CDPL::Chem Namespace Reference

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

Namespaces
	AtomConfiguration
	Provides constants that are used to specify the configuration of stereogenic 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 labeling the endpoints of bonds matched by BRICS fragmentation rules.
	BRICSRuleID
	Provides constants for the identification of BRICS fragmentation rules.
	CIPDescriptor
	Provides constants for the specification of stereogenic atom/bond configurations determined by the Cahn-Ingold-Prelog (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 (CTAB) and Rxn-File version for the I/O of molecular graphs and reactions in an MDL CTFile based data format.
	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 Sybyl MOL2 files.
	MOL2MoleculeType
	Provides constants for the specification of the molecule type in Sybyl 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 labeling the endpoints of bonds matched by RECAP fragmentation rules.
	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 numeric identifiers for built-in Chem::TautomerizationRule implementations.

Classes
class	AmideImidicAcidTautomerization
	Implementation of the amide ↔ imidic-acid tautomerization rule. More...
class	ANDMatchExpressionList
	Chem::MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND). More...
class	ANDMatchExpressionList< ObjType, void >
	Chem::MatchExpressionList specialization (single-object form) that evaluates the stored expressions as a logical conjunction (AND). More...
class	AromaticRingSet
	Implements the perception of aromatic rings in a molecular graph. More...
class	AromaticSSSRSubset
	Implements the extraction of the aromatic rings in the SSSR of a molecular graph. More...
class	AromaticSubstructure
	Implements the perception of aromatic atoms and bonds in a molecular graph. More...
class	Atom
	Abstract base class representing a chemical atom and its bonded neighborhood. More...
class	Atom2DCoordinatesCalculator
	Generates 2D coordinates for the atoms of a molecular graph. More...
struct	Atom3DCoordinatesFunctor
	Helper-functor for retrieving the 3D coordinates of an atom (via the Chem::AtomProperty::COORDINATES_3D property). More...
class	AtomArray3DCoordinatesFunctor
	Functor for retrieving atom 3D coordinates from a provided coordinates array via index of the atoms in a specified molecular graph. More...
class	AtomBondMapping
	Data structure for the common storage of related atom to atom and bond to bond mappings. More...
class	AtomConfigurationMatchExpression
	Chem::MatchExpression that constrains target atoms by their stereo configuration relative to a query atom. More...
class	AtomConformer3DCoordinatesFunctor
	Functor for retrieving atom 3D coordinates from a specific conformer. More...
class	AtomContainer
	Common interface for data structures that support a random access to stored Chem::Atom instances. More...
class	AtomDictionary
	A global dictionary for the lookup of data associated with the atom types defined in namespace Chem::AtomType. More...
class	AtomEnvironmentMatchExpression
	Chem::MatchExpression that constrains target atoms by the structural environment encoded as a SMARTS substructure pattern. More...
class	AtomMapping
	Data type for the storage and lookup of arbitrary atom to atom mappings. More...
class	AtomSSSRRingSizeMatchExpression
	Chem::MatchExpression that constrains target atoms by the size of the SSSR ring(s) containing them. More...
class	AtomTypeMatchExpression
	MatchExpression that checks the atom type of a target atom against a query atom type. More...
class	AutomorphismGroupSearch
	Enumerates the atom and bond self-mappings (automorphism group) of a molecular graph. More...
class	BasicAtom
	Default implementation of the Chem::Atom interface. More...
class	BasicBond
	Default implementation of the Chem::Bond interface. More...
class	BasicMolecule
	Default implementation of the Chem::Molecule interface. More...
class	BasicReaction
	Default implementation of the Chem::Reaction interface. More...
class	BemisMurckoAnalyzer
	Decomposes a molecular graph into its Bemis-Murcko framework, ring systems, linkers and side chains. More...
class	Bond
	Abstract base class representing a chemical bond between two atoms (represented by Chem::Atom instances). More...
class	BondConfigurationMatchExpression
	Chem::MatchExpression that constrains target bonds by their stereo configuration relative to a query bond. More...
class	BondContainer
	Common interface for data structures that support a random access to stored Chem::Bond instances. More...
class	BondDirectionMatchExpression
	Chem::MatchExpression that constrains target bonds by their SMILES/SMARTS bond direction. More...
class	BondMapping
	Data type for the storage and lookup of arbitrary bond to bond mappings. More...
class	BondOrderCalculator
	Perceives bond orders of a molecular graph from its 3D structure and atom connectivity. More...
class	BondReactionCenterStatusMatchExpression
	Chem::MatchExpression that constrains target bonds by their reaction-center status (see Chem::ReactionCenterStatus). More...
class	BondStereoFlagCalculator
	Calculator that derives 2D wedge/hash bond stereo flags from atom 2D coordinates and stereochemical descriptors of a molecular graph. More...
class	BondSubstituentDirectionMatchExpression
	Chem::MatchExpression that constrains target double bond geometry via the per-substituent bond-direction annotations carried by the query (in the style of Daylight SMARTS [SMARTS] cis/trans patterns). More...
class	BRICSFragmentGenerator
	Molecular graph fragment generator implementing the BRICS bond-cleavage rule set. More...
class	CanonicalNumberingCalculator
	Computes canonical atom numberings for molecular graphs using McKay's algorithm. More...
class	CDFMolecularGraphWriter
	Writer for molecular graph data in the native I/O format of the CDPL. More...
class	CDFMoleculeReader
	Reader for molecule data in the native I/O format of the CDPL. More...
class	CDFReactionReader
	Reader for reaction data in the native I/O format of the CDPL. More...
class	CDFReactionWriter
	Writer for reaction data in the native I/O format of the CDPL. More...
class	ChEMBLStandardizer
	Implementation of the ChEMBL structure preprocessing pipeline. More...
class	CIPConfigurationLabeler
	Assigns Cahn-Ingold-Prelog (CIP) configuration labels to stereogenic atoms and bonds of a molecular graph. More...
class	CIPPriorityCalculator
	Computes a topological approximation of CIP (Cahn-Ingold-Prelog) priorities for the atoms of a molecular graph. More...
class	CMLMolecularGraphWriter
	Writer for molecular graph data in the Chemical Markup Language [CML] format. More...
class	CMLMoleculeReader
	Reader for molecule data in the Chemical Markup Language [CML] format. More...
class	CommonConnectedSubstructureSearch
	Enumerates all maximal common connected substructures shared between a query and a target molecular graph. More...
class	CompleteRingSet
	Implements the exhaustive perception of rings in a molecular graph. More...
class	ComponentSet
	Implements the perception of molecular graph components. More...
class	ConjugatedRingBondPatternSwitching
	Chem::TautomerizationRule implementation that enumerates tautomers obtained by switching the single/double bond pattern of conjugated rings (e.g. the two Kekulé forms of benzene). More...
class	ConnectedSubstructureSet
	Enumerates the connected substructures of a molecular graph of a specified bond count. More...
class	CyclicSubstructure
	Implements the perception of ring atoms and bonds in a molecular graph. More...
class	DefaultMultiConfMoleculeInputProcessor
	Default Chem::MultiConfMoleculeInputProcessor implementation that detects multi-conformer input by comparing atom and bond properties (and optionally molecule names) between successively read molecules. More...
class	DefaultTautomerGenerator
	Tautomer generator implementation preconfigured with the default set of tautomerization rules. More...
class	ElectronSystem
	Describes an electron system of a molecule in terms of involved atoms and their electron contributions. More...
class	ElectronSystemList
	Data structure for the storage of Chem::ElectronSystem objects. More...
class	Entity3D
	Base class for objects that have a position in 3D space (e.g. Chem::Atom and Chem::Feature). More...
class	Entity3DContainer
	Common interface for data structures that support a random access to stored Chem::Entity3D instances. More...
struct	Entity3DCoordinatesFunctor
	Helper-functor for retrieving the 3D coordinates of an Chem::Entity3D object (via the Chem::Entity3DProperty::COORDINATES_3D property). More...
class	Entity3DMapping
	Data type for the storage and lookup of arbitrary entity to entity mappings. More...
class	ExtendedSSSR
	Implements the perception of the Extended Smallest Set of Smallest Rings (ESSSR) of a molecular graph. More...
class	Fragment
	Concrete implementation of the Chem::MolecularGraph interface that stores references to selectable Chem::Atom and Chem::Bond instances. More...
class	FragmentGenerator
	Generic rule-based molecule fragmentation engine that splits a molecular graph along bonds matching user-defined fragmentation rules. More...
class	FragmentList
	Data structure for the storage of Chem::Fragment objects. More...
class	GenericHydrogen13ShiftTautomerization
	Chem::TautomerizationRule implementation for the generation of tautomeric forms that result from proton migration between susceptible atoms separated by two bonds. More...
class	GenericHydrogen15ShiftTautomerization
	Chem::TautomerizationRule implementation for the generation of tautomeric forms that result from proton migration between susceptible atoms separated by four bonds. More...
class	HashCodeCalculator
	Computes 64-bit hash codes that are characteristic for the topology of a molecular graph and the properties of its atoms and bonds. More...
class	Hydrogen3DCoordinatesCalculator
	Generates 3D coordinates for the hydrogen atoms of a molecular graph from the existing positions of their heavy atom neighbors. More...
class	ImineEnamineTautomerization
	Chem::TautomerizationRule implementation for the generation of imine ⇄ enamine tautomers. More...
class	INCHIMolecularGraphWriter
	Writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	INCHIMoleculeReader
	Reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
class	JMEMolecularGraphWriter
	Writer for molecular graph data in the native I/O format of the JME Molecular Editor [JME] Java applet. More...
class	JMEMoleculeReader
	Reader for molecule data in the native I/O format of the JME Molecular Editor [JME] Java applet. More...
class	JMEReactionReader
	Reader for reaction data in the native I/O format of the JME Molecular Editor [JME] Java applet. More...
class	JMEReactionWriter
	Writer for reaction data in the native I/O format of the JME Molecular Editor [JME] Java applet. More...
class	KekuleStructureCalculator
	Assigns an alternating single/double bond pattern (Kekulé structure) to undefined bonds of a molecular graph. More...
class	KeteneYnolTautomerization
	Chem::TautomerizationRule implementation for the generation of ketene ⇄ ynol tautomers. More...
class	KetoEnolTautomerization
	Chem::TautomerizationRule implementation for the generation of keto ⇄ enol tautomers. More...
class	LactamLactimTautomerization
	Chem::TautomerizationRule implementation for the generation of lactam ⇄ lactim tautomers. More...
class	MatchConstraint
	Describes a single attribute comparison constraint between a query and a target object. More...
class	MatchConstraintList
	Data structure storing a set of Chem::MatchConstraint objects together with a logical type. More...
class	MatchExpression
	Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	MatchExpression< ObjType, void >
	Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms. More...
class	MatchExpressionList
	Container for the storage and evaluation of logical match expression lists. More...
class	MaxCommonAtomSubstructureSearch
	Searches for the maximum common atom substructures between a query and a target molecular graph. More...
class	MaxCommonBondSubstructureSearch
	Searches for the maximum common bond substructures between a query and a target molecular graph. More...
class	MOL2MolecularGraphWriter
	Writer for molecular graph data in the Sybyl MOL2 format. More...
class	MOL2MoleculeReader
	Reader for molecule data in the Sybyl MOL2 format. More...
class	MolecularGraph
	Abstract base class for data structures that represent chemical structures as molecular graphs. More...
class	MolecularGraphComponentGroupingMatchExpression
	Chem::MatchExpression implementation that constrains the substructure mapping by the query's component-level groupings. More...
class	Molecule
	Abstract base class representing a mutable molecular graph that owns and manages its atoms and bonds. More...
class	MOLMolecularGraphWriter
	Writer for molecular graph data in the MDL Mol-File [CTFILE] format. More...
class	MOLMoleculeReader
	Reader for molecule data in the MDL Mol-File [CTFILE] format. More...
class	MorganNumberingCalculator
	Computes canonical atom numberings for molecular graphs using Morgan's algorithm. More...
class	MultiConfMoleculeInputProcessor
	Abstract base for classes that detect and assemble multi-conformer molecules from a stream of successive single-conformer input molecules. More...
class	MultiSubstructureSearch
	Evaluates a boolean expression over multiple substructure queries against a target molecular graph. More...
class	NitroAciTautomerization
	Implementation of the nitro ↔ aci-nitro tautomerization rule. More...
class	NitrosoOximeTautomerization
	Chem::TautomerizationRule implementation for the generation of nitroso ⇄ oxime tautomers. More...
class	NOTMatchExpression
	Chem::MatchExpression decorator that negates the result of a wrapped Chem::MatchExpression instance. More...
class	NOTMatchExpression< ObjType, void >
	Chem::MatchExpression decorator that negates the result of a wrapped Chem::MatchExpression instance. More...
class	ORMatchExpressionList
	Chem::MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR). More...
class	ORMatchExpressionList< ObjType, void >
	Chem::MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR). More...
class	PatternAtomTyper
	Assigns numeric labels to specific atoms of a molecular graph that are described by substructure patterns. More...
class	PatternBasedTautomerizationRule
	Substructure search pattern-based implementation of the Chem::TautomerizationRule interface. More...
class	PhosphinicAcidTautomerization
	Chem::TautomerizationRule implementation for the generation of phosphinic acid tautomers. More...
class	PiElectronSystemList
	Implements the perception of all π-electron systems present in a molecule. More...
class	PropertyMatchExpression
	Generic Chem::MatchExpression specialization for the binary comparison between a query- and a target-derived property value retrieved through a user-supplied accessor function. More...
class	PropertyMatchExpression< ValueType, MatchFunc, ObjType, void >
	Single-object specialization of Chem::PropertyMatchExpression for the binary comparison between a query- and a target-derived property value retrieved through a user-supplied accessor function. More...
class	ProtonationStateStandardizer
	Adjusts the protonation state of a molecule (atom formal charges and bonded hydrogen counts) according to one of several pre-defined objectives. More...
class	RDFReactionReader
	Reader for reaction data in the MDL RD-File [CTFILE] format. More...
