
	DefaultTautomerGenerator. More...
class	ElectronSystem
	Describes an electron system of a molecule in terms of involved atoms and their electron contributions. More...
class	ElectronSystemList
	A data type for the storage of Chem::ElectronSystem objects. More...
class	Entity3D
	Entity3D. More...
class	Entity3DContainer
	A common interface for data-structures that support a random access to stored Chem::Entity3D instances. More...
struct	Entity3DCoordinatesFunctor
	Entity3DCoordinatesFunctor. More...
class	Entity3DMapping
	A data type for the storage and lookup of arbitrary entity to entity mappings. More...
class	Fragment
	Fragment. More...
class	FragmentGenerator
	FragmentGenerator. More...
class	FragmentList
	A data type for the storage of Chem::Fragment objects. More...
class	GenericHydrogen13ShiftTautomerization
	GenericHydrogen13ShiftTautomerizationRule. More...
class	GenericHydrogen15ShiftTautomerization
	GenericHydrogen15ShiftTautomerizationRule. More...
class	HashCodeCalculator
	HashCodeCalculator. More...
class	Hydrogen3DCoordinatesCalculator
	Hydrogen3DCoordinatesCalculator. More...
class	ImineEnamineTautomerization
	ImineEnamineTautomerizationRule. More...
class	INCHIMolecularGraphWriter
	A writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	INCHIMoleculeReader
	A reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	JMEMolecularGraphWriter
	A writer for molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEMoleculeReader
	A reader for molecule data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionReader
	A reader for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	JMEReactionWriter
	A writer for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
class	KekuleStructureCalculator
	KekuleStructureCalculator. More...
class	KeteneYnolTautomerization
	KeteneYnolTautomerizationRule. More...
class	KetoEnolTautomerization
	KetoEnolTautomerizationRule. More...
class	LactamLactimTautomerization
	LactamLactimTautomerizationRule. More...
class	MatchConstraint
	MatchConstraint. More...
class	MatchConstraintList
	MatchConstraintList. More...
class	MatchExpression
	A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	MatchExpression< ObjType, void >
	A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	MatchExpressionList
	A container for the storage and evaluation of logical match expression lists. More...
class	MaxCommonAtomSubstructureSearch
	MaxCommonAtomSubstructureSearch. More...
class	MaxCommonBondSubstructureSearch
	MaxCommonBondSubstructureSearch. More...
class	MOL2MolecularGraphWriter
class	MOL2MoleculeReader
class	MolecularGraph
	MolecularGraph. More...
class	MolecularGraphComponentGroupingMatchExpression
	MolecularGraphComponentGroupingMatchExpression. More...
class	Molecule
	Molecule. More...
class	MOLMolecularGraphWriter
	A writer for molecular graph data in the MDL Mol-File [CTFILE] format. More...
class	MOLMoleculeReader
	A reader for molecule data in the MDL Mol-File [CTFILE] format. More...
class	MorganNumberingCalculator
	MorganNumberingCalculator. More...
class	MultiConfMoleculeInputProcessor
	MultiConfMoleculeInputProcessor. More...
class	NitroAciTautomerization
	NitroAciTautomerizationRule. More...
class	NitrosoOximeTautomerization
	NitrosoOximeTautomerizationRule. More...
class	NOTMatchExpression
	NOTMatchExpression. More...
class	NOTMatchExpression< ObjType, void >
	NOTMatchExpression. More...
class	ORMatchExpressionList
	ORMatchExpressionList. More...
class	ORMatchExpressionList< ObjType, void >
	ORMatchExpressionList. More...
class	PatternAtomTyper
	PatternAtomTyper. More...
class	PatternBasedTautomerizationRule
	PatternBasedTautomerizationRule. More...
class	PhosphinicAcidTautomerization
	PhosphinicAcidTautomerizationRule. More...
class	PiElectronSystemList
	Implements the perception of all pi electron systems present in a molecule. More...
class	PropertyMatchExpression
	PropertyMatchExpression. More...
class	PropertyMatchExpression< ValueType, MatchFunc, ObjType, void >
	PropertyMatchExpression. More...
class	ProtonationStateStandardizer
	Sets the protation state of molecules according to desired objectives. More...
class	RDFReactionReader
	A reader for reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFReactionWriter
	A writer for reaction data in the MDL RD-File [CTFILE] format. More...
class	Reaction
	Reaction. More...
class	ReactionAtomMappingMatchExpression
	ReactionAtomMappingMatchExpression. More...
class	ReactionComponentGroupingMatchExpression
	ReactionComponentGroupingMatchExpression. More...
class	ReactionSubstructureSearch
	ReactionSubstructureSearch. More...
class	Reactor
	Reactor. More...
class	RECAPFragmentGenerator
	RECAPFragmentGenerator. More...
class	ResonanceStructureGenerator
	ResonanceStructureGenerator. More...
class	RXNReactionReader
	A reader for reaction data in the MDL Rxn-File [CTFILE] format. More...
class	RXNReactionWriter
	A writer for reaction data in the MDL Rxn-File [CTFILE] format. More...
class	SDFMolecularGraphWriter
	A writer for molecular graph data in the MDL Mol-File [CTFILE] format. More...
class	SDFMoleculeReader
	A Reader for molecule data in the MDL SD-File [CTFILE] format. More...
class	SmallestSetOfSmallestRings
	Implements the perception of the Smallest Set of Smallest Rings (SSSR) of a molecular graphs. More...
class	SMARTSMolecularGraphWriter
	A writer for molecular graph data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSMoleculeReader
	A reader for molecule data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionReader
	A reader for reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionWriter
	A writer for reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMILESMolecularGraphWriter
	A writer for molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESMoleculeReader
	A reader for molecule data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionReader
	A reader for reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionWriter
	A writer for reaction data in the Daylight SMILES [SMILES] format. More...
class	SpatialEntityAlignment
	SpatialEntityAlignment. More...
class	StereoDescriptor
	A data structure for the storage and retrieval of stereochemical information about atoms and bonds. More...
class	StereoisomerGenerator
	StereoisomerGenerator. More...
class	StringDataBlock
	An array of Chem::StringDataBlockEntry objects used to store the structure or reaction data block of a STRING SD- or RD-File data record (see [CTFILE]). More...
class	StringDataBlockEntry
	Represents a data item in the structure or reaction data block of a MDL SD- or RD-File data record (see [CTFILE]). More...
class	SubstructureHistogramCalculator
	SubstructureHistogramCalculator. More...
class	SubstructureSearch
	SubstructureSearch. More...
class	SulfenicAcidTautomerization
	SulfenicAcidTautomerizationRule. More...
class	SurfaceAtomExtractor
	SurfaceAtomExtractor. More...
class	SymmetryClassCalculator
	SymmetryClassCalculator. More...
class	TautomerGenerator
	TautomerGenerator. More...
class	TautomerizationRule
	TautomerizationRule. More...
class	TautomerScore
	TautomerScore. More...
class	TopologicalEntityAlignment
	TopologicalEntityAlignment. More...
class	XYZMolecularGraphWriter
class	XYZMoleculeReader

Typedefs
typedef std::function< const Math::Vector3D &(const Chem::Atom &)>	Atom3DCoordinatesFunction
	A generic wrapper class used to store a user-defined Chem::Atom 3D-coordinates function. More...
typedef std::function< bool(const Chem::Atom &, const Chem::Atom &)>	AtomCompareFunction
	A generic wrapper class used to store a user-defined atom compare function. More...
typedef std::function< bool(const Chem::Atom &)>	AtomPredicate
	A generic wrapper class used to store a user-defined atom predicate. More...
typedef std::function< std::size_t(const Chem::Atom &)>	AtomPriorityFunction
	A generic wrapper class used to store a user-defined atom priority function. More...
typedef std::function< bool(const Chem::Bond &, const Chem::Bond &)>	BondCompareFunction
	A generic wrapper class used to store a user-defined bond compare function. More...
typedef std::function< bool(const Chem::Bond &)>	BondPredicate
	A generic wrapper class used to store a user-defined bond predicate. More...
typedef Util::DefaultDataOutputHandler< CDFBZ2MolecularGraphWriter, DataFormat::CDF_BZ2 >	CDFBZ2MolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataWriter< CDFMolecularGraphWriter, Util::BZip2OStream >	CDFBZ2MolecularGraphWriter
typedef Util::DefaultDataInputHandler< CDFBZ2MoleculeReader, DataFormat::CDF_BZ2 >	CDFBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataReader< CDFMoleculeReader, Util::BZip2IStream >	CDFBZ2MoleculeReader
typedef Util::DefaultDataInputHandler< CDFBZ2ReactionReader, DataFormat::CDF_BZ2 >	CDFBZ2ReactionInputHandler
	A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataOutputHandler< CDFBZ2ReactionWriter, DataFormat::CDF_BZ2 >	CDFBZ2ReactionOutputHandler
	A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataReader< CDFReactionReader, Util::BZip2IStream >	CDFBZ2ReactionReader
typedef Util::CompressedDataWriter< CDFReactionWriter, Util::BZip2OStream >	CDFBZ2ReactionWriter
typedef Util::DefaultDataOutputHandler< CDFGZMolecularGraphWriter, DataFormat::CDF_GZ >	CDFGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataWriter< CDFMolecularGraphWriter, Util::GZipOStream >	CDFGZMolecularGraphWriter
typedef Util::DefaultDataInputHandler< CDFGZMoleculeReader, DataFormat::CDF_GZ >	CDFGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataReader< CDFMoleculeReader, Util::GZipIStream >	CDFGZMoleculeReader
typedef Util::DefaultDataInputHandler< CDFGZReactionReader, DataFormat::CDF_GZ >	CDFGZReactionInputHandler
	A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataOutputHandler< CDFGZReactionWriter, DataFormat::CDF_GZ >	CDFGZReactionOutputHandler
	A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataReader< CDFReactionReader, Util::GZipIStream >	CDFGZReactionReader
typedef Util::CompressedDataWriter< CDFReactionWriter, Util::GZipOStream >	CDFGZReactionWriter
typedef Util::DefaultDataOutputHandler< CDFMolecularGraphWriter, DataFormat::CDF >	CDFMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataInputHandler< CDFMoleculeReader, DataFormat::CDF >	CDFMoleculeInputHandler
	A handler for the input of molecule data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataInputHandler< CDFReactionReader, DataFormat::CDF >	CDFReactionInputHandler
	A handler for the input of reaction data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataOutputHandler< CDFReactionWriter, DataFormat::CDF >	CDFReactionOutputHandler
	A handler for the output of reaction data in the native I/O format of the CDPL. More...
typedef std::function< const Math::Vector3D &(const Chem::Entity &)>	Entity3DCoordinatesFunction
	A generic wrapper class used to store a user-defined Chem::Entity3D coordinates function. More...
typedef Util::DefaultDataOutputHandler< INCHIMolecularGraphWriter, DataFormat::INCHI >	INCHIMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
typedef Util::DefaultDataInputHandler< INCHIMoleculeReader, DataFormat::INCHI >	INCHIMoleculeInputHandler
	A handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
typedef Util::DefaultDataOutputHandler< JMEMolecularGraphWriter, DataFormat::JME >	JMEMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
typedef Util::DefaultDataInputHandler< JMEMoleculeReader, DataFormat::JME >	JMEMoleculeInputHandler
	A handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
typedef Util::DefaultDataInputHandler< JMEReactionReader, DataFormat::JME >	JMEReactionInputHandler
	A handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
typedef Util::DefaultDataOutputHandler< JMEReactionWriter, DataFormat::JME >	JMEReactionOutputHandler
	A handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
typedef Util::DefaultDataOutputHandler< MOL2BZ2MolecularGraphWriter, DataFormat::MOL2_BZ2 >	MOL2BZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format. More...
typedef Util::CompressedDataWriter< MOL2MolecularGraphWriter, Util::BZip2OStream >	MOL2BZ2MolecularGraphWriter
typedef Util::DefaultDataInputHandler< MOL2BZ2MoleculeReader, DataFormat::MOL2_BZ2 >	MOL2BZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format. More...
typedef Util::CompressedDataReader< MOL2MoleculeReader, Util::BZip2IStream >	MOL2BZ2MoleculeReader
typedef Util::DefaultDataOutputHandler< MOL2GZMolecularGraphWriter, DataFormat::MOL2_GZ >	MOL2GZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format. More...
typedef Util::CompressedDataWriter< MOL2MolecularGraphWriter, Util::GZipOStream >	MOL2GZMolecularGraphWriter
typedef Util::DefaultDataInputHandler< MOL2GZMoleculeReader, DataFormat::MOL2_GZ >	MOL2GZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format. More...
typedef Util::CompressedDataReader< MOL2MoleculeReader, Util::GZipIStream >	MOL2GZMoleculeReader
typedef Util::DefaultDataOutputHandler< MOL2MolecularGraphWriter, DataFormat::MOL2 >	MOL2MolecularGraphOutputHandler
	A handler for the output of molecular graph data in the Sybyl MOL2 format. More...
typedef Util::DefaultDataInputHandler< MOL2MoleculeReader, DataFormat::MOL2 >	MOL2MoleculeInputHandler
	A handler for the input of molecule data in the Sybyl MOL2 format. More...
typedef Util::MultiFormatDataWriter< MolecularGraph >	MolecularGraphWriter
	Writer for molecule data in any supported format. More...
typedef Util::MultiFormatDataReader< Molecule >	MoleculeReader
	Reader for molecule data in any supported format. More...
typedef Util::DefaultDataOutputHandler< MOLMolecularGraphWriter, DataFormat::MOL >	MOLMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< MOLMoleculeReader, DataFormat::MOL >	MOLMoleculeInputHandler
	A handler for the input of molecule data in the MDL Mol-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< RDFBZ2ReactionReader, DataFormat::RDF_BZ2 >	RDFBZ2ReactionInputHandler
	A handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< RDFBZ2ReactionWriter, DataFormat::RDF_BZ2 >	RDFBZ2ReactionOutputHandler
	A handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
typedef Util::CompressedDataReader< RDFReactionReader, Util::BZip2IStream >	RDFBZ2ReactionReader
typedef Util::CompressedDataWriter< RDFReactionWriter, Util::BZip2OStream >	RDFBZ2ReactionWriter
typedef Util::DefaultDataInputHandler< RDFGZReactionReader, DataFormat::RDF_GZ >	RDFGZReactionInputHandler
	A handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< RDFGZReactionWriter, DataFormat::RDF_GZ >	RDFGZReactionOutputHandler
	A handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
typedef Util::CompressedDataReader< RDFReactionReader, Util::GZipIStream >	RDFGZReactionReader
typedef Util::CompressedDataWriter< RDFReactionWriter, Util::GZipOStream >	RDFGZReactionWriter
typedef Util::DefaultDataInputHandler< RDFReactionReader, DataFormat::RDF >	RDFReactionInputHandler
	A handler for the input of reaction data in the MDL RD-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< RDFReactionWriter, DataFormat::RDF >	RDFReactionOutputHandler
	A handler for the output of reaction data in the MDL RD-File [CTFILE] format. More...
typedef Util::MultiFormatDataReader< Reaction >	ReactionReader
	Reader for reaction data in any supported format. More...
typedef Util::MultiFormatDataWriter< Reaction >	ReactionWriter
	Writer for reaction data in any supported format. More...
typedef Util::DefaultDataInputHandler< RXNReactionReader, DataFormat::RXN >	RXNReactionInputHandler
	A handler for the input of reaction data in the MDL Rxn-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< RXNReactionWriter, DataFormat::RXN >	RXNReactionOutputHandler
	A handler for the output of reaction data in the MDL Rxn-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< SDFBZ2MolecularGraphWriter, DataFormat::SDF_BZ2 >	SDFBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
typedef Util::CompressedDataWriter< SDFMolecularGraphWriter, Util::BZip2OStream >	SDFBZ2MolecularGraphWriter
typedef Util::DefaultDataInputHandler< SDFBZ2MoleculeReader, DataFormat::SDF_BZ2 >	SDFBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format. More...
typedef Util::CompressedDataReader< SDFMoleculeReader, Util::BZip2IStream >	SDFBZ2MoleculeReader
typedef Util::DefaultDataOutputHandler< SDFGZMolecularGraphWriter, DataFormat::SDF_GZ >	SDFGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
typedef Util::CompressedDataWriter< SDFMolecularGraphWriter, Util::GZipOStream >	SDFGZMolecularGraphWriter
typedef Util::DefaultDataInputHandler< SDFGZMoleculeReader, DataFormat::SDF_GZ >	SDFGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format. More...
typedef Util::CompressedDataReader< SDFMoleculeReader, Util::GZipIStream >	SDFGZMoleculeReader
typedef Util::DefaultDataOutputHandler< SDFMolecularGraphWriter, DataFormat::SDF >	SDFMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the MDL SD-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< SDFMoleculeReader, DataFormat::SDF >	SDFMoleculeInputHandler
	A handler for the input of molecule data in the MDL SD-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< SMARTSMolecularGraphWriter, DataFormat::SMARTS >	SMARTSMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format. More...
typedef Util::DefaultDataInputHandler< SMARTSMoleculeReader, DataFormat::SMARTS >	SMARTSMoleculeInputHandler
	A handler for the input of molecule data in the Daylight SMARTS [SMARTS] format. More...
typedef Util::DefaultDataInputHandler< SMARTSReactionReader, DataFormat::SMARTS >	SMARTSReactionInputHandler
	A handler for the input of reaction data in the Daylight SMARTS [SMARTS] format. More...
typedef Util::DefaultDataOutputHandler< SMARTSReactionWriter, DataFormat::SMARTS >	SMARTSReactionOutputHandler
	A handler for the output of reaction data in the Daylight SMARTS [SMARTS] format. More...
typedef Util::DefaultDataOutputHandler< SMILESBZ2MolecularGraphWriter, DataFormat::SMILES_BZ2 >	SMILESBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataWriter< SMILESMolecularGraphWriter, Util::BZip2OStream >	SMILESBZ2MolecularGraphWriter
typedef Util::DefaultDataInputHandler< SMILESBZ2MoleculeReader, DataFormat::SMILES_BZ2 >	SMILESBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataReader< SMILESMoleculeReader, Util::BZip2IStream >	SMILESBZ2MoleculeReader
typedef Util::DefaultDataInputHandler< SMILESBZ2ReactionReader, DataFormat::SMILES_BZ2 >	SMILESBZ2ReactionInputHandler
	A handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< SMILESBZ2ReactionWriter, DataFormat::SMILES_BZ2 >	SMILESBZ2ReactionOutputHandler
	A handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataReader< SMILESReactionReader, Util::BZip2IStream >	SMILESBZ2ReactionReader
typedef Util::CompressedDataWriter< SMILESReactionWriter, Util::BZip2OStream >	SMILESBZ2ReactionWriter
typedef Util::DefaultDataOutputHandler< SMILESGZMolecularGraphWriter, DataFormat::SMILES_GZ >	SMILESGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataWriter< SMILESMolecularGraphWriter, Util::GZipOStream >	SMILESGZMolecularGraphWriter
typedef Util::DefaultDataInputHandler< SMILESGZMoleculeReader, DataFormat::SMILES_GZ >	SMILESGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataReader< SMILESMoleculeReader, Util::GZipIStream >	SMILESGZMoleculeReader
typedef Util::DefaultDataInputHandler< SMILESGZReactionReader, DataFormat::SMILES_GZ >	SMILESGZReactionInputHandler
	A handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< SMILESGZReactionWriter, DataFormat::SMILES_GZ >	SMILESGZReactionOutputHandler
	A handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataReader< SMILESReactionReader, Util::GZipIStream >	SMILESGZReactionReader
typedef Util::CompressedDataWriter< SMILESReactionWriter, Util::GZipOStream >	SMILESGZReactionWriter
typedef Util::DefaultDataOutputHandler< SMILESMolecularGraphWriter, DataFormat::SMILES >	SMILESMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataInputHandler< SMILESMoleculeReader, DataFormat::SMILES >	SMILESMoleculeInputHandler
	A handler for the input of molecule data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataInputHandler< SMILESReactionReader, DataFormat::SMILES >	SMILESReactionInputHandler
	A handler for the input of reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< SMILESReactionWriter, DataFormat::SMILES >	SMILESReactionOutputHandler
	A handler for the output of reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< XYZBZ2MolecularGraphWriter, DataFormat::XYZ_BZ2 >	XYZBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the XYZ format. More...
typedef Util::CompressedDataWriter< XYZMolecularGraphWriter, Util::BZip2OStream >	XYZBZ2MolecularGraphWriter
typedef Util::DefaultDataInputHandler< XYZBZ2MoleculeReader, DataFormat::XYZ_BZ2 >	XYZBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the XYZ format. More...
typedef Util::CompressedDataReader< XYZMoleculeReader, Util::BZip2IStream >	XYZBZ2MoleculeReader
typedef Util::DefaultDataOutputHandler< XYZGZMolecularGraphWriter, DataFormat::XYZ_GZ >	XYZGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the XYZ format. More...
typedef Util::CompressedDataWriter< XYZMolecularGraphWriter, Util::GZipOStream >	XYZGZMolecularGraphWriter
typedef Util::DefaultDataInputHandler< XYZGZMoleculeReader, DataFormat::XYZ_GZ >	XYZGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the XYZ format. More...
typedef Util::CompressedDataReader< XYZMoleculeReader, Util::GZipIStream >	XYZGZMoleculeReader
typedef Util::DefaultDataOutputHandler< XYZMolecularGraphWriter, DataFormat::XYZ >	XYZMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the XYZ format. More...
typedef Util::DefaultDataInputHandler< XYZMoleculeReader, DataFormat::XYZ >	XYZMoleculeInputHandler
	A handler for the input of molecule data in the XYZ format. More...