class	RDFReactionWriter
	Writer for reaction data in the MDL RD-File [CTFILE] format. More...
class	Reaction
	Abstract base class for chemical reactions composed of role-tagged reaction components of type Chem::Molecule. More...
class	ReactionAtomMappingMatchExpression
	Chem::MatchExpression that constrains reaction substructure matches by a required reactant-to-product atom mapping. More...
class	ReactionComponentGroupingMatchExpression
	Chem::MatchExpression that constrains reaction substructure matches by the query's component-level groupings (typically derived from the parenthesization of a Daylight SMARTS [SMARTS] pattern). More...
class	ReactionSubstructureSearch
	Searches for substructures of the components of a target reaction that match a given query reaction pattern. More...
class	Reactor
	Applies a Chem::Reaction template to the reactant components of a target Chem::Reaction to generate the corresponding product molecules. More...
class	RECAPFragmentGenerator
	Molecular graph fragment generator implementing the RECAP bond-cleavage rule set. More...
class	ResonanceStructureGenerator
	Enumerates the resonance structures of a molecular graph by redistributing π-electrons across conjugated bonds. More...
class	RXNReactionReader
	Reader for reaction data in the MDL Rxn-File [CTFILE] format. More...
class	RXNReactionWriter
	Writer for reaction data in the MDL Rxn-File [CTFILE] format. More...
class	SDFMolecularGraphWriter
	Writer for molecular graph data in the MDL SD-File [CTFILE] format. More...
class	SDFMoleculeReader
	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
	Writer for molecular graph data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSMoleculeReader
	Reader for molecule data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionReader
	Reader for reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMARTSReactionWriter
	Writer for reaction data in the Daylight SMARTS [SMARTS] format. More...
class	SMILESMolecularGraphWriter
	Writer for molecular graph data in the Daylight SMILES [SMILES] format. More...
class	SMILESMoleculeReader
	Reader for molecule data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionReader
	Reader for reaction data in the Daylight SMILES [SMILES] format. More...
class	SMILESReactionWriter
	Writer for reaction data in the Daylight SMILES [SMILES] format. More...
class	SpatialEntityAlignment
	Computes a spatial alignment between two sets of 3D entities by combining topological entity matching with Kabsch-style 3D superposition. More...
class	StereoDescriptor
	Data structure for the storage and retrieval of stereochemical information about atoms and bonds. More...
class	StereoisomerGenerator
	Enumerates the stereoisomers of a molecular graph by flipping the configurations of selected atom and bond stereocenters. More...
class	StringDataBlockEntry
	Represents a data item consisting of a header and a data payload. More...
class	StringDataBlock
	Array of Chem::StringDataBlockEntry objects. More...
class	SubstructureEditor
	Pattern-driven editor that rewrites matched substructures of a molecule according to a given editing template. More...
class	SubstructureHistogramCalculator
	Counts occurrences of registered substructure patterns in a molecular graph, emitting the per-pattern hit counts into a user-supplied histogram container. More...
class	SubstructureSearch
	Searches for substructures of a target molecular graph that match the topology of a given query molecular graph. More...
class	SulfenicAcidTautomerization
	Chem::TautomerizationRule implementation for the generation of sulfenic acid tautomers. More...
class	SurfaceAtomExtractor
	Identifies the accessible surface atoms in a given set of atoms. More...
class	SymmetryClassCalculator
	Perceives the topological symmetry classes of the atoms in a molecular graph. More...
class	TautomerGenerator
	Enumerates the tautomers of a molecular graph by iteratively applying a configurable set of Chem::TautomerizationRule instances and reporting each accepted tautomer to a user-supplied callback. More...
class	TautomerizationRule
	Abstract base class for tautomerization rule implementations employed by the Chem::TautomerGenerator class. More...
class	TautomerScore
	Functor for the calculation of a heuristic stability score of a tautomeric form represented as a molecular graph. More...
class	TopologicalEntityAlignment
	Computes a topological alignment between two sets of arbitrary entities by performing a maximum common subgraph search on a entity pair compatibility graph. More...
class	XYZMolecularGraphWriter
	Writer for molecular graph data in XYZ format to an output stream. More...
class	XYZMoleculeReader
	Reader for molecule data in XYZ format from an input stream. More...

Typedefs
typedef std::function< const Math::Vector3D &(const Chem::Atom &)>	Atom3DCoordinatesFunction
	Generic wrapper class used to store a user-defined Chem::Atom 3D coordinates function. More...
typedef std::function< bool(const Atom &, const Atom &)>	AtomCompareFunction
	Generic wrapper class used to store a user-defined atom compare function. More...
typedef std::function< bool(const Chem::Atom &)>	AtomPredicate
	Generic wrapper class used to store a user-defined atom predicate. More...
typedef std::function< std::size_t(const Chem::Atom &)>	AtomPriorityFunction
	Generic wrapper class used to store a user-defined atom priority function. More...
typedef std::function< bool(const Chem::Bond &, const Chem::Bond &)>	BondCompareFunction
	Generic wrapper class used to store a user-defined bond compare function. More...
typedef std::function< bool(const Chem::Bond &)>	BondPredicate
	Generic wrapper class used to store a user-defined bond predicate. More...
typedef Util::DefaultDataOutputHandler< CDFBZ2MolecularGraphWriter, DataFormat::CDF_BZ2 >	CDFBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataWriter< CDFMolecularGraphWriter, Util::BZip2OStream >	CDFBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed native I/O format of the CDPL. More...
typedef Util::DefaultDataInputHandler< CDFBZ2MoleculeReader, DataFormat::CDF_BZ2 >	CDFBZ2MoleculeInputHandler
	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
	Reader for molecule data in the bzip2-compressed native I/O format of the CDPL. More...
typedef Util::DefaultDataInputHandler< CDFBZ2ReactionReader, DataFormat::CDF_BZ2 >	CDFBZ2ReactionInputHandler
	Handler for the input of bzip2-compressed reaction data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataOutputHandler< CDFBZ2ReactionWriter, DataFormat::CDF_BZ2 >	CDFBZ2ReactionOutputHandler
	Handler for the output of bzip2-compressed reaction data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataReader< CDFReactionReader, Util::BZip2IStream >	CDFBZ2ReactionReader
	Reader for reaction data in the bzip2-compressed native I/O format of the CDPL. More...
typedef Util::CompressedDataWriter< CDFReactionWriter, Util::BZip2OStream >	CDFBZ2ReactionWriter
	Writer for reaction data in the bzip2-compressed native I/O format of the CDPL. More...
typedef Util::DefaultDataOutputHandler< CDFGZMolecularGraphWriter, DataFormat::CDF_GZ >	CDFGZMolecularGraphOutputHandler
	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
	Writer for molecular graph data in the gzip-compressed native I/O format of the CDPL. More...
typedef Util::DefaultDataInputHandler< CDFGZMoleculeReader, DataFormat::CDF_GZ >	CDFGZMoleculeInputHandler
	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
	Reader for molecule data in the gzip-compressed native I/O format of the CDPL. More...
typedef Util::DefaultDataInputHandler< CDFGZReactionReader, DataFormat::CDF_GZ >	CDFGZReactionInputHandler
	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
	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
	Reader for reaction data in the gzip-compressed native I/O format of the CDPL. More...
typedef Util::CompressedDataWriter< CDFReactionWriter, Util::GZipOStream >	CDFGZReactionWriter
	Writer for reaction data in the gzip-compressed native I/O format of the CDPL. More...
typedef Util::DefaultDataOutputHandler< CDFMolecularGraphWriter, DataFormat::CDF >	CDFMolecularGraphOutputHandler
	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
	Handler for the input of molecule data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataInputHandler< CDFReactionReader, DataFormat::CDF >	CDFReactionInputHandler
	Handler for the input of reaction data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataOutputHandler< CDFReactionWriter, DataFormat::CDF >	CDFReactionOutputHandler
	Handler for the output of reaction data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataOutputHandler< CMLBZ2MolecularGraphWriter, DataFormat::CML_BZ2 >	CMLBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the Chemical Markup Language [CML] format. More...
typedef Util::CompressedDataWriter< CMLMolecularGraphWriter, Util::BZip2OStream >	CMLBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Chemical Markup Language [CML] format. More...
typedef Util::DefaultDataInputHandler< CMLBZ2MoleculeReader, DataFormat::CML_BZ2 >	CMLBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Chemical Markup Language [CML] format. More...
typedef Util::CompressedDataReader< CMLMoleculeReader, Util::BZip2IStream >	CMLBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Chemical Markup Language [CML] format. More...
typedef Util::DefaultDataOutputHandler< CMLGZMolecularGraphWriter, DataFormat::CML_GZ >	CMLGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the Chemical Markup Language [CML] format. More...
typedef Util::CompressedDataWriter< CMLMolecularGraphWriter, Util::GZipOStream >	CMLGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Chemical Markup Language [CML] format. More...
typedef Util::DefaultDataInputHandler< CMLGZMoleculeReader, DataFormat::CML_GZ >	CMLGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the Chemical Markup Language [CML] format. More...
typedef Util::CompressedDataReader< CMLMoleculeReader, Util::GZipIStream >	CMLGZMoleculeReader
	Reader for molecule data in the gzip-compressed Chemical Markup Language [CML] format. More...
typedef Util::DefaultDataOutputHandler< CMLMolecularGraphWriter, DataFormat::CML >	CMLMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Chemical Markup Language [CML] format. More...
typedef Util::DefaultDataInputHandler< CMLMoleculeReader, DataFormat::CML >	CMLMoleculeInputHandler
	Handler for the input of molecule data in the Chemical Markup Language [CML] format. More...
typedef std::function< const Math::Vector3D &(const Chem::Entity &)>	Entity3DCoordinatesFunction
	Generic wrapper class used to store a user-defined Chem::Entity3D coordinates function. More...
typedef Util::DefaultDataOutputHandler< INCHIMolecularGraphWriter, DataFormat::INCHI >	INCHIMolecularGraphOutputHandler
	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
	Handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
typedef Util::DefaultDataOutputHandler< JMEMolecularGraphWriter, DataFormat::JME >	JMEMolecularGraphOutputHandler
	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
	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
	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
	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
	Handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format. More...
typedef Util::CompressedDataWriter< MOL2MolecularGraphWriter, Util::BZip2OStream >	MOL2BZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Sybyl MOL2 format. More...
typedef Util::DefaultDataInputHandler< MOL2BZ2MoleculeReader, DataFormat::MOL2_BZ2 >	MOL2BZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format. More...
typedef Util::CompressedDataReader< MOL2MoleculeReader, Util::BZip2IStream >	MOL2BZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Sybyl MOL2 format. More...
typedef Util::DefaultDataOutputHandler< MOL2GZMolecularGraphWriter, DataFormat::MOL2_GZ >	MOL2GZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format. More...
typedef Util::CompressedDataWriter< MOL2MolecularGraphWriter, Util::GZipOStream >	MOL2GZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Sybyl MOL2 format. More...
typedef Util::DefaultDataInputHandler< MOL2GZMoleculeReader, DataFormat::MOL2_GZ >	MOL2GZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format. More...
typedef Util::CompressedDataReader< MOL2MoleculeReader, Util::GZipIStream >	MOL2GZMoleculeReader
	Reader for molecule data in the gzip-compressed Sybyl MOL2 format. More...
typedef Util::DefaultDataOutputHandler< MOL2MolecularGraphWriter, DataFormat::MOL2 >	MOL2MolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Sybyl MOL2 format. More...
typedef Util::DefaultDataInputHandler< MOL2MoleculeReader, DataFormat::MOL2 >	MOL2MoleculeInputHandler
	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
	Handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< MOLMoleculeReader, DataFormat::MOL >	MOLMoleculeInputHandler
	Handler for the input of molecule data in the MDL Mol-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< RDFBZ2ReactionReader, DataFormat::RDF_BZ2 >	RDFBZ2ReactionInputHandler
	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
	Handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
typedef Util::CompressedDataReader< RDFReactionReader, Util::BZip2IStream >	RDFBZ2ReactionReader
	Reader for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format. More...
typedef Util::CompressedDataWriter< RDFReactionWriter, Util::BZip2OStream >	RDFBZ2ReactionWriter
	Writer for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< RDFGZReactionReader, DataFormat::RDF_GZ >	RDFGZReactionInputHandler
	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
	Handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
typedef Util::CompressedDataReader< RDFReactionReader, Util::GZipIStream >	RDFGZReactionReader
	Reader for reaction data in the gzip-compressed MDL RD-File [CTFILE] format. More...
typedef Util::CompressedDataWriter< RDFReactionWriter, Util::GZipOStream >	RDFGZReactionWriter
	Writer for reaction data in the gzip-compressed MDL RD-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< RDFReactionReader, DataFormat::RDF >	RDFReactionInputHandler
	Handler for the input of reaction data in the MDL RD-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< RDFReactionWriter, DataFormat::RDF >	RDFReactionOutputHandler
	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
	Handler for the input of reaction data in the MDL Rxn-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< RXNReactionWriter, DataFormat::RXN >	RXNReactionOutputHandler
	Handler for the output of reaction data in the MDL Rxn-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< SDFBZ2MolecularGraphWriter, DataFormat::SDF_BZ2 >	SDFBZ2MolecularGraphOutputHandler
	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
	Writer for molecular graph data in the bzip2-compressed MDL SD-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< SDFBZ2MoleculeReader, DataFormat::SDF_BZ2 >	SDFBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format. More...
typedef Util::CompressedDataReader< SDFMoleculeReader, Util::BZip2IStream >	SDFBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed MDL SD-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< SDFGZMolecularGraphWriter, DataFormat::SDF_GZ >	SDFGZMolecularGraphOutputHandler
	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
	Writer for molecular graph data in the gzip-compressed MDL SD-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< SDFGZMoleculeReader, DataFormat::SDF_GZ >	SDFGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format. More...
typedef Util::CompressedDataReader< SDFMoleculeReader, Util::GZipIStream >	SDFGZMoleculeReader
	Reader for molecule data in the gzip-compressed MDL SD-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< SDFMolecularGraphWriter, DataFormat::SDF >	SDFMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the MDL SD-File [CTFILE] format. More...
typedef Util::DefaultDataInputHandler< SDFMoleculeReader, DataFormat::SDF >	SDFMoleculeInputHandler
	Handler for the input of molecule data in the MDL SD-File [CTFILE] format. More...
typedef Util::DefaultDataOutputHandler< SMARTSMolecularGraphWriter, DataFormat::SMARTS >	SMARTSMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format. More...
typedef Util::DefaultDataInputHandler< SMARTSMoleculeReader, DataFormat::SMARTS >	SMARTSMoleculeInputHandler
	Handler for the input of molecule data in the Daylight SMARTS [SMARTS] format. More...
typedef Util::DefaultDataInputHandler< SMARTSReactionReader, DataFormat::SMARTS >	SMARTSReactionInputHandler
	Handler for the input of reaction data in the Daylight SMARTS [SMARTS] format. More...
typedef Util::DefaultDataOutputHandler< SMARTSReactionWriter, DataFormat::SMARTS >	SMARTSReactionOutputHandler
	Handler for the output of reaction data in the Daylight SMARTS [SMARTS] format. More...
typedef Util::DefaultDataOutputHandler< SMILESBZ2MolecularGraphWriter, DataFormat::SMILES_BZ2 >	SMILESBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataWriter< SMILESMolecularGraphWriter, Util::BZip2OStream >	SMILESBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataInputHandler< SMILESBZ2MoleculeReader, DataFormat::SMILES_BZ2 >	SMILESBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataReader< SMILESMoleculeReader, Util::BZip2IStream >	SMILESBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataInputHandler< SMILESBZ2ReactionReader, DataFormat::SMILES_BZ2 >	SMILESBZ2ReactionInputHandler
	Handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< SMILESBZ2ReactionWriter, DataFormat::SMILES_BZ2 >	SMILESBZ2ReactionOutputHandler
	Handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataReader< SMILESReactionReader, Util::BZip2IStream >	SMILESBZ2ReactionReader
	Reader for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataWriter< SMILESReactionWriter, Util::BZip2OStream >	SMILESBZ2ReactionWriter
	Writer for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< SMILESGZMolecularGraphWriter, DataFormat::SMILES_GZ >	SMILESGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataWriter< SMILESMolecularGraphWriter, Util::GZipOStream >	SMILESGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataInputHandler< SMILESGZMoleculeReader, DataFormat::SMILES_GZ >	SMILESGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataReader< SMILESMoleculeReader, Util::GZipIStream >	SMILESGZMoleculeReader
	Reader for molecule data in the gzip-compressed Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataInputHandler< SMILESGZReactionReader, DataFormat::SMILES_GZ >	SMILESGZReactionInputHandler
	Handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< SMILESGZReactionWriter, DataFormat::SMILES_GZ >	SMILESGZReactionOutputHandler
	Handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataReader< SMILESReactionReader, Util::GZipIStream >	SMILESGZReactionReader
	Reader for reaction data in the gzip-compressed Daylight SMILES [SMILES] format. More...
typedef Util::CompressedDataWriter< SMILESReactionWriter, Util::GZipOStream >	SMILESGZReactionWriter
	Writer for reaction data in the gzip-compressed Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< SMILESMolecularGraphWriter, DataFormat::SMILES >	SMILESMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataInputHandler< SMILESMoleculeReader, DataFormat::SMILES >	SMILESMoleculeInputHandler
	Handler for the input of molecule data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataInputHandler< SMILESReactionReader, DataFormat::SMILES >	SMILESReactionInputHandler
	Handler for the input of reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< SMILESReactionWriter, DataFormat::SMILES >	SMILESReactionOutputHandler
	Handler for the output of reaction data in the Daylight SMILES [SMILES] format. More...
typedef Util::DefaultDataOutputHandler< XYZBZ2MolecularGraphWriter, DataFormat::XYZ_BZ2 >	XYZBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the XYZ format. More...
typedef Util::CompressedDataWriter< XYZMolecularGraphWriter, Util::BZip2OStream >	XYZBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed XYZ format. More...
typedef Util::DefaultDataInputHandler< XYZBZ2MoleculeReader, DataFormat::XYZ_BZ2 >	XYZBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the XYZ format. More...
typedef Util::CompressedDataReader< XYZMoleculeReader, Util::BZip2IStream >	XYZBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed XYZ format. More...
typedef Util::DefaultDataOutputHandler< XYZGZMolecularGraphWriter, DataFormat::XYZ_GZ >	XYZGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the XYZ format. More...
typedef Util::CompressedDataWriter< XYZMolecularGraphWriter, Util::GZipOStream >	XYZGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed XYZ format. More...
typedef Util::DefaultDataInputHandler< XYZGZMoleculeReader, DataFormat::XYZ_GZ >	XYZGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the XYZ format. More...
typedef Util::CompressedDataReader< XYZMoleculeReader, Util::GZipIStream >	XYZGZMoleculeReader
	Reader for molecule data in the gzip-compressed XYZ format. More...
typedef Util::DefaultDataOutputHandler< XYZMolecularGraphWriter, DataFormat::XYZ >	XYZMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the XYZ format. More...
typedef Util::DefaultDataInputHandler< XYZMoleculeReader, DataFormat::XYZ >	XYZMoleculeInputHandler
	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)
	Tells whether all atoms of cntnr carry coordinates of the given dimensionality. More...
CDPL_CHEM_API void	get2DCoordinates (const AtomContainer &cntnr, Math::Vector2DArray &coords, bool append=false)
	Extracts the 2D coordinates of all atoms in cntnr into coords. More...
CDPL_CHEM_API void	set2DCoordinates (AtomContainer &cntnr, const Math::Vector2DArray &coords)
	Writes the 2D coordinates in coords back to the corresponding atoms of cntnr. More...
CDPL_CHEM_API void	transform2DCoordinates (AtomContainer &cntnr, const Math::Matrix3D &mtx)
	Transforms the 2D coordinates of all atoms in cntnr by the affine 3×3 matrix mtx. More...
CDPL_CHEM_API void	get3DCoordinates (const AtomContainer &cntnr, Math::Vector3DArray &coords, const Atom3DCoordinatesFunction &coords_func, bool append=false)
	Extracts the 3D coordinates of all atoms in cntnr into coords using the per-atom coordinate lookup function coords_func. More...
CDPL_CHEM_API void	clearConformations (AtomContainer &cntnr)
	Removes all stored conformations from the atoms of cntnr. More...
CDPL_CHEM_API std::size_t	getNumConformations (const AtomContainer &cntnr)
	Returns the number of conformations stored on the atoms of cntnr. More...
CDPL_CHEM_API void	applyConformation (AtomContainer &cntnr, std::size_t conf_idx)
	Promotes the stored conformation at index conf_idx to the active per-atom 3D coordinates. More...
CDPL_CHEM_API void	getConformation (const AtomContainer &cntnr, std::size_t conf_idx, Math::Vector3DArray &coords, bool append=false)
	Extracts the conformation at index conf_idx into coords. More...
CDPL_CHEM_API void	setConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Vector3DArray &coords)
	Overwrites the conformation at index conf_idx with the supplied 3D coordinates. More...
CDPL_CHEM_API void	addConformation (AtomContainer &cntnr, const Math::Vector3DArray &coords)
	Appends a new conformation built from the supplied 3D coordinates to the atoms of cntnr. More...
CDPL_CHEM_API void	transformConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Matrix4D &mtx)
	Transforms the conformation at index conf_idx by the homogeneous 4×4 matrix mtx. More...
CDPL_CHEM_API void	transformConformations (AtomContainer &cntnr, const Math::Matrix4D &mtx)
	Transforms every stored conformation of the atoms in cntnr by the homogeneous 4×4 matrix mtx. More...
CDPL_CHEM_API bool	alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms, const Math::Vector3DArray &ref_coords)
	Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms flagged in ref_atoms as alignment anchors. More...
CDPL_CHEM_API bool	alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms, const Math::Vector3DArray &ref_coords)
	Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms of ref_atoms as alignment anchors. More...
CDPL_CHEM_API bool	alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms)
	Aligns each stored conformation of cntnr to the first conformation using the atoms flagged in ref_atoms as alignment anchors. More...
CDPL_CHEM_API bool	alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms)
	Aligns each stored conformation of cntnr to the first conformation using the atoms of ref_atoms as alignment anchors. More...
CDPL_CHEM_API std::size_t	getMaxComponentGroupID (const AtomContainer &cntnr)
	Returns the largest component-group ID assigned to any atom of cntnr. More...
CDPL_CHEM_API std::size_t	getMaxAtomMappingID (const AtomContainer &cntnr)
	Returns the largest atom mapping ID assigned to any atom of cntnr. More...
CDPL_CHEM_API std::size_t	createAtomTypeMask (const AtomContainer &cntnr, Util::BitSet &mask, unsigned int type, bool reset=true, bool strict=true)
	Sets bits in mask corresponding to atoms of cntnr whose atom type matches type. More...
CDPL_CHEM_API void	copyAtomsIf (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false)
	Copies every atom of cntnr that satisfies pred into the molecule mol. More...
CDPL_CHEM_API void	copyAtomsIf (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false)
	Copies every atom of cntnr that satisfies pred into the fragment frag. More...
CDPL_CHEM_API void	copyAtomsIfNot (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false)
	Copies every atom of cntnr that does not satisfy pred into the molecule mol. More...
CDPL_CHEM_API void	copyAtomsIfNot (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false)
	Copies every atom of cntnr that does not satisfy pred into the fragment frag. More...
CDPL_CHEM_API bool	calcCenterOfMass (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr)
	Computes the mass-weighted center of mass of the atoms in cntnr. More...
CDPL_CHEM_API bool	calcCentroid (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr)
	Computes the unweighted centroid (arithmetic mean of atom coordinates) of cntnr. More...
CDPL_CHEM_API void	calcBoundingBox (const AtomContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func, bool reset=true)
	Computes the axis-aligned bounding box enclosing the atoms of cntnr. More...
CDPL_CHEM_API bool	insideBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func)
	Tells whether every atom of cntnr lies inside the axis-aligned bounding box defined by min and max. More...
CDPL_CHEM_API bool	intersectsBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func)
	Tells whether at least one atom of cntnr lies inside the axis-aligned bounding box defined by min and max. More...
CDPL_CHEM_API const std::string &	getName (const Atom &atom)
	Returns the value of the Chem::AtomProperty::NAME property of the atom atom. More...
CDPL_CHEM_API void	setName (Atom &atom, const std::string &name)
	Sets the value of the Chem::AtomProperty::NAME property of the atom atom to name. More...
CDPL_CHEM_API void	clearName (Atom &atom)
	Clears the value of the Chem::AtomProperty::NAME property of the atom atom. More...
CDPL_CHEM_API bool	hasName (const Atom &atom)
	Tells whether the Chem::AtomProperty::NAME property of the atom atom is set. More...
CDPL_CHEM_API const std::string &	getSymbol (const Atom &atom)
	Returns the value of the Chem::AtomProperty::SYMBOL property of the atom atom. More...
CDPL_CHEM_API void	setSymbol (Atom &atom, const std::string &symbol)
	Sets the value of the Chem::AtomProperty::SYMBOL property of the atom atom to symbol. More...
CDPL_CHEM_API void	clearSymbol (Atom &atom)
	Clears the value of the Chem::AtomProperty::SYMBOL property of the atom atom. More...
CDPL_CHEM_API bool	hasSymbol (const Atom &atom)
	Tells whether the Chem::AtomProperty::SYMBOL property of the atom atom is set. More...
CDPL_CHEM_API const std::string &	getSymbolForType (const Atom &atom)
	Returns the symbol that corresponds to the numeric type property of the atom atom. More...
CDPL_CHEM_API unsigned int	getType (const Atom &atom)
	Returns the value of the Chem::AtomProperty::TYPE property of the atom atom. More...
CDPL_CHEM_API void	setType (Atom &atom, unsigned int type)
	Sets the value of the Chem::AtomProperty::TYPE property of the atom atom to type. More...
CDPL_CHEM_API void	clearType (Atom &atom)
	Clears the value of the Chem::AtomProperty::TYPE property of the atom atom. More...
CDPL_CHEM_API bool	hasType (const Atom &atom)
	Tells whether the Chem::AtomProperty::TYPE property of the atom atom is set. More...
CDPL_CHEM_API unsigned int	getTypeForSymbol (const Atom &atom)
	Returns the numeric atom type that corresponds to the symbol property of the atom atom. More...
CDPL_CHEM_API unsigned int	getGenericType (const Atom &atom)
	Returns the generic atom type associated with numeric type property of the atom atom. More...
CDPL_CHEM_API long	getFormalCharge (const Atom &atom)
	Returns the value of the Chem::AtomProperty::FORMAL_CHARGE property of the atom atom. More...
CDPL_CHEM_API void	setFormalCharge (Atom &atom, long charge)
	Sets the value of the Chem::AtomProperty::FORMAL_CHARGE property of the atom atom to charge. More...
CDPL_CHEM_API void	clearFormalCharge (Atom &atom)
	Clears the value of the Chem::AtomProperty::FORMAL_CHARGE property of the atom atom. More...
CDPL_CHEM_API bool	hasFormalCharge (const Atom &atom)
	Tells whether the Chem::AtomProperty::FORMAL_CHARGE property of the atom atom is set. More...
CDPL_CHEM_API long	calcFormalCharge (const Atom &atom, const MolecularGraph &molgraph)
	Computes the formal charge of the atom atom from its connectivity in the molecular graph molgraph. More...
CDPL_CHEM_API std::size_t	getIsotope (const Atom &atom)
	Returns the value of the Chem::AtomProperty::ISOTOPE property of the atom atom. More...
CDPL_CHEM_API void	setIsotope (Atom &atom, std::size_t isotope)
	Sets the value of the Chem::AtomProperty::ISOTOPE property of the atom atom to isotope. More...