Functions
CDPL_CHEM_API bool	hasCoordinates (const AtomContainer &cntnr, std::size_t dim)
CDPL_CHEM_API void	get2DCoordinates (const AtomContainer &cntnr, Math::Vector2DArray &coords, bool append=false)
CDPL_CHEM_API void	set2DCoordinates (AtomContainer &cntnr, const Math::Vector2DArray &coords)
CDPL_CHEM_API void	transform2DCoordinates (AtomContainer &cntnr, const Math::Matrix3D &mtx)
CDPL_CHEM_API void	get3DCoordinates (const AtomContainer &cntnr, Math::Vector3DArray &coords, const Atom3DCoordinatesFunction &coords_func, bool append=false)
CDPL_CHEM_API void	clearConformations (AtomContainer &cntnr)
CDPL_CHEM_API std::size_t	getNumConformations (const AtomContainer &cntnr)
CDPL_CHEM_API void	applyConformation (AtomContainer &cntnr, std::size_t conf_idx)
CDPL_CHEM_API void	getConformation (const AtomContainer &cntnr, std::size_t conf_idx, Math::Vector3DArray &coords, bool append=false)
CDPL_CHEM_API void	setConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Vector3DArray &coords)
CDPL_CHEM_API void	addConformation (AtomContainer &cntnr, const Math::Vector3DArray &coords)
CDPL_CHEM_API void	transformConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Matrix4D &mtx)
CDPL_CHEM_API void	transformConformations (AtomContainer &cntnr, const Math::Matrix4D &mtx)
CDPL_CHEM_API bool	alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms, const Math::Vector3DArray &ref_coords)
CDPL_CHEM_API bool	alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms, const Math::Vector3DArray &ref_coords)
CDPL_CHEM_API bool	alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms)
CDPL_CHEM_API bool	alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms)
CDPL_CHEM_API std::size_t	getMaxComponentGroupID (const AtomContainer &cntnr)
CDPL_CHEM_API std::size_t	getMaxAtomMappingID (const AtomContainer &cntnr)
CDPL_CHEM_API std::size_t	createAtomTypeMask (const AtomContainer &cntnr, Util::BitSet &mask, unsigned int type, bool reset=true, bool strict=true)
CDPL_CHEM_API void	copyAtomsIf (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false)
CDPL_CHEM_API void	copyAtomsIf (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false)
CDPL_CHEM_API void	copyAtomsIfNot (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false)
CDPL_CHEM_API void	copyAtomsIfNot (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false)
CDPL_CHEM_API bool	calcCenterOfMass (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr)
CDPL_CHEM_API bool	calcCentroid (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr)
CDPL_CHEM_API void	calcBoundingBox (const AtomContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func, bool reset=true)
CDPL_CHEM_API bool	insideBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func)
CDPL_CHEM_API bool	intersectsBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func)
CDPL_CHEM_API const std::string &	getName (const Atom &atom)
CDPL_CHEM_API void	setName (Atom &atom, const std::string &name)
CDPL_CHEM_API void	clearName (Atom &atom)
CDPL_CHEM_API bool	hasName (const Atom &atom)
CDPL_CHEM_API const std::string &	getSymbol (const Atom &atom)
CDPL_CHEM_API void	setSymbol (Atom &atom, const std::string &symbol)
CDPL_CHEM_API void	clearSymbol (Atom &atom)
CDPL_CHEM_API bool	hasSymbol (const Atom &atom)
CDPL_CHEM_API const std::string &	getSymbolForType (const Atom &atom)
CDPL_CHEM_API unsigned int	getType (const Atom &atom)
CDPL_CHEM_API void	setType (Atom &atom, unsigned int type)
CDPL_CHEM_API void	clearType (Atom &atom)
CDPL_CHEM_API bool	hasType (const Atom &atom)
CDPL_CHEM_API unsigned int	getTypeForSymbol (const Atom &atom)
CDPL_CHEM_API unsigned int	getGenericType (const Atom &atom)
CDPL_CHEM_API long	getFormalCharge (const Atom &atom)
CDPL_CHEM_API void	setFormalCharge (Atom &atom, long charge)
CDPL_CHEM_API void	clearFormalCharge (Atom &atom)
CDPL_CHEM_API bool	hasFormalCharge (const Atom &atom)
CDPL_CHEM_API long	calcFormalCharge (const Atom &atom, const MolecularGraph &molgraph)
CDPL_CHEM_API std::size_t	getIsotope (const Atom &atom)
CDPL_CHEM_API void	setIsotope (Atom &atom, std::size_t isotope)
CDPL_CHEM_API void	clearIsotope (Atom &atom)
CDPL_CHEM_API bool	hasIsotope (const Atom &atom)
CDPL_CHEM_API unsigned int	getRadicalType (const Atom &atom)
CDPL_CHEM_API void	setRadicalType (Atom &atom, unsigned int type)
CDPL_CHEM_API void	clearRadicalType (Atom &atom)
CDPL_CHEM_API bool	hasRadicalType (const Atom &atom)
CDPL_CHEM_API unsigned int	getHybridizationState (const Atom &atom)
CDPL_CHEM_API void	setHybridizationState (Atom &atom, unsigned int state)
CDPL_CHEM_API void	clearHybridizationState (Atom &atom)
CDPL_CHEM_API bool	hasHybridizationState (const Atom &atom)
CDPL_CHEM_API unsigned int	perceiveHybridizationState (const Atom &atom, const MolecularGraph &molgraph)
CDPL_CHEM_API bool	getRingFlag (const Atom &atom)
CDPL_CHEM_API void	setRingFlag (Atom &atom, bool in_ring)
CDPL_CHEM_API void	clearRingFlag (Atom &atom)
CDPL_CHEM_API bool	hasRingFlag (const Atom &atom)
CDPL_CHEM_API bool	isInFragmentOfSize (const Atom &atom, const FragmentList &frag_list, std::size_t size)
CDPL_CHEM_API std::size_t	getSizeOfSmallestContainingFragment (const Atom &atom, const FragmentList &frag_list)
CDPL_CHEM_API std::size_t	getSizeOfLargestContainingFragment (const Atom &atom, const FragmentList &frag_list)
CDPL_CHEM_API std::size_t	getNumContainingFragments (const Atom &atom, const FragmentList &frag_list)
CDPL_CHEM_API void	getContainingFragments (const Atom &atom, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false)
CDPL_CHEM_API bool	getAromaticityFlag (const Atom &atom)
CDPL_CHEM_API void	setAromaticityFlag (Atom &atom, bool aromatic)
CDPL_CHEM_API void	clearAromaticityFlag (Atom &atom)
CDPL_CHEM_API bool	hasAromaticityFlag (const Atom &atom)
CDPL_CHEM_API std::size_t	getUnpairedElectronCount (const Atom &atom)
CDPL_CHEM_API void	setUnpairedElectronCount (Atom &atom, std::size_t count)
CDPL_CHEM_API void	clearUnpairedElectronCount (Atom &atom)
CDPL_CHEM_API bool	hasUnpairedElectronCount (const Atom &atom)
CDPL_CHEM_API std::size_t	getImplicitHydrogenCount (const Atom &atom)
CDPL_CHEM_API void	setImplicitHydrogenCount (Atom &atom, std::size_t count)
CDPL_CHEM_API void	clearImplicitHydrogenCount (Atom &atom)
CDPL_CHEM_API bool	hasImplicitHydrogenCount (const Atom &atom)
CDPL_CHEM_API std::size_t	calcImplicitHydrogenCount (const Atom &atom, const MolecularGraph &molgraph)
CDPL_CHEM_API const Math::Vector2D &	get2DCoordinates (const Atom &atom)
CDPL_CHEM_API void	set2DCoordinates (Atom &atom, const Math::Vector2D &coords)
CDPL_CHEM_API void	clear2DCoordinates (Atom &atom)
CDPL_CHEM_API bool	has2DCoordinates (const Atom &atom)
CDPL_CHEM_API const Math::Vector3D &	getConformer3DCoordinates (const Atom &atom, std::size_t conf_idx)
CDPL_CHEM_API const Math::Vector3DArray::SharedPointer &	get3DCoordinatesArray (const Atom &atom)
CDPL_CHEM_API void	set3DCoordinatesArray (Atom &atom, const Math::Vector3DArray::SharedPointer &coords_array)
CDPL_CHEM_API void	clear3DCoordinatesArray (Atom &atom)
CDPL_CHEM_API bool	has3DCoordinatesArray (const Atom &atom)
CDPL_CHEM_API std::size_t	getMorganNumber (const Atom &atom)
CDPL_CHEM_API void	setMorganNumber (Atom &atom, std::size_t num)
CDPL_CHEM_API void	clearMorganNumber (Atom &atom)
CDPL_CHEM_API bool	hasMorganNumber (const Atom &atom)
CDPL_CHEM_API std::size_t	getCanonicalNumber (const Atom &atom)
CDPL_CHEM_API void	setCanonicalNumber (Atom &atom, std::size_t num)
CDPL_CHEM_API void	clearCanonicalNumber (Atom &atom)
CDPL_CHEM_API bool	hasCanonicalNumber (const Atom &atom)
CDPL_CHEM_API std::size_t	getCIPPriority (const Atom &atom)
CDPL_CHEM_API void	setCIPPriority (Atom &atom, std::size_t priority)
CDPL_CHEM_API void	clearCIPPriority (Atom &atom)
CDPL_CHEM_API bool	hasCIPPriority (const Atom &atom)
CDPL_CHEM_API std::size_t	getSymmetryClass (const Atom &atom)
CDPL_CHEM_API void	setSymmetryClass (Atom &atom, std::size_t class_id)
CDPL_CHEM_API void	clearSymmetryClass (Atom &atom)
CDPL_CHEM_API bool	hasSymmetryClass (const Atom &atom)
CDPL_CHEM_API unsigned int	getCIPConfiguration (const Atom &atom)
CDPL_CHEM_API void	setCIPConfiguration (Atom &atom, unsigned int config)
CDPL_CHEM_API void	clearCIPConfiguration (Atom &atom)
CDPL_CHEM_API bool	hasCIPConfiguration (const Atom &atom)
CDPL_CHEM_API const StereoDescriptor &	getStereoDescriptor (const Atom &atom)
CDPL_CHEM_API void	setStereoDescriptor (Atom &atom, const StereoDescriptor &descr)
CDPL_CHEM_API void	clearStereoDescriptor (Atom &atom)
CDPL_CHEM_API bool	hasStereoDescriptor (const Atom &atom)
CDPL_CHEM_API StereoDescriptor	calcStereoDescriptor (const Atom &atom, const MolecularGraph &molgraph, std::size_t dim=1)
CDPL_CHEM_API StereoDescriptor	calcStereoDescriptorFromMDLParity (const Atom &atom, const MolecularGraph &molgraph)
CDPL_CHEM_API unsigned int	calcConfiguration (const Atom &atom, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords)
CDPL_CHEM_API bool	getStereoCenterFlag (const Atom &atom)
CDPL_CHEM_API void	setStereoCenterFlag (Atom &atom, bool is_center)
CDPL_CHEM_API void	clearStereoCenterFlag (Atom &atom)
CDPL_CHEM_API bool	hasStereoCenterFlag (const Atom &atom)
CDPL_CHEM_API bool	isStereoCenter (const Atom &atom, const 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)
CDPL_CHEM_API unsigned int	getSybylType (const Atom &atom)
CDPL_CHEM_API void	setSybylType (Atom &atom, unsigned int type)
CDPL_CHEM_API void	clearSybylType (Atom &atom)
CDPL_CHEM_API bool	hasSybylType (const Atom &atom)
CDPL_CHEM_API unsigned int	perceiveSybylType (const Atom &atom, const MolecularGraph &molgraph)
CDPL_CHEM_API const std::string &	getMOL2Name (const Atom &atom)
CDPL_CHEM_API void	setMOL2Name (Atom &atom, const std::string &name)
CDPL_CHEM_API void	clearMOL2Name (Atom &atom)
CDPL_CHEM_API bool	hasMOL2Name (const Atom &atom)
CDPL_CHEM_API double	getMOL2Charge (const Atom &atom)
CDPL_CHEM_API void	setMOL2Charge (Atom &atom, double charge)
CDPL_CHEM_API void	clearMOL2Charge (Atom &atom)
CDPL_CHEM_API bool	hasMOL2Charge (const Atom &atom)
CDPL_CHEM_API std::size_t	getMOL2SubstructureID (const Atom &atom)
CDPL_CHEM_API void	setMOL2SubstructureID (Atom &atom, std::size_t id)
CDPL_CHEM_API void	clearMOL2SubstructureID (Atom &atom)
CDPL_CHEM_API bool	hasMOL2SubstructureID (const Atom &atom)
CDPL_CHEM_API const std::string &	getMOL2SubstructureName (const Atom &atom)
CDPL_CHEM_API void	setMOL2SubstructureName (Atom &atom, const std::string &id)
CDPL_CHEM_API void	clearMOL2SubstructureName (Atom &atom)
CDPL_CHEM_API bool	hasMOL2SubstructureName (const Atom &atom)
CDPL_CHEM_API const std::string &	getMOL2SubstructureSubtype (const Atom &atom)
CDPL_CHEM_API void	setMOL2SubstructureSubtype (Atom &atom, const std::string &subtype)
CDPL_CHEM_API void	clearMOL2SubstructureSubtype (Atom &atom)
CDPL_CHEM_API bool	hasMOL2SubstructureSubtype (const Atom &atom)
CDPL_CHEM_API const std::string &	getMOL2SubstructureChain (const Atom &atom)
CDPL_CHEM_API void	setMOL2SubstructureChain (Atom &atom, const std::string &chain)
CDPL_CHEM_API void	clearMOL2SubstructureChain (Atom &atom)
CDPL_CHEM_API bool	hasMOL2SubstructureChain (const Atom &atom)
CDPL_CHEM_API unsigned int	getMDLParity (const Atom &atom)
CDPL_CHEM_API void	setMDLParity (Atom &atom, unsigned int parity)
CDPL_CHEM_API void	clearMDLParity (Atom &atom)
CDPL_CHEM_API bool	hasMDLParity (const Atom &atom)
CDPL_CHEM_API unsigned int	calcMDLParity (const Atom &atom, const MolecularGraph &molgraph)
CDPL_CHEM_API bool	getMDLStereoCareFlag (const Atom &atom)
CDPL_CHEM_API void	setMDLStereoCareFlag (Atom &atom, bool flag)
CDPL_CHEM_API void	clearMDLStereoCareFlag (Atom &atom)
CDPL_CHEM_API bool	hasMDLStereoCareFlag (const Atom &atom)
CDPL_CHEM_API unsigned int	getReactionCenterStatus (const Atom &atom)
CDPL_CHEM_API void	setReactionCenterStatus (Atom &atom, unsigned int status)
CDPL_CHEM_API void	clearReactionCenterStatus (Atom &atom)
CDPL_CHEM_API bool	hasReactionCenterStatus (const Atom &atom)
CDPL_CHEM_API std::size_t	getAtomMappingID (const Atom &atom)
CDPL_CHEM_API void	setAtomMappingID (Atom &atom, std::size_t id)
CDPL_CHEM_API void	clearAtomMappingID (Atom &atom)
CDPL_CHEM_API bool	hasAtomMappingID (const Atom &atom)
CDPL_CHEM_API std::size_t	getComponentGroupID (const Atom &atom)
CDPL_CHEM_API void	setComponentGroupID (Atom &atom, std::size_t id)
CDPL_CHEM_API void	clearComponentGroupID (Atom &atom)
CDPL_CHEM_API bool	hasComponentGroupID (const Atom &atom)
CDPL_CHEM_API const MatchConstraintList::SharedPointer &	getMatchConstraints (const Atom &atom)
CDPL_CHEM_API void	setMatchConstraints (Atom &atom, const MatchConstraintList::SharedPointer &constr)
CDPL_CHEM_API void	clearMatchConstraints (Atom &atom)
CDPL_CHEM_API bool	hasMatchConstraints (const Atom &atom)
CDPL_CHEM_API const MatchExpression< Atom, MolecularGraph >::SharedPointer &	getMatchExpression (const Atom &atom)
CDPL_CHEM_API void	setMatchExpression (Atom &atom, const MatchExpression< Atom, MolecularGraph >::SharedPointer &expr)
CDPL_CHEM_API void	clearMatchExpression (Atom &atom)
CDPL_CHEM_API bool	hasMatchExpression (const Atom &atom)
CDPL_CHEM_API MatchExpression< Atom, MolecularGraph >::SharedPointer	generateMatchExpression (const Atom &atom, const MolecularGraph &molgraph)
CDPL_CHEM_API const std::string &	getMatchExpressionString (const Atom &atom)
CDPL_CHEM_API void	setMatchExpressionString (Atom &atom, const std::string &expr_str)
CDPL_CHEM_API void	clearMatchExpressionString (Atom &atom)
CDPL_CHEM_API bool	hasMatchExpressionString (const Atom &atom)
CDPL_CHEM_API void	generateMatchExpressionString (const Atom &atom, const MolecularGraph &molgraph, std::string &expr_str)
CDPL_CHEM_API void	markReachableAtoms (const Atom &atom, const MolecularGraph &molgraph, Util::BitSet &atom_mask, bool reset=true)
CDPL_CHEM_API std::size_t	getTopologicalDistance (const Atom &atom1, const Atom &atom2, const MolecularGraph &molgraph)
CDPL_CHEM_API std::size_t	getEnvironment (const Atom &atom, const MolecularGraph &molgraph, std::size_t max_dist, Fragment &env, bool append=false)
template<typename AtomType , typename OutputIterator >
std::size_t	getConnectedAtoms (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0)
template<typename AtomType , typename OutputIterator >
std::size_t	getIncidentBonds (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0)
template<typename AtomType , typename AtomOutputIterator , typename BondOutputIterator >
std::size_t	getConnectedAtomsAndBonds (AtomType &atom, const MolecularGraph &molgraph, AtomOutputIterator ao_it, BondOutputIterator bo_it, AtomType *excl_atom=0)
CDPL_CHEM_API std::size_t	getOrder (const Bond &bond)
CDPL_CHEM_API void	setOrder (Bond &bond, std::size_t order)
CDPL_CHEM_API void	clearOrder (Bond &bond)
CDPL_CHEM_API bool	hasOrder (const Bond &bond)
CDPL_CHEM_API bool	getRingFlag (const Bond &bond)
CDPL_CHEM_API void	setRingFlag (Bond &bond, bool in_ring)
CDPL_CHEM_API void	clearRingFlag (Bond &bond)
CDPL_CHEM_API bool	hasRingFlag (const Bond &bond)
CDPL_CHEM_API bool	isInFragmentOfSize (const Bond &bond, const FragmentList &frag_list, std::size_t size)
CDPL_CHEM_API std::size_t	getSizeOfSmallestContainingFragment (const Bond &bond, const FragmentList &frag_list)
CDPL_CHEM_API std::size_t	getSizeOfLargestContainingFragment (const Bond &bond, const FragmentList &frag_list)
CDPL_CHEM_API std::size_t	getNumContainingFragments (const Bond &bond, const FragmentList &frag_list)
CDPL_CHEM_API void	getContainingFragments (const Bond &bond, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false)
CDPL_CHEM_API bool	getAromaticityFlag (const Bond &bond)
CDPL_CHEM_API void	setAromaticityFlag (Bond &bond, bool aromatic)
CDPL_CHEM_API void	clearAromaticityFlag (Bond &bond)
CDPL_CHEM_API bool	hasAromaticityFlag (const Bond &bond)
CDPL_CHEM_API unsigned int	get2DStereoFlag (const Bond &bond)
CDPL_CHEM_API void	set2DStereoFlag (Bond &bond, unsigned int flag)
CDPL_CHEM_API void	clear2DStereoFlag (Bond &bond)
CDPL_CHEM_API bool	has2DStereoFlag (const Bond &bond)
CDPL_CHEM_API unsigned int	getCIPConfiguration (const Bond &bond)
CDPL_CHEM_API void	setCIPConfiguration (Bond &bond, unsigned int config)
CDPL_CHEM_API void	clearCIPConfiguration (Bond &bond)
CDPL_CHEM_API bool	hasCIPConfiguration (const Bond &bond)
CDPL_CHEM_API const StereoDescriptor &	getStereoDescriptor (const Bond &bond)
CDPL_CHEM_API void	setStereoDescriptor (Bond &bond, const StereoDescriptor &descr)
CDPL_CHEM_API void	clearStereoDescriptor (Bond &bond)
CDPL_CHEM_API bool	hasStereoDescriptor (const Bond &bond)
CDPL_CHEM_API StereoDescriptor	calcStereoDescriptor (const Bond &bond, const MolecularGraph &molgraph, std::size_t dim=1)
CDPL_CHEM_API unsigned int	calcConfiguration (const Bond &bond, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords)
CDPL_CHEM_API bool	getStereoCenterFlag (const Bond &bond)
CDPL_CHEM_API void	setStereoCenterFlag (Bond &bond, bool is_center)
CDPL_CHEM_API void	clearStereoCenterFlag (Bond &bond)
CDPL_CHEM_API bool	hasStereoCenterFlag (const Bond &bond)
CDPL_CHEM_API bool	isStereoCenter (const Bond &bond, const MolecularGraph &molgraph, bool check_asym=true, bool check_term_n=true, bool check_order=true, std::size_t min_ring_size=8)
CDPL_CHEM_API unsigned int	getDirection (const Bond &bond)
CDPL_CHEM_API void	setDirection (Bond &bond, unsigned int dir)
CDPL_CHEM_API void	clearDirection (Bond &bond)
CDPL_CHEM_API bool	hasDirection (const Bond &bond)
CDPL_CHEM_API unsigned int	getReactionCenterStatus (const Bond &bond)
CDPL_CHEM_API void	setReactionCenterStatus (Bond &bond, unsigned int status)
CDPL_CHEM_API void	clearReactionCenterStatus (Bond &bond)
CDPL_CHEM_API bool	hasReactionCenterStatus (const Bond &bond)
CDPL_CHEM_API const MatchConstraintList::SharedPointer &	getMatchConstraints (const Bond &bond)
CDPL_CHEM_API void	setMatchConstraints (Bond &bond, const MatchConstraintList::SharedPointer &constr)
CDPL_CHEM_API void	clearMatchConstraints (Bond &bond)
CDPL_CHEM_API bool	hasMatchConstraints (const Bond &bond)
CDPL_CHEM_API const MatchExpression< Bond, MolecularGraph >::SharedPointer &	getMatchExpression (const Bond &bond)
CDPL_CHEM_API void	setMatchExpression (Bond &bond, const MatchExpression< Bond, MolecularGraph >::SharedPointer &expr)
CDPL_CHEM_API void	clearMatchExpression (Bond &bond)
CDPL_CHEM_API bool	hasMatchExpression (const Bond &bond)
CDPL_CHEM_API MatchExpression< Bond, MolecularGraph >::SharedPointer	generateMatchExpression (const Bond &bond, const MolecularGraph &molgraph)
CDPL_CHEM_API const std::string &	getMatchExpressionString (const Bond &bond)
CDPL_CHEM_API void	setMatchExpressionString (Bond &bond, const std::string &expr_str)
CDPL_CHEM_API void	clearMatchExpressionString (Bond &bond)
CDPL_CHEM_API bool	hasMatchExpressionString (const Bond &bond)
CDPL_CHEM_API void	generateMatchExpressionString (const Bond &bond, const MolecularGraph &molgraph, std::string &str)
CDPL_CHEM_API unsigned int	getSybylType (const Bond &bond)
CDPL_CHEM_API void	setSybylType (Bond &bond, unsigned int type)
CDPL_CHEM_API void	clearSybylType (Bond &bond)
CDPL_CHEM_API bool	hasSybylType (const Bond &bond)
CDPL_CHEM_API unsigned int	perceiveSybylType (const Bond &bond, const MolecularGraph &molgraph)
CDPL_CHEM_API bool	getOrdinaryHydrogenDepleteParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setOrdinaryHydrogenDepleteParameter (Base::ControlParameterContainer &cntnr, bool deplete)
CDPL_CHEM_API bool	hasOrdinaryHydrogenDepleteParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearOrdinaryHydrogenDepleteParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API std::size_t	getCoordinatesDimensionParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setCoordinatesDimensionParameter (Base::ControlParameterContainer &cntnr, std::size_t dim)
CDPL_CHEM_API bool	hasCoordinatesDimensionParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearCoordinatesDimensionParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict)
CDPL_CHEM_API bool	hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API const std::string &	getRecordSeparatorParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setRecordSeparatorParameter (Base::ControlParameterContainer &cntnr, const std::string &sep)
CDPL_CHEM_API bool	hasRecordSeparatorParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearRecordSeparatorParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getBondMemberSwapStereoFixParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setBondMemberSwapStereoFixParameter (Base::ControlParameterContainer &cntnr, bool fix)
CDPL_CHEM_API bool	hasBondMemberSwapStereoFixParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearBondMemberSwapStereoFixParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setCheckLineLengthParameter (Base::ControlParameterContainer &cntnr, bool check)
CDPL_CHEM_API bool	hasCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearCheckLineLengthParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API unsigned int	getMDLCTABVersionParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLCTABVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int version)
CDPL_CHEM_API bool	hasMDLCTABVersionParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLCTABVersionParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMDLIgnoreParityParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLIgnoreParityParameter (Base::ControlParameterContainer &cntnr, bool ignore)
CDPL_CHEM_API bool	hasMDLIgnoreParityParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLIgnoreParityParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMDLUpdateTimestampParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLUpdateTimestampParameter (Base::ControlParameterContainer &cntnr, bool update)
CDPL_CHEM_API bool	hasMDLUpdateTimestampParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLUpdateTimestampParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMDLTrimStringsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLTrimStringsParameter (Base::ControlParameterContainer &cntnr, bool trim)
CDPL_CHEM_API bool	hasMDLTrimStringsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLTrimStringsParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMDLTrimLinesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLTrimLinesParameter (Base::ControlParameterContainer &cntnr, bool trim)
CDPL_CHEM_API bool	hasMDLTrimLinesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLTrimLinesParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMDLTruncateStringsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLTruncateStringsParameter (Base::ControlParameterContainer &cntnr, bool trunc)
CDPL_CHEM_API bool	hasMDLTruncateStringsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLTruncateStringsParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMDLTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLTruncateLinesParameter (Base::ControlParameterContainer &cntnr, bool trunc)
CDPL_CHEM_API bool	hasMDLTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLTruncateLinesParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API unsigned int	getMDLRXNFileVersionParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLRXNFileVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int version)
CDPL_CHEM_API bool	hasMDLRXNFileVersionParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLRXNFileVersionParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMDLOutputConfEnergyToEnergyFieldParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLOutputConfEnergyToEnergyFieldParameter (Base::ControlParameterContainer &cntnr, bool output)
CDPL_CHEM_API bool	hasMDLOutputConfEnergyToEnergyFieldParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLOutputConfEnergyToEnergyFieldParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMDLOutputConfEnergyAsSDEntryParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLOutputConfEnergyAsSDEntryParameter (Base::ControlParameterContainer &cntnr, bool output)
CDPL_CHEM_API bool	hasMDLOutputConfEnergyAsSDEntryParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLOutputConfEnergyAsSDEntryParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API const std::string &	getMDLConfEnergySDTagParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMDLConfEnergySDTagParameter (Base::ControlParameterContainer &cntnr, const std::string &tag)
CDPL_CHEM_API bool	hasMDLConfEnergySDTagParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMDLConfEnergySDTagParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getJMESeparateComponentsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setJMESeparateComponentsParameter (Base::ControlParameterContainer &cntnr, bool separate)
CDPL_CHEM_API bool	hasJMESeparateComponentsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearJMESeparateComponentsParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API const std::string &	getSMILESRecordFormatParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESRecordFormatParameter (Base::ControlParameterContainer &cntnr, const std::string &format)
CDPL_CHEM_API bool	hasSMILESRecordFormatParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESRecordFormatParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESWriteCanonicalFormParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESWriteCanonicalFormParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESWriteCanonicalFormParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESWriteCanonicalFormParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESWriteKekuleFormParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESWriteKekuleFormParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESWriteKekuleFormParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESWriteKekuleFormParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESWriteAtomStereoParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESWriteAtomStereoParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESWriteAtomStereoParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESWriteAtomStereoParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESWriteBondStereoParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESWriteBondStereoParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESWriteBondStereoParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESWriteBondStereoParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESWriteRingBondStereoParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESWriteRingBondStereoParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESWriteRingBondStereoParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESWriteRingBondStereoParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API std::size_t	getSMILESMinStereoBondRingSizeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESMinStereoBondRingSizeParameter (Base::ControlParameterContainer &cntnr, std::size_t min_size)
CDPL_CHEM_API bool	hasSMILESMinStereoBondRingSizeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESMinStereoBondRingSizeParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESWriteIsotopeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESWriteIsotopeParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESWriteIsotopeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESWriteIsotopeParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESMolWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESMolWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESMolWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESMolWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESRxnWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESRxnWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESRxnWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESRxnWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESWriteSingleBondsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESWriteSingleBondsParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESWriteSingleBondsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESWriteSingleBondsParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESWriteAromaticBondsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESWriteAromaticBondsParameter (Base::ControlParameterContainer &cntnr, bool write)
CDPL_CHEM_API bool	hasSMILESWriteAromaticBondsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESWriteAromaticBondsParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getSMILESNoOrganicSubsetParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setSMILESNoOrganicSubsetParameter (Base::ControlParameterContainer &cntnr, bool no_subset)
CDPL_CHEM_API bool	hasSMILESNoOrganicSubsetParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearSMILESNoOrganicSubsetParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API const std::string &	getINCHIInputOptionsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setINCHIInputOptionsParameter (Base::ControlParameterContainer &cntnr, const std::string &opts)
CDPL_CHEM_API bool	hasINCHIInputOptionsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearINCHIInputOptionsParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API const std::string &	getINCHIOutputOptionsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setINCHIOutputOptionsParameter (Base::ControlParameterContainer &cntnr, const std::string &opts)
CDPL_CHEM_API bool	hasINCHIOutputOptionsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearINCHIOutputOptionsParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMultiConfImportParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMultiConfImportParameter (Base::ControlParameterContainer &cntnr, bool multi_conf)
CDPL_CHEM_API bool	hasMultiConfImportParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMultiConfImportParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMultiConfExportParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMultiConfExportParameter (Base::ControlParameterContainer &cntnr, bool multi_conf)
CDPL_CHEM_API bool	hasMultiConfExportParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMultiConfExportParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getOutputConfEnergyAsCommentParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setOutputConfEnergyAsCommentParameter (Base::ControlParameterContainer &cntnr, bool output)
CDPL_CHEM_API bool	hasOutputConfEnergyAsCommentParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearOutputConfEnergyAsCommentParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API const std::string &	getConfIndexNameSuffixPatternParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setConfIndexNameSuffixPatternParameter (Base::ControlParameterContainer &cntnr, const std::string &pattern)
CDPL_CHEM_API bool	hasConfIndexNameSuffixPatternParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearConfIndexNameSuffixPatternParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API const MultiConfMoleculeInputProcessor::SharedPointer &	getMultiConfInputProcessorParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMultiConfInputProcessorParameter (Base::ControlParameterContainer &cntnr, const MultiConfMoleculeInputProcessor::SharedPointer &proc)