CDPL_CHEM_API void	clearIsotope (Atom &atom)
	Clears the value of the Chem::AtomProperty::ISOTOPE property of the atom atom. More...
CDPL_CHEM_API bool	hasIsotope (const Atom &atom)
	Tells whether the Chem::AtomProperty::ISOTOPE property of the atom atom is set. More...
CDPL_CHEM_API unsigned int	getRadicalType (const Atom &atom)
	Returns the value of the Chem::AtomProperty::RADICAL_TYPE property of the atom atom. More...
CDPL_CHEM_API void	setRadicalType (Atom &atom, unsigned int type)
	Sets the value of the Chem::AtomProperty::RADICAL_TYPE property of the atom atom to type. More...
CDPL_CHEM_API void	clearRadicalType (Atom &atom)
	Clears the value of the Chem::AtomProperty::RADICAL_TYPE property of the atom atom. More...
CDPL_CHEM_API bool	hasRadicalType (const Atom &atom)
	Tells whether the Chem::AtomProperty::RADICAL_TYPE property of the atom atom is set. More...
CDPL_CHEM_API unsigned int	getHybridizationState (const Atom &atom)
	Returns the value of the Chem::AtomProperty::HYBRIDIZATION property of the atom atom. More...
CDPL_CHEM_API void	setHybridizationState (Atom &atom, unsigned int state)
	Sets the value of the Chem::AtomProperty::HYBRIDIZATION property of the atom atom to state. More...
CDPL_CHEM_API void	clearHybridizationState (Atom &atom)
	Clears the value of the Chem::AtomProperty::HYBRIDIZATION property of the atom atom. More...
CDPL_CHEM_API bool	hasHybridizationState (const Atom &atom)
	Tells whether the Chem::AtomProperty::HYBRIDIZATION property of the atom atom is set. More...
CDPL_CHEM_API unsigned int	perceiveHybridizationState (const Atom &atom, const MolecularGraph &molgraph)
	Derives the hybridization state of the atom atom from its connectivity in the molecular graph molgraph. More...
CDPL_CHEM_API bool	getRingFlag (const Atom &atom)
	Returns the value of the Chem::AtomProperty::RING_FLAG property of the atom atom. More...
CDPL_CHEM_API void	setRingFlag (Atom &atom, bool in_ring)
	Sets the value of the Chem::AtomProperty::RING_FLAG property of the atom atom to in_ring. More...
CDPL_CHEM_API void	clearRingFlag (Atom &atom)
	Clears the value of the Chem::AtomProperty::RING_FLAG property of the atom atom. More...
CDPL_CHEM_API bool	hasRingFlag (const Atom &atom)
	Tells whether the Chem::AtomProperty::RING_FLAG property of the atom atom is set. More...
CDPL_CHEM_API bool	isInFragmentOfSize (const Atom &atom, const FragmentList &frag_list, std::size_t size)
	Tells whether the atom atom is a member of any fragment in frag_list whose size matches size. More...
CDPL_CHEM_API std::size_t	getSizeOfSmallestContainingFragment (const Atom &atom, const FragmentList &frag_list)
	Returns the size (in atoms) of the smallest fragment in frag_list that contains the atom atom. More...
CDPL_CHEM_API std::size_t	getSizeOfLargestContainingFragment (const Atom &atom, const FragmentList &frag_list)
	Returns the size (in atoms) of the largest fragment in frag_list that contains the atom atom. More...
CDPL_CHEM_API std::size_t	getNumContainingFragments (const Atom &atom, const FragmentList &frag_list)
	Returns the number of fragments in frag_list that contain the atom atom. More...
CDPL_CHEM_API void	getContainingFragments (const Atom &atom, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false)
	Collects the fragments in frag_list that contain the atom atom into cont_frag_list. More...
CDPL_CHEM_API bool	getAromaticityFlag (const Atom &atom)
	Returns the value of the Chem::AtomProperty::AROMATICITY_FLAG property of the atom atom. More...
CDPL_CHEM_API void	setAromaticityFlag (Atom &atom, bool aromatic)
	Sets the value of the Chem::AtomProperty::AROMATICITY_FLAG property of the atom atom to aromatic. More...
CDPL_CHEM_API void	clearAromaticityFlag (Atom &atom)
	Clears the value of the Chem::AtomProperty::AROMATICITY_FLAG property of the atom atom. More...
CDPL_CHEM_API bool	hasAromaticityFlag (const Atom &atom)
	Tells whether the Chem::AtomProperty::AROMATICITY_FLAG property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	getUnpairedElectronCount (const Atom &atom)
	Returns the value of the Chem::AtomProperty::UNPAIRED_ELECTRON_COUNT property of the atom atom. More...
CDPL_CHEM_API void	setUnpairedElectronCount (Atom &atom, std::size_t count)
	Sets the value of the Chem::AtomProperty::UNPAIRED_ELECTRON_COUNT property of the atom atom to count. More...
CDPL_CHEM_API void	clearUnpairedElectronCount (Atom &atom)
	Clears the value of the Chem::AtomProperty::UNPAIRED_ELECTRON_COUNT property of the atom atom. More...
CDPL_CHEM_API bool	hasUnpairedElectronCount (const Atom &atom)
	Tells whether the Chem::AtomProperty::UNPAIRED_ELECTRON_COUNT property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	getImplicitHydrogenCount (const Atom &atom)
	Returns the value of the Chem::AtomProperty::IMPLICIT_HYDROGEN_COUNT property of the atom atom. More...
CDPL_CHEM_API void	setImplicitHydrogenCount (Atom &atom, std::size_t count)
	Sets the value of the Chem::AtomProperty::IMPLICIT_HYDROGEN_COUNT property of the atom atom to count. More...
CDPL_CHEM_API void	clearImplicitHydrogenCount (Atom &atom)
	Clears the value of the Chem::AtomProperty::IMPLICIT_HYDROGEN_COUNT property of the atom atom. More...
CDPL_CHEM_API bool	hasImplicitHydrogenCount (const Atom &atom)
	Tells whether the Chem::AtomProperty::IMPLICIT_HYDROGEN_COUNT property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	calcImplicitHydrogenCount (const Atom &atom, const MolecularGraph &molgraph)
	Computes the implicit hydrogen count of the atom atom from its connectivity in the molecular graph molgraph. More...
CDPL_CHEM_API const Math::Vector2D &	get2DCoordinates (const Atom &atom)
	Returns the value of the Chem::AtomProperty::COORDINATES_2D property of the atom atom. More...
CDPL_CHEM_API void	set2DCoordinates (Atom &atom, const Math::Vector2D &coords)
	Sets the value of the Chem::AtomProperty::COORDINATES_2D property of the atom atom to coords. More...
CDPL_CHEM_API void	clear2DCoordinates (Atom &atom)
	Clears the value of the Chem::AtomProperty::COORDINATES_2D property of the atom atom. More...
CDPL_CHEM_API bool	has2DCoordinates (const Atom &atom)
	Tells whether the Chem::AtomProperty::COORDINATES_2D property of the atom atom is set. More...
CDPL_CHEM_API const Math::Vector3D &	getConformer3DCoordinates (const Atom &atom, std::size_t conf_idx)
	Returns the 3D coordinates of the atom atom in the conformer with index conf_idx. More...
CDPL_CHEM_API const Math::Vector3DArray::SharedPointer &	get3DCoordinatesArray (const Atom &atom)
	Returns the value of the Chem::AtomProperty::COORDINATES_3D_ARRAY property of the atom atom. More...
CDPL_CHEM_API void	set3DCoordinatesArray (Atom &atom, const Math::Vector3DArray::SharedPointer &coords_array)
	Sets the value of the Chem::AtomProperty::COORDINATES_3D_ARRAY property of the atom atom to coords_array. More...
CDPL_CHEM_API void	clear3DCoordinatesArray (Atom &atom)
	Clears the value of the Chem::AtomProperty::COORDINATES_3D_ARRAY property of the atom atom. More...
CDPL_CHEM_API bool	has3DCoordinatesArray (const Atom &atom)
	Tells whether the Chem::AtomProperty::COORDINATES_3D_ARRAY property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	getMorganNumber (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MORGAN_NUMBER property of the atom atom. More...
CDPL_CHEM_API void	setMorganNumber (Atom &atom, std::size_t num)
	Sets the value of the Chem::AtomProperty::MORGAN_NUMBER property of the atom atom to num. More...
CDPL_CHEM_API void	clearMorganNumber (Atom &atom)
	Clears the value of the Chem::AtomProperty::MORGAN_NUMBER property of the atom atom. More...
CDPL_CHEM_API bool	hasMorganNumber (const Atom &atom)
	Tells whether the Chem::AtomProperty::MORGAN_NUMBER property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	getCanonicalNumber (const Atom &atom)
	Returns the value of the Chem::AtomProperty::CANONICAL_NUMBER property of the atom atom. More...
CDPL_CHEM_API void	setCanonicalNumber (Atom &atom, std::size_t num)
	Sets the value of the Chem::AtomProperty::CANONICAL_NUMBER property of the atom atom to num. More...
CDPL_CHEM_API void	clearCanonicalNumber (Atom &atom)
	Clears the value of the Chem::AtomProperty::CANONICAL_NUMBER property of the atom atom. More...
CDPL_CHEM_API bool	hasCanonicalNumber (const Atom &atom)
	Tells whether the Chem::AtomProperty::CANONICAL_NUMBER property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	getCIPPriority (const Atom &atom)
	Returns the value of the Chem::AtomProperty::CIP_PRIORITY property of the atom atom. More...
CDPL_CHEM_API void	setCIPPriority (Atom &atom, std::size_t priority)
	Sets the value of the Chem::AtomProperty::CIP_PRIORITY property of the atom atom to priority. More...
CDPL_CHEM_API void	clearCIPPriority (Atom &atom)
	Clears the value of the Chem::AtomProperty::CIP_PRIORITY property of the atom atom. More...
CDPL_CHEM_API bool	hasCIPPriority (const Atom &atom)
	Tells whether the Chem::AtomProperty::CIP_PRIORITY property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	getSymmetryClass (const Atom &atom)
	Returns the value of the Chem::AtomProperty::SYMMETRY_CLASS property of the atom atom. More...
CDPL_CHEM_API void	setSymmetryClass (Atom &atom, std::size_t class_id)
	Sets the value of the Chem::AtomProperty::SYMMETRY_CLASS property of the atom atom to class_id. More...
CDPL_CHEM_API void	clearSymmetryClass (Atom &atom)
	Clears the value of the Chem::AtomProperty::SYMMETRY_CLASS property of the atom atom. More...
CDPL_CHEM_API bool	hasSymmetryClass (const Atom &atom)
	Tells whether the Chem::AtomProperty::SYMMETRY_CLASS property of the atom atom is set. More...
CDPL_CHEM_API unsigned int	getCIPConfiguration (const Atom &atom)
	Returns the value of the Chem::AtomProperty::CIP_CONFIGURATION property of the atom atom. More...
CDPL_CHEM_API void	setCIPConfiguration (Atom &atom, unsigned int config)
	Sets the value of the Chem::AtomProperty::CIP_CONFIGURATION property of the atom atom to config. More...
CDPL_CHEM_API void	clearCIPConfiguration (Atom &atom)
	Clears the value of the Chem::AtomProperty::CIP_CONFIGURATION property of the atom atom. More...
CDPL_CHEM_API bool	hasCIPConfiguration (const Atom &atom)
	Tells whether the Chem::AtomProperty::CIP_CONFIGURATION property of the atom atom is set. More...
CDPL_CHEM_API const StereoDescriptor &	getStereoDescriptor (const Atom &atom)
	Returns the value of the Chem::AtomProperty::STEREO_DESCRIPTOR property of the atom atom. More...
CDPL_CHEM_API void	setStereoDescriptor (Atom &atom, const StereoDescriptor &descr)
	Sets the value of the Chem::AtomProperty::STEREO_DESCRIPTOR property of the atom atom to descr. More...
CDPL_CHEM_API void	clearStereoDescriptor (Atom &atom)
	Clears the value of the Chem::AtomProperty::STEREO_DESCRIPTOR property of the atom atom. More...
CDPL_CHEM_API bool	hasStereoDescriptor (const Atom &atom)
	Tells whether the Chem::AtomProperty::STEREO_DESCRIPTOR property of the atom atom is set. More...
CDPL_CHEM_API StereoDescriptor	calcStereoDescriptor (const Atom &atom, const MolecularGraph &molgraph, std::size_t dim=1)
	Computes the stereo descriptor for the atom atom in the molecular graph molgraph. More...
CDPL_CHEM_API StereoDescriptor	calcStereoDescriptorFromMDLParity (const Atom &atom, const MolecularGraph &molgraph)
	Calculates the stereo descriptor of the atom atom from its MDL parity in the molecular graph molgraph. More...
CDPL_CHEM_API unsigned int	calcConfiguration (const Atom &atom, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords)
	Calculates the atom configuration from the supplied descriptor and reference atom 3D coordinates. More...
CDPL_CHEM_API bool	getStereoCenterFlag (const Atom &atom)
	Returns the value of the Chem::AtomProperty::STEREO_CENTER_FLAG property of the atom atom. More...
CDPL_CHEM_API void	setStereoCenterFlag (Atom &atom, bool is_center)
	Sets the value of the Chem::AtomProperty::STEREO_CENTER_FLAG property of the atom atom to is_center. More...
CDPL_CHEM_API void	clearStereoCenterFlag (Atom &atom)
	Clears the value of the Chem::AtomProperty::STEREO_CENTER_FLAG property of the atom atom. More...
CDPL_CHEM_API bool	hasStereoCenterFlag (const Atom &atom)
	Tells whether the Chem::AtomProperty::STEREO_CENTER_FLAG property of the atom atom is set. More...
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)
	Tells whether the atom atom qualifies as a stereo center in the context of the molecular graph molgraph. More...
CDPL_CHEM_API unsigned int	getSybylType (const Atom &atom)
	Returns the value of the Chem::AtomProperty::SYBYL_TYPE property of the atom atom. More...