CDPL_CHEM_API bool	hasMultiConfInputProcessorParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMultiConfInputProcessorParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr, bool single_prec)
CDPL_CHEM_API bool	hasCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMOL2EnableExtendedAtomTypesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMOL2EnableExtendedAtomTypesParameter (Base::ControlParameterContainer &cntnr, bool enable)
CDPL_CHEM_API bool	hasMOL2EnableExtendedAtomTypesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMOL2EnableExtendedAtomTypesParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMOL2EnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMOL2EnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr, bool enable)
CDPL_CHEM_API bool	hasMOL2EnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMOL2EnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMOL2CalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMOL2CalcFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc)
CDPL_CHEM_API bool	hasMOL2CalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMOL2CalcFormalChargesParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API unsigned int	getMOL2ChargeTypeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMOL2ChargeTypeParameter (Base::ControlParameterContainer &cntnr, unsigned int type)
CDPL_CHEM_API bool	hasMOL2ChargeTypeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMOL2ChargeTypeParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API unsigned int	getMOL2MoleculeTypeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMOL2MoleculeTypeParameter (Base::ControlParameterContainer &cntnr, unsigned int type)
CDPL_CHEM_API bool	hasMOL2MoleculeTypeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMOL2MoleculeTypeParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getMOL2OutputSubstructuresParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setMOL2OutputSubstructuresParameter (Base::ControlParameterContainer &cntnr, bool output)
CDPL_CHEM_API bool	hasMOL2OutputSubstructuresParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearMOL2OutputSubstructuresParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getXYZCommentIsNameParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setXYZCommentIsNameParameter (Base::ControlParameterContainer &cntnr, bool is_name)
CDPL_CHEM_API bool	hasXYZCommentIsNameParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearXYZCommentIsNameParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getXYZPerceiveConnectivityParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setXYZPerceiveConnectivityParameter (Base::ControlParameterContainer &cntnr, bool perceive)
CDPL_CHEM_API bool	hasXYZPerceiveConnectivityParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearXYZPerceiveConnectivityParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getXYZPerceiveBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setXYZPerceiveBondOrdersParameter (Base::ControlParameterContainer &cntnr, bool perceive)
CDPL_CHEM_API bool	hasXYZPerceiveBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearXYZPerceiveBondOrdersParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API bool	getXYZCalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	setXYZCalcFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc)
CDPL_CHEM_API bool	hasXYZCalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	clearXYZCalcFormalChargesParameter (Base::ControlParameterContainer &cntnr)
CDPL_CHEM_API void	calcGeometricalDistanceMatrix (const Entity3DContainer &cntnr, Math::DMatrix &mtx)
CDPL_CHEM_API void	get3DCoordinates (const Entity3DContainer &cntnr, Math::Vector3DArray &coords, bool append=false)
CDPL_CHEM_API void	set3DCoordinates (Entity3DContainer &cntnr, const Math::Vector3DArray &coords)
CDPL_CHEM_API void	transform3DCoordinates (Entity3DContainer &cntnr, const Math::Matrix4D &mtx)
CDPL_CHEM_API bool	align3DCoordinates (Entity3DContainer &cntnr, const Entity3DContainer &ref_entities, const Math::Vector3DArray &ref_coords)
CDPL_CHEM_API bool	calcCentroid (const Entity3DContainer &cntnr, Math::Vector3D &ctr)
CDPL_CHEM_API void	calcBoundingBox (const Entity3DContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, bool reset=true)
CDPL_CHEM_API bool	insideBoundingBox (const Entity3DContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max)
CDPL_CHEM_API bool	intersectsBoundingBox (const Entity3DContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max)
CDPL_CHEM_API const Math::Vector3D &	get3DCoordinates (const Entity3D &entity)
CDPL_CHEM_API void	set3DCoordinates (Entity3D &entity, const Math::Vector3D &coords)
CDPL_CHEM_API void	clear3DCoordinates (Entity3D &entity)
CDPL_CHEM_API bool	has3DCoordinates (const Entity3D &entity)
CDPL_CHEM_API bool	makeHydrogenDeplete (Fragment &frag)
	Removes all explicit hydrogen atoms from the fragment frag. More...
CDPL_CHEM_API bool	makeOrdinaryHydrogenDeplete (Fragment &frag, unsigned int flags)
	Removes all explicit ordinary hydrogen atoms from the fragment frag. More...
CDPL_CHEM_API void	removeAtomsIf (Fragment &frag, const AtomPredicate &pred)
CDPL_CHEM_API void	removeAtomsIfNot (Fragment &frag, const AtomPredicate &pred)
CDPL_CHEM_API const std::string &	getName (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setName (MolecularGraph &molgraph, const std::string &name)
CDPL_CHEM_API void	clearName (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasName (const MolecularGraph &molgraph)
CDPL_CHEM_API std::time_t	getTimestamp (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setTimestamp (MolecularGraph &molgraph, std::time_t time)
CDPL_CHEM_API void	clearTimestamp (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasTimestamp (const MolecularGraph &molgraph)
CDPL_CHEM_API const std::string &	getComment (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setComment (MolecularGraph &molgraph, const std::string &comment)
CDPL_CHEM_API void	clearComment (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasComment (const MolecularGraph &molgraph)
CDPL_CHEM_API const MatchConstraintList::SharedPointer &	getMatchConstraints (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr)
CDPL_CHEM_API void	clearMatchConstraints (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMatchConstraints (const MolecularGraph &molgraph)
CDPL_CHEM_API const MatchExpression< MolecularGraph >::SharedPointer &	getMatchExpression (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMatchExpression (MolecularGraph &molgraph, const MatchExpression< MolecularGraph >::SharedPointer &expr)
CDPL_CHEM_API void	clearMatchExpression (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMatchExpression (const MolecularGraph &molgraph)
CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer	generateMatchExpression (const MolecularGraph &molgraph)
CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer	generateMatchExpression (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API const FragmentList::SharedPointer &	getRings (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setRings (MolecularGraph &molgraph, const FragmentList::SharedPointer &rings)
CDPL_CHEM_API void	clearRings (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasRings (const MolecularGraph &molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveRings (const MolecularGraph &molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveRings (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API const FragmentList::SharedPointer &	getSSSR (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setSSSR (MolecularGraph &molgraph, const FragmentList::SharedPointer &sssr)
CDPL_CHEM_API void	clearSSSR (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasSSSR (const MolecularGraph &molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveSSSR (const MolecularGraph &molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveSSSR (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API FragmentList::SharedPointer	extractSSSRSubset (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	extractSSSRSubset (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite)
CDPL_CHEM_API const Fragment::SharedPointer &	getCyclicSubstructure (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setCyclicSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct)
CDPL_CHEM_API void	clearCyclicSubstructure (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasCyclicSubstructure (const MolecularGraph &molgraph)
CDPL_CHEM_API Fragment::SharedPointer	perceiveCyclicSubstructure (const MolecularGraph &molgraph)
CDPL_CHEM_API Fragment::SharedPointer	perceiveCyclicSubstructure (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API const FragmentList::SharedPointer &	getComponents (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setComponents (MolecularGraph &molgraph, const FragmentList::SharedPointer &comps)
CDPL_CHEM_API void	clearComponents (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasComponents (const MolecularGraph &molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponents (const MolecularGraph &molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponents (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API const FragmentList::SharedPointer &	getComponentGroups (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setComponentGroups (MolecularGraph &molgraph, const FragmentList::SharedPointer &comp_groups)
CDPL_CHEM_API void	clearComponentGroups (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasComponentGroups (const MolecularGraph &molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponentGroups (const MolecularGraph &molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponentGroups (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API std::size_t	getConformationIndex (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setConformationIndex (MolecularGraph &molgraph, std::size_t index)
CDPL_CHEM_API void	clearConformationIndex (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasConformationIndex (const MolecularGraph &molgraph)
CDPL_CHEM_API const Util::DArray::SharedPointer &	getConformerEnergies (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setConformerEnergies (MolecularGraph &molgraph, const Util::DArray::SharedPointer &energies)
CDPL_CHEM_API void	clearConformerEnergies (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasConformerEnergies (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setConformation (MolecularGraph &molgraph, std::size_t conf_idx, const Math::Vector3DArray &coords, double energy)
CDPL_CHEM_API void	addConformation (MolecularGraph &molgraph, const Math::Vector3DArray &coords, double energy)
CDPL_CHEM_API double	getConformationEnergy (const MolecularGraph &molgraph, std::size_t conf_idx)
CDPL_CHEM_API std::uint64_t	getHashCode (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setHashCode (MolecularGraph &molgraph, std::uint64_t hash_code)
CDPL_CHEM_API void	clearHashCode (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasHashCode (const MolecularGraph &molgraph)
CDPL_CHEM_API std::uint64_t	calcHashCode (const MolecularGraph &molgraph, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool ord_h_deplete=true)
CDPL_CHEM_API void	extractReactionCenter (const MolecularGraph &molgraph, Fragment &rxn_center)
CDPL_CHEM_API double	getStoichiometricNumber (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setStoichiometricNumber (MolecularGraph &molgraph, double num)
CDPL_CHEM_API void	clearStoichiometricNumber (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasStoichiometricNumber (const MolecularGraph &molgraph)
CDPL_CHEM_API const std::string &	getMDLUserInitials (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMDLUserInitials (MolecularGraph &molgraph, const std::string &initials)
CDPL_CHEM_API void	clearMDLUserInitials (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMDLUserInitials (const MolecularGraph &molgraph)
CDPL_CHEM_API const std::string &	getMDLProgramName (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMDLProgramName (MolecularGraph &molgraph, const std::string &name)
CDPL_CHEM_API void	clearMDLProgramName (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMDLProgramName (const MolecularGraph &molgraph)
CDPL_CHEM_API std::size_t	getMDLRegistryNumber (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMDLRegistryNumber (MolecularGraph &molgraph, std::size_t reg_no)
CDPL_CHEM_API void	clearMDLRegistryNumber (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMDLRegistryNumber (const MolecularGraph &molgraph)
CDPL_CHEM_API unsigned int	getMDLCTABVersion (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMDLCTABVersion (MolecularGraph &molgraph, unsigned int version)
CDPL_CHEM_API void	clearMDLCTABVersion (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMDLCTABVersion (const MolecularGraph &molgraph)
CDPL_CHEM_API const StringDataBlock::SharedPointer &	getStructureData (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setStructureData (MolecularGraph &molgraph, const StringDataBlock::SharedPointer &data)
CDPL_CHEM_API void	clearStructureData (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasStructureData (const MolecularGraph &molgraph)
CDPL_CHEM_API std::size_t	getMDLDimensionality (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMDLDimensionality (MolecularGraph &molgraph, std::size_t dim)
CDPL_CHEM_API void	clearMDLDimensionality (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMDLDimensionality (const MolecularGraph &molgraph)
CDPL_CHEM_API long	getMDLScalingFactor1 (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMDLScalingFactor1 (MolecularGraph &molgraph, long factor)
CDPL_CHEM_API void	clearMDLScalingFactor1 (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMDLScalingFactor1 (const MolecularGraph &molgraph)
CDPL_CHEM_API double	getMDLScalingFactor2 (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMDLScalingFactor2 (MolecularGraph &molgraph, double factor)
CDPL_CHEM_API void	clearMDLScalingFactor2 (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMDLScalingFactor2 (const MolecularGraph &molgraph)
CDPL_CHEM_API double	getMDLEnergy (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMDLEnergy (MolecularGraph &molgraph, double energy)
CDPL_CHEM_API void	clearMDLEnergy (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMDLEnergy (const MolecularGraph &molgraph)
CDPL_CHEM_API bool	getMDLChiralFlag (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMDLChiralFlag (MolecularGraph &molgraph, bool flag)
CDPL_CHEM_API void	clearMDLChiralFlag (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMDLChiralFlag (const MolecularGraph &molgraph)
CDPL_CHEM_API unsigned int	getMOL2MoleculeType (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMOL2MoleculeType (MolecularGraph &molgraph, unsigned int type)
CDPL_CHEM_API void	clearMOL2MoleculeType (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMOL2MoleculeType (const MolecularGraph &molgraph)
CDPL_CHEM_API unsigned int	getMOL2ChargeType (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setMOL2ChargeType (MolecularGraph &molgraph, unsigned int type)
CDPL_CHEM_API void	clearMOL2ChargeType (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasMOL2ChargeType (const MolecularGraph &molgraph)
CDPL_CHEM_API void	generateAdjacencyMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
CDPL_CHEM_API void	generateIncidenceMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
CDPL_CHEM_API void	generateBondMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
CDPL_CHEM_API void	generateBondElectronMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
CDPL_CHEM_API void	generateBondAtomTypeMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
CDPL_CHEM_API const Math::ULMatrix::SharedPointer &	getTopologicalDistanceMatrix (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setTopologicalDistanceMatrix (MolecularGraph &molgraph, const Math::ULMatrix::SharedPointer &mtx)
CDPL_CHEM_API void	clearTopologicalDistanceMatrix (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasTopologicalDistanceMatrix (const MolecularGraph &molgraph)
CDPL_CHEM_API Math::ULMatrix::SharedPointer	calcTopologicalDistanceMatrix (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	calcTopologicalDistanceMatrix (const MolecularGraph &molgraph, Math::ULMatrix &mtx)
CDPL_CHEM_API Math::ULMatrix::SharedPointer	extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite)
CDPL_CHEM_API void	extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph, Math::ULMatrix &mtx)
CDPL_CHEM_API const Math::DMatrix::SharedPointer &	getGeometricalDistanceMatrix (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setGeometricalDistanceMatrix (MolecularGraph &molgraph, const Math::DMatrix::SharedPointer &mtx)
CDPL_CHEM_API void	clearGeometricalDistanceMatrix (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasGeometricalDistanceMatrix (const MolecularGraph &molgraph)
CDPL_CHEM_API Math::DMatrix::SharedPointer	calcGeometricalDistanceMatrix (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API const Fragment::SharedPointer &	getAromaticSubstructure (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setAromaticSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct)
CDPL_CHEM_API void	clearAromaticSubstructure (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasAromaticSubstructure (const MolecularGraph &molgraph)
CDPL_CHEM_API Fragment::SharedPointer	perceiveAromaticSubstructure (const MolecularGraph &molgraph)
CDPL_CHEM_API Fragment::SharedPointer	perceiveAromaticSubstructure (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API const ElectronSystemList::SharedPointer &	getPiElectronSystems (const MolecularGraph &molgraph)
CDPL_CHEM_API void	setPiElectronSystems (MolecularGraph &molgraph, const ElectronSystemList::SharedPointer &pi_systems)
CDPL_CHEM_API void	clearPiElectronSystems (MolecularGraph &molgraph)
CDPL_CHEM_API bool	hasPiElectronSystems (const MolecularGraph &molgraph)
CDPL_CHEM_API ElectronSystemList::SharedPointer	perceivePiElectronSystems (const MolecularGraph &molgraph)
CDPL_CHEM_API ElectronSystemList::SharedPointer	perceivePiElectronSystems (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API bool	generateSMILES (const MolecularGraph &molgraph, std::string &smiles, bool canonical=false, bool ord_h_deplete=true, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT)
CDPL_CHEM_API int	generateINCHI (const MolecularGraph &molgraph, std::string &inchi, const std::string &options=ControlParameterDefault::INCHI_OUTPUT_OPTIONS, std::size_t dim=0)
CDPL_CHEM_API int	generateINCHIKey (const MolecularGraph &molgraph, std::string &inchi_key)
CDPL_CHEM_API void	canonicalize (MolecularGraph &molgraph, const AtomCompareFunction &func, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false)
CDPL_CHEM_API void	canonicalize (MolecularGraph &molgraph, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false)
CDPL_CHEM_API void	calc2DCoordinates (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	calcHydrogen3DCoordinates (MolecularGraph &molgraph, bool undef_only=true)
CDPL_CHEM_API void	calcBond2DStereoFlags (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	calcCIPPriorities (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	perceiveSymmetryClasses (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool inc_impl_h=true)
CDPL_CHEM_API void	calcCanonicalNumbering (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT)
CDPL_CHEM_API void	calcMorganNumbering (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	calcImplicitHydrogenCounts (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	calcFormalCharges (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	perceiveHybridizationStates (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	perceiveBondOrders (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	kekulizeBonds (MolecularGraph &molgraph)
CDPL_CHEM_API void	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)
CDPL_CHEM_API void	perceiveBondStereoCenters (MolecularGraph &molgraph, bool overwrite, bool check_asym=true, bool check_term_n=true, bool check_order=true, std::size_t min_ring_size=8)
CDPL_CHEM_API void	calcMDLParities (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	calcAtomStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true)
CDPL_CHEM_API void	calcAtomStereoDescriptorsFromMDLParities (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	calcBondStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true)
CDPL_CHEM_API void	calcAtomCIPConfigurations (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	calcBondCIPConfigurations (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	setAtomMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite)
CDPL_CHEM_API void	setBondMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite)
CDPL_CHEM_API void	generateMatchExpressions (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	generateMatchExpressionStrings (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	initSubstructureSearchQuery (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	initSubstructureSearchTarget (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	setAromaticityFlags (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	setRingFlags (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	setAtomTypesFromSymbols (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	setAtomSymbolsFromTypes (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API void	perceiveSybylAtomTypes (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API FragmentList::SharedPointer	getAromaticRings (const MolecularGraph &molgraph)
CDPL_CHEM_API FragmentList::SharedPointer	getAromaticSSSRSubset (const MolecularGraph &molgraph)
CDPL_CHEM_API bool	containsMolecularGraph (const MolecularGraph &molgraph, const MolecularGraph &sub_molgraph, bool atoms=true, bool bonds=true)
CDPL_CHEM_API void	getContainedFragments (const MolecularGraph &molgraph, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false, bool atoms=true, bool bonds=true)
CDPL_CHEM_API void	getContainingFragments (const MolecularGraph &molgraph, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false, bool atoms=true, bool bonds=true)
CDPL_CHEM_API void	translateFragment (const MolecularGraph &src_molgraph, const Fragment &src_frag, const MolecularGraph &tgt_molgraph, Fragment &tgt_frag, bool append=false)
CDPL_CHEM_API void	translateFragments (const MolecularGraph &src_molgraph, const FragmentList &src_frag_list, const MolecularGraph &tgt_molgraph, FragmentList &tgt_frag_list, bool append=false)
CDPL_CHEM_API void	splitIntoFragments (const MolecularGraph &molgraph, FragmentList &frag_list, const Util::BitSet &split_bond_mask, bool append=false)
CDPL_CHEM_API std::size_t	getCompleteBondCount (const MolecularGraph &molgraph)
CDPL_CHEM_API void	calcBasicProperties (MolecularGraph &molgraph, bool overwrite)
CDPL_CHEM_API bool	makeHydrogenDeplete (Molecule &mol, bool corr_impl_h_count=true)
	Removes all explicit hydrogen atoms from the molecule mol. More...
CDPL_CHEM_API bool	makeOrdinaryHydrogenDeplete (Molecule &mol, unsigned int flags, bool corr_impl_h_count=true)
	Removes all explicit ordinary hydrogen atoms from the molecule mol. More...
CDPL_CHEM_API bool	makeHydrogenComplete (Molecule &mol, bool corr_impl_h_count=true)
	Converts all implicit hydrogens of the molecule mol to explicit hydrogen atoms. More...
CDPL_CHEM_API void	connectAtoms (Molecule &mol, double dist_tol=0.3, std::size_t atom_idx_offs=0)
CDPL_CHEM_API void	connectAtoms (Molecule &mol, const Atom3DCoordinatesFunction &coords_func, double dist_tol=0.3, std::size_t atom_idx_offs=0)
CDPL_CHEM_API void	removeAtomsIf (Molecule &mol, const AtomPredicate &pred)
CDPL_CHEM_API void	removeAtomsIfNot (Molecule &mol, const AtomPredicate &pred)
CDPL_CHEM_API const std::string &	getName (const Reaction &rxn)
CDPL_CHEM_API void	setName (Reaction &rxn, const std::string &name)
CDPL_CHEM_API void	clearName (Reaction &rxn)
CDPL_CHEM_API bool	hasName (const Reaction &rxn)
CDPL_CHEM_API std::time_t	getTimestamp (const Reaction &rxn)
CDPL_CHEM_API void	setTimestamp (Reaction &rxn, std::time_t time)
CDPL_CHEM_API void	clearTimestamp (Reaction &rxn)
CDPL_CHEM_API bool	hasTimestamp (const Reaction &rxn)
CDPL_CHEM_API const std::string &	getComment (const Reaction &rxn)
CDPL_CHEM_API void	setComment (Reaction &rxn, const std::string &comment)
CDPL_CHEM_API void	clearComment (Reaction &rxn)
CDPL_CHEM_API bool	hasComment (const Reaction &rxn)
CDPL_CHEM_API const MatchExpression< Reaction >::SharedPointer &	getMatchExpression (const Reaction &rxn)
CDPL_CHEM_API void	setMatchExpression (Reaction &rxn, const MatchExpression< Reaction >::SharedPointer &expr)
CDPL_CHEM_API void	clearMatchExpression (Reaction &rxn)
CDPL_CHEM_API bool	hasMatchExpression (const Reaction &rxn)
CDPL_CHEM_API MatchExpression< Reaction >::SharedPointer	generateMatchExpression (const Reaction &rxn)
CDPL_CHEM_API MatchExpression< Reaction >::SharedPointer	generateMatchExpression (Reaction &rxn, bool overwrite)
CDPL_CHEM_API const MatchConstraintList::SharedPointer &	getMatchConstraints (const Reaction &rxn)
CDPL_CHEM_API void	setMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr)
CDPL_CHEM_API void	clearMatchConstraints (Reaction &rxn)
CDPL_CHEM_API bool	hasMatchConstraints (const Reaction &rxn)
CDPL_CHEM_API const FragmentList::SharedPointer &	getComponentGroups (const Reaction &rxn)
CDPL_CHEM_API void	setComponentGroups (Reaction &rxn, const FragmentList::SharedPointer &comp_groups)
CDPL_CHEM_API void	clearComponentGroups (Reaction &rxn)
CDPL_CHEM_API bool	hasComponentGroups (const Reaction &rxn)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponentGroups (const Reaction &rxn)
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponentGroups (Reaction &rxn, bool overwrite)
CDPL_CHEM_API const AtomMapping::SharedPointer &	getAtomMapping (const Reaction &rxn)
CDPL_CHEM_API void	setAtomMapping (Reaction &rxn, const AtomMapping::SharedPointer &mapping)
CDPL_CHEM_API void	clearAtomMapping (Reaction &rxn)
CDPL_CHEM_API bool	hasAtomMapping (const Reaction &rxn)
CDPL_CHEM_API AtomMapping::SharedPointer	perceiveAtomMapping (const Reaction &rxn)
CDPL_CHEM_API AtomMapping::SharedPointer	perceiveAtomMapping (Reaction &rxn, bool overwrite)
CDPL_CHEM_API bool	generateSMILES (const Reaction &rxn, std::string &smiles, bool canonical=false, bool ord_h_deplete=true, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT)
CDPL_CHEM_API std::uint64_t	calcHashCode (const Reaction &rxn, unsigned int role_mask=ReactionRole::ALL, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool ord_h_deplete=true)
CDPL_CHEM_API const std::string &	getMDLUserInitials (const Reaction &rxn)
CDPL_CHEM_API void	setMDLUserInitials (Reaction &rxn, const std::string &initials)
CDPL_CHEM_API void	clearMDLUserInitials (Reaction &rxn)
CDPL_CHEM_API bool	hasMDLUserInitials (const Reaction &rxn)
CDPL_CHEM_API const std::string &	getMDLProgramName (const Reaction &rxn)
CDPL_CHEM_API void	setMDLProgramName (Reaction &rxn, const std::string &name)
CDPL_CHEM_API void	clearMDLProgramName (Reaction &rxn)
CDPL_CHEM_API bool	hasMDLProgramName (const Reaction &rxn)
CDPL_CHEM_API std::size_t	getMDLRegistryNumber (const Reaction &rxn)
CDPL_CHEM_API void	setMDLRegistryNumber (Reaction &rxn, std::size_t reg_no)
CDPL_CHEM_API void	clearMDLRegistryNumber (Reaction &rxn)
CDPL_CHEM_API bool	hasMDLRegistryNumber (const Reaction &rxn)
CDPL_CHEM_API const StringDataBlock::SharedPointer &	getReactionData (const Reaction &rxn)
CDPL_CHEM_API void	setReactionData (Reaction &rxn, const StringDataBlock::SharedPointer &data)
CDPL_CHEM_API void	clearReactionData (Reaction &rxn)
CDPL_CHEM_API bool	hasReactionData (const Reaction &rxn)
CDPL_CHEM_API const Molecule::SharedPointer &	getMDLMoleculeRecord (const Reaction &rxn)
CDPL_CHEM_API void	setMDLMoleculeRecord (Reaction &rxn, const Molecule::SharedPointer &mol_rec)
CDPL_CHEM_API void	clearMDLMoleculeRecord (Reaction &rxn)
CDPL_CHEM_API bool	hasMDLMoleculeRecord (const Reaction &rxn)
CDPL_CHEM_API const std::string &	getMDLInternalRegistryNumber (const Reaction &rxn)
CDPL_CHEM_API void	setMDLInternalRegistryNumber (Reaction &rxn, const std::string &reg_no)
CDPL_CHEM_API void	clearMDLInternalRegistryNumber (Reaction &rxn)
CDPL_CHEM_API bool	hasMDLInternalRegistryNumber (const Reaction &rxn)
CDPL_CHEM_API const std::string &	getMDLExternalRegistryNumber (const Reaction &rxn)
CDPL_CHEM_API void	setMDLExternalRegistryNumber (Reaction &rxn, const std::string &reg_no)
CDPL_CHEM_API void	clearMDLExternalRegistryNumber (Reaction &rxn)
CDPL_CHEM_API bool	hasMDLExternalRegistryNumber (const Reaction &rxn)
CDPL_CHEM_API unsigned int	getMDLRXNFileVersion (const Reaction &rxn)
CDPL_CHEM_API void	setMDLRXNFileVersion (Reaction &rxn, unsigned int version)
CDPL_CHEM_API void	clearMDLRXNFileVersion (Reaction &rxn)
CDPL_CHEM_API bool	hasMDLRXNFileVersion (const Reaction &rxn)
CDPL_CHEM_API std::size_t	getMaxComponentGroupID (const Reaction &rxn)
CDPL_CHEM_API std::size_t	getMaxAtomMappingID (const Reaction &rxn)
CDPL_CHEM_API void	setAtomMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite)
CDPL_CHEM_API void	setBondMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite)
CDPL_CHEM_API void	setComponentMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite)
CDPL_CHEM_API void	generateMatchExpressions (Reaction &rxn, bool overwrite)
CDPL_CHEM_API void	initSubstructureSearchQuery (Reaction &rxn, bool overwrite)
CDPL_CHEM_API void	initSubstructureSearchTarget (Reaction &rxn, bool overwrite)
CDPL_CHEM_API void	calcBasicProperties (Reaction &rxn, bool overwrite)
CDPL_CHEM_API Molecule::SharedPointer	parseSMARTS (const std::string &smarts, bool init_qry=true)
CDPL_CHEM_API bool	parseSMARTS (const std::string &smarts, Molecule &mol, bool init_qry=true)
CDPL_CHEM_API Molecule::SharedPointer	parseSMILES (const std::string &smiles)
CDPL_CHEM_API bool	parseSMILES (const std::string &smiles, Molecule &mol)
CDPL_CHEM_API void	extendBoundingBox (Math::Vector3D &min, Math::Vector3D &max, const Math::Vector3D &coords, bool reset=false)
CDPL_CHEM_API bool	insideBoundingBox (const Math::Vector3D &min, const Math::Vector3D &max, const Math::Vector3D &coords)
CDPL_CHEM_API bool	isAromatic (const Fragment &ring, const MolecularGraph &molgraph, const Util::BitSet &arom_bond_mask)
CDPL_CHEM_API bool	isNotAromatic (const Fragment &ring, const MolecularGraph &molgraph)
CDPL_CHEM_API bool	containsFragmentWithBond (const FragmentList &frag_list, const Bond &bond)
CDPL_CHEM_API bool	containsFragmentWithMinSize (const FragmentList &frag_list, std::size_t min_size)
CDPL_CHEM_API bool	atomTypesMatch (unsigned int qry_type, unsigned int tgt_type)
CDPL_CHEM_API unsigned int	sybylToAtomType (unsigned int sybyl_type)
CDPL_CHEM_API const std::string &	getSybylAtomTypeString (unsigned int sybyl_type)
CDPL_CHEM_API const std::string &	getSybylBondTypeString (unsigned int sybyl_type)

Detailed Description

Contains classes and functions related to chemistry.

Typedef Documentation

Atom3DCoordinatesFunction

typedef std::function<const Math::Vector3D&(const Chem::Atom&)> CDPL::Chem::Atom3DCoordinatesFunction

A generic wrapper class used to store a user-defined Chem::Atom 3D-coordinates function.

AtomCompareFunction

typedef std::function<bool(const Chem::Atom&, const Chem::Atom&)> CDPL::Chem::AtomCompareFunction

A generic wrapper class used to store a user-defined atom compare function.

AtomPredicate

typedef std::function<bool(const Chem::Atom&)> CDPL::Chem::AtomPredicate

A generic wrapper class used to store a user-defined atom predicate.

AtomPriorityFunction

typedef std::function<std::size_t(const Chem::Atom&)> CDPL::Chem::AtomPriorityFunction

A generic wrapper class used to store a user-defined atom priority function.

BondCompareFunction

typedef std::function<bool(const Chem::Bond&, const Chem::Bond&)> CDPL::Chem::BondCompareFunction

A generic wrapper class used to store a user-defined bond compare function.

BondPredicate

typedef std::function<bool(const Chem::Bond&)> CDPL::Chem::BondPredicate

A generic wrapper class used to store a user-defined bond predicate.

CDFBZ2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<CDFBZ2MolecularGraphWriter, DataFormat::CDF_BZ2> CDPL::Chem::CDFBZ2MolecularGraphOutputHandler

A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL.

CDFBZ2MolecularGraphWriter

typedef Util::CompressedDataWriter<CDFMolecularGraphWriter, Util::BZip2OStream> CDPL::Chem::CDFBZ2MolecularGraphWriter

CDFBZ2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<CDFBZ2MoleculeReader, DataFormat::CDF_BZ2> CDPL::Chem::CDFBZ2MoleculeInputHandler

A handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL.

CDFBZ2MoleculeReader

typedef Util::CompressedDataReader<CDFMoleculeReader, Util::BZip2IStream> CDPL::Chem::CDFBZ2MoleculeReader

CDFBZ2ReactionInputHandler

typedef Util::DefaultDataInputHandler<CDFBZ2ReactionReader, DataFormat::CDF_BZ2> CDPL::Chem::CDFBZ2ReactionInputHandler

A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL.

CDFBZ2ReactionOutputHandler

typedef Util::DefaultDataOutputHandler<CDFBZ2ReactionWriter, DataFormat::CDF_BZ2> CDPL::Chem::CDFBZ2ReactionOutputHandler

A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL.

CDFBZ2ReactionReader

typedef Util::CompressedDataReader<CDFReactionReader, Util::BZip2IStream> CDPL::Chem::CDFBZ2ReactionReader

CDFBZ2ReactionWriter

typedef Util::CompressedDataWriter<CDFReactionWriter, Util::BZip2OStream> CDPL::Chem::CDFBZ2ReactionWriter

CDFGZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<CDFGZMolecularGraphWriter, DataFormat::CDF_GZ> CDPL::Chem::CDFGZMolecularGraphOutputHandler

A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL.

CDFGZMolecularGraphWriter

typedef Util::CompressedDataWriter<CDFMolecularGraphWriter, Util::GZipOStream> CDPL::Chem::CDFGZMolecularGraphWriter

CDFGZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<CDFGZMoleculeReader, DataFormat::CDF_GZ> CDPL::Chem::CDFGZMoleculeInputHandler

A handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL.

CDFGZMoleculeReader

typedef Util::CompressedDataReader<CDFMoleculeReader, Util::GZipIStream> CDPL::Chem::CDFGZMoleculeReader

CDFGZReactionInputHandler

typedef Util::DefaultDataInputHandler<CDFGZReactionReader, DataFormat::CDF_GZ> CDPL::Chem::CDFGZReactionInputHandler

A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL.

CDFGZReactionOutputHandler

typedef Util::DefaultDataOutputHandler<CDFGZReactionWriter, DataFormat::CDF_GZ> CDPL::Chem::CDFGZReactionOutputHandler

A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL.

CDFGZReactionReader

typedef Util::CompressedDataReader<CDFReactionReader, Util::GZipIStream> CDPL::Chem::CDFGZReactionReader

CDFGZReactionWriter

typedef Util::CompressedDataWriter<CDFReactionWriter, Util::GZipOStream> CDPL::Chem::CDFGZReactionWriter

CDFMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<CDFMolecularGraphWriter, DataFormat::CDF> CDPL::Chem::CDFMolecularGraphOutputHandler

A handler for the output of molecular graph data in the native I/O format of the CDPL.

CDFMoleculeInputHandler

typedef Util::DefaultDataInputHandler<CDFMoleculeReader, DataFormat::CDF> CDPL::Chem::CDFMoleculeInputHandler

A handler for the input of molecule data in the native I/O format of the CDPL.

CDFReactionInputHandler

typedef Util::DefaultDataInputHandler<CDFReactionReader, DataFormat::CDF> CDPL::Chem::CDFReactionInputHandler

A handler for the input of reaction data in the native I/O format of the CDPL.

CDFReactionOutputHandler

typedef Util::DefaultDataOutputHandler<CDFReactionWriter, DataFormat::CDF> CDPL::Chem::CDFReactionOutputHandler

A handler for the output of reaction data in the native I/O format of the CDPL.

Entity3DCoordinatesFunction

typedef std::function<const Math::Vector3D&(const Chem::Entity&)> CDPL::Chem::Entity3DCoordinatesFunction

A generic wrapper class used to store a user-defined Chem::Entity3D coordinates function.

INCHIMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<INCHIMolecularGraphWriter, DataFormat::INCHI> CDPL::Chem::INCHIMolecularGraphOutputHandler

A handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format.

INCHIMoleculeInputHandler

typedef Util::DefaultDataInputHandler<INCHIMoleculeReader, DataFormat::INCHI> CDPL::Chem::INCHIMoleculeInputHandler

A handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format.

JMEMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<JMEMolecularGraphWriter, DataFormat::JME> CDPL::Chem::JMEMolecularGraphOutputHandler

A handler for the output of molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet.

JMEMoleculeInputHandler

typedef Util::DefaultDataInputHandler<JMEMoleculeReader, DataFormat::JME> CDPL::Chem::JMEMoleculeInputHandler

A handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME] java applet.

JMEReactionInputHandler

typedef Util::DefaultDataInputHandler<JMEReactionReader, DataFormat::JME> CDPL::Chem::JMEReactionInputHandler

A handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet.

JMEReactionOutputHandler

typedef Util::DefaultDataOutputHandler<JMEReactionWriter, DataFormat::JME> CDPL::Chem::JMEReactionOutputHandler

A handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet.

MOL2BZ2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MOL2BZ2MolecularGraphWriter, DataFormat::MOL2_BZ2> CDPL::Chem::MOL2BZ2MolecularGraphOutputHandler

A handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format.

MOL2BZ2MolecularGraphWriter

typedef Util::CompressedDataWriter<MOL2MolecularGraphWriter, Util::BZip2OStream> CDPL::Chem::MOL2BZ2MolecularGraphWriter

MOL2BZ2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<MOL2BZ2MoleculeReader, DataFormat::MOL2_BZ2> CDPL::Chem::MOL2BZ2MoleculeInputHandler

A handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format.

MOL2BZ2MoleculeReader

typedef Util::CompressedDataReader<MOL2MoleculeReader, Util::BZip2IStream> CDPL::Chem::MOL2BZ2MoleculeReader

MOL2GZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MOL2GZMolecularGraphWriter, DataFormat::MOL2_GZ> CDPL::Chem::MOL2GZMolecularGraphOutputHandler

A handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format.

MOL2GZMolecularGraphWriter

typedef Util::CompressedDataWriter<MOL2MolecularGraphWriter, Util::GZipOStream> CDPL::Chem::MOL2GZMolecularGraphWriter

MOL2GZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<MOL2GZMoleculeReader, DataFormat::MOL2_GZ> CDPL::Chem::MOL2GZMoleculeInputHandler

A handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format.

MOL2GZMoleculeReader

typedef Util::CompressedDataReader<MOL2MoleculeReader, Util::GZipIStream> CDPL::Chem::MOL2GZMoleculeReader

MOL2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MOL2MolecularGraphWriter, DataFormat::MOL2> CDPL::Chem::MOL2MolecularGraphOutputHandler

A handler for the output of molecular graph data in the Sybyl MOL2 format.

MOL2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<MOL2MoleculeReader, DataFormat::MOL2> CDPL::Chem::MOL2MoleculeInputHandler

A handler for the input of molecule data in the Sybyl MOL2 format.

MolecularGraphWriter

typedef Util::MultiFormatDataWriter<MolecularGraph> CDPL::Chem::MolecularGraphWriter

Writer for molecule data in any supported format.

MoleculeReader

typedef Util::MultiFormatDataReader<Molecule> CDPL::Chem::MoleculeReader

Reader for molecule data in any supported format.

MOLMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MOLMolecularGraphWriter, DataFormat::MOL> CDPL::Chem::MOLMolecularGraphOutputHandler

A handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format.

MOLMoleculeInputHandler

typedef Util::DefaultDataInputHandler<MOLMoleculeReader, DataFormat::MOL> CDPL::Chem::MOLMoleculeInputHandler

A handler for the input of molecule data in the MDL Mol-File [CTFILE] format.

RDFBZ2ReactionInputHandler

typedef Util::DefaultDataInputHandler<RDFBZ2ReactionReader, DataFormat::RDF_BZ2> CDPL::Chem::RDFBZ2ReactionInputHandler

A handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format.

RDFBZ2ReactionOutputHandler

typedef Util::DefaultDataOutputHandler<RDFBZ2ReactionWriter, DataFormat::RDF_BZ2> CDPL::Chem::RDFBZ2ReactionOutputHandler

A handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format.

RDFBZ2ReactionReader

typedef Util::CompressedDataReader<RDFReactionReader, Util::BZip2IStream> CDPL::Chem::RDFBZ2ReactionReader

RDFBZ2ReactionWriter

typedef Util::CompressedDataWriter<RDFReactionWriter, Util::BZip2OStream> CDPL::Chem::RDFBZ2ReactionWriter

RDFGZReactionInputHandler

typedef Util::DefaultDataInputHandler<RDFGZReactionReader, DataFormat::RDF_GZ> CDPL::Chem::RDFGZReactionInputHandler

A handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE] format.

RDFGZReactionOutputHandler

typedef Util::DefaultDataOutputHandler<RDFGZReactionWriter, DataFormat::RDF_GZ> CDPL::Chem::RDFGZReactionOutputHandler

A handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format.

RDFGZReactionReader

typedef Util::CompressedDataReader<RDFReactionReader, Util::GZipIStream> CDPL::Chem::RDFGZReactionReader

RDFGZReactionWriter

typedef Util::CompressedDataWriter<RDFReactionWriter, Util::GZipOStream> CDPL::Chem::RDFGZReactionWriter

RDFReactionInputHandler

typedef Util::DefaultDataInputHandler<RDFReactionReader, DataFormat::RDF> CDPL::Chem::RDFReactionInputHandler

A handler for the input of reaction data in the MDL RD-File [CTFILE] format.

RDFReactionOutputHandler

typedef Util::DefaultDataOutputHandler<RDFReactionWriter, DataFormat::RDF> CDPL::Chem::RDFReactionOutputHandler

A handler for the output of reaction data in the MDL RD-File [CTFILE] format.

ReactionReader

typedef Util::MultiFormatDataReader<Reaction> CDPL::Chem::ReactionReader

Reader for reaction data in any supported format.

ReactionWriter

typedef Util::MultiFormatDataWriter<Reaction> CDPL::Chem::ReactionWriter

Writer for reaction data in any supported format.

RXNReactionInputHandler

typedef Util::DefaultDataInputHandler<RXNReactionReader, DataFormat::RXN> CDPL::Chem::RXNReactionInputHandler

A handler for the input of reaction data in the MDL Rxn-File [CTFILE] format.

RXNReactionOutputHandler

typedef Util::DefaultDataOutputHandler<RXNReactionWriter, DataFormat::RXN> CDPL::Chem::RXNReactionOutputHandler

A handler for the output of reaction data in the MDL Rxn-File [CTFILE] format.

SDFBZ2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<SDFBZ2MolecularGraphWriter, DataFormat::SDF_BZ2> CDPL::Chem::SDFBZ2MolecularGraphOutputHandler

A handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE] format.

SDFBZ2MolecularGraphWriter

typedef Util::CompressedDataWriter<SDFMolecularGraphWriter, Util::BZip2OStream> CDPL::Chem::SDFBZ2MolecularGraphWriter

SDFBZ2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<SDFBZ2MoleculeReader, DataFormat::SDF_BZ2> CDPL::Chem::SDFBZ2MoleculeInputHandler

A handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format.

SDFBZ2MoleculeReader

typedef Util::CompressedDataReader<SDFMoleculeReader, Util::BZip2IStream> CDPL::Chem::SDFBZ2MoleculeReader

SDFGZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<SDFGZMolecularGraphWriter, DataFormat::SDF_GZ> CDPL::Chem::SDFGZMolecularGraphOutputHandler

A handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE] format.

SDFGZMolecularGraphWriter

typedef Util::CompressedDataWriter<SDFMolecularGraphWriter, Util::GZipOStream> CDPL::Chem::SDFGZMolecularGraphWriter

SDFGZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<SDFGZMoleculeReader, DataFormat::SDF_GZ> CDPL::Chem::SDFGZMoleculeInputHandler

A handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format.

SDFGZMoleculeReader

typedef Util::CompressedDataReader<SDFMoleculeReader, Util::GZipIStream> CDPL::Chem::SDFGZMoleculeReader

SDFMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<SDFMolecularGraphWriter, DataFormat::SDF> CDPL::Chem::SDFMolecularGraphOutputHandler

A handler for the output of molecular graph data in the MDL SD-File [CTFILE] format.

SDFMoleculeInputHandler

typedef Util::DefaultDataInputHandler<SDFMoleculeReader, DataFormat::SDF> CDPL::Chem::SDFMoleculeInputHandler

A handler for the input of molecule data in the MDL SD-File [CTFILE] format.

SMARTSMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<SMARTSMolecularGraphWriter, DataFormat::SMARTS> CDPL::Chem::SMARTSMolecularGraphOutputHandler

A handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format.

SMARTSMoleculeInputHandler

typedef Util::DefaultDataInputHandler<SMARTSMoleculeReader, DataFormat::SMARTS> CDPL::Chem::SMARTSMoleculeInputHandler

A handler for the input of molecule data in the Daylight SMARTS [SMARTS] format.

SMARTSReactionInputHandler

typedef Util::DefaultDataInputHandler<SMARTSReactionReader, DataFormat::SMARTS> CDPL::Chem::SMARTSReactionInputHandler

A handler for the input of reaction data in the Daylight SMARTS [SMARTS] format.

SMARTSReactionOutputHandler

typedef Util::DefaultDataOutputHandler<SMARTSReactionWriter, DataFormat::SMARTS> CDPL::Chem::SMARTSReactionOutputHandler

A handler for the output of reaction data in the Daylight SMARTS [SMARTS] format.

SMILESBZ2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<SMILESBZ2MolecularGraphWriter, DataFormat::SMILES_BZ2> CDPL::Chem::SMILESBZ2MolecularGraphOutputHandler

A handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format.

SMILESBZ2MolecularGraphWriter

typedef Util::CompressedDataWriter<SMILESMolecularGraphWriter, Util::BZip2OStream> CDPL::Chem::SMILESBZ2MolecularGraphWriter

SMILESBZ2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<SMILESBZ2MoleculeReader, DataFormat::SMILES_BZ2> CDPL::Chem::SMILESBZ2MoleculeInputHandler

A handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format.

SMILESBZ2MoleculeReader

typedef Util::CompressedDataReader<SMILESMoleculeReader, Util::BZip2IStream> CDPL::Chem::SMILESBZ2MoleculeReader

SMILESBZ2ReactionInputHandler

typedef Util::DefaultDataInputHandler<SMILESBZ2ReactionReader, DataFormat::SMILES_BZ2> CDPL::Chem::SMILESBZ2ReactionInputHandler

A handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format.

SMILESBZ2ReactionOutputHandler

typedef Util::DefaultDataOutputHandler<SMILESBZ2ReactionWriter, DataFormat::SMILES_BZ2> CDPL::Chem::SMILESBZ2ReactionOutputHandler

A handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format.

SMILESBZ2ReactionReader

typedef Util::CompressedDataReader<SMILESReactionReader, Util::BZip2IStream> CDPL::Chem::SMILESBZ2ReactionReader

SMILESBZ2ReactionWriter

typedef Util::CompressedDataWriter<SMILESReactionWriter, Util::BZip2OStream> CDPL::Chem::SMILESBZ2ReactionWriter

SMILESGZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<SMILESGZMolecularGraphWriter, DataFormat::SMILES_GZ> CDPL::Chem::SMILESGZMolecularGraphOutputHandler

A handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format.

SMILESGZMolecularGraphWriter

typedef Util::CompressedDataWriter<SMILESMolecularGraphWriter, Util::GZipOStream> CDPL::Chem::SMILESGZMolecularGraphWriter

SMILESGZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<SMILESGZMoleculeReader, DataFormat::SMILES_GZ> CDPL::Chem::SMILESGZMoleculeInputHandler

A handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format.

SMILESGZMoleculeReader

typedef Util::CompressedDataReader<SMILESMoleculeReader, Util::GZipIStream> CDPL::Chem::SMILESGZMoleculeReader

SMILESGZReactionInputHandler

typedef Util::DefaultDataInputHandler<SMILESGZReactionReader, DataFormat::SMILES_GZ> CDPL::Chem::SMILESGZReactionInputHandler

A handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format.

SMILESGZReactionOutputHandler

typedef Util::DefaultDataOutputHandler<SMILESGZReactionWriter, DataFormat::SMILES_GZ> CDPL::Chem::SMILESGZReactionOutputHandler

A handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format.

SMILESGZReactionReader

typedef Util::CompressedDataReader<SMILESReactionReader, Util::GZipIStream> CDPL::Chem::SMILESGZReactionReader

SMILESGZReactionWriter

typedef Util::CompressedDataWriter<SMILESReactionWriter, Util::GZipOStream> CDPL::Chem::SMILESGZReactionWriter

SMILESMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<SMILESMolecularGraphWriter, DataFormat::SMILES> CDPL::Chem::SMILESMolecularGraphOutputHandler

A handler for the output of molecular graph data in the Daylight SMILES [SMILES] format.

SMILESMoleculeInputHandler

typedef Util::DefaultDataInputHandler<SMILESMoleculeReader, DataFormat::SMILES> CDPL::Chem::SMILESMoleculeInputHandler

A handler for the input of molecule data in the Daylight SMILES [SMILES] format.

SMILESReactionInputHandler

typedef Util::DefaultDataInputHandler<SMILESReactionReader, DataFormat::SMILES> CDPL::Chem::SMILESReactionInputHandler

A handler for the input of reaction data in the Daylight SMILES [SMILES] format.

SMILESReactionOutputHandler

typedef Util::DefaultDataOutputHandler<SMILESReactionWriter, DataFormat::SMILES> CDPL::Chem::SMILESReactionOutputHandler

A handler for the output of reaction data in the Daylight SMILES [SMILES] format.

XYZBZ2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<XYZBZ2MolecularGraphWriter, DataFormat::XYZ_BZ2> CDPL::Chem::XYZBZ2MolecularGraphOutputHandler

A handler for the output of bzip2-compressed molecular graph data in the XYZ format.

XYZBZ2MolecularGraphWriter

typedef Util::CompressedDataWriter<XYZMolecularGraphWriter, Util::BZip2OStream> CDPL::Chem::XYZBZ2MolecularGraphWriter

XYZBZ2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<XYZBZ2MoleculeReader, DataFormat::XYZ_BZ2> CDPL::Chem::XYZBZ2MoleculeInputHandler

A handler for the input of bzip2-compressed molecule data in the XYZ format.

XYZBZ2MoleculeReader

typedef Util::CompressedDataReader<XYZMoleculeReader, Util::BZip2IStream> CDPL::Chem::XYZBZ2MoleculeReader

XYZGZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<XYZGZMolecularGraphWriter, DataFormat::XYZ_GZ> CDPL::Chem::XYZGZMolecularGraphOutputHandler

A handler for the output of gzip-compressed molecular graph data in the XYZ format.

XYZGZMolecularGraphWriter

typedef Util::CompressedDataWriter<XYZMolecularGraphWriter, Util::GZipOStream> CDPL::Chem::XYZGZMolecularGraphWriter

XYZGZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<XYZGZMoleculeReader, DataFormat::XYZ_GZ> CDPL::Chem::XYZGZMoleculeInputHandler

A handler for the input of gzip-compressed molecule data in the XYZ format.

XYZGZMoleculeReader

typedef Util::CompressedDataReader<XYZMoleculeReader, Util::GZipIStream> CDPL::Chem::XYZGZMoleculeReader

XYZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<XYZMolecularGraphWriter, DataFormat::XYZ> CDPL::Chem::XYZMolecularGraphOutputHandler

A handler for the output of molecular graph data in the XYZ format.

XYZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<XYZMoleculeReader, DataFormat::XYZ> CDPL::Chem::XYZMoleculeInputHandler

A handler for the input of molecule data in the XYZ format.