CDPL_CHEM_API void	setSybylType (Atom &atom, unsigned int type)
	Sets the value of the Chem::AtomProperty::SYBYL_TYPE property of the atom atom to type. More...
CDPL_CHEM_API void	clearSybylType (Atom &atom)
	Clears the value of the Chem::AtomProperty::SYBYL_TYPE property of the atom atom. More...
CDPL_CHEM_API bool	hasSybylType (const Atom &atom)
	Tells whether the Chem::AtomProperty::SYBYL_TYPE property of the atom atom is set. More...
CDPL_CHEM_API unsigned int	perceiveSybylType (const Atom &atom, const MolecularGraph &molgraph)
	Derives the Sybyl MOL2 atom type of the atom atom in the molecular graph molgraph. More...
CDPL_CHEM_API const std::string &	getMOL2Name (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MOL2_NAME property of the atom atom. More...
CDPL_CHEM_API void	setMOL2Name (Atom &atom, const std::string &name)
	Sets the value of the Chem::AtomProperty::MOL2_NAME property of the atom atom to name. More...
CDPL_CHEM_API void	clearMOL2Name (Atom &atom)
	Clears the value of the Chem::AtomProperty::MOL2_NAME property of the atom atom. More...
CDPL_CHEM_API bool	hasMOL2Name (const Atom &atom)
	Tells whether the Chem::AtomProperty::MOL2_NAME property of the atom atom is set. More...
CDPL_CHEM_API double	getMOL2Charge (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MOL2_CHARGE property of the atom atom. More...
CDPL_CHEM_API void	setMOL2Charge (Atom &atom, double charge)
	Sets the value of the Chem::AtomProperty::MOL2_CHARGE property of the atom atom to charge. More...
CDPL_CHEM_API void	clearMOL2Charge (Atom &atom)
	Clears the value of the Chem::AtomProperty::MOL2_CHARGE property of the atom atom. More...
CDPL_CHEM_API bool	hasMOL2Charge (const Atom &atom)
	Tells whether the Chem::AtomProperty::MOL2_CHARGE property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	getMOL2SubstructureID (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_ID property of the atom atom. More...
CDPL_CHEM_API void	setMOL2SubstructureID (Atom &atom, std::size_t id)
	Sets the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_ID property of the atom atom to id. More...
CDPL_CHEM_API void	clearMOL2SubstructureID (Atom &atom)
	Clears the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_ID property of the atom atom. More...
CDPL_CHEM_API bool	hasMOL2SubstructureID (const Atom &atom)
	Tells whether the Chem::AtomProperty::MOL2_SUBSTRUCTURE_ID property of the atom atom is set. More...
CDPL_CHEM_API const std::string &	getMOL2SubstructureName (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_NAME property of the atom atom. More...
CDPL_CHEM_API void	setMOL2SubstructureName (Atom &atom, const std::string &id)
	Sets the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_NAME property of the atom atom to id. More...
CDPL_CHEM_API void	clearMOL2SubstructureName (Atom &atom)
	Clears the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_NAME property of the atom atom. More...
CDPL_CHEM_API bool	hasMOL2SubstructureName (const Atom &atom)
	Tells whether the Chem::AtomProperty::MOL2_SUBSTRUCTURE_NAME property of the atom atom is set. More...
CDPL_CHEM_API const std::string &	getMOL2SubstructureSubtype (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom. More...
CDPL_CHEM_API void	setMOL2SubstructureSubtype (Atom &atom, const std::string &subtype)
	Sets the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom to subtype. More...
CDPL_CHEM_API void	clearMOL2SubstructureSubtype (Atom &atom)
	Clears the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom. More...
CDPL_CHEM_API bool	hasMOL2SubstructureSubtype (const Atom &atom)
	Tells whether the Chem::AtomProperty::MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom is set. More...
CDPL_CHEM_API const std::string &	getMOL2SubstructureChain (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_CHAIN property of the atom atom. More...
CDPL_CHEM_API void	setMOL2SubstructureChain (Atom &atom, const std::string &chain)
	Sets the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_CHAIN property of the atom atom to chain. More...
CDPL_CHEM_API void	clearMOL2SubstructureChain (Atom &atom)
	Clears the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_CHAIN property of the atom atom. More...
CDPL_CHEM_API bool	hasMOL2SubstructureChain (const Atom &atom)
	Tells whether the Chem::AtomProperty::MOL2_SUBSTRUCTURE_CHAIN property of the atom atom is set. More...
CDPL_CHEM_API unsigned int	getMDLParity (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MDL_PARITY property of the atom atom. More...
CDPL_CHEM_API void	setMDLParity (Atom &atom, unsigned int parity)
	Sets the value of the Chem::AtomProperty::MDL_PARITY property of the atom atom to parity. More...
CDPL_CHEM_API void	clearMDLParity (Atom &atom)
	Clears the value of the Chem::AtomProperty::MDL_PARITY property of the atom atom. More...
CDPL_CHEM_API bool	hasMDLParity (const Atom &atom)
	Tells whether the Chem::AtomProperty::MDL_PARITY property of the atom atom is set. More...
CDPL_CHEM_API unsigned int	calcMDLParity (const Atom &atom, const MolecularGraph &molgraph)
	Calculates the MDL parity of the atom atom in the molecular graph molgraph. More...
CDPL_CHEM_API bool	getMDLStereoCareFlag (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MDL_DB_STEREO_CARE_FLAG property of the atom atom. More...
CDPL_CHEM_API void	setMDLStereoCareFlag (Atom &atom, bool flag)
	Sets the value of the Chem::AtomProperty::MDL_DB_STEREO_CARE_FLAG property of the atom atom to flag. More...
CDPL_CHEM_API void	clearMDLStereoCareFlag (Atom &atom)
	Clears the value of the Chem::AtomProperty::MDL_DB_STEREO_CARE_FLAG property of the atom atom. More...
CDPL_CHEM_API bool	hasMDLStereoCareFlag (const Atom &atom)
	Tells whether the Chem::AtomProperty::MDL_DB_STEREO_CARE_FLAG property of the atom atom is set. More...
CDPL_CHEM_API unsigned int	getReactionCenterStatus (const Atom &atom)
	Returns the value of the Chem::AtomProperty::REACTION_CENTER_STATUS property of the atom atom. More...
CDPL_CHEM_API void	setReactionCenterStatus (Atom &atom, unsigned int status)
	Sets the value of the Chem::AtomProperty::REACTION_CENTER_STATUS property of the atom atom to status. More...
CDPL_CHEM_API void	clearReactionCenterStatus (Atom &atom)
	Clears the value of the Chem::AtomProperty::REACTION_CENTER_STATUS property of the atom atom. More...
CDPL_CHEM_API bool	hasReactionCenterStatus (const Atom &atom)
	Tells whether the Chem::AtomProperty::REACTION_CENTER_STATUS property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	getAtomMappingID (const Atom &atom)
	Returns the value of the Chem::AtomProperty::ATOM_MAPPING_ID property of the atom atom. More...
CDPL_CHEM_API void	setAtomMappingID (Atom &atom, std::size_t id)
	Sets the value of the Chem::AtomProperty::ATOM_MAPPING_ID property of the atom atom to id. More...
CDPL_CHEM_API void	clearAtomMappingID (Atom &atom)
	Clears the value of the Chem::AtomProperty::ATOM_MAPPING_ID property of the atom atom. More...
CDPL_CHEM_API bool	hasAtomMappingID (const Atom &atom)
	Tells whether the Chem::AtomProperty::ATOM_MAPPING_ID property of the atom atom is set. More...
CDPL_CHEM_API std::size_t	getComponentGroupID (const Atom &atom)
	Returns the value of the Chem::AtomProperty::COMPONENT_GROUP_ID property of the atom atom. More...
CDPL_CHEM_API void	setComponentGroupID (Atom &atom, std::size_t id)
	Sets the value of the Chem::AtomProperty::COMPONENT_GROUP_ID property of the atom atom to id. More...
CDPL_CHEM_API void	clearComponentGroupID (Atom &atom)
	Clears the value of the Chem::AtomProperty::COMPONENT_GROUP_ID property of the atom atom. More...
CDPL_CHEM_API bool	hasComponentGroupID (const Atom &atom)
	Tells whether the Chem::AtomProperty::COMPONENT_GROUP_ID property of the atom atom is set. More...
CDPL_CHEM_API const MatchConstraintList::SharedPointer &	getMatchConstraints (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MATCH_CONSTRAINTS property of the atom atom. More...
CDPL_CHEM_API void	setMatchConstraints (Atom &atom, const MatchConstraintList::SharedPointer &constr)
	Sets the value of the Chem::AtomProperty::MATCH_CONSTRAINTS property of the atom atom to constr. More...
CDPL_CHEM_API void	clearMatchConstraints (Atom &atom)
	Clears the value of the Chem::AtomProperty::MATCH_CONSTRAINTS property of the atom atom. More...
CDPL_CHEM_API bool	hasMatchConstraints (const Atom &atom)
	Tells whether the Chem::AtomProperty::MATCH_CONSTRAINTS property of the atom atom is set. More...
CDPL_CHEM_API const MatchExpression< Atom, MolecularGraph >::SharedPointer &	getMatchExpression (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MATCH_EXPRESSION property of the atom atom. More...
CDPL_CHEM_API void	setMatchExpression (Atom &atom, const MatchExpression< Atom, MolecularGraph >::SharedPointer &expr)
	Sets the value of the Chem::AtomProperty::MATCH_EXPRESSION property of the atom atom to expr. More...
CDPL_CHEM_API void	clearMatchExpression (Atom &atom)
	Clears the value of the Chem::AtomProperty::MATCH_EXPRESSION property of the atom atom. More...
CDPL_CHEM_API bool	hasMatchExpression (const Atom &atom)
	Tells whether the Chem::AtomProperty::MATCH_EXPRESSION property of the atom atom is set. More...
CDPL_CHEM_API MatchExpression< Atom, MolecularGraph >::SharedPointer	generateMatchExpression (const Atom &atom, const MolecularGraph &molgraph)
	Builds an match expression from the match constraint list attached to the atom atom. More...
CDPL_CHEM_API const std::string &	getMatchExpressionString (const Atom &atom)
	Returns the value of the Chem::AtomProperty::MATCH_EXPRESSION_STRING property of the atom atom. More...
CDPL_CHEM_API void	setMatchExpressionString (Atom &atom, const std::string &expr_str)
	Sets the value of the Chem::AtomProperty::MATCH_EXPRESSION_STRING property of the atom atom to expr_str. More...
CDPL_CHEM_API void	clearMatchExpressionString (Atom &atom)
	Clears the value of the Chem::AtomProperty::MATCH_EXPRESSION_STRING property of the atom atom. More...
CDPL_CHEM_API bool	hasMatchExpressionString (const Atom &atom)
	Tells whether the Chem::AtomProperty::MATCH_EXPRESSION_STRING property of the atom atom is set. More...
CDPL_CHEM_API void	generateMatchExpressionString (const Atom &atom, const MolecularGraph &molgraph, std::string &expr_str)
	Generates a textual representation of the match expression resulting from the match constraint list attached to the atom atom. More...
CDPL_CHEM_API void	markReachableAtoms (const Atom &atom, const MolecularGraph &molgraph, Util::BitSet &atom_mask, bool reset=true)
	Sets bits in atom_mask for every atom of the molecular graph molgraph that is reachable from the atom atom through the bonds of molgraph. More...
CDPL_CHEM_API std::size_t	getTopologicalDistance (const Atom &atom1, const Atom &atom2, const MolecularGraph &molgraph)
	Returns the topological distance between the two atoms in the molecular graph molgraph. More...
CDPL_CHEM_API std::size_t	getEnvironment (const Atom &atom, const MolecularGraph &molgraph, std::size_t max_dist, Fragment &env, bool append=false)
	Collects every atom of the molecular graph molgraph that is within max_dist bonds of the atom atom into the fragment env. More...
template<typename AtomType , typename OutputIterator >
std::size_t	getConnectedAtoms (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0)
	Writes every neighbor of the atom atom that is connected by a bond belonging to the molecular graph molgraph into the output iterator it, skipping excl_atom. More...
template<typename AtomType , typename OutputIterator >
std::size_t	getIncidentBonds (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0)
	Writes every bond incident to the atom atom where the bond itself and both atoms are members of the molecular graph molgraph into the output iterator it, skipping bonds to excl_atom. More...
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)
	Writes every connected neighbor of the atom atom and the corresponding incident bond that are both members of molecular graph molgraph into the supplied output iterators. More...
CDPL_CHEM_API std::size_t	getOrder (const Bond &bond)
	Returns the value of the Chem::BondProperty::ORDER property of the bond bond. More...
CDPL_CHEM_API void	setOrder (Bond &bond, std::size_t order)
	Sets the value of the Chem::BondProperty::ORDER property of the bond bond to order. More...
CDPL_CHEM_API void	clearOrder (Bond &bond)
	Clears the value of the Chem::BondProperty::ORDER property of the bond bond. More...
CDPL_CHEM_API bool	hasOrder (const Bond &bond)
	Tells whether the Chem::BondProperty::ORDER property of the bond bond is set. More...
CDPL_CHEM_API bool	getRingFlag (const Bond &bond)
	Returns the value of the Chem::BondProperty::RING_FLAG property of the bond bond. More...
CDPL_CHEM_API void	setRingFlag (Bond &bond, bool in_ring)
	Sets the value of the Chem::BondProperty::RING_FLAG property of the bond bond to in_ring. More...
CDPL_CHEM_API void	clearRingFlag (Bond &bond)
	Clears the value of the Chem::BondProperty::RING_FLAG property of the bond bond. More...
CDPL_CHEM_API bool	hasRingFlag (const Bond &bond)
	Tells whether the Chem::BondProperty::RING_FLAG property of the bond bond is set. More...
CDPL_CHEM_API bool	isInFragmentOfSize (const Bond &bond, const FragmentList &frag_list, std::size_t size)
	Tells whether the bond bond is a member of any fragment in frag_list whose size matches size. More...