Function Documentation

hasCoordinates()

CDPL_CHEM_API bool CDPL::Chem::hasCoordinates	(	const AtomContainer &	cntnr,
		std::size_t	dim
	)

get2DCoordinates() [1/2]

CDPL_CHEM_API void CDPL::Chem::get2DCoordinates	(	const AtomContainer &	cntnr,
		Math::Vector2DArray &	coords,
		bool	append = false
	)

set2DCoordinates() [1/2]

CDPL_CHEM_API void CDPL::Chem::set2DCoordinates	(	AtomContainer &	cntnr,
		const Math::Vector2DArray &	coords
	)

transform2DCoordinates()

CDPL_CHEM_API void CDPL::Chem::transform2DCoordinates	(	AtomContainer &	cntnr,
		const Math::Matrix3D &	mtx
	)

get3DCoordinates() [1/3]

CDPL_CHEM_API void CDPL::Chem::get3DCoordinates	(	const AtomContainer &	cntnr,
		Math::Vector3DArray &	coords,
		const Atom3DCoordinatesFunction &	coords_func,
		bool	append = false
	)

clearConformations()

CDPL_CHEM_API void CDPL::Chem::clearConformations

(

AtomContainer &

cntnr

)

getNumConformations()

CDPL_CHEM_API std::size_t CDPL::Chem::getNumConformations

(

const AtomContainer &

cntnr

)

applyConformation()

CDPL_CHEM_API void CDPL::Chem::applyConformation	(	AtomContainer &	cntnr,
		std::size_t	conf_idx
	)

getConformation()

CDPL_CHEM_API void CDPL::Chem::getConformation	(	const AtomContainer &	cntnr,
		std::size_t	conf_idx,
		Math::Vector3DArray &	coords,
		bool	append = false
	)

setConformation() [1/2]

CDPL_CHEM_API void CDPL::Chem::setConformation	(	AtomContainer &	cntnr,
		std::size_t	conf_idx,
		const Math::Vector3DArray &	coords
	)

addConformation() [1/2]

CDPL_CHEM_API void CDPL::Chem::addConformation	(	AtomContainer &	cntnr,
		const Math::Vector3DArray &	coords
	)

transformConformation()

CDPL_CHEM_API void CDPL::Chem::transformConformation	(	AtomContainer &	cntnr,
		std::size_t	conf_idx,
		const Math::Matrix4D &	mtx
	)

transformConformations()

CDPL_CHEM_API void CDPL::Chem::transformConformations	(	AtomContainer &	cntnr,
		const Math::Matrix4D &	mtx
	)

alignConformations() [1/4]

CDPL_CHEM_API bool CDPL::Chem::alignConformations	(	AtomContainer &	cntnr,
		const Util::BitSet &	ref_atoms,
		const Math::Vector3DArray &	ref_coords
	)

alignConformations() [2/4]

CDPL_CHEM_API bool CDPL::Chem::alignConformations	(	AtomContainer &	cntnr,
		const AtomContainer &	ref_atoms,
		const Math::Vector3DArray &	ref_coords
	)

alignConformations() [3/4]

CDPL_CHEM_API bool CDPL::Chem::alignConformations	(	AtomContainer &	cntnr,
		const Util::BitSet &	ref_atoms
	)

alignConformations() [4/4]

CDPL_CHEM_API bool CDPL::Chem::alignConformations	(	AtomContainer &	cntnr,
		const AtomContainer &	ref_atoms
	)

getMaxComponentGroupID() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxComponentGroupID

(

const AtomContainer &

cntnr

)

getMaxAtomMappingID() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxAtomMappingID

(

const AtomContainer &

cntnr

)

createAtomTypeMask()

CDPL_CHEM_API std::size_t CDPL::Chem::createAtomTypeMask	(	const AtomContainer &	cntnr,
		Util::BitSet &	mask,
		unsigned int	type,
		bool	reset = true,
		bool	strict = true
	)

copyAtomsIf() [1/2]

CDPL_CHEM_API void CDPL::Chem::copyAtomsIf	(	const AtomContainer &	cntnr,
		Molecule &	mol,
		const AtomPredicate &	pred,
		bool	append = false
	)

copyAtomsIf() [2/2]

CDPL_CHEM_API void CDPL::Chem::copyAtomsIf	(	const AtomContainer &	cntnr,
		Fragment &	frag,
		const AtomPredicate &	pred,
		bool	append = false
	)

copyAtomsIfNot() [1/2]

CDPL_CHEM_API void CDPL::Chem::copyAtomsIfNot	(	const AtomContainer &	cntnr,
		Molecule &	mol,
		const AtomPredicate &	pred,
		bool	append = false
	)

copyAtomsIfNot() [2/2]

CDPL_CHEM_API void CDPL::Chem::copyAtomsIfNot	(	const AtomContainer &	cntnr,
		Fragment &	frag,
		const AtomPredicate &	pred,
		bool	append = false
	)

calcCenterOfMass()

CDPL_CHEM_API bool CDPL::Chem::calcCenterOfMass	(	const AtomContainer &	cntnr,
		const Atom3DCoordinatesFunction &	coords_func,
		Math::Vector3D &	ctr
	)

calcCentroid() [1/2]

CDPL_CHEM_API bool CDPL::Chem::calcCentroid	(	const AtomContainer &	cntnr,
		const Atom3DCoordinatesFunction &	coords_func,
		Math::Vector3D &	ctr
	)

calcBoundingBox() [1/2]

CDPL_CHEM_API void CDPL::Chem::calcBoundingBox	(	const AtomContainer &	cntnr,
		Math::Vector3D &	min,
		Math::Vector3D &	max,
		const Atom3DCoordinatesFunction &	coords_func,
		bool	reset = true
	)

insideBoundingBox() [1/3]

CDPL_CHEM_API bool CDPL::Chem::insideBoundingBox	(	const AtomContainer &	cntnr,
		const Math::Vector3D &	min,
		const Math::Vector3D &	max,
		const Atom3DCoordinatesFunction &	coords_func
	)

intersectsBoundingBox() [1/2]

CDPL_CHEM_API bool CDPL::Chem::intersectsBoundingBox	(	const AtomContainer &	cntnr,
		const Math::Vector3D &	min,
		const Math::Vector3D &	max,
		const Atom3DCoordinatesFunction &	coords_func
	)

getName() [1/3]

CDPL_CHEM_API const std::string& CDPL::Chem::getName

(

const Atom &

atom

)

setName() [1/3]

CDPL_CHEM_API void CDPL::Chem::setName	(	Atom &	atom,
		const std::string &	name
	)

clearName() [1/3]

CDPL_CHEM_API void CDPL::Chem::clearName

(

Atom &

atom

)

hasName() [1/3]

CDPL_CHEM_API bool CDPL::Chem::hasName

(

const Atom &

atom

)

getSymbol()

CDPL_CHEM_API const std::string& CDPL::Chem::getSymbol

(

const Atom &

atom

)

setSymbol()

CDPL_CHEM_API void CDPL::Chem::setSymbol	(	Atom &	atom,
		const std::string &	symbol
	)

clearSymbol()

CDPL_CHEM_API void CDPL::Chem::clearSymbol

(

Atom &

atom

)

hasSymbol()

CDPL_CHEM_API bool CDPL::Chem::hasSymbol

(

const Atom &

atom

)

getSymbolForType()

CDPL_CHEM_API const std::string& CDPL::Chem::getSymbolForType

(

const Atom &

atom

)

getType()

CDPL_CHEM_API unsigned int CDPL::Chem::getType

(

const Atom &

atom

)

setType()

CDPL_CHEM_API void CDPL::Chem::setType	(	Atom &	atom,
		unsigned int	type
	)

clearType()

CDPL_CHEM_API void CDPL::Chem::clearType

(

Atom &

atom

)

hasType()

CDPL_CHEM_API bool CDPL::Chem::hasType

(

const Atom &

atom

)

getTypeForSymbol()

CDPL_CHEM_API unsigned int CDPL::Chem::getTypeForSymbol

(

const Atom &

atom

)

getGenericType()

CDPL_CHEM_API unsigned int CDPL::Chem::getGenericType

(

const Atom &

atom

)

getFormalCharge()

CDPL_CHEM_API long CDPL::Chem::getFormalCharge

(

const Atom &

atom

)

setFormalCharge()

CDPL_CHEM_API void CDPL::Chem::setFormalCharge	(	Atom &	atom,
		long	charge
	)

clearFormalCharge()

CDPL_CHEM_API void CDPL::Chem::clearFormalCharge

(

Atom &

atom

)

hasFormalCharge()

CDPL_CHEM_API bool CDPL::Chem::hasFormalCharge

(

const Atom &

atom

)

calcFormalCharge()

CDPL_CHEM_API long CDPL::Chem::calcFormalCharge	(	const Atom &	atom,
		const MolecularGraph &	molgraph
	)

getIsotope()

CDPL_CHEM_API std::size_t CDPL::Chem::getIsotope

(

const Atom &

atom

)

setIsotope()

CDPL_CHEM_API void CDPL::Chem::setIsotope	(	Atom &	atom,
		std::size_t	isotope
	)

clearIsotope()

CDPL_CHEM_API void CDPL::Chem::clearIsotope

(

Atom &

atom

)

hasIsotope()

CDPL_CHEM_API bool CDPL::Chem::hasIsotope

(

const Atom &

atom

)

getRadicalType()

CDPL_CHEM_API unsigned int CDPL::Chem::getRadicalType

(

const Atom &

atom

)

setRadicalType()

CDPL_CHEM_API void CDPL::Chem::setRadicalType	(	Atom &	atom,
		unsigned int	type
	)

clearRadicalType()

CDPL_CHEM_API void CDPL::Chem::clearRadicalType

(

Atom &

atom

)

hasRadicalType()

CDPL_CHEM_API bool CDPL::Chem::hasRadicalType

(

const Atom &

atom

)

getHybridizationState()

CDPL_CHEM_API unsigned int CDPL::Chem::getHybridizationState

(

const Atom &

atom

)

setHybridizationState()

CDPL_CHEM_API void CDPL::Chem::setHybridizationState	(	Atom &	atom,
		unsigned int	state
	)

clearHybridizationState()

CDPL_CHEM_API void CDPL::Chem::clearHybridizationState

(

Atom &

atom

)

hasHybridizationState()

CDPL_CHEM_API bool CDPL::Chem::hasHybridizationState

(

const Atom &

atom

)

perceiveHybridizationState()

CDPL_CHEM_API unsigned int CDPL::Chem::perceiveHybridizationState	(	const Atom &	atom,
		const MolecularGraph &	molgraph
	)

getRingFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::getRingFlag

(

const Atom &

atom

)

setRingFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::setRingFlag	(	Atom &	atom,
		bool	in_ring
	)

clearRingFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearRingFlag

(

Atom &

atom

)

hasRingFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasRingFlag

(

const Atom &

atom

)

isInFragmentOfSize() [1/2]

CDPL_CHEM_API bool CDPL::Chem::isInFragmentOfSize	(	const Atom &	atom,
		const FragmentList &	frag_list,
		std::size_t	size
	)

getSizeOfSmallestContainingFragment() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getSizeOfSmallestContainingFragment	(	const Atom &	atom,
		const FragmentList &	frag_list
	)

getSizeOfLargestContainingFragment() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getSizeOfLargestContainingFragment	(	const Atom &	atom,
		const FragmentList &	frag_list
	)

getNumContainingFragments() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getNumContainingFragments	(	const Atom &	atom,
		const FragmentList &	frag_list
	)

getContainingFragments() [1/3]

CDPL_CHEM_API void CDPL::Chem::getContainingFragments	(	const Atom &	atom,
		const FragmentList &	frag_list,
		FragmentList &	cont_frag_list,
		bool	append = false
	)

getAromaticityFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::getAromaticityFlag

(

const Atom &

atom

)

setAromaticityFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::setAromaticityFlag	(	Atom &	atom,
		bool	aromatic
	)

clearAromaticityFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearAromaticityFlag

(

Atom &

atom

)

hasAromaticityFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasAromaticityFlag

(

const Atom &

atom

)

getUnpairedElectronCount()

CDPL_CHEM_API std::size_t CDPL::Chem::getUnpairedElectronCount

(

const Atom &

atom

)

setUnpairedElectronCount()

CDPL_CHEM_API void CDPL::Chem::setUnpairedElectronCount	(	Atom &	atom,
		std::size_t	count
	)

clearUnpairedElectronCount()

CDPL_CHEM_API void CDPL::Chem::clearUnpairedElectronCount

(

Atom &

atom

)

hasUnpairedElectronCount()

CDPL_CHEM_API bool CDPL::Chem::hasUnpairedElectronCount

(

const Atom &

atom

)

getImplicitHydrogenCount()

CDPL_CHEM_API std::size_t CDPL::Chem::getImplicitHydrogenCount

(

const Atom &

atom

)

setImplicitHydrogenCount()

CDPL_CHEM_API void CDPL::Chem::setImplicitHydrogenCount	(	Atom &	atom,
		std::size_t	count
	)

clearImplicitHydrogenCount()

CDPL_CHEM_API void CDPL::Chem::clearImplicitHydrogenCount

(

Atom &

atom

)

hasImplicitHydrogenCount()

CDPL_CHEM_API bool CDPL::Chem::hasImplicitHydrogenCount

(

const Atom &

atom

)

calcImplicitHydrogenCount()

CDPL_CHEM_API std::size_t CDPL::Chem::calcImplicitHydrogenCount	(	const Atom &	atom,
		const MolecularGraph &	molgraph
	)

get2DCoordinates() [2/2]

CDPL_CHEM_API const Math::Vector2D& CDPL::Chem::get2DCoordinates

(

const Atom &

atom

)

set2DCoordinates() [2/2]

CDPL_CHEM_API void CDPL::Chem::set2DCoordinates	(	Atom &	atom,
		const Math::Vector2D &	coords
	)

clear2DCoordinates()

CDPL_CHEM_API void CDPL::Chem::clear2DCoordinates

(

Atom &

atom

)

has2DCoordinates()

CDPL_CHEM_API bool CDPL::Chem::has2DCoordinates

(

const Atom &

atom

)

getConformer3DCoordinates()

CDPL_CHEM_API const Math::Vector3D& CDPL::Chem::getConformer3DCoordinates	(	const Atom &	atom,
		std::size_t	conf_idx
	)

get3DCoordinatesArray()

CDPL_CHEM_API const Math::Vector3DArray::SharedPointer& CDPL::Chem::get3DCoordinatesArray

(

const Atom &

atom

)

set3DCoordinatesArray()

CDPL_CHEM_API void CDPL::Chem::set3DCoordinatesArray	(	Atom &	atom,
		const Math::Vector3DArray::SharedPointer &	coords_array
	)

clear3DCoordinatesArray()

CDPL_CHEM_API void CDPL::Chem::clear3DCoordinatesArray

(

Atom &

atom

)

has3DCoordinatesArray()

CDPL_CHEM_API bool CDPL::Chem::has3DCoordinatesArray

(

const Atom &

atom

)

getMorganNumber()

CDPL_CHEM_API std::size_t CDPL::Chem::getMorganNumber

(

const Atom &

atom

)

setMorganNumber()

CDPL_CHEM_API void CDPL::Chem::setMorganNumber	(	Atom &	atom,
		std::size_t	num
	)

clearMorganNumber()

CDPL_CHEM_API void CDPL::Chem::clearMorganNumber

(

Atom &

atom

)

hasMorganNumber()

CDPL_CHEM_API bool CDPL::Chem::hasMorganNumber

(

const Atom &

atom

)

getCanonicalNumber()

CDPL_CHEM_API std::size_t CDPL::Chem::getCanonicalNumber

(

const Atom &

atom

)

setCanonicalNumber()

CDPL_CHEM_API void CDPL::Chem::setCanonicalNumber	(	Atom &	atom,
		std::size_t	num
	)

clearCanonicalNumber()

CDPL_CHEM_API void CDPL::Chem::clearCanonicalNumber

(

Atom &

atom

)

hasCanonicalNumber()

CDPL_CHEM_API bool CDPL::Chem::hasCanonicalNumber

(

const Atom &

atom

)

getCIPPriority()

CDPL_CHEM_API std::size_t CDPL::Chem::getCIPPriority

(

const Atom &

atom

)

setCIPPriority()

CDPL_CHEM_API void CDPL::Chem::setCIPPriority	(	Atom &	atom,
		std::size_t	priority
	)

clearCIPPriority()

CDPL_CHEM_API void CDPL::Chem::clearCIPPriority

(

Atom &

atom

)

hasCIPPriority()

CDPL_CHEM_API bool CDPL::Chem::hasCIPPriority

(

const Atom &

atom

)

getSymmetryClass()

CDPL_CHEM_API std::size_t CDPL::Chem::getSymmetryClass

(

const Atom &

atom

)

setSymmetryClass()

CDPL_CHEM_API void CDPL::Chem::setSymmetryClass	(	Atom &	atom,
		std::size_t	class_id
	)

clearSymmetryClass()

CDPL_CHEM_API void CDPL::Chem::clearSymmetryClass

(

Atom &

atom

)

hasSymmetryClass()

CDPL_CHEM_API bool CDPL::Chem::hasSymmetryClass

(

const Atom &

atom

)

getCIPConfiguration() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getCIPConfiguration

(

const Atom &

atom

)

setCIPConfiguration() [1/2]

CDPL_CHEM_API void CDPL::Chem::setCIPConfiguration	(	Atom &	atom,
		unsigned int	config
	)

clearCIPConfiguration() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearCIPConfiguration

(

Atom &

atom

)

hasCIPConfiguration() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasCIPConfiguration

(

const Atom &

atom

)

getStereoDescriptor() [1/2]

CDPL_CHEM_API const StereoDescriptor& CDPL::Chem::getStereoDescriptor

(

const Atom &

atom

)

setStereoDescriptor() [1/2]

CDPL_CHEM_API void CDPL::Chem::setStereoDescriptor	(	Atom &	atom,
		const StereoDescriptor &	descr
	)

clearStereoDescriptor() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoDescriptor

(

Atom &

atom

)

hasStereoDescriptor() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoDescriptor

(

const Atom &

atom

)

calcStereoDescriptor() [1/2]

CDPL_CHEM_API StereoDescriptor CDPL::Chem::calcStereoDescriptor	(	const Atom &	atom,
		const MolecularGraph &	molgraph,
		std::size_t	dim = 1
	)

calcStereoDescriptorFromMDLParity()

CDPL_CHEM_API StereoDescriptor CDPL::Chem::calcStereoDescriptorFromMDLParity	(	const Atom &	atom,
		const MolecularGraph &	molgraph
	)

calcConfiguration() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::calcConfiguration	(	const Atom &	atom,
		const MolecularGraph &	molgraph,
		const StereoDescriptor &	descr,
		const Math::Vector3DArray &	coords
	)

getStereoCenterFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::getStereoCenterFlag

(

const Atom &

atom

)

setStereoCenterFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::setStereoCenterFlag	(	Atom &	atom,
		bool	is_center
	)

clearStereoCenterFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoCenterFlag

(

Atom &

atom

)

hasStereoCenterFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoCenterFlag

(

const Atom &

atom

)

isStereoCenter() [1/2]

CDPL_CHEM_API bool CDPL::Chem::isStereoCenter	(	const Atom &	atom,
		const 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
	)

getSybylType() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getSybylType

(

const Atom &

atom

)

setSybylType() [1/2]

CDPL_CHEM_API void CDPL::Chem::setSybylType	(	Atom &	atom,
		unsigned int	type
	)

clearSybylType() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearSybylType

(

Atom &

atom

)

hasSybylType() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasSybylType

(

const Atom &

atom

)

perceiveSybylType() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::perceiveSybylType	(	const Atom &	atom,
		const MolecularGraph &	molgraph
	)

getMOL2Name()

CDPL_CHEM_API const std::string& CDPL::Chem::getMOL2Name

(

const Atom &

atom

)

setMOL2Name()

CDPL_CHEM_API void CDPL::Chem::setMOL2Name	(	Atom &	atom,
		const std::string &	name
	)

clearMOL2Name()

CDPL_CHEM_API void CDPL::Chem::clearMOL2Name

(

Atom &

atom

)

hasMOL2Name()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2Name

(

const Atom &

atom

)

getMOL2Charge()

CDPL_CHEM_API double CDPL::Chem::getMOL2Charge

(

const Atom &

atom

)

setMOL2Charge()

CDPL_CHEM_API void CDPL::Chem::setMOL2Charge	(	Atom &	atom,
		double	charge
	)

clearMOL2Charge()

CDPL_CHEM_API void CDPL::Chem::clearMOL2Charge

(

Atom &

atom

)

hasMOL2Charge()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2Charge

(

const Atom &

atom

)

getMOL2SubstructureID()

CDPL_CHEM_API std::size_t CDPL::Chem::getMOL2SubstructureID

(

const Atom &

atom

)

setMOL2SubstructureID()

CDPL_CHEM_API void CDPL::Chem::setMOL2SubstructureID	(	Atom &	atom,
		std::size_t	id
	)

clearMOL2SubstructureID()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureID

(

Atom &

atom

)

hasMOL2SubstructureID()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureID

(

const Atom &

atom

)

getMOL2SubstructureName()

CDPL_CHEM_API const std::string& CDPL::Chem::getMOL2SubstructureName

(

const Atom &

atom

)

setMOL2SubstructureName()

CDPL_CHEM_API void CDPL::Chem::setMOL2SubstructureName	(	Atom &	atom,
		const std::string &	id
	)

clearMOL2SubstructureName()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureName

(

Atom &

atom

)

hasMOL2SubstructureName()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureName

(

const Atom &

atom

)

getMOL2SubstructureSubtype()

CDPL_CHEM_API const std::string& CDPL::Chem::getMOL2SubstructureSubtype

(

const Atom &

atom

)

setMOL2SubstructureSubtype()

CDPL_CHEM_API void CDPL::Chem::setMOL2SubstructureSubtype	(	Atom &	atom,
		const std::string &	subtype
	)

clearMOL2SubstructureSubtype()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureSubtype

(

Atom &

atom

)

hasMOL2SubstructureSubtype()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureSubtype

(

const Atom &

atom

)

getMOL2SubstructureChain()

CDPL_CHEM_API const std::string& CDPL::Chem::getMOL2SubstructureChain

(

const Atom &

atom

)

setMOL2SubstructureChain()

CDPL_CHEM_API void CDPL::Chem::setMOL2SubstructureChain	(	Atom &	atom,
		const std::string &	chain
	)

clearMOL2SubstructureChain()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureChain

(

Atom &

atom

)

hasMOL2SubstructureChain()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureChain

(

const Atom &

atom

)

getMDLParity()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLParity

(

const Atom &

atom

)

setMDLParity()

CDPL_CHEM_API void CDPL::Chem::setMDLParity	(	Atom &	atom,
		unsigned int	parity
	)

clearMDLParity()

CDPL_CHEM_API void CDPL::Chem::clearMDLParity

(

Atom &

atom

)

hasMDLParity()

CDPL_CHEM_API bool CDPL::Chem::hasMDLParity

(

const Atom &

atom

)

calcMDLParity()

CDPL_CHEM_API unsigned int CDPL::Chem::calcMDLParity	(	const Atom &	atom,
		const MolecularGraph &	molgraph
	)

getMDLStereoCareFlag()

CDPL_CHEM_API bool CDPL::Chem::getMDLStereoCareFlag

(

const Atom &

atom

)

setMDLStereoCareFlag()

CDPL_CHEM_API void CDPL::Chem::setMDLStereoCareFlag	(	Atom &	atom,
		bool	flag
	)

clearMDLStereoCareFlag()

CDPL_CHEM_API void CDPL::Chem::clearMDLStereoCareFlag

(

Atom &

atom

)

hasMDLStereoCareFlag()

CDPL_CHEM_API bool CDPL::Chem::hasMDLStereoCareFlag

(

const Atom &

atom

)

getReactionCenterStatus() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getReactionCenterStatus

(

const Atom &

atom

)

setReactionCenterStatus() [1/2]

CDPL_CHEM_API void CDPL::Chem::setReactionCenterStatus	(	Atom &	atom,
		unsigned int	status
	)

clearReactionCenterStatus() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearReactionCenterStatus

(

Atom &

atom

)

hasReactionCenterStatus() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasReactionCenterStatus

(

const Atom &

atom

)

getAtomMappingID()

CDPL_CHEM_API std::size_t CDPL::Chem::getAtomMappingID

(

const Atom &

atom

)

setAtomMappingID()

CDPL_CHEM_API void CDPL::Chem::setAtomMappingID	(	Atom &	atom,
		std::size_t	id
	)

clearAtomMappingID()

CDPL_CHEM_API void CDPL::Chem::clearAtomMappingID

(

Atom &

atom

)

hasAtomMappingID()

CDPL_CHEM_API bool CDPL::Chem::hasAtomMappingID

(

const Atom &

atom

)

getComponentGroupID()

CDPL_CHEM_API std::size_t CDPL::Chem::getComponentGroupID

(

const Atom &

atom

)

setComponentGroupID()

CDPL_CHEM_API void CDPL::Chem::setComponentGroupID	(	Atom &	atom,
		std::size_t	id
	)

clearComponentGroupID()

CDPL_CHEM_API void CDPL::Chem::clearComponentGroupID

(

Atom &

atom

)

hasComponentGroupID()

CDPL_CHEM_API bool CDPL::Chem::hasComponentGroupID

(

const Atom &

atom

)

getMatchConstraints() [1/4]

CDPL_CHEM_API const MatchConstraintList::SharedPointer& CDPL::Chem::getMatchConstraints

(

const Atom &

atom

)

setMatchConstraints() [1/4]

CDPL_CHEM_API void CDPL::Chem::setMatchConstraints	(	Atom &	atom,
		const MatchConstraintList::SharedPointer &	constr
	)

clearMatchConstraints() [1/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints

(

Atom &

atom

)

hasMatchConstraints() [1/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints

(

const Atom &

atom

)

getMatchExpression() [1/4]

CDPL_CHEM_API const MatchExpression<Atom, MolecularGraph>::SharedPointer& CDPL::Chem::getMatchExpression

(

const Atom &

atom

)

setMatchExpression() [1/4]

CDPL_CHEM_API void CDPL::Chem::setMatchExpression	(	Atom &	atom,
		const MatchExpression< Atom, MolecularGraph >::SharedPointer &	expr
	)

clearMatchExpression() [1/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression

(

Atom &

atom

)

hasMatchExpression() [1/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression

(

const Atom &

atom

)

generateMatchExpression() [1/6]

CDPL_CHEM_API MatchExpression<Atom, MolecularGraph>::SharedPointer CDPL::Chem::generateMatchExpression	(	const Atom &	atom,
		const MolecularGraph &	molgraph
	)

getMatchExpressionString() [1/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMatchExpressionString

(

const Atom &

atom

)

setMatchExpressionString() [1/2]

CDPL_CHEM_API void CDPL::Chem::setMatchExpressionString	(	Atom &	atom,
		const std::string &	expr_str
	)

clearMatchExpressionString() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpressionString

(

Atom &

atom

)

hasMatchExpressionString() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpressionString

(

const Atom &

atom

)

generateMatchExpressionString() [1/2]

CDPL_CHEM_API void CDPL::Chem::generateMatchExpressionString	(	const Atom &	atom,
		const MolecularGraph &	molgraph,
		std::string &	expr_str
	)

markReachableAtoms()

CDPL_CHEM_API void CDPL::Chem::markReachableAtoms	(	const Atom &	atom,
		const MolecularGraph &	molgraph,
		Util::BitSet &	atom_mask,
		bool	reset = true
	)

getTopologicalDistance()

CDPL_CHEM_API std::size_t CDPL::Chem::getTopologicalDistance	(	const Atom &	atom1,
		const Atom &	atom2,
		const MolecularGraph &	molgraph
	)

getEnvironment()

CDPL_CHEM_API std::size_t CDPL::Chem::getEnvironment	(	const Atom &	atom,
		const MolecularGraph &	molgraph,
		std::size_t	max_dist,
		Fragment &	env,
		bool	append = false
	)

getConnectedAtoms()

template<typename AtomType , typename OutputIterator >

std::size_t CDPL::Chem::getConnectedAtoms	(	AtomType &	atom,
		const MolecularGraph &	molgraph,
		OutputIterator	it,
		AtomType *	excl_atom = 0
	)

getIncidentBonds()

template<typename AtomType , typename OutputIterator >

std::size_t CDPL::Chem::getIncidentBonds	(	AtomType &	atom,
		const MolecularGraph &	molgraph,
		OutputIterator	it,
		AtomType *	excl_atom = 0
	)

getConnectedAtomsAndBonds()

template<typename AtomType , typename AtomOutputIterator , typename BondOutputIterator >

std::size_t CDPL::Chem::getConnectedAtomsAndBonds	(	AtomType &	atom,
		const MolecularGraph &	molgraph,
		AtomOutputIterator	ao_it,
		BondOutputIterator	bo_it,
		AtomType *	excl_atom = 0
	)

getOrder()

CDPL_CHEM_API std::size_t CDPL::Chem::getOrder

(

const Bond &

bond

)

setOrder()

CDPL_CHEM_API void CDPL::Chem::setOrder	(	Bond &	bond,
		std::size_t	order
	)

clearOrder()

CDPL_CHEM_API void CDPL::Chem::clearOrder

(

Bond &

bond

)

hasOrder()

CDPL_CHEM_API bool CDPL::Chem::hasOrder

(

const Bond &

bond

)

getRingFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::getRingFlag

(

const Bond &

bond

)

setRingFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::setRingFlag	(	Bond &	bond,
		bool	in_ring
	)

clearRingFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearRingFlag

(

Bond &

bond

)

hasRingFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasRingFlag

(

const Bond &

bond

)

isInFragmentOfSize() [2/2]

CDPL_CHEM_API bool CDPL::Chem::isInFragmentOfSize	(	const Bond &	bond,
		const FragmentList &	frag_list,
		std::size_t	size
	)

getSizeOfSmallestContainingFragment() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getSizeOfSmallestContainingFragment	(	const Bond &	bond,
		const FragmentList &	frag_list
	)

getSizeOfLargestContainingFragment() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getSizeOfLargestContainingFragment	(	const Bond &	bond,
		const FragmentList &	frag_list
	)

getNumContainingFragments() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getNumContainingFragments	(	const Bond &	bond,
		const FragmentList &	frag_list
	)

getContainingFragments() [2/3]

CDPL_CHEM_API void CDPL::Chem::getContainingFragments	(	const Bond &	bond,
		const FragmentList &	frag_list,
		FragmentList &	cont_frag_list,
		bool	append = false
	)

getAromaticityFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::getAromaticityFlag

(

const Bond &

bond

)

setAromaticityFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::setAromaticityFlag	(	Bond &	bond,
		bool	aromatic
	)

clearAromaticityFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearAromaticityFlag

(

Bond &

bond

)

hasAromaticityFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasAromaticityFlag

(

const Bond &

bond

)

get2DStereoFlag()

CDPL_CHEM_API unsigned int CDPL::Chem::get2DStereoFlag

(

const Bond &

bond

)

set2DStereoFlag()

CDPL_CHEM_API void CDPL::Chem::set2DStereoFlag	(	Bond &	bond,
		unsigned int	flag
	)

clear2DStereoFlag()

CDPL_CHEM_API void CDPL::Chem::clear2DStereoFlag

(

Bond &

bond

)

has2DStereoFlag()

CDPL_CHEM_API bool CDPL::Chem::has2DStereoFlag

(

const Bond &

bond

)

getCIPConfiguration() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getCIPConfiguration

(

const Bond &

bond

)

setCIPConfiguration() [2/2]

CDPL_CHEM_API void CDPL::Chem::setCIPConfiguration	(	Bond &	bond,
		unsigned int	config
	)

clearCIPConfiguration() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearCIPConfiguration

(

Bond &

bond

)

hasCIPConfiguration() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasCIPConfiguration

(

const Bond &

bond

)

getStereoDescriptor() [2/2]

CDPL_CHEM_API const StereoDescriptor& CDPL::Chem::getStereoDescriptor

(

const Bond &

bond

)

setStereoDescriptor() [2/2]

CDPL_CHEM_API void CDPL::Chem::setStereoDescriptor	(	Bond &	bond,
		const StereoDescriptor &	descr
	)

clearStereoDescriptor() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoDescriptor

(

Bond &

bond

)

hasStereoDescriptor() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoDescriptor

(

const Bond &

bond

)

calcStereoDescriptor() [2/2]

CDPL_CHEM_API StereoDescriptor CDPL::Chem::calcStereoDescriptor	(	const Bond &	bond,
		const MolecularGraph &	molgraph,
		std::size_t	dim = 1
	)

calcConfiguration() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::calcConfiguration	(	const Bond &	bond,
		const MolecularGraph &	molgraph,
		const StereoDescriptor &	descr,
		const Math::Vector3DArray &	coords
	)

getStereoCenterFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::getStereoCenterFlag

(

const Bond &

bond

)

setStereoCenterFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::setStereoCenterFlag	(	Bond &	bond,
		bool	is_center
	)

clearStereoCenterFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoCenterFlag

(

Bond &

bond

)

hasStereoCenterFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoCenterFlag

(

const Bond &

bond

)

isStereoCenter() [2/2]

CDPL_CHEM_API bool CDPL::Chem::isStereoCenter	(	const Bond &	bond,
		const MolecularGraph &	molgraph,
		bool	check_asym = true,
		bool	check_term_n = true,
		bool	check_order = true,
		std::size_t	min_ring_size = 8
	)

getDirection()

CDPL_CHEM_API unsigned int CDPL::Chem::getDirection

(

const Bond &

bond

)

setDirection()

CDPL_CHEM_API void CDPL::Chem::setDirection	(	Bond &	bond,
		unsigned int	dir
	)

clearDirection()

CDPL_CHEM_API void CDPL::Chem::clearDirection

(

Bond &

bond

)

hasDirection()

CDPL_CHEM_API bool CDPL::Chem::hasDirection

(

const Bond &

bond

)

getReactionCenterStatus() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getReactionCenterStatus

(

const Bond &

bond

)

setReactionCenterStatus() [2/2]

CDPL_CHEM_API void CDPL::Chem::setReactionCenterStatus	(	Bond &	bond,
		unsigned int	status
	)

clearReactionCenterStatus() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearReactionCenterStatus

(

Bond &

bond

)

hasReactionCenterStatus() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasReactionCenterStatus

(

const Bond &

bond

)

getMatchConstraints() [2/4]

CDPL_CHEM_API const MatchConstraintList::SharedPointer& CDPL::Chem::getMatchConstraints

(

const Bond &

bond

)

setMatchConstraints() [2/4]

CDPL_CHEM_API void CDPL::Chem::setMatchConstraints	(	Bond &	bond,
		const MatchConstraintList::SharedPointer &	constr
	)

clearMatchConstraints() [2/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints

(

Bond &

bond

)

hasMatchConstraints() [2/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints

(

const Bond &

bond

)

getMatchExpression() [2/4]

CDPL_CHEM_API const MatchExpression<Bond, MolecularGraph>::SharedPointer& CDPL::Chem::getMatchExpression

(

const Bond &

bond

)

setMatchExpression() [2/4]

CDPL_CHEM_API void CDPL::Chem::setMatchExpression	(	Bond &	bond,
		const MatchExpression< Bond, MolecularGraph >::SharedPointer &	expr
	)

clearMatchExpression() [2/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression

(

Bond &

bond

)

hasMatchExpression() [2/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression

(

const Bond &

bond

)

generateMatchExpression() [2/6]

CDPL_CHEM_API MatchExpression<Bond, MolecularGraph>::SharedPointer CDPL::Chem::generateMatchExpression	(	const Bond &	bond,
		const MolecularGraph &	molgraph
	)

getMatchExpressionString() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMatchExpressionString

(

const Bond &

bond

)

setMatchExpressionString() [2/2]

CDPL_CHEM_API void CDPL::Chem::setMatchExpressionString	(	Bond &	bond,
		const std::string &	expr_str
	)

clearMatchExpressionString() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpressionString

(

Bond &

bond

)

hasMatchExpressionString() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpressionString

(

const Bond &

bond

)

generateMatchExpressionString() [2/2]

CDPL_CHEM_API void CDPL::Chem::generateMatchExpressionString	(	const Bond &	bond,
		const MolecularGraph &	molgraph,
		std::string &	str
	)

getSybylType() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getSybylType

(

const Bond &

bond

)

setSybylType() [2/2]

CDPL_CHEM_API void CDPL::Chem::setSybylType	(	Bond &	bond,
		unsigned int	type
	)

clearSybylType() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearSybylType

(

Bond &

bond

)

hasSybylType() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasSybylType

(

const Bond &

bond

)

perceiveSybylType() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::perceiveSybylType	(	const Bond &	bond,
		const MolecularGraph &	molgraph
	)

getOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API bool CDPL::Chem::getOrdinaryHydrogenDepleteParameter

(

const Base::ControlParameterContainer &

cntnr

)

setOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API void CDPL::Chem::setOrdinaryHydrogenDepleteParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	deplete
	)

hasOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API bool CDPL::Chem::hasOrdinaryHydrogenDepleteParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API void CDPL::Chem::clearOrdinaryHydrogenDepleteParameter

(

Base::ControlParameterContainer &

cntnr

)

getCoordinatesDimensionParameter()

CDPL_CHEM_API std::size_t CDPL::Chem::getCoordinatesDimensionParameter

(

const Base::ControlParameterContainer &

cntnr

)

setCoordinatesDimensionParameter()

CDPL_CHEM_API void CDPL::Chem::setCoordinatesDimensionParameter	(	Base::ControlParameterContainer &	cntnr,
		std::size_t	dim
	)

hasCoordinatesDimensionParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCoordinatesDimensionParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearCoordinatesDimensionParameter()

CDPL_CHEM_API void CDPL::Chem::clearCoordinatesDimensionParameter

(

Base::ControlParameterContainer &

cntnr

)

getStrictErrorCheckingParameter()

CDPL_CHEM_API bool CDPL::Chem::getStrictErrorCheckingParameter

(

const Base::ControlParameterContainer &

cntnr

)

setStrictErrorCheckingParameter()

CDPL_CHEM_API void CDPL::Chem::setStrictErrorCheckingParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	strict
	)

hasStrictErrorCheckingParameter()

CDPL_CHEM_API bool CDPL::Chem::hasStrictErrorCheckingParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearStrictErrorCheckingParameter()

CDPL_CHEM_API void CDPL::Chem::clearStrictErrorCheckingParameter

(

Base::ControlParameterContainer &

cntnr

)

getRecordSeparatorParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getRecordSeparatorParameter

(

const Base::ControlParameterContainer &

cntnr

)

setRecordSeparatorParameter()

CDPL_CHEM_API void CDPL::Chem::setRecordSeparatorParameter	(	Base::ControlParameterContainer &	cntnr,
		const std::string &	sep
	)

hasRecordSeparatorParameter()

CDPL_CHEM_API bool CDPL::Chem::hasRecordSeparatorParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearRecordSeparatorParameter()

CDPL_CHEM_API void CDPL::Chem::clearRecordSeparatorParameter

(

Base::ControlParameterContainer &

cntnr

)

getBondMemberSwapStereoFixParameter()

CDPL_CHEM_API bool CDPL::Chem::getBondMemberSwapStereoFixParameter

(

const Base::ControlParameterContainer &

cntnr

)

setBondMemberSwapStereoFixParameter()

CDPL_CHEM_API void CDPL::Chem::setBondMemberSwapStereoFixParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	fix
	)

hasBondMemberSwapStereoFixParameter()

CDPL_CHEM_API bool CDPL::Chem::hasBondMemberSwapStereoFixParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearBondMemberSwapStereoFixParameter()

CDPL_CHEM_API void CDPL::Chem::clearBondMemberSwapStereoFixParameter

(

Base::ControlParameterContainer &

cntnr

)

getCheckLineLengthParameter()

CDPL_CHEM_API bool CDPL::Chem::getCheckLineLengthParameter

(

const Base::ControlParameterContainer &

cntnr

)

setCheckLineLengthParameter()

CDPL_CHEM_API void CDPL::Chem::setCheckLineLengthParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	check
	)

hasCheckLineLengthParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCheckLineLengthParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearCheckLineLengthParameter()

CDPL_CHEM_API void CDPL::Chem::clearCheckLineLengthParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLCTABVersionParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLCTABVersionParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLCTABVersionParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLCTABVersionParameter	(	Base::ControlParameterContainer &	cntnr,
		unsigned int	version
	)

hasMDLCTABVersionParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLCTABVersionParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLCTABVersionParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLCTABVersionParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLIgnoreParityParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLIgnoreParityParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLIgnoreParityParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLIgnoreParityParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	ignore
	)

hasMDLIgnoreParityParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLIgnoreParityParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLIgnoreParityParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLIgnoreParityParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLUpdateTimestampParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLUpdateTimestampParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLUpdateTimestampParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLUpdateTimestampParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	update
	)

hasMDLUpdateTimestampParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLUpdateTimestampParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLUpdateTimestampParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLUpdateTimestampParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLTrimStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTrimStringsParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLTrimStringsParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLTrimStringsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	trim
	)

hasMDLTrimStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTrimStringsParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLTrimStringsParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTrimStringsParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLTrimLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTrimLinesParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLTrimLinesParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLTrimLinesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	trim
	)

hasMDLTrimLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTrimLinesParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLTrimLinesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTrimLinesParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLTruncateStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTruncateStringsParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLTruncateStringsParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLTruncateStringsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	trunc
	)

hasMDLTruncateStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTruncateStringsParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLTruncateStringsParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTruncateStringsParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLTruncateLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTruncateLinesParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLTruncateLinesParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLTruncateLinesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	trunc
	)

hasMDLTruncateLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTruncateLinesParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLTruncateLinesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTruncateLinesParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLRXNFileVersionParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLRXNFileVersionParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLRXNFileVersionParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLRXNFileVersionParameter	(	Base::ControlParameterContainer &	cntnr,
		unsigned int	version
	)

hasMDLRXNFileVersionParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLRXNFileVersionParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLRXNFileVersionParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLRXNFileVersionParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLOutputConfEnergyToEnergyFieldParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLOutputConfEnergyToEnergyFieldParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	output
	)

hasMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLOutputConfEnergyToEnergyFieldParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLOutputConfEnergyToEnergyFieldParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLOutputConfEnergyAsSDEntryParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLOutputConfEnergyAsSDEntryParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	output
	)

hasMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLOutputConfEnergyAsSDEntryParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLOutputConfEnergyAsSDEntryParameter

(

Base::ControlParameterContainer &

cntnr

)

getMDLConfEnergySDTagParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLConfEnergySDTagParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMDLConfEnergySDTagParameter()

CDPL_CHEM_API void CDPL::Chem::setMDLConfEnergySDTagParameter	(	Base::ControlParameterContainer &	cntnr,
		const std::string &	tag
	)

hasMDLConfEnergySDTagParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLConfEnergySDTagParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMDLConfEnergySDTagParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLConfEnergySDTagParameter

(

Base::ControlParameterContainer &

cntnr

)

getJMESeparateComponentsParameter()

CDPL_CHEM_API bool CDPL::Chem::getJMESeparateComponentsParameter

(

const Base::ControlParameterContainer &

cntnr

)

setJMESeparateComponentsParameter()

CDPL_CHEM_API void CDPL::Chem::setJMESeparateComponentsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	separate
	)

hasJMESeparateComponentsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasJMESeparateComponentsParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearJMESeparateComponentsParameter()

CDPL_CHEM_API void CDPL::Chem::clearJMESeparateComponentsParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESRecordFormatParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getSMILESRecordFormatParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESRecordFormatParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESRecordFormatParameter	(	Base::ControlParameterContainer &	cntnr,
		const std::string &	format
	)

hasSMILESRecordFormatParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESRecordFormatParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESRecordFormatParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESRecordFormatParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESWriteCanonicalFormParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteCanonicalFormParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESWriteCanonicalFormParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESWriteCanonicalFormParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESWriteCanonicalFormParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteCanonicalFormParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESWriteCanonicalFormParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteCanonicalFormParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESWriteKekuleFormParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteKekuleFormParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESWriteKekuleFormParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESWriteKekuleFormParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESWriteKekuleFormParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteKekuleFormParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESWriteKekuleFormParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteKekuleFormParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESWriteAtomStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteAtomStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESWriteAtomStereoParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESWriteAtomStereoParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESWriteAtomStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteAtomStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESWriteAtomStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteAtomStereoParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESWriteBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESWriteBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESWriteBondStereoParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESWriteBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESWriteBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteBondStereoParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESWriteRingBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteRingBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESWriteRingBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESWriteRingBondStereoParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESWriteRingBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteRingBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESWriteRingBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteRingBondStereoParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESMinStereoBondRingSizeParameter()

CDPL_CHEM_API std::size_t CDPL::Chem::getSMILESMinStereoBondRingSizeParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESMinStereoBondRingSizeParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESMinStereoBondRingSizeParameter	(	Base::ControlParameterContainer &	cntnr,
		std::size_t	min_size
	)

hasSMILESMinStereoBondRingSizeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESMinStereoBondRingSizeParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESMinStereoBondRingSizeParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESMinStereoBondRingSizeParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESWriteIsotopeParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteIsotopeParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESWriteIsotopeParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESWriteIsotopeParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESWriteIsotopeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteIsotopeParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESWriteIsotopeParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteIsotopeParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESMolWriteAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESMolWriteAtomMappingIDParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESMolWriteAtomMappingIDParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESMolWriteAtomMappingIDParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESMolWriteAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESMolWriteAtomMappingIDParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESMolWriteAtomMappingIDParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESMolWriteAtomMappingIDParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESRxnWriteAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESRxnWriteAtomMappingIDParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESRxnWriteAtomMappingIDParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESRxnWriteAtomMappingIDParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESRxnWriteAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESRxnWriteAtomMappingIDParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESRxnWriteAtomMappingIDParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESRxnWriteAtomMappingIDParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESWriteSingleBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteSingleBondsParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESWriteSingleBondsParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESWriteSingleBondsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESWriteSingleBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteSingleBondsParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESWriteSingleBondsParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteSingleBondsParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESWriteAromaticBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteAromaticBondsParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESWriteAromaticBondsParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESWriteAromaticBondsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

hasSMILESWriteAromaticBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteAromaticBondsParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESWriteAromaticBondsParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteAromaticBondsParameter

(

Base::ControlParameterContainer &

cntnr

)

getSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESNoOrganicSubsetParameter

(

const Base::ControlParameterContainer &

cntnr

)

setSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API void CDPL::Chem::setSMILESNoOrganicSubsetParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	no_subset
	)

hasSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESNoOrganicSubsetParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESNoOrganicSubsetParameter

(

Base::ControlParameterContainer &

cntnr

)

getINCHIInputOptionsParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getINCHIInputOptionsParameter

(

const Base::ControlParameterContainer &

cntnr

)

setINCHIInputOptionsParameter()

CDPL_CHEM_API void CDPL::Chem::setINCHIInputOptionsParameter	(	Base::ControlParameterContainer &	cntnr,
		const std::string &	opts
	)

hasINCHIInputOptionsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasINCHIInputOptionsParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearINCHIInputOptionsParameter()

CDPL_CHEM_API void CDPL::Chem::clearINCHIInputOptionsParameter

(

Base::ControlParameterContainer &

cntnr

)

getINCHIOutputOptionsParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getINCHIOutputOptionsParameter

(

const Base::ControlParameterContainer &

cntnr

)

setINCHIOutputOptionsParameter()

CDPL_CHEM_API void CDPL::Chem::setINCHIOutputOptionsParameter	(	Base::ControlParameterContainer &	cntnr,
		const std::string &	opts
	)

hasINCHIOutputOptionsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasINCHIOutputOptionsParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearINCHIOutputOptionsParameter()

CDPL_CHEM_API void CDPL::Chem::clearINCHIOutputOptionsParameter

(

Base::ControlParameterContainer &

cntnr

)

getMultiConfImportParameter()

CDPL_CHEM_API bool CDPL::Chem::getMultiConfImportParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMultiConfImportParameter()

CDPL_CHEM_API void CDPL::Chem::setMultiConfImportParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	multi_conf
	)

hasMultiConfImportParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMultiConfImportParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMultiConfImportParameter()

CDPL_CHEM_API void CDPL::Chem::clearMultiConfImportParameter

(

Base::ControlParameterContainer &

cntnr

)

getMultiConfExportParameter()

CDPL_CHEM_API bool CDPL::Chem::getMultiConfExportParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMultiConfExportParameter()

CDPL_CHEM_API void CDPL::Chem::setMultiConfExportParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	multi_conf
	)

hasMultiConfExportParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMultiConfExportParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMultiConfExportParameter()

CDPL_CHEM_API void CDPL::Chem::clearMultiConfExportParameter

(

Base::ControlParameterContainer &

cntnr

)

getOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API bool CDPL::Chem::getOutputConfEnergyAsCommentParameter

(

const Base::ControlParameterContainer &

cntnr

)

setOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API void CDPL::Chem::setOutputConfEnergyAsCommentParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	output
	)

hasOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API bool CDPL::Chem::hasOutputConfEnergyAsCommentParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API void CDPL::Chem::clearOutputConfEnergyAsCommentParameter

(

Base::ControlParameterContainer &

cntnr

)

getConfIndexNameSuffixPatternParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getConfIndexNameSuffixPatternParameter

(

const Base::ControlParameterContainer &

cntnr

)

setConfIndexNameSuffixPatternParameter()

CDPL_CHEM_API void CDPL::Chem::setConfIndexNameSuffixPatternParameter	(	Base::ControlParameterContainer &	cntnr,
		const std::string &	pattern
	)

hasConfIndexNameSuffixPatternParameter()

CDPL_CHEM_API bool CDPL::Chem::hasConfIndexNameSuffixPatternParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearConfIndexNameSuffixPatternParameter()

CDPL_CHEM_API void CDPL::Chem::clearConfIndexNameSuffixPatternParameter

(

Base::ControlParameterContainer &

cntnr

)

getMultiConfInputProcessorParameter()

CDPL_CHEM_API const MultiConfMoleculeInputProcessor::SharedPointer& CDPL::Chem::getMultiConfInputProcessorParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMultiConfInputProcessorParameter()

CDPL_CHEM_API void CDPL::Chem::setMultiConfInputProcessorParameter	(	Base::ControlParameterContainer &	cntnr,
		const MultiConfMoleculeInputProcessor::SharedPointer &	proc
	)

hasMultiConfInputProcessorParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMultiConfInputProcessorParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMultiConfInputProcessorParameter()

CDPL_CHEM_API void CDPL::Chem::clearMultiConfInputProcessorParameter

(

Base::ControlParameterContainer &

cntnr

)

getCDFWriteSinglePrecisionFloatsParameter()

CDPL_CHEM_API bool CDPL::Chem::getCDFWriteSinglePrecisionFloatsParameter

(

const Base::ControlParameterContainer &

cntnr

)

setCDFWriteSinglePrecisionFloatsParameter()

CDPL_CHEM_API void CDPL::Chem::setCDFWriteSinglePrecisionFloatsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	single_prec
	)

hasCDFWriteSinglePrecisionFloatsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCDFWriteSinglePrecisionFloatsParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearCDFWriteSinglePrecisionFloatsParameter()

CDPL_CHEM_API void CDPL::Chem::clearCDFWriteSinglePrecisionFloatsParameter

(

Base::ControlParameterContainer &

cntnr

)

getMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2EnableExtendedAtomTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API void CDPL::Chem::setMOL2EnableExtendedAtomTypesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	enable
	)

hasMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2EnableExtendedAtomTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2EnableExtendedAtomTypesParameter

(

Base::ControlParameterContainer &

cntnr

)

getMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2EnableAromaticBondTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API void CDPL::Chem::setMOL2EnableAromaticBondTypesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	enable
	)

hasMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2EnableAromaticBondTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2EnableAromaticBondTypesParameter

(

Base::ControlParameterContainer &

cntnr

)

getMOL2CalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2CalcFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMOL2CalcFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::setMOL2CalcFormalChargesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	calc
	)

hasMOL2CalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2CalcFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMOL2CalcFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2CalcFormalChargesParameter

(

Base::ControlParameterContainer &

cntnr

)

getMOL2ChargeTypeParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2ChargeTypeParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMOL2ChargeTypeParameter()

CDPL_CHEM_API void CDPL::Chem::setMOL2ChargeTypeParameter	(	Base::ControlParameterContainer &	cntnr,
		unsigned int	type
	)

hasMOL2ChargeTypeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2ChargeTypeParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMOL2ChargeTypeParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2ChargeTypeParameter