CDPL_CHEM_API std::size_t	getSizeOfSmallestContainingFragment (const Bond &bond, const FragmentList &frag_list)
	Returns the size (in atoms) of the smallest fragment in frag_list that contains the bond bond. More...
CDPL_CHEM_API std::size_t	getSizeOfLargestContainingFragment (const Bond &bond, const FragmentList &frag_list)
	Returns the size (in atoms) of the largest fragment in frag_list that contains the bond bond. More...
CDPL_CHEM_API std::size_t	getNumContainingFragments (const Bond &bond, const FragmentList &frag_list)
	Returns the number of fragments in frag_list that contain the bond bond. More...
CDPL_CHEM_API void	getContainingFragments (const Bond &bond, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false)
	Collects the fragments in frag_list that contain the bond bond into cont_frag_list. More...
CDPL_CHEM_API bool	getAromaticityFlag (const Bond &bond)
	Returns the value of the Chem::BondProperty::AROMATICITY_FLAG property of the bond bond. More...
CDPL_CHEM_API void	setAromaticityFlag (Bond &bond, bool aromatic)
	Sets the value of the Chem::BondProperty::AROMATICITY_FLAG property of the bond bond to aromatic. More...
CDPL_CHEM_API void	clearAromaticityFlag (Bond &bond)
	Clears the value of the Chem::BondProperty::AROMATICITY_FLAG property of the bond bond. More...
CDPL_CHEM_API bool	hasAromaticityFlag (const Bond &bond)
	Tells whether the Chem::BondProperty::AROMATICITY_FLAG property of the bond bond is set. More...
CDPL_CHEM_API unsigned int	get2DStereoFlag (const Bond &bond)
	Returns the value of the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond. More...
CDPL_CHEM_API void	set2DStereoFlag (Bond &bond, unsigned int flag)
	Sets the value of the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond to flag. More...
CDPL_CHEM_API void	clear2DStereoFlag (Bond &bond)
	Clears the value of the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond. More...
CDPL_CHEM_API bool	has2DStereoFlag (const Bond &bond)
	Tells whether the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond is set. More...
CDPL_CHEM_API unsigned int	getCIPConfiguration (const Bond &bond)
	Returns the value of the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond. More...
CDPL_CHEM_API void	setCIPConfiguration (Bond &bond, unsigned int config)
	Sets the value of the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond to config. More...
CDPL_CHEM_API void	clearCIPConfiguration (Bond &bond)
	Clears the value of the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond. More...
CDPL_CHEM_API bool	hasCIPConfiguration (const Bond &bond)
	Tells whether the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond is set. More...
CDPL_CHEM_API const StereoDescriptor &	getStereoDescriptor (const Bond &bond)
	Returns the value of the Chem::BondProperty::STEREO_DESCRIPTOR property of the bond bond. More...
CDPL_CHEM_API void	setStereoDescriptor (Bond &bond, const StereoDescriptor &descr)
	Sets the value of the Chem::BondProperty::STEREO_DESCRIPTOR property of the bond bond to descr. More...
CDPL_CHEM_API void	clearStereoDescriptor (Bond &bond)
	Clears the value of the Chem::BondProperty::STEREO_DESCRIPTOR property of the bond bond. More...
CDPL_CHEM_API bool	hasStereoDescriptor (const Bond &bond)
	Tells whether the Chem::BondProperty::STEREO_DESCRIPTOR property of the bond bond is set. More...
CDPL_CHEM_API StereoDescriptor	calcStereoDescriptor (const Bond &bond, const MolecularGraph &molgraph, std::size_t dim=1)
	Computes the stereo descriptor for the bond bond in the molecular graph molgraph. More...
CDPL_CHEM_API unsigned int	calcConfiguration (const Bond &bond, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords)
	Calculates the bond configuration from the supplied descriptor and reference atom 3D coordinates. More...
CDPL_CHEM_API bool	getStereoCenterFlag (const Bond &bond)
	Returns the value of the Chem::BondProperty::STEREO_CENTER_FLAG property of the bond bond. More...
CDPL_CHEM_API void	setStereoCenterFlag (Bond &bond, bool is_center)
	Sets the value of the Chem::BondProperty::STEREO_CENTER_FLAG property of the bond bond to is_center. More...
CDPL_CHEM_API void	clearStereoCenterFlag (Bond &bond)
	Clears the value of the Chem::BondProperty::STEREO_CENTER_FLAG property of the bond bond. More...
CDPL_CHEM_API bool	hasStereoCenterFlag (const Bond &bond)
	Tells whether the Chem::BondProperty::STEREO_CENTER_FLAG property of the bond bond is set. More...
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)
	Tells whether the bond bond qualifies as a stereo center in the context of the molecular graph molgraph. More...
CDPL_CHEM_API unsigned int	getDirection (const Bond &bond)
	Returns the value of the Chem::BondProperty::DIRECTION property of the bond bond. More...
CDPL_CHEM_API void	setDirection (Bond &bond, unsigned int dir)
	Sets the value of the Chem::BondProperty::DIRECTION property of the bond bond to dir. More...
CDPL_CHEM_API void	clearDirection (Bond &bond)
	Clears the value of the Chem::BondProperty::DIRECTION property of the bond bond. More...
CDPL_CHEM_API bool	hasDirection (const Bond &bond)
	Tells whether the Chem::BondProperty::DIRECTION property of the bond bond is set. More...
CDPL_CHEM_API unsigned int	getReactionCenterStatus (const Bond &bond)
	Returns the value of the Chem::BondProperty::REACTION_CENTER_STATUS property of the bond bond. More...
CDPL_CHEM_API void	setReactionCenterStatus (Bond &bond, unsigned int status)
	Sets the value of the Chem::BondProperty::REACTION_CENTER_STATUS property of the bond bond to status. More...
CDPL_CHEM_API void	clearReactionCenterStatus (Bond &bond)
	Clears the value of the Chem::BondProperty::REACTION_CENTER_STATUS property of the bond bond. More...
CDPL_CHEM_API bool	hasReactionCenterStatus (const Bond &bond)
	Tells whether the Chem::BondProperty::REACTION_CENTER_STATUS property of the bond bond is set. More...
CDPL_CHEM_API const MatchConstraintList::SharedPointer &	getMatchConstraints (const Bond &bond)
	Returns the value of the Chem::BondProperty::MATCH_CONSTRAINTS property of the bond bond. More...
CDPL_CHEM_API void	setMatchConstraints (Bond &bond, const MatchConstraintList::SharedPointer &constr)
	Sets the value of the Chem::BondProperty::MATCH_CONSTRAINTS property of the bond bond to constr. More...
CDPL_CHEM_API void	clearMatchConstraints (Bond &bond)
	Clears the value of the Chem::BondProperty::MATCH_CONSTRAINTS property of the bond bond. More...
CDPL_CHEM_API bool	hasMatchConstraints (const Bond &bond)
	Tells whether the Chem::BondProperty::MATCH_CONSTRAINTS property of the bond bond is set. More...
CDPL_CHEM_API const MatchExpression< Bond, MolecularGraph >::SharedPointer &	getMatchExpression (const Bond &bond)
	Returns the value of the Chem::BondProperty::MATCH_EXPRESSION property of the bond bond. More...
CDPL_CHEM_API void	setMatchExpression (Bond &bond, const MatchExpression< Bond, MolecularGraph >::SharedPointer &expr)
	Sets the value of the Chem::BondProperty::MATCH_EXPRESSION property of the bond bond to expr. More...
CDPL_CHEM_API void	clearMatchExpression (Bond &bond)
	Clears the value of the Chem::BondProperty::MATCH_EXPRESSION property of the bond bond. More...
CDPL_CHEM_API bool	hasMatchExpression (const Bond &bond)
	Tells whether the Chem::BondProperty::MATCH_EXPRESSION property of the bond bond is set. More...
CDPL_CHEM_API MatchExpression< Bond, MolecularGraph >::SharedPointer	generateMatchExpression (const Bond &bond, const MolecularGraph &molgraph)
	Builds a match expression from the match constraint list attached to the bond bond. More...
CDPL_CHEM_API const std::string &	getMatchExpressionString (const Bond &bond)
	Returns the value of the Chem::BondProperty::MATCH_EXPRESSION_STRING property of the bond bond. More...
CDPL_CHEM_API void	setMatchExpressionString (Bond &bond, const std::string &expr_str)
	Sets the value of the Chem::BondProperty::MATCH_EXPRESSION_STRING property of the bond bond to expr_str. More...
CDPL_CHEM_API void	clearMatchExpressionString (Bond &bond)
	Clears the value of the Chem::BondProperty::MATCH_EXPRESSION_STRING property of the bond bond. More...
CDPL_CHEM_API bool	hasMatchExpressionString (const Bond &bond)
	Tells whether the Chem::BondProperty::MATCH_EXPRESSION_STRING property of the bond bond is set. More...
CDPL_CHEM_API void	generateMatchExpressionString (const Bond &bond, const MolecularGraph &molgraph, std::string &str)
	Generates a textual representation of the match expression resulting from the match constraint list attached to the bond bond. More...
CDPL_CHEM_API unsigned int	getSybylType (const Bond &bond)
	Returns the value of the Chem::BondProperty::SYBYL_TYPE property of the bond bond. More...
CDPL_CHEM_API void	setSybylType (Bond &bond, unsigned int type)
	Sets the value of the Chem::BondProperty::SYBYL_TYPE property of the bond bond to type. More...
CDPL_CHEM_API void	clearSybylType (Bond &bond)
	Clears the value of the Chem::BondProperty::SYBYL_TYPE property of the bond bond. More...
CDPL_CHEM_API bool	hasSybylType (const Bond &bond)
	Tells whether the Chem::BondProperty::SYBYL_TYPE property of the bond bond is set. More...
CDPL_CHEM_API unsigned int	perceiveSybylType (const Bond &bond, const MolecularGraph &molgraph)
	Derives the Sybyl MOL2 bond type of the bond bond in the molecular graph molgraph. More...
CDPL_CHEM_API bool	getOrdinaryHydrogenDepleteParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE parameter stored in cntnr. More...
CDPL_CHEM_API void	setOrdinaryHydrogenDepleteParameter (Base::ControlParameterContainer &cntnr, bool deplete)
	Sets the value of the Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE parameter of cntnr to deplete. More...
CDPL_CHEM_API bool	hasOrdinaryHydrogenDepleteParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE parameter of cntnr is set. More...
CDPL_CHEM_API void	clearOrdinaryHydrogenDepleteParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE parameter from cntnr. More...
CDPL_CHEM_API std::size_t	getCoordinatesDimensionParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::COORDINATES_DIMENSION parameter stored in cntnr. More...
CDPL_CHEM_API void	setCoordinatesDimensionParameter (Base::ControlParameterContainer &cntnr, std::size_t dim)
	Sets the value of the Chem::ControlParameter::COORDINATES_DIMENSION parameter of cntnr to dim. More...
CDPL_CHEM_API bool	hasCoordinatesDimensionParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::COORDINATES_DIMENSION parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCoordinatesDimensionParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::COORDINATES_DIMENSION parameter from cntnr. More...
CDPL_CHEM_API bool	getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::STRICT_ERROR_CHECKING parameter stored in cntnr. More...
CDPL_CHEM_API void	setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict)
	Sets the value of the Chem::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr to strict. More...
CDPL_CHEM_API bool	hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr is set. More...
CDPL_CHEM_API void	clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::STRICT_ERROR_CHECKING parameter from cntnr. More...
CDPL_CHEM_API const std::string &	getRecordSeparatorParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::RECORD_SEPARATOR parameter stored in cntnr. More...
CDPL_CHEM_API void	setRecordSeparatorParameter (Base::ControlParameterContainer &cntnr, const std::string &sep)
	Sets the value of the Chem::ControlParameter::RECORD_SEPARATOR parameter of cntnr to sep. More...
CDPL_CHEM_API bool	hasRecordSeparatorParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::RECORD_SEPARATOR parameter of cntnr is set. More...
CDPL_CHEM_API void	clearRecordSeparatorParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::RECORD_SEPARATOR parameter from cntnr. More...
CDPL_CHEM_API bool	getBondMemberSwapStereoFixParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX parameter stored in cntnr. More...
CDPL_CHEM_API void	setBondMemberSwapStereoFixParameter (Base::ControlParameterContainer &cntnr, bool fix)
	Sets the value of the Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr to fix. More...
CDPL_CHEM_API bool	hasBondMemberSwapStereoFixParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr is set. More...
CDPL_CHEM_API void	clearBondMemberSwapStereoFixParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX parameter from cntnr. More...
CDPL_CHEM_API bool	getCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CHECK_LINE_LENGTH parameter stored in cntnr. More...
CDPL_CHEM_API void	setCheckLineLengthParameter (Base::ControlParameterContainer &cntnr, bool check)
	Sets the value of the Chem::ControlParameter::CHECK_LINE_LENGTH parameter of cntnr to check. More...
CDPL_CHEM_API bool	hasCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CHECK_LINE_LENGTH parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCheckLineLengthParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CHECK_LINE_LENGTH parameter from cntnr. More...
CDPL_CHEM_API unsigned int	getMDLCTABVersionParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_CTAB_VERSION parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLCTABVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int version)
	Sets the value of the Chem::ControlParameter::MDL_CTAB_VERSION parameter of cntnr to version. More...
CDPL_CHEM_API bool	hasMDLCTABVersionParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_CTAB_VERSION parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLCTABVersionParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_CTAB_VERSION parameter from cntnr. More...
CDPL_CHEM_API bool	getMDLIgnoreParityParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_IGNORE_PARITY parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLIgnoreParityParameter (Base::ControlParameterContainer &cntnr, bool ignore)
	Sets the value of the Chem::ControlParameter::MDL_IGNORE_PARITY parameter of cntnr to ignore. More...
CDPL_CHEM_API bool	hasMDLIgnoreParityParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_IGNORE_PARITY parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLIgnoreParityParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_IGNORE_PARITY parameter from cntnr. More...