(

Base::ControlParameterContainer &

cntnr

)

getMOL2MoleculeTypeParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2MoleculeTypeParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMOL2MoleculeTypeParameter()

CDPL_CHEM_API void CDPL::Chem::setMOL2MoleculeTypeParameter	(	Base::ControlParameterContainer &	cntnr,
		unsigned int	type
	)

hasMOL2MoleculeTypeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2MoleculeTypeParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMOL2MoleculeTypeParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2MoleculeTypeParameter

(

Base::ControlParameterContainer &

cntnr

)

getMOL2OutputSubstructuresParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2OutputSubstructuresParameter

(

const Base::ControlParameterContainer &

cntnr

)

setMOL2OutputSubstructuresParameter()

CDPL_CHEM_API void CDPL::Chem::setMOL2OutputSubstructuresParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	output
	)

hasMOL2OutputSubstructuresParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2OutputSubstructuresParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearMOL2OutputSubstructuresParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2OutputSubstructuresParameter

(

Base::ControlParameterContainer &

cntnr

)

getXYZCommentIsNameParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZCommentIsNameParameter

(

const Base::ControlParameterContainer &

cntnr

)

setXYZCommentIsNameParameter()

CDPL_CHEM_API void CDPL::Chem::setXYZCommentIsNameParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	is_name
	)

hasXYZCommentIsNameParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZCommentIsNameParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearXYZCommentIsNameParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZCommentIsNameParameter

(

Base::ControlParameterContainer &

cntnr

)

getXYZPerceiveConnectivityParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZPerceiveConnectivityParameter

(

const Base::ControlParameterContainer &

cntnr

)

setXYZPerceiveConnectivityParameter()

CDPL_CHEM_API void CDPL::Chem::setXYZPerceiveConnectivityParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	perceive
	)

hasXYZPerceiveConnectivityParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZPerceiveConnectivityParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearXYZPerceiveConnectivityParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZPerceiveConnectivityParameter

(

Base::ControlParameterContainer &

cntnr

)

getXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZPerceiveBondOrdersParameter

(

const Base::ControlParameterContainer &

cntnr

)

setXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API void CDPL::Chem::setXYZPerceiveBondOrdersParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	perceive
	)

hasXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZPerceiveBondOrdersParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZPerceiveBondOrdersParameter

(

Base::ControlParameterContainer &

cntnr

)

getXYZCalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZCalcFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

setXYZCalcFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::setXYZCalcFormalChargesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	calc
	)

hasXYZCalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZCalcFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearXYZCalcFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZCalcFormalChargesParameter

(

Base::ControlParameterContainer &

cntnr

)

calcGeometricalDistanceMatrix() [1/2]

CDPL_CHEM_API void CDPL::Chem::calcGeometricalDistanceMatrix	(	const Entity3DContainer &	cntnr,
		Math::DMatrix &	mtx
	)

get3DCoordinates() [2/3]

CDPL_CHEM_API void CDPL::Chem::get3DCoordinates	(	const Entity3DContainer &	cntnr,
		Math::Vector3DArray &	coords,
		bool	append = false
	)

set3DCoordinates() [1/2]

CDPL_CHEM_API void CDPL::Chem::set3DCoordinates	(	Entity3DContainer &	cntnr,
		const Math::Vector3DArray &	coords
	)

transform3DCoordinates()

CDPL_CHEM_API void CDPL::Chem::transform3DCoordinates	(	Entity3DContainer &	cntnr,
		const Math::Matrix4D &	mtx
	)

align3DCoordinates()

CDPL_CHEM_API bool CDPL::Chem::align3DCoordinates	(	Entity3DContainer &	cntnr,
		const Entity3DContainer &	ref_entities,
		const Math::Vector3DArray &	ref_coords
	)

calcCentroid() [2/2]

CDPL_CHEM_API bool CDPL::Chem::calcCentroid	(	const Entity3DContainer &	cntnr,
		Math::Vector3D &	ctr
	)

calcBoundingBox() [2/2]

CDPL_CHEM_API void CDPL::Chem::calcBoundingBox	(	const Entity3DContainer &	cntnr,
		Math::Vector3D &	min,
		Math::Vector3D &	max,
		bool	reset = true
	)

insideBoundingBox() [2/3]

CDPL_CHEM_API bool CDPL::Chem::insideBoundingBox	(	const Entity3DContainer &	cntnr,
		const Math::Vector3D &	min,
		const Math::Vector3D &	max
	)

intersectsBoundingBox() [2/2]

CDPL_CHEM_API bool CDPL::Chem::intersectsBoundingBox	(	const Entity3DContainer &	cntnr,
		const Math::Vector3D &	min,
		const Math::Vector3D &	max
	)

get3DCoordinates() [3/3]

CDPL_CHEM_API const Math::Vector3D& CDPL::Chem::get3DCoordinates

(

const Entity3D &

entity

)

set3DCoordinates() [2/2]

CDPL_CHEM_API void CDPL::Chem::set3DCoordinates	(	Entity3D &	entity,
		const Math::Vector3D &	coords
	)

clear3DCoordinates()

CDPL_CHEM_API void CDPL::Chem::clear3DCoordinates

(

Entity3D &

entity

)

has3DCoordinates()

CDPL_CHEM_API bool CDPL::Chem::has3DCoordinates

(

const Entity3D &

entity

)

makeHydrogenDeplete() [1/2]

CDPL_CHEM_API bool CDPL::Chem::makeHydrogenDeplete

(

Fragment &

frag

)

Removes all explicit hydrogen atoms from the fragment frag.

Parameters

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

Returns

false if frag was not altered, true otherwise.

makeOrdinaryHydrogenDeplete() [1/2]

CDPL_CHEM_API bool CDPL::Chem::makeOrdinaryHydrogenDeplete	(	Fragment &	frag,
		unsigned int	flags
	)

Removes all explicit ordinary hydrogen atoms from the fragment frag.

Parameters

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

Returns

false if frag was not altered, true otherwise.

See also

Chem::isOrdinaryHydrogen

removeAtomsIf() [1/2]

CDPL_CHEM_API void CDPL::Chem::removeAtomsIf	(	Fragment &	frag,
		const AtomPredicate &	pred
	)

removeAtomsIfNot() [1/2]

CDPL_CHEM_API void CDPL::Chem::removeAtomsIfNot	(	Fragment &	frag,
		const AtomPredicate &	pred
	)

getName() [2/3]

CDPL_CHEM_API const std::string& CDPL::Chem::getName

(

const MolecularGraph &

molgraph

)

setName() [2/3]

CDPL_CHEM_API void CDPL::Chem::setName	(	MolecularGraph &	molgraph,
		const std::string &	name
	)

clearName() [2/3]

CDPL_CHEM_API void CDPL::Chem::clearName

(

MolecularGraph &

molgraph

)

hasName() [2/3]

CDPL_CHEM_API bool CDPL::Chem::hasName

(

const MolecularGraph &

molgraph

)

getTimestamp() [1/2]

CDPL_CHEM_API std::time_t CDPL::Chem::getTimestamp

(

const MolecularGraph &

molgraph

)

setTimestamp() [1/2]

CDPL_CHEM_API void CDPL::Chem::setTimestamp	(	MolecularGraph &	molgraph,
		std::time_t	time
	)

clearTimestamp() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearTimestamp

(

MolecularGraph &

molgraph

)

hasTimestamp() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasTimestamp

(

const MolecularGraph &

molgraph

)

getComment() [1/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getComment

(

const MolecularGraph &

molgraph

)

setComment() [1/2]

CDPL_CHEM_API void CDPL::Chem::setComment	(	MolecularGraph &	molgraph,
		const std::string &	comment
	)

clearComment() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearComment

(

MolecularGraph &

molgraph

)

hasComment() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasComment

(

const MolecularGraph &

molgraph

)

getMatchConstraints() [3/4]

CDPL_CHEM_API const MatchConstraintList::SharedPointer& CDPL::Chem::getMatchConstraints

(

const MolecularGraph &

molgraph

)

setMatchConstraints() [3/4]

CDPL_CHEM_API void CDPL::Chem::setMatchConstraints	(	MolecularGraph &	molgraph,
		const MatchConstraintList::SharedPointer &	constr
	)

clearMatchConstraints() [3/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints

(

MolecularGraph &

molgraph

)

hasMatchConstraints() [3/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints

(

const MolecularGraph &

molgraph

)

getMatchExpression() [3/4]

CDPL_CHEM_API const MatchExpression<MolecularGraph>::SharedPointer& CDPL::Chem::getMatchExpression

(

const MolecularGraph &

molgraph

)

setMatchExpression() [3/4]

CDPL_CHEM_API void CDPL::Chem::setMatchExpression	(	MolecularGraph &	molgraph,
		const MatchExpression< MolecularGraph >::SharedPointer &	expr
	)

clearMatchExpression() [3/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression

(

MolecularGraph &

molgraph

)

hasMatchExpression() [3/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression

(

const MolecularGraph &

molgraph

)

generateMatchExpression() [3/6]

CDPL_CHEM_API MatchExpression<MolecularGraph>::SharedPointer CDPL::Chem::generateMatchExpression

(

const MolecularGraph &

molgraph

)

generateMatchExpression() [4/6]

CDPL_CHEM_API MatchExpression<MolecularGraph>::SharedPointer CDPL::Chem::generateMatchExpression	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

getRings()

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getRings

(

const MolecularGraph &

molgraph

)

setRings()

CDPL_CHEM_API void CDPL::Chem::setRings	(	MolecularGraph &	molgraph,
		const FragmentList::SharedPointer &	rings
	)

clearRings()

CDPL_CHEM_API void CDPL::Chem::clearRings

(

MolecularGraph &

molgraph

)

hasRings()

CDPL_CHEM_API bool CDPL::Chem::hasRings

(

const MolecularGraph &

molgraph

)

perceiveRings() [1/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveRings

(

const MolecularGraph &

molgraph

)

perceiveRings() [2/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveRings	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

getSSSR()

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getSSSR

(

const MolecularGraph &

molgraph

)

setSSSR()

CDPL_CHEM_API void CDPL::Chem::setSSSR	(	MolecularGraph &	molgraph,
		const FragmentList::SharedPointer &	sssr
	)

clearSSSR()

CDPL_CHEM_API void CDPL::Chem::clearSSSR

(

MolecularGraph &

molgraph

)

hasSSSR()

CDPL_CHEM_API bool CDPL::Chem::hasSSSR

(

const MolecularGraph &

molgraph

)

perceiveSSSR() [1/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveSSSR

(

const MolecularGraph &

molgraph

)

perceiveSSSR() [2/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveSSSR	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

extractSSSRSubset() [1/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::extractSSSRSubset	(	const MolecularGraph &	src_molgraph,
		const MolecularGraph &	tgt_molgraph
	)

extractSSSRSubset() [2/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::extractSSSRSubset	(	const MolecularGraph &	src_molgraph,
		MolecularGraph &	tgt_molgraph,
		bool	overwrite
	)

getCyclicSubstructure()

CDPL_CHEM_API const Fragment::SharedPointer& CDPL::Chem::getCyclicSubstructure

(

const MolecularGraph &

molgraph

)

setCyclicSubstructure()

CDPL_CHEM_API void CDPL::Chem::setCyclicSubstructure	(	MolecularGraph &	molgraph,
		const Fragment::SharedPointer &	substruct
	)

clearCyclicSubstructure()

CDPL_CHEM_API void CDPL::Chem::clearCyclicSubstructure

(

MolecularGraph &

molgraph

)

hasCyclicSubstructure()

CDPL_CHEM_API bool CDPL::Chem::hasCyclicSubstructure

(

const MolecularGraph &

molgraph

)

perceiveCyclicSubstructure() [1/2]

CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveCyclicSubstructure

(

const MolecularGraph &

molgraph

)

perceiveCyclicSubstructure() [2/2]

CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveCyclicSubstructure	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

getComponents()

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getComponents

(

const MolecularGraph &

molgraph

)

setComponents()

CDPL_CHEM_API void CDPL::Chem::setComponents	(	MolecularGraph &	molgraph,
		const FragmentList::SharedPointer &	comps
	)

clearComponents()

CDPL_CHEM_API void CDPL::Chem::clearComponents

(

MolecularGraph &

molgraph

)

hasComponents()

CDPL_CHEM_API bool CDPL::Chem::hasComponents

(

const MolecularGraph &

molgraph

)

perceiveComponents() [1/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponents

(

const MolecularGraph &

molgraph

)

perceiveComponents() [2/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponents	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

getComponentGroups() [1/2]

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getComponentGroups

(

const MolecularGraph &

molgraph

)

setComponentGroups() [1/2]

CDPL_CHEM_API void CDPL::Chem::setComponentGroups	(	MolecularGraph &	molgraph,
		const FragmentList::SharedPointer &	comp_groups
	)

clearComponentGroups() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearComponentGroups

(

MolecularGraph &

molgraph

)

hasComponentGroups() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasComponentGroups

(

const MolecularGraph &

molgraph

)

perceiveComponentGroups() [1/4]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups

(

const MolecularGraph &

molgraph

)

perceiveComponentGroups() [2/4]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

getConformationIndex()

CDPL_CHEM_API std::size_t CDPL::Chem::getConformationIndex

(

const MolecularGraph &

molgraph

)

setConformationIndex()

CDPL_CHEM_API void CDPL::Chem::setConformationIndex	(	MolecularGraph &	molgraph,
		std::size_t	index
	)

clearConformationIndex()

CDPL_CHEM_API void CDPL::Chem::clearConformationIndex

(

MolecularGraph &

molgraph

)

hasConformationIndex()

CDPL_CHEM_API bool CDPL::Chem::hasConformationIndex

(

const MolecularGraph &

molgraph

)

getConformerEnergies()

CDPL_CHEM_API const Util::DArray::SharedPointer& CDPL::Chem::getConformerEnergies

(

const MolecularGraph &

molgraph

)

setConformerEnergies()

CDPL_CHEM_API void CDPL::Chem::setConformerEnergies	(	MolecularGraph &	molgraph,
		const Util::DArray::SharedPointer &	energies
	)

clearConformerEnergies()

CDPL_CHEM_API void CDPL::Chem::clearConformerEnergies

(

MolecularGraph &

molgraph

)

hasConformerEnergies()

CDPL_CHEM_API bool CDPL::Chem::hasConformerEnergies

(

const MolecularGraph &

molgraph

)

setConformation() [2/2]

CDPL_CHEM_API void CDPL::Chem::setConformation	(	MolecularGraph &	molgraph,
		std::size_t	conf_idx,
		const Math::Vector3DArray &	coords,
		double	energy
	)

addConformation() [2/2]

CDPL_CHEM_API void CDPL::Chem::addConformation	(	MolecularGraph &	molgraph,
		const Math::Vector3DArray &	coords,
		double	energy
	)

getConformationEnergy()

CDPL_CHEM_API double CDPL::Chem::getConformationEnergy	(	const MolecularGraph &	molgraph,
		std::size_t	conf_idx
	)

getHashCode()

CDPL_CHEM_API std::uint64_t CDPL::Chem::getHashCode

(

const MolecularGraph &

molgraph

)

setHashCode()

CDPL_CHEM_API void CDPL::Chem::setHashCode	(	MolecularGraph &	molgraph,
		std::uint64_t	hash_code
	)

clearHashCode()

CDPL_CHEM_API void CDPL::Chem::clearHashCode

(

MolecularGraph &

molgraph

)

hasHashCode()

CDPL_CHEM_API bool CDPL::Chem::hasHashCode

(

const MolecularGraph &

molgraph

)

calcHashCode() [1/2]

CDPL_CHEM_API std::uint64_t CDPL::Chem::calcHashCode	(	const MolecularGraph &	molgraph,
		unsigned int	atom_flags = AtomPropertyFlag::DEFAULT,
		unsigned int	bond_flags = BondPropertyFlag::DEFAULT,
		bool	ord_h_deplete = true
	)

extractReactionCenter()

CDPL_CHEM_API void CDPL::Chem::extractReactionCenter	(	const MolecularGraph &	molgraph,
		Fragment &	rxn_center
	)

getStoichiometricNumber()

CDPL_CHEM_API double CDPL::Chem::getStoichiometricNumber

(

const MolecularGraph &

molgraph

)

setStoichiometricNumber()

CDPL_CHEM_API void CDPL::Chem::setStoichiometricNumber	(	MolecularGraph &	molgraph,
		double	num
	)

clearStoichiometricNumber()

CDPL_CHEM_API void CDPL::Chem::clearStoichiometricNumber

(

MolecularGraph &

molgraph

)

hasStoichiometricNumber()

CDPL_CHEM_API bool CDPL::Chem::hasStoichiometricNumber

(

const MolecularGraph &

molgraph

)

getMDLUserInitials() [1/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLUserInitials

(

const MolecularGraph &

molgraph

)

setMDLUserInitials() [1/2]

CDPL_CHEM_API void CDPL::Chem::setMDLUserInitials	(	MolecularGraph &	molgraph,
		const std::string &	initials
	)

clearMDLUserInitials() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLUserInitials

(

MolecularGraph &

molgraph

)

hasMDLUserInitials() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLUserInitials

(

const MolecularGraph &

molgraph

)

getMDLProgramName() [1/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLProgramName

(

const MolecularGraph &

molgraph

)

setMDLProgramName() [1/2]

CDPL_CHEM_API void CDPL::Chem::setMDLProgramName	(	MolecularGraph &	molgraph,
		const std::string &	name
	)

clearMDLProgramName() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLProgramName

(

MolecularGraph &

molgraph

)

hasMDLProgramName() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLProgramName

(

const MolecularGraph &

molgraph

)

getMDLRegistryNumber() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMDLRegistryNumber

(

const MolecularGraph &

molgraph

)

setMDLRegistryNumber() [1/2]

CDPL_CHEM_API void CDPL::Chem::setMDLRegistryNumber	(	MolecularGraph &	molgraph,
		std::size_t	reg_no
	)

clearMDLRegistryNumber() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLRegistryNumber

(

MolecularGraph &

molgraph

)

hasMDLRegistryNumber() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLRegistryNumber

(

const MolecularGraph &

molgraph

)

getMDLCTABVersion()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLCTABVersion

(

const MolecularGraph &

molgraph

)

setMDLCTABVersion()

CDPL_CHEM_API void CDPL::Chem::setMDLCTABVersion	(	MolecularGraph &	molgraph,
		unsigned int	version
	)

clearMDLCTABVersion()

CDPL_CHEM_API void CDPL::Chem::clearMDLCTABVersion

(

MolecularGraph &

molgraph

)

hasMDLCTABVersion()

CDPL_CHEM_API bool CDPL::Chem::hasMDLCTABVersion

(

const MolecularGraph &

molgraph

)

getStructureData()

CDPL_CHEM_API const StringDataBlock::SharedPointer& CDPL::Chem::getStructureData

(

const MolecularGraph &

molgraph

)

setStructureData()

CDPL_CHEM_API void CDPL::Chem::setStructureData	(	MolecularGraph &	molgraph,
		const StringDataBlock::SharedPointer &	data
	)

clearStructureData()

CDPL_CHEM_API void CDPL::Chem::clearStructureData

(

MolecularGraph &

molgraph

)

hasStructureData()

CDPL_CHEM_API bool CDPL::Chem::hasStructureData

(

const MolecularGraph &

molgraph

)

getMDLDimensionality()

CDPL_CHEM_API std::size_t CDPL::Chem::getMDLDimensionality

(

const MolecularGraph &

molgraph

)

setMDLDimensionality()

CDPL_CHEM_API void CDPL::Chem::setMDLDimensionality	(	MolecularGraph &	molgraph,
		std::size_t	dim
	)

clearMDLDimensionality()

CDPL_CHEM_API void CDPL::Chem::clearMDLDimensionality

(

MolecularGraph &

molgraph

)

hasMDLDimensionality()

CDPL_CHEM_API bool CDPL::Chem::hasMDLDimensionality

(

const MolecularGraph &

molgraph

)

getMDLScalingFactor1()

CDPL_CHEM_API long CDPL::Chem::getMDLScalingFactor1

(

const MolecularGraph &

molgraph

)

setMDLScalingFactor1()

CDPL_CHEM_API void CDPL::Chem::setMDLScalingFactor1	(	MolecularGraph &	molgraph,
		long	factor
	)

clearMDLScalingFactor1()

CDPL_CHEM_API void CDPL::Chem::clearMDLScalingFactor1

(

MolecularGraph &

molgraph

)

hasMDLScalingFactor1()

CDPL_CHEM_API bool CDPL::Chem::hasMDLScalingFactor1

(

const MolecularGraph &

molgraph

)

getMDLScalingFactor2()

CDPL_CHEM_API double CDPL::Chem::getMDLScalingFactor2

(

const MolecularGraph &

molgraph

)

setMDLScalingFactor2()

CDPL_CHEM_API void CDPL::Chem::setMDLScalingFactor2	(	MolecularGraph &	molgraph,
		double	factor
	)

clearMDLScalingFactor2()

CDPL_CHEM_API void CDPL::Chem::clearMDLScalingFactor2

(

MolecularGraph &

molgraph

)

hasMDLScalingFactor2()

CDPL_CHEM_API bool CDPL::Chem::hasMDLScalingFactor2

(

const MolecularGraph &

molgraph

)

getMDLEnergy()

CDPL_CHEM_API double CDPL::Chem::getMDLEnergy

(

const MolecularGraph &

molgraph

)

setMDLEnergy()

CDPL_CHEM_API void CDPL::Chem::setMDLEnergy	(	MolecularGraph &	molgraph,
		double	energy
	)

clearMDLEnergy()

CDPL_CHEM_API void CDPL::Chem::clearMDLEnergy

(

MolecularGraph &

molgraph

)

hasMDLEnergy()

CDPL_CHEM_API bool CDPL::Chem::hasMDLEnergy

(

const MolecularGraph &

molgraph

)

getMDLChiralFlag()

CDPL_CHEM_API bool CDPL::Chem::getMDLChiralFlag

(

const MolecularGraph &

molgraph

)

setMDLChiralFlag()

CDPL_CHEM_API void CDPL::Chem::setMDLChiralFlag	(	MolecularGraph &	molgraph,
		bool	flag
	)

clearMDLChiralFlag()

CDPL_CHEM_API void CDPL::Chem::clearMDLChiralFlag

(

MolecularGraph &

molgraph

)

hasMDLChiralFlag()

CDPL_CHEM_API bool CDPL::Chem::hasMDLChiralFlag

(

const MolecularGraph &

molgraph

)

getMOL2MoleculeType()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2MoleculeType

(

const MolecularGraph &

molgraph

)

setMOL2MoleculeType()

CDPL_CHEM_API void CDPL::Chem::setMOL2MoleculeType	(	MolecularGraph &	molgraph,
		unsigned int	type
	)

clearMOL2MoleculeType()

CDPL_CHEM_API void CDPL::Chem::clearMOL2MoleculeType

(

MolecularGraph &

molgraph

)

hasMOL2MoleculeType()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2MoleculeType

(

const MolecularGraph &

molgraph

)

getMOL2ChargeType()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2ChargeType

(

const MolecularGraph &

molgraph

)

setMOL2ChargeType()

CDPL_CHEM_API void CDPL::Chem::setMOL2ChargeType	(	MolecularGraph &	molgraph,
		unsigned int	type
	)

clearMOL2ChargeType()

CDPL_CHEM_API void CDPL::Chem::clearMOL2ChargeType

(

MolecularGraph &

molgraph

)

hasMOL2ChargeType()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2ChargeType

(

const MolecularGraph &

molgraph

)

generateAdjacencyMatrix()

CDPL_CHEM_API void CDPL::Chem::generateAdjacencyMatrix	(	const MolecularGraph &	molgraph,
		Math::SparseULMatrix &	mtx
	)

generateIncidenceMatrix()

CDPL_CHEM_API void CDPL::Chem::generateIncidenceMatrix	(	const MolecularGraph &	molgraph,
		Math::SparseULMatrix &	mtx
	)

generateBondMatrix()

CDPL_CHEM_API void CDPL::Chem::generateBondMatrix	(	const MolecularGraph &	molgraph,
		Math::SparseULMatrix &	mtx
	)

generateBondElectronMatrix()

CDPL_CHEM_API void CDPL::Chem::generateBondElectronMatrix	(	const MolecularGraph &	molgraph,
		Math::SparseULMatrix &	mtx
	)

generateBondAtomTypeMatrix()

CDPL_CHEM_API void CDPL::Chem::generateBondAtomTypeMatrix	(	const MolecularGraph &	molgraph,
		Math::SparseULMatrix &	mtx
	)

getTopologicalDistanceMatrix()

CDPL_CHEM_API const Math::ULMatrix::SharedPointer& CDPL::Chem::getTopologicalDistanceMatrix

(

const MolecularGraph &

molgraph

)

setTopologicalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::setTopologicalDistanceMatrix	(	MolecularGraph &	molgraph,
		const Math::ULMatrix::SharedPointer &	mtx
	)

clearTopologicalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::clearTopologicalDistanceMatrix

(

MolecularGraph &

molgraph

)

hasTopologicalDistanceMatrix()

CDPL_CHEM_API bool CDPL::Chem::hasTopologicalDistanceMatrix

(

const MolecularGraph &

molgraph

)

calcTopologicalDistanceMatrix() [1/2]

CDPL_CHEM_API Math::ULMatrix::SharedPointer CDPL::Chem::calcTopologicalDistanceMatrix	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

calcTopologicalDistanceMatrix() [2/2]

CDPL_CHEM_API void CDPL::Chem::calcTopologicalDistanceMatrix	(	const MolecularGraph &	molgraph,
		Math::ULMatrix &	mtx
	)

extractTopologicalDistanceSubMatrix() [1/2]

CDPL_CHEM_API Math::ULMatrix::SharedPointer CDPL::Chem::extractTopologicalDistanceSubMatrix	(	const MolecularGraph &	src_molgraph,
		MolecularGraph &	tgt_molgraph,
		bool	overwrite
	)

extractTopologicalDistanceSubMatrix() [2/2]