CDPL_CHEM_API bool	getMDLUpdateTimestampParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_UPDATE_TIMESTAMP parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLUpdateTimestampParameter (Base::ControlParameterContainer &cntnr, bool update)
	Sets the value of the Chem::ControlParameter::MDL_UPDATE_TIMESTAMP parameter of cntnr to update. More...
CDPL_CHEM_API bool	hasMDLUpdateTimestampParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_UPDATE_TIMESTAMP parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLUpdateTimestampParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_UPDATE_TIMESTAMP parameter from cntnr. More...
CDPL_CHEM_API bool	getMDLTrimStringsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_TRIM_STRINGS parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLTrimStringsParameter (Base::ControlParameterContainer &cntnr, bool trim)
	Sets the value of the Chem::ControlParameter::MDL_TRIM_STRINGS parameter of cntnr to trim. More...
CDPL_CHEM_API bool	hasMDLTrimStringsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_TRIM_STRINGS parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLTrimStringsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_TRIM_STRINGS parameter from cntnr. More...
CDPL_CHEM_API bool	getMDLTrimLinesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_TRIM_LINES parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLTrimLinesParameter (Base::ControlParameterContainer &cntnr, bool trim)
	Sets the value of the Chem::ControlParameter::MDL_TRIM_LINES parameter of cntnr to trim. More...
CDPL_CHEM_API bool	hasMDLTrimLinesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_TRIM_LINES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLTrimLinesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_TRIM_LINES parameter from cntnr. More...
CDPL_CHEM_API bool	getMDLTruncateStringsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_TRUNCATE_STRINGS parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLTruncateStringsParameter (Base::ControlParameterContainer &cntnr, bool trunc)
	Sets the value of the Chem::ControlParameter::MDL_TRUNCATE_STRINGS parameter of cntnr to trunc. More...
CDPL_CHEM_API bool	hasMDLTruncateStringsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_TRUNCATE_STRINGS parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLTruncateStringsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_TRUNCATE_STRINGS parameter from cntnr. More...
CDPL_CHEM_API bool	getMDLTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_TRUNCATE_LINES parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLTruncateLinesParameter (Base::ControlParameterContainer &cntnr, bool trunc)
	Sets the value of the Chem::ControlParameter::MDL_TRUNCATE_LINES parameter of cntnr to trunc. More...
CDPL_CHEM_API bool	hasMDLTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_TRUNCATE_LINES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLTruncateLinesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_TRUNCATE_LINES parameter from cntnr. More...
CDPL_CHEM_API unsigned int	getMDLRXNFileVersionParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_RXN_FILE_VERSION parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLRXNFileVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int version)
	Sets the value of the Chem::ControlParameter::MDL_RXN_FILE_VERSION parameter of cntnr to version. More...
CDPL_CHEM_API bool	hasMDLRXNFileVersionParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_RXN_FILE_VERSION parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLRXNFileVersionParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_RXN_FILE_VERSION parameter from cntnr. More...
CDPL_CHEM_API bool	getMDLOutputConfEnergyToEnergyFieldParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLOutputConfEnergyToEnergyFieldParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasMDLOutputConfEnergyToEnergyFieldParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLOutputConfEnergyToEnergyFieldParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter from cntnr. More...
CDPL_CHEM_API bool	getMDLOutputConfEnergyAsSDEntryParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLOutputConfEnergyAsSDEntryParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasMDLOutputConfEnergyAsSDEntryParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLOutputConfEnergyAsSDEntryParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter from cntnr. More...
CDPL_CHEM_API bool	getMDLEnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLEnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr, bool enable)
	Sets the value of the Chem::ControlParameter::MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable. More...
CDPL_CHEM_API bool	hasMDLEnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLEnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr. More...
CDPL_CHEM_API const std::string &	getMDLConfEnergySDTagParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MDL_CONF_ENERGY_SD_TAG parameter stored in cntnr. More...
CDPL_CHEM_API void	setMDLConfEnergySDTagParameter (Base::ControlParameterContainer &cntnr, const std::string &tag)
	Sets the value of the Chem::ControlParameter::MDL_CONF_ENERGY_SD_TAG parameter of cntnr to tag. More...
CDPL_CHEM_API bool	hasMDLConfEnergySDTagParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MDL_CONF_ENERGY_SD_TAG parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMDLConfEnergySDTagParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MDL_CONF_ENERGY_SD_TAG parameter from cntnr. More...
CDPL_CHEM_API bool	getJMESeparateComponentsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::JME_SEPARATE_COMPONENTS parameter stored in cntnr. More...
CDPL_CHEM_API void	setJMESeparateComponentsParameter (Base::ControlParameterContainer &cntnr, bool separate)
	Sets the value of the Chem::ControlParameter::JME_SEPARATE_COMPONENTS parameter of cntnr to separate. More...
CDPL_CHEM_API bool	hasJMESeparateComponentsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::JME_SEPARATE_COMPONENTS parameter of cntnr is set. More...
CDPL_CHEM_API void	clearJMESeparateComponentsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::JME_SEPARATE_COMPONENTS parameter from cntnr. More...
CDPL_CHEM_API const std::string &	getSMILESRecordFormatParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_RECORD_FORMAT parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESRecordFormatParameter (Base::ControlParameterContainer &cntnr, const std::string &format)
	Sets the value of the Chem::ControlParameter::SMILES_RECORD_FORMAT parameter of cntnr to format. More...
CDPL_CHEM_API bool	hasSMILESRecordFormatParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_RECORD_FORMAT parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESRecordFormatParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_RECORD_FORMAT parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESOutputCanonicalFormParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_CANONICAL_FORM parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESOutputCanonicalFormParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESOutputCanonicalFormParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESOutputCanonicalFormParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_OUTPUT_CANONICAL_FORM parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESOutputKekuleFormParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_KEKULE_FORM parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESOutputKekuleFormParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_KEKULE_FORM parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESOutputKekuleFormParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_OUTPUT_KEKULE_FORM parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESOutputKekuleFormParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_OUTPUT_KEKULE_FORM parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESOutputAtomStereoParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_ATOM_STEREO parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESOutputAtomStereoParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_ATOM_STEREO parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESOutputAtomStereoParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_OUTPUT_ATOM_STEREO parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESOutputAtomStereoParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_OUTPUT_ATOM_STEREO parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESOutputBondStereoParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_BOND_STEREO parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESOutputBondStereoParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_BOND_STEREO parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESOutputBondStereoParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_OUTPUT_BOND_STEREO parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESOutputBondStereoParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_OUTPUT_BOND_STEREO parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESOutputRingBondStereoParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_RING_BOND_STEREO parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESOutputRingBondStereoParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESOutputRingBondStereoParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESOutputRingBondStereoParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_OUTPUT_RING_BOND_STEREO parameter from cntnr. More...
CDPL_CHEM_API std::size_t	getSMILESMinStereoBondRingSizeParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESMinStereoBondRingSizeParameter (Base::ControlParameterContainer &cntnr, std::size_t min_size)
	Sets the value of the Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr to min_size. More...
CDPL_CHEM_API bool	hasSMILESMinStereoBondRingSizeParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESMinStereoBondRingSizeParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESOutputIsotopeParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_ISOTOPE parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESOutputIsotopeParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_ISOTOPE parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESOutputIsotopeParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_OUTPUT_ISOTOPE parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESOutputIsotopeParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_OUTPUT_ISOTOPE parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESOutputHydrogenCountParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_HYDROGEN_COUNT parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESOutputHydrogenCountParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESOutputHydrogenCountParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESOutputHydrogenCountParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_OUTPUT_HYDROGEN_COUNT parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESMolOutputAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESMolOutputAtomMappingIDParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESMolOutputAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESMolOutputAtomMappingIDParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESRxnOutputAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESRxnOutputAtomMappingIDParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESRxnOutputAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESRxnOutputAtomMappingIDParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESOutputSingleBondsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_SINGLE_BONDS parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESOutputSingleBondsParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESOutputSingleBondsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESOutputSingleBondsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_OUTPUT_SINGLE_BONDS parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESOutputAromaticBondsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_AROMATIC_BONDS parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESOutputAromaticBondsParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasSMILESOutputAromaticBondsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESOutputAromaticBondsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_OUTPUT_AROMATIC_BONDS parameter from cntnr. More...
CDPL_CHEM_API bool	getSMILESNoOrganicSubsetParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET parameter stored in cntnr. More...
CDPL_CHEM_API void	setSMILESNoOrganicSubsetParameter (Base::ControlParameterContainer &cntnr, bool no_subset)
	Sets the value of the Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET parameter of cntnr to no_subset. More...
CDPL_CHEM_API bool	hasSMILESNoOrganicSubsetParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET parameter of cntnr is set. More...
CDPL_CHEM_API void	clearSMILESNoOrganicSubsetParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET parameter from cntnr. More...
CDPL_CHEM_API const std::string &	getINCHIInputOptionsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::INCHI_INPUT_OPTIONS parameter stored in cntnr. More...
CDPL_CHEM_API void	setINCHIInputOptionsParameter (Base::ControlParameterContainer &cntnr, const std::string &opts)
	Sets the value of the Chem::ControlParameter::INCHI_INPUT_OPTIONS parameter of cntnr to opts. More...
CDPL_CHEM_API bool	hasINCHIInputOptionsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::INCHI_INPUT_OPTIONS parameter of cntnr is set. More...
CDPL_CHEM_API void	clearINCHIInputOptionsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::INCHI_INPUT_OPTIONS parameter from cntnr. More...
CDPL_CHEM_API const std::string &	getINCHIOutputOptionsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::INCHI_OUTPUT_OPTIONS parameter stored in cntnr. More...
CDPL_CHEM_API void	setINCHIOutputOptionsParameter (Base::ControlParameterContainer &cntnr, const std::string &opts)
	Sets the value of the Chem::ControlParameter::INCHI_OUTPUT_OPTIONS parameter of cntnr to opts. More...
CDPL_CHEM_API bool	hasINCHIOutputOptionsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::INCHI_OUTPUT_OPTIONS parameter of cntnr is set. More...
CDPL_CHEM_API void	clearINCHIOutputOptionsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::INCHI_OUTPUT_OPTIONS parameter from cntnr. More...
CDPL_CHEM_API bool	getMultiConfImportParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MULTI_CONF_IMPORT parameter stored in cntnr. More...
CDPL_CHEM_API void	setMultiConfImportParameter (Base::ControlParameterContainer &cntnr, bool multi_conf)
	Sets the value of the Chem::ControlParameter::MULTI_CONF_IMPORT parameter of cntnr to multi_conf. More...
CDPL_CHEM_API bool	hasMultiConfImportParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MULTI_CONF_IMPORT parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMultiConfImportParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MULTI_CONF_IMPORT parameter from cntnr. More...
CDPL_CHEM_API bool	getMultiConfExportParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MULTI_CONF_EXPORT parameter stored in cntnr. More...
CDPL_CHEM_API void	setMultiConfExportParameter (Base::ControlParameterContainer &cntnr, bool multi_conf)
	Sets the value of the Chem::ControlParameter::MULTI_CONF_EXPORT parameter of cntnr to multi_conf. More...
CDPL_CHEM_API bool	hasMultiConfExportParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MULTI_CONF_EXPORT parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMultiConfExportParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MULTI_CONF_EXPORT parameter from cntnr. More...
CDPL_CHEM_API bool	getOutputConfEnergyAsCommentParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COMMENT parameter stored in cntnr. More...
CDPL_CHEM_API void	setOutputConfEnergyAsCommentParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasOutputConfEnergyAsCommentParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr is set. More...
CDPL_CHEM_API void	clearOutputConfEnergyAsCommentParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COMMENT parameter from cntnr. More...
CDPL_CHEM_API const std::string &	getConfIndexNameSuffixPatternParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CONF_INDEX_NAME_SUFFIX_PATTERN parameter stored in cntnr. More...
CDPL_CHEM_API void	setConfIndexNameSuffixPatternParameter (Base::ControlParameterContainer &cntnr, const std::string &pattern)
	Sets the value of the Chem::ControlParameter::CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr to pattern. More...
CDPL_CHEM_API bool	hasConfIndexNameSuffixPatternParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr is set. More...
CDPL_CHEM_API void	clearConfIndexNameSuffixPatternParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CONF_INDEX_NAME_SUFFIX_PATTERN parameter from cntnr. More...
CDPL_CHEM_API const MultiConfMoleculeInputProcessor::SharedPointer &	getMultiConfInputProcessorParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR parameter stored in cntnr. More...
CDPL_CHEM_API void	setMultiConfInputProcessorParameter (Base::ControlParameterContainer &cntnr, const MultiConfMoleculeInputProcessor::SharedPointer &proc)
	Sets the value of the Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR parameter of cntnr to proc. More...
CDPL_CHEM_API bool	hasMultiConfInputProcessorParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMultiConfInputProcessorParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR parameter from cntnr. More...
CDPL_CHEM_API bool	getCDFOutputSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter stored in cntnr. More...
CDPL_CHEM_API void	setCDFOutputSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr, bool single_prec)
	Sets the value of the Chem::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr to single_prec. More...
CDPL_CHEM_API bool	hasCDFOutputSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCDFOutputSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter from cntnr. More...
CDPL_CHEM_API bool	getMOL2EnableExtendedAtomTypesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter stored in cntnr. More...
CDPL_CHEM_API void	setMOL2EnableExtendedAtomTypesParameter (Base::ControlParameterContainer &cntnr, bool enable)
	Sets the value of the Chem::ControlParameter::MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr to enable. More...
CDPL_CHEM_API bool	hasMOL2EnableExtendedAtomTypesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMOL2EnableExtendedAtomTypesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter from cntnr. More...
CDPL_CHEM_API bool	getMOL2EnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MOL2_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr. More...
CDPL_CHEM_API void	setMOL2EnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr, bool enable)
	Sets the value of the Chem::ControlParameter::MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable. More...