CDPL_CHEM_API void CDPL::Chem::extractTopologicalDistanceSubMatrix	(	const MolecularGraph &	src_molgraph,
		const MolecularGraph &	tgt_molgraph,
		Math::ULMatrix &	mtx
	)

getGeometricalDistanceMatrix()

CDPL_CHEM_API const Math::DMatrix::SharedPointer& CDPL::Chem::getGeometricalDistanceMatrix

(

const MolecularGraph &

molgraph

)

setGeometricalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::setGeometricalDistanceMatrix	(	MolecularGraph &	molgraph,
		const Math::DMatrix::SharedPointer &	mtx
	)

clearGeometricalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::clearGeometricalDistanceMatrix

(

MolecularGraph &

molgraph

)

hasGeometricalDistanceMatrix()

CDPL_CHEM_API bool CDPL::Chem::hasGeometricalDistanceMatrix

(

const MolecularGraph &

molgraph

)

calcGeometricalDistanceMatrix() [2/2]

CDPL_CHEM_API Math::DMatrix::SharedPointer CDPL::Chem::calcGeometricalDistanceMatrix	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

getAromaticSubstructure()

CDPL_CHEM_API const Fragment::SharedPointer& CDPL::Chem::getAromaticSubstructure

(

const MolecularGraph &

molgraph

)

setAromaticSubstructure()

CDPL_CHEM_API void CDPL::Chem::setAromaticSubstructure	(	MolecularGraph &	molgraph,
		const Fragment::SharedPointer &	substruct
	)

clearAromaticSubstructure()

CDPL_CHEM_API void CDPL::Chem::clearAromaticSubstructure

(

MolecularGraph &

molgraph

)

hasAromaticSubstructure()

CDPL_CHEM_API bool CDPL::Chem::hasAromaticSubstructure

(

const MolecularGraph &

molgraph

)

perceiveAromaticSubstructure() [1/2]

CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveAromaticSubstructure

(

const MolecularGraph &

molgraph

)

perceiveAromaticSubstructure() [2/2]

CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveAromaticSubstructure	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

getPiElectronSystems()

CDPL_CHEM_API const ElectronSystemList::SharedPointer& CDPL::Chem::getPiElectronSystems

(

const MolecularGraph &

molgraph

)

setPiElectronSystems()

CDPL_CHEM_API void CDPL::Chem::setPiElectronSystems	(	MolecularGraph &	molgraph,
		const ElectronSystemList::SharedPointer &	pi_systems
	)

clearPiElectronSystems()

CDPL_CHEM_API void CDPL::Chem::clearPiElectronSystems

(

MolecularGraph &

molgraph

)

hasPiElectronSystems()

CDPL_CHEM_API bool CDPL::Chem::hasPiElectronSystems

(

const MolecularGraph &

molgraph

)

perceivePiElectronSystems() [1/2]

CDPL_CHEM_API ElectronSystemList::SharedPointer CDPL::Chem::perceivePiElectronSystems

(

const MolecularGraph &

molgraph

)

perceivePiElectronSystems() [2/2]

CDPL_CHEM_API ElectronSystemList::SharedPointer CDPL::Chem::perceivePiElectronSystems	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

generateSMILES() [1/2]

CDPL_CHEM_API bool CDPL::Chem::generateSMILES	(	const MolecularGraph &	molgraph,
		std::string &	smiles,
		bool	canonical = false,
		bool	ord_h_deplete = true,
		unsigned int	atom_flags = AtomPropertyFlag::DEFAULT,
		unsigned int	bond_flags = BondPropertyFlag::DEFAULT
	)

generateINCHI()

CDPL_CHEM_API int CDPL::Chem::generateINCHI	(	const MolecularGraph &	molgraph,
		std::string &	inchi,
		const std::string &	options = ControlParameterDefault::INCHI_OUTPUT_OPTIONS,
		std::size_t	dim = 0
	)

generateINCHIKey()

CDPL_CHEM_API int CDPL::Chem::generateINCHIKey	(	const MolecularGraph &	molgraph,
		std::string &	inchi_key
	)

canonicalize() [1/2]

CDPL_CHEM_API void CDPL::Chem::canonicalize	(	MolecularGraph &	molgraph,
		const AtomCompareFunction &	func,
		bool	atoms = true,
		bool	atom_nbrs = true,
		bool	bonds = true,
		bool	bond_atoms = false
	)

canonicalize() [2/2]

CDPL_CHEM_API void CDPL::Chem::canonicalize	(	MolecularGraph &	molgraph,
		bool	atoms = true,
		bool	atom_nbrs = true,
		bool	bonds = true,
		bool	bond_atoms = false
	)

calc2DCoordinates()

CDPL_CHEM_API void CDPL::Chem::calc2DCoordinates	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

calcHydrogen3DCoordinates()

CDPL_CHEM_API void CDPL::Chem::calcHydrogen3DCoordinates	(	MolecularGraph &	molgraph,
		bool	undef_only = true
	)

calcBond2DStereoFlags()

CDPL_CHEM_API void CDPL::Chem::calcBond2DStereoFlags	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

calcCIPPriorities()

CDPL_CHEM_API void CDPL::Chem::calcCIPPriorities	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

perceiveSymmetryClasses()

CDPL_CHEM_API void CDPL::Chem::perceiveSymmetryClasses	(	MolecularGraph &	molgraph,
		bool	overwrite,
		unsigned int	atom_flags = AtomPropertyFlag::DEFAULT,
		unsigned int	bond_flags = BondPropertyFlag::DEFAULT,
		bool	inc_impl_h = true
	)

calcCanonicalNumbering()

CDPL_CHEM_API void CDPL::Chem::calcCanonicalNumbering	(	MolecularGraph &	molgraph,
		bool	overwrite,
		unsigned int	atom_flags = AtomPropertyFlag::DEFAULT,
		unsigned int	bond_flags = BondPropertyFlag::DEFAULT
	)

calcMorganNumbering()

CDPL_CHEM_API void CDPL::Chem::calcMorganNumbering	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

calcImplicitHydrogenCounts()

CDPL_CHEM_API void CDPL::Chem::calcImplicitHydrogenCounts	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

calcFormalCharges()

CDPL_CHEM_API void CDPL::Chem::calcFormalCharges	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

perceiveHybridizationStates()

CDPL_CHEM_API void CDPL::Chem::perceiveHybridizationStates	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

perceiveBondOrders()

CDPL_CHEM_API void CDPL::Chem::perceiveBondOrders	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

kekulizeBonds()

CDPL_CHEM_API void CDPL::Chem::kekulizeBonds

(

MolecularGraph &

molgraph

)

perceiveAtomStereoCenters()

CDPL_CHEM_API void 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
	)

perceiveBondStereoCenters()

CDPL_CHEM_API void CDPL::Chem::perceiveBondStereoCenters	(	MolecularGraph &	molgraph,
		bool	overwrite,
		bool	check_asym = true,
		bool	check_term_n = true,
		bool	check_order = true,
		std::size_t	min_ring_size = 8
	)

calcMDLParities()

CDPL_CHEM_API void CDPL::Chem::calcMDLParities	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

calcAtomStereoDescriptors()

CDPL_CHEM_API void CDPL::Chem::calcAtomStereoDescriptors	(	MolecularGraph &	molgraph,
		bool	overwrite,
		std::size_t	dim = 1,
		bool	check_stc_flag = true
	)

calcAtomStereoDescriptorsFromMDLParities()

CDPL_CHEM_API void CDPL::Chem::calcAtomStereoDescriptorsFromMDLParities	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

calcBondStereoDescriptors()

CDPL_CHEM_API void CDPL::Chem::calcBondStereoDescriptors	(	MolecularGraph &	molgraph,
		bool	overwrite,
		std::size_t	dim = 1,
		bool	check_stc_flag = true
	)

calcAtomCIPConfigurations()

CDPL_CHEM_API void CDPL::Chem::calcAtomCIPConfigurations	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

calcBondCIPConfigurations()

CDPL_CHEM_API void CDPL::Chem::calcBondCIPConfigurations	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

setAtomMatchConstraints() [1/2]

CDPL_CHEM_API void CDPL::Chem::setAtomMatchConstraints	(	MolecularGraph &	molgraph,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

setBondMatchConstraints() [1/2]

CDPL_CHEM_API void CDPL::Chem::setBondMatchConstraints	(	MolecularGraph &	molgraph,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

generateMatchExpressions() [1/2]

CDPL_CHEM_API void CDPL::Chem::generateMatchExpressions	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

generateMatchExpressionStrings()

CDPL_CHEM_API void CDPL::Chem::generateMatchExpressionStrings	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

initSubstructureSearchQuery() [1/2]

CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchQuery	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

initSubstructureSearchTarget() [1/2]

CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchTarget	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

setAromaticityFlags()

CDPL_CHEM_API void CDPL::Chem::setAromaticityFlags	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

setRingFlags()

CDPL_CHEM_API void CDPL::Chem::setRingFlags	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

setAtomTypesFromSymbols()

CDPL_CHEM_API void CDPL::Chem::setAtomTypesFromSymbols	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

setAtomSymbolsFromTypes()

CDPL_CHEM_API void CDPL::Chem::setAtomSymbolsFromTypes	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

perceiveSybylAtomTypes()

CDPL_CHEM_API void CDPL::Chem::perceiveSybylAtomTypes	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

getAromaticRings()

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::getAromaticRings

(

const MolecularGraph &

molgraph

)

getAromaticSSSRSubset()

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::getAromaticSSSRSubset

(

const MolecularGraph &

molgraph

)

containsMolecularGraph()

CDPL_CHEM_API bool CDPL::Chem::containsMolecularGraph	(	const MolecularGraph &	molgraph,
		const MolecularGraph &	sub_molgraph,
		bool	atoms = true,
		bool	bonds = true
	)

getContainedFragments()

CDPL_CHEM_API void CDPL::Chem::getContainedFragments	(	const MolecularGraph &	molgraph,
		const FragmentList &	frag_list,
		FragmentList &	cont_frag_list,
		bool	append = false,
		bool	atoms = true,
		bool	bonds = true
	)

getContainingFragments() [3/3]

CDPL_CHEM_API void CDPL::Chem::getContainingFragments	(	const MolecularGraph &	molgraph,
		const FragmentList &	frag_list,
		FragmentList &	cont_frag_list,
		bool	append = false,
		bool	atoms = true,
		bool	bonds = true
	)

translateFragment()

CDPL_CHEM_API void CDPL::Chem::translateFragment	(	const MolecularGraph &	src_molgraph,
		const Fragment &	src_frag,
		const MolecularGraph &	tgt_molgraph,
		Fragment &	tgt_frag,
		bool	append = false
	)

translateFragments()

CDPL_CHEM_API void CDPL::Chem::translateFragments	(	const MolecularGraph &	src_molgraph,
		const FragmentList &	src_frag_list,
		const MolecularGraph &	tgt_molgraph,
		FragmentList &	tgt_frag_list,
		bool	append = false
	)

splitIntoFragments()

CDPL_CHEM_API void CDPL::Chem::splitIntoFragments	(	const MolecularGraph &	molgraph,
		FragmentList &	frag_list,
		const Util::BitSet &	split_bond_mask,
		bool	append = false
	)

getCompleteBondCount()

CDPL_CHEM_API std::size_t CDPL::Chem::getCompleteBondCount

(

const MolecularGraph &

molgraph

)

calcBasicProperties() [1/2]

CDPL_CHEM_API void CDPL::Chem::calcBasicProperties	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Since

1.1

makeHydrogenDeplete() [2/2]

CDPL_CHEM_API bool CDPL::Chem::makeHydrogenDeplete	(	Molecule &	mol,
		bool	corr_impl_h_count = true
	)

Removes all explicit hydrogen atoms from the molecule mol.

Parameters

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

Returns

false if mol was not altered, true otherwise.

makeOrdinaryHydrogenDeplete() [2/2]

CDPL_CHEM_API bool CDPL::Chem::makeOrdinaryHydrogenDeplete	(	Molecule &	mol,
		unsigned int	flags,
		bool	corr_impl_h_count = true
	)

Removes all explicit ordinary hydrogen atoms from the molecule mol.

Parameters

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

Returns

false if mol was not altered, true otherwise.

See also

Chem::isOrdinaryHydrogen

makeHydrogenComplete()

CDPL_CHEM_API 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.

connectAtoms() [1/2]

CDPL_CHEM_API void CDPL::Chem::connectAtoms	(	Molecule &	mol,
		double	dist_tol = 0.3,
		std::size_t	atom_idx_offs = 0
	)

connectAtoms() [2/2]

CDPL_CHEM_API void CDPL::Chem::connectAtoms	(	Molecule &	mol,
		const Atom3DCoordinatesFunction &	coords_func,
		double	dist_tol = 0.3,
		std::size_t	atom_idx_offs = 0
	)

removeAtomsIf() [2/2]

CDPL_CHEM_API void CDPL::Chem::removeAtomsIf	(	Molecule &	mol,
		const AtomPredicate &	pred
	)

removeAtomsIfNot() [2/2]

CDPL_CHEM_API void CDPL::Chem::removeAtomsIfNot	(	Molecule &	mol,
		const AtomPredicate &	pred
	)

getName() [3/3]

CDPL_CHEM_API const std::string& CDPL::Chem::getName

(

const Reaction &

rxn

)

setName() [3/3]

CDPL_CHEM_API void CDPL::Chem::setName	(	Reaction &	rxn,
		const std::string &	name
	)

clearName() [3/3]

CDPL_CHEM_API void CDPL::Chem::clearName

(

Reaction &

rxn

)

hasName() [3/3]

CDPL_CHEM_API bool CDPL::Chem::hasName

(

const Reaction &

rxn

)

getTimestamp() [2/2]

CDPL_CHEM_API std::time_t CDPL::Chem::getTimestamp

(

const Reaction &

rxn

)

setTimestamp() [2/2]

CDPL_CHEM_API void CDPL::Chem::setTimestamp	(	Reaction &	rxn,
		std::time_t	time
	)

clearTimestamp() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearTimestamp

(

Reaction &

rxn

)

hasTimestamp() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasTimestamp

(

const Reaction &

rxn

)

getComment() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getComment

(

const Reaction &

rxn

)

setComment() [2/2]

CDPL_CHEM_API void CDPL::Chem::setComment	(	Reaction &	rxn,
		const std::string &	comment
	)

clearComment() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearComment

(

Reaction &

rxn

)

hasComment() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasComment

(

const Reaction &

rxn

)

getMatchExpression() [4/4]

CDPL_CHEM_API const MatchExpression<Reaction>::SharedPointer& CDPL::Chem::getMatchExpression

(

const Reaction &

rxn

)

setMatchExpression() [4/4]

CDPL_CHEM_API void CDPL::Chem::setMatchExpression	(	Reaction &	rxn,
		const MatchExpression< Reaction >::SharedPointer &	expr
	)

clearMatchExpression() [4/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression

(

Reaction &

rxn

)

hasMatchExpression() [4/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression

(

const Reaction &

rxn

)

generateMatchExpression() [5/6]

CDPL_CHEM_API MatchExpression<Reaction>::SharedPointer CDPL::Chem::generateMatchExpression

(

const Reaction &

rxn

)

generateMatchExpression() [6/6]

CDPL_CHEM_API MatchExpression<Reaction>::SharedPointer CDPL::Chem::generateMatchExpression	(	Reaction &	rxn,
		bool	overwrite
	)

getMatchConstraints() [4/4]

CDPL_CHEM_API const MatchConstraintList::SharedPointer& CDPL::Chem::getMatchConstraints

(

const Reaction &

rxn

)

setMatchConstraints() [4/4]

CDPL_CHEM_API void CDPL::Chem::setMatchConstraints	(	Reaction &	rxn,
		const MatchConstraintList::SharedPointer &	constr
	)

clearMatchConstraints() [4/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints

(

Reaction &

rxn

)

hasMatchConstraints() [4/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints

(

const Reaction &

rxn

)

getComponentGroups() [2/2]

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getComponentGroups

(

const Reaction &

rxn

)

setComponentGroups() [2/2]

CDPL_CHEM_API void CDPL::Chem::setComponentGroups	(	Reaction &	rxn,
		const FragmentList::SharedPointer &	comp_groups
	)

clearComponentGroups() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearComponentGroups

(

Reaction &

rxn

)

hasComponentGroups() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasComponentGroups

(

const Reaction &

rxn

)

perceiveComponentGroups() [3/4]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups

(

const Reaction &

rxn

)

perceiveComponentGroups() [4/4]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups	(	Reaction &	rxn,
		bool	overwrite
	)

getAtomMapping()

CDPL_CHEM_API const AtomMapping::SharedPointer& CDPL::Chem::getAtomMapping

(

const Reaction &

rxn

)

setAtomMapping()

CDPL_CHEM_API void CDPL::Chem::setAtomMapping	(	Reaction &	rxn,
		const AtomMapping::SharedPointer &	mapping
	)

clearAtomMapping()

CDPL_CHEM_API void CDPL::Chem::clearAtomMapping

(

Reaction &

rxn

)

hasAtomMapping()

CDPL_CHEM_API bool CDPL::Chem::hasAtomMapping

(

const Reaction &

rxn

)

perceiveAtomMapping() [1/2]

CDPL_CHEM_API AtomMapping::SharedPointer CDPL::Chem::perceiveAtomMapping

(

const Reaction &

rxn

)

perceiveAtomMapping() [2/2]

CDPL_CHEM_API AtomMapping::SharedPointer CDPL::Chem::perceiveAtomMapping	(	Reaction &	rxn,
		bool	overwrite
	)

generateSMILES() [2/2]

CDPL_CHEM_API bool CDPL::Chem::generateSMILES	(	const Reaction &	rxn,
		std::string &	smiles,
		bool	canonical = false,
		bool	ord_h_deplete = true,
		unsigned int	atom_flags = AtomPropertyFlag::DEFAULT,
		unsigned int	bond_flags = BondPropertyFlag::DEFAULT
	)

calcHashCode() [2/2]

CDPL_CHEM_API std::uint64_t CDPL::Chem::calcHashCode	(	const Reaction &	rxn,
		unsigned int	role_mask = ReactionRole::ALL,
		unsigned int	atom_flags = AtomPropertyFlag::DEFAULT,
		unsigned int	bond_flags = BondPropertyFlag::DEFAULT,
		bool	ord_h_deplete = true
	)

getMDLUserInitials() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLUserInitials

(

const Reaction &

rxn

)

setMDLUserInitials() [2/2]

CDPL_CHEM_API void CDPL::Chem::setMDLUserInitials	(	Reaction &	rxn,
		const std::string &	initials
	)

clearMDLUserInitials() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLUserInitials

(

Reaction &

rxn

)

hasMDLUserInitials() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLUserInitials

(

const Reaction &

rxn

)

getMDLProgramName() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLProgramName

(

const Reaction &

rxn

)

setMDLProgramName() [2/2]

CDPL_CHEM_API void CDPL::Chem::setMDLProgramName	(	Reaction &	rxn,
		const std::string &	name
	)

clearMDLProgramName() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLProgramName

(

Reaction &

rxn

)

hasMDLProgramName() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLProgramName

(

const Reaction &

rxn

)

getMDLRegistryNumber() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMDLRegistryNumber

(

const Reaction &

rxn

)

setMDLRegistryNumber() [2/2]

CDPL_CHEM_API void CDPL::Chem::setMDLRegistryNumber	(	Reaction &	rxn,
		std::size_t	reg_no
	)

clearMDLRegistryNumber() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLRegistryNumber

(

Reaction &

rxn

)

hasMDLRegistryNumber() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLRegistryNumber

(

const Reaction &

rxn

)

getReactionData()

CDPL_CHEM_API const StringDataBlock::SharedPointer& CDPL::Chem::getReactionData

(

const Reaction &

rxn

)

setReactionData()

CDPL_CHEM_API void CDPL::Chem::setReactionData	(	Reaction &	rxn,
		const StringDataBlock::SharedPointer &	data
	)

clearReactionData()

CDPL_CHEM_API void CDPL::Chem::clearReactionData

(

Reaction &

rxn

)

hasReactionData()

CDPL_CHEM_API bool CDPL::Chem::hasReactionData

(

const Reaction &

rxn

)

getMDLMoleculeRecord()

CDPL_CHEM_API const Molecule::SharedPointer& CDPL::Chem::getMDLMoleculeRecord

(

const Reaction &

rxn

)

setMDLMoleculeRecord()

CDPL_CHEM_API void CDPL::Chem::setMDLMoleculeRecord	(	Reaction &	rxn,
		const Molecule::SharedPointer &	mol_rec
	)

clearMDLMoleculeRecord()

CDPL_CHEM_API void CDPL::Chem::clearMDLMoleculeRecord

(

Reaction &

rxn

)

hasMDLMoleculeRecord()

CDPL_CHEM_API bool CDPL::Chem::hasMDLMoleculeRecord

(

const Reaction &

rxn

)

getMDLInternalRegistryNumber()

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLInternalRegistryNumber

(

const Reaction &

rxn

)

setMDLInternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::setMDLInternalRegistryNumber	(	Reaction &	rxn,
		const std::string &	reg_no
	)

clearMDLInternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::clearMDLInternalRegistryNumber

(

Reaction &

rxn

)

hasMDLInternalRegistryNumber()

CDPL_CHEM_API bool CDPL::Chem::hasMDLInternalRegistryNumber

(

const Reaction &

rxn

)

getMDLExternalRegistryNumber()

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLExternalRegistryNumber

(

const Reaction &

rxn

)

setMDLExternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::setMDLExternalRegistryNumber	(	Reaction &	rxn,
		const std::string &	reg_no
	)

clearMDLExternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::clearMDLExternalRegistryNumber

(

Reaction &

rxn

)

hasMDLExternalRegistryNumber()

CDPL_CHEM_API bool CDPL::Chem::hasMDLExternalRegistryNumber

(

const Reaction &

rxn

)

getMDLRXNFileVersion()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLRXNFileVersion

(

const Reaction &

rxn

)

setMDLRXNFileVersion()

CDPL_CHEM_API void CDPL::Chem::setMDLRXNFileVersion	(	Reaction &	rxn,
		unsigned int	version
	)

clearMDLRXNFileVersion()

CDPL_CHEM_API void CDPL::Chem::clearMDLRXNFileVersion

(

Reaction &

rxn

)

hasMDLRXNFileVersion()

CDPL_CHEM_API bool CDPL::Chem::hasMDLRXNFileVersion

(

const Reaction &

rxn

)

getMaxComponentGroupID() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxComponentGroupID

(

const Reaction &

rxn

)

getMaxAtomMappingID() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxAtomMappingID

(

const Reaction &

rxn

)

setAtomMatchConstraints() [2/2]

CDPL_CHEM_API void CDPL::Chem::setAtomMatchConstraints	(	Reaction &	rxn,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

setBondMatchConstraints() [2/2]

CDPL_CHEM_API void CDPL::Chem::setBondMatchConstraints	(	Reaction &	rxn,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

setComponentMatchConstraints()

CDPL_CHEM_API void CDPL::Chem::setComponentMatchConstraints	(	Reaction &	rxn,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

generateMatchExpressions() [2/2]

CDPL_CHEM_API void CDPL::Chem::generateMatchExpressions	(	Reaction &	rxn,
		bool	overwrite
	)

initSubstructureSearchQuery() [2/2]

CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchQuery	(	Reaction &	rxn,
		bool	overwrite
	)

initSubstructureSearchTarget() [2/2]

CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchTarget	(	Reaction &	rxn,
		bool	overwrite
	)

calcBasicProperties() [2/2]

CDPL_CHEM_API void CDPL::Chem::calcBasicProperties	(	Reaction &	rxn,
		bool	overwrite
	)

Since

1.1

parseSMARTS() [1/2]

CDPL_CHEM_API Molecule::SharedPointer CDPL::Chem::parseSMARTS	(	const std::string &	smarts,
		bool	init_qry = true
	)

parseSMARTS() [2/2]

CDPL_CHEM_API bool CDPL::Chem::parseSMARTS	(	const std::string &	smarts,
		Molecule &	mol,
		bool	init_qry = true
	)

parseSMILES() [1/2]

CDPL_CHEM_API Molecule::SharedPointer CDPL::Chem::parseSMILES

(

const std::string &

smiles

)

parseSMILES() [2/2]

CDPL_CHEM_API bool CDPL::Chem::parseSMILES	(	const std::string &	smiles,
		Molecule &	mol
	)

extendBoundingBox()

CDPL_CHEM_API void CDPL::Chem::extendBoundingBox	(	Math::Vector3D &	min,
		Math::Vector3D &	max,
		const Math::Vector3D &	coords,
		bool	reset = false
	)

insideBoundingBox() [3/3]

CDPL_CHEM_API bool CDPL::Chem::insideBoundingBox	(	const Math::Vector3D &	min,
		const Math::Vector3D &	max,
		const Math::Vector3D &	coords
	)

isAromatic()

CDPL_CHEM_API bool CDPL::Chem::isAromatic	(	const Fragment &	ring,
		const MolecularGraph &	molgraph,
		const Util::BitSet &	arom_bond_mask
	)

isNotAromatic()

CDPL_CHEM_API bool CDPL::Chem::isNotAromatic	(	const Fragment &	ring,
		const MolecularGraph &	molgraph
	)

containsFragmentWithBond()

CDPL_CHEM_API bool CDPL::Chem::containsFragmentWithBond	(	const FragmentList &	frag_list,
		const Bond &	bond
	)

containsFragmentWithMinSize()

CDPL_CHEM_API bool CDPL::Chem::containsFragmentWithMinSize	(	const FragmentList &	frag_list,
		std::size_t	min_size
	)

atomTypesMatch()

CDPL_CHEM_API bool CDPL::Chem::atomTypesMatch	(	unsigned int	qry_type,
		unsigned int	tgt_type
	)

sybylToAtomType()

CDPL_CHEM_API unsigned int CDPL::Chem::sybylToAtomType

(

unsigned int

sybyl_type

)

getSybylAtomTypeString()

CDPL_CHEM_API const std::string& CDPL::Chem::getSybylAtomTypeString

(

unsigned int

sybyl_type

)

getSybylBondTypeString()

CDPL_CHEM_API const std::string& CDPL::Chem::getSybylBondTypeString

(

unsigned int

sybyl_type

)