CDPL_CHEM_API bool	hasMOL2EnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMOL2EnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MOL2_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr. More...
CDPL_CHEM_API bool	getMOL2ReadPartialAsFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter stored in cntnr. More...
CDPL_CHEM_API void	setMOL2ReadPartialAsFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool read)
	Sets the value of the Chem::ControlParameter::MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr to read. More...
CDPL_CHEM_API bool	hasMOL2ReadPartialAsFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMOL2ReadPartialAsFormalChargesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter from cntnr. More...
CDPL_CHEM_API bool	getMOL2CalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MOL2_CALC_FORMAL_CHARGES parameter stored in cntnr. More...
CDPL_CHEM_API void	setMOL2CalcFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc)
	Sets the value of the Chem::ControlParameter::MOL2_CALC_FORMAL_CHARGES parameter of cntnr to calc. More...
CDPL_CHEM_API bool	hasMOL2CalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MOL2_CALC_FORMAL_CHARGES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMOL2CalcFormalChargesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MOL2_CALC_FORMAL_CHARGES parameter from cntnr. More...
CDPL_CHEM_API unsigned int	getMOL2ChargeTypeParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MOL2_CHARGE_TYPE parameter stored in cntnr. More...
CDPL_CHEM_API void	setMOL2ChargeTypeParameter (Base::ControlParameterContainer &cntnr, unsigned int type)
	Sets the value of the Chem::ControlParameter::MOL2_CHARGE_TYPE parameter of cntnr to type. More...
CDPL_CHEM_API bool	hasMOL2ChargeTypeParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MOL2_CHARGE_TYPE parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMOL2ChargeTypeParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MOL2_CHARGE_TYPE parameter from cntnr. More...
CDPL_CHEM_API unsigned int	getMOL2MoleculeTypeParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MOL2_MOLECULE_TYPE parameter stored in cntnr. More...
CDPL_CHEM_API void	setMOL2MoleculeTypeParameter (Base::ControlParameterContainer &cntnr, unsigned int type)
	Sets the value of the Chem::ControlParameter::MOL2_MOLECULE_TYPE parameter of cntnr to type. More...
CDPL_CHEM_API bool	hasMOL2MoleculeTypeParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MOL2_MOLECULE_TYPE parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMOL2MoleculeTypeParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MOL2_MOLECULE_TYPE parameter from cntnr. More...
CDPL_CHEM_API bool	getMOL2OutputSubstructuresParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MOL2_OUTPUT_SUBSTRUCTURES parameter stored in cntnr. More...
CDPL_CHEM_API void	setMOL2OutputSubstructuresParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasMOL2OutputSubstructuresParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMOL2OutputSubstructuresParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MOL2_OUTPUT_SUBSTRUCTURES parameter from cntnr. More...
CDPL_CHEM_API bool	getMOL2OutputFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::MOL2_OUTPUT_FORMAL_CHARGES parameter stored in cntnr. More...
CDPL_CHEM_API void	setMOL2OutputFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasMOL2OutputFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearMOL2OutputFormalChargesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::MOL2_OUTPUT_FORMAL_CHARGES parameter from cntnr. More...
CDPL_CHEM_API bool	getXYZCommentIsNameParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::XYZ_COMMENT_IS_NAME parameter stored in cntnr. More...
CDPL_CHEM_API void	setXYZCommentIsNameParameter (Base::ControlParameterContainer &cntnr, bool is_name)
	Sets the value of the Chem::ControlParameter::XYZ_COMMENT_IS_NAME parameter of cntnr to is_name. More...
CDPL_CHEM_API bool	hasXYZCommentIsNameParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::XYZ_COMMENT_IS_NAME parameter of cntnr is set. More...
CDPL_CHEM_API void	clearXYZCommentIsNameParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::XYZ_COMMENT_IS_NAME parameter from cntnr. More...
CDPL_CHEM_API bool	getXYZPerceiveConnectivityParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::XYZ_PERCEIVE_CONNECTIVITY parameter stored in cntnr. More...
CDPL_CHEM_API void	setXYZPerceiveConnectivityParameter (Base::ControlParameterContainer &cntnr, bool perceive)
	Sets the value of the Chem::ControlParameter::XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr to perceive. More...
CDPL_CHEM_API bool	hasXYZPerceiveConnectivityParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr is set. More...
CDPL_CHEM_API void	clearXYZPerceiveConnectivityParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::XYZ_PERCEIVE_CONNECTIVITY parameter from cntnr. More...
CDPL_CHEM_API bool	getXYZPerceiveBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::XYZ_PERCEIVE_BOND_ORDERS parameter stored in cntnr. More...
CDPL_CHEM_API void	setXYZPerceiveBondOrdersParameter (Base::ControlParameterContainer &cntnr, bool perceive)
	Sets the value of the Chem::ControlParameter::XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr to perceive. More...
CDPL_CHEM_API bool	hasXYZPerceiveBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr is set. More...
CDPL_CHEM_API void	clearXYZPerceiveBondOrdersParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::XYZ_PERCEIVE_BOND_ORDERS parameter from cntnr. More...
CDPL_CHEM_API bool	getXYZCalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::XYZ_CALC_FORMAL_CHARGES parameter stored in cntnr. More...
CDPL_CHEM_API void	setXYZCalcFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc)
	Sets the value of the Chem::ControlParameter::XYZ_CALC_FORMAL_CHARGES parameter of cntnr to calc. More...
CDPL_CHEM_API bool	hasXYZCalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::XYZ_CALC_FORMAL_CHARGES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearXYZCalcFormalChargesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::XYZ_CALC_FORMAL_CHARGES parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputXMLDeclarationParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_XML_DECLARATION parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputXMLDeclarationParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_XML_DECLARATION parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputXMLDeclarationParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_XML_DECLARATION parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputXMLDeclarationParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_XML_DECLARATION parameter from cntnr. More...
CDPL_CHEM_API const std::string &	getCMLOutputElementNamespaceParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_ELEMENT_NAMESPACE parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputElementNamespaceParameter (Base::ControlParameterContainer &cntnr, const std::string &ns)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr to ns. More...
CDPL_CHEM_API bool	hasCMLOutputElementNamespaceParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputElementNamespaceParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_ELEMENT_NAMESPACE parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputAtomParityParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_ATOM_PARITY parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputAtomParityParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_ATOM_PARITY parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputAtomParityParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_ATOM_PARITY parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputAtomParityParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_ATOM_PARITY parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputSingleBondStereoParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_SINGLE_BOND_STEREO parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputSingleBondStereoParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputSingleBondStereoParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputSingleBondStereoParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_SINGLE_BOND_STEREO parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputDoubleBondStereoParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_DOUBLE_BOND_STEREO parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputDoubleBondStereoParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputDoubleBondStereoParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputDoubleBondStereoParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_DOUBLE_BOND_STEREO parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLEnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLEnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr, bool enable)
	Sets the value of the Chem::ControlParameter::CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable. More...
CDPL_CHEM_API bool	hasCMLEnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLEnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputMoleculeNameParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_MOLECULE_NAME parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputMoleculeNameParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_MOLECULE_NAME parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputMoleculeNameParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_MOLECULE_NAME parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputMoleculeNameParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_MOLECULE_NAME parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputStructureDataParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_STRUCTURE_DATA parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputStructureDataParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_STRUCTURE_DATA parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputStructureDataParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_STRUCTURE_DATA parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputStructureDataParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_STRUCTURE_DATA parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputIsotopeParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_ISOTOPE parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputIsotopeParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_ISOTOPE parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputIsotopeParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_ISOTOPE parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputIsotopeParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_ISOTOPE parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputSpinMultiplicityParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_SPIN_MULTIPLICITY parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputSpinMultiplicityParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputSpinMultiplicityParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputSpinMultiplicityParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_SPIN_MULTIPLICITY parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputCompactAtomDataParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_COMPACT_ATOM_DATA parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputCompactAtomDataParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputCompactAtomDataParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputCompactAtomDataParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_COMPACT_ATOM_DATA parameter from cntnr. More...
CDPL_CHEM_API bool	getCMLOutputCompactBondDataParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Chem::ControlParameter::CML_OUTPUT_COMPACT_BOND_DATA parameter stored in cntnr. More...
CDPL_CHEM_API void	setCMLOutputCompactBondDataParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the value of the Chem::ControlParameter::CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr to output. More...
CDPL_CHEM_API bool	hasCMLOutputCompactBondDataParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Chem::ControlParameter::CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr is set. More...
CDPL_CHEM_API void	clearCMLOutputCompactBondDataParameter (Base::ControlParameterContainer &cntnr)
	Removes the Chem::ControlParameter::CML_OUTPUT_COMPACT_BOND_DATA parameter from cntnr. More...
CDPL_CHEM_API void	calcGeometricalDistanceMatrix (const Entity3DContainer &cntnr, Math::DMatrix &mtx)
	Calculates the inter-entity geometric distance matrix for the entities of cntnr. More...
CDPL_CHEM_API void	get3DCoordinates (const Entity3DContainer &cntnr, Math::Vector3DArray &coords, bool append=false)
	Stores the 3D coordinates of the entities of cntnr in coords. More...
CDPL_CHEM_API void	set3DCoordinates (Entity3DContainer &cntnr, const Math::Vector3DArray &coords)
	Sets the 3D coordinates of the entities of cntnr from coords. More...
CDPL_CHEM_API void	transform3DCoordinates (Entity3DContainer &cntnr, const Math::Matrix4D &mtx)
	Transforms the 3D coordinates of the entities of cntnr by the affine matrix mtx. More...
CDPL_CHEM_API bool	align3DCoordinates (Entity3DContainer &cntnr, const Entity3DContainer &ref_entities, const Math::Vector3DArray &ref_coords)
	Transforms the 3D coordinates of the entities of cntnr by the affine matrix that is calculated for the rigid-body alignment of the 3D coordinates of the entities of ref_entities with the given reference coordinates ref_coords. More...
CDPL_CHEM_API bool	calcCentroid (const Entity3DContainer &cntnr, Math::Vector3D &ctr)
	Calculates the geometric centroid of the 3D coordinates of the entities of cntnr. More...
CDPL_CHEM_API void	calcBoundingBox (const Entity3DContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, bool reset=true)
	Calculates the axis-aligned bounding box of the 3D coordinates of the entities of cntnr. More...
CDPL_CHEM_API bool	insideBoundingBox (const Entity3DContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max)
	Tells whether all 3D coordinates of the entities of cntnr lie within the axis-aligned bounding box defined by min and max. More...
CDPL_CHEM_API bool	intersectsBoundingBox (const Entity3DContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max)
	Tells whether at least one entity of cntnr lies within the axis-aligned bounding box defined by min and max. More...
CDPL_CHEM_API const Math::Vector3D &	get3DCoordinates (const Entity3D &entity)
	Returns the value of the Chem::Entity3DProperty::COORDINATES_3D property of the 3D entity entity. More...
CDPL_CHEM_API void	set3DCoordinates (Entity3D &entity, const Math::Vector3D &coords)
	Sets the value of the Chem::Entity3DProperty::COORDINATES_3D property of the 3D entity entity to coords. More...
CDPL_CHEM_API void	clear3DCoordinates (Entity3D &entity)
	Clears the value of the Chem::Entity3DProperty::COORDINATES_3D property of the 3D entity entity. More...
CDPL_CHEM_API bool	has3DCoordinates (const Entity3D &entity)
	Tells whether the Chem::Entity3DProperty::COORDINATES_3D property of the 3D entity entity is set. More...
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)
	Removes all atoms of the fragment frag for which the predicate pred returns true. More...
CDPL_CHEM_API void	removeAtomsIfNot (Fragment &frag, const AtomPredicate &pred)
	Removes all atoms of the fragment frag for which the predicate pred returns false. More...
CDPL_CHEM_API const std::string &	getName (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::NAME property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setName (MolecularGraph &molgraph, const std::string &name)
	Sets the value of the Chem::MolecularGraphProperty::NAME property of the molecular graph molgraph to name. More...
CDPL_CHEM_API void	clearName (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::NAME property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasName (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::NAME property of the molecular graph molgraph is set. More...
CDPL_CHEM_API std::time_t	getTimestamp (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::TIMESTAMP property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setTimestamp (MolecularGraph &molgraph, std::time_t time)
	Sets the value of the Chem::MolecularGraphProperty::TIMESTAMP property of the molecular graph molgraph to time. More...
CDPL_CHEM_API void	clearTimestamp (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::TIMESTAMP property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasTimestamp (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::TIMESTAMP property of the molecular graph molgraph is set. More...
CDPL_CHEM_API const std::string &	getComment (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::COMMENT property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setComment (MolecularGraph &molgraph, const std::string &comment)
	Sets the value of the Chem::MolecularGraphProperty::COMMENT property of the molecular graph molgraph to comment. More...
CDPL_CHEM_API void	clearComment (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::COMMENT property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasComment (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::COMMENT property of the molecular graph molgraph is set. More...
CDPL_CHEM_API const MatchConstraintList::SharedPointer &	getMatchConstraints (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MATCH_CONSTRAINTS property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr)
	Sets the value of the Chem::MolecularGraphProperty::MATCH_CONSTRAINTS property of the molecular graph molgraph to constr. More...
CDPL_CHEM_API void	clearMatchConstraints (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MATCH_CONSTRAINTS property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMatchConstraints (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MATCH_CONSTRAINTS property of the molecular graph molgraph is set. More...
CDPL_CHEM_API const MatchExpression< MolecularGraph >::SharedPointer &	getMatchExpression (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MATCH_EXPRESSION property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMatchExpression (MolecularGraph &molgraph, const MatchExpression< MolecularGraph >::SharedPointer &expr)
	Sets the value of the Chem::MolecularGraphProperty::MATCH_EXPRESSION property of the molecular graph molgraph to expr. More...
CDPL_CHEM_API void	clearMatchExpression (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MATCH_EXPRESSION property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMatchExpression (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MATCH_EXPRESSION property of the molecular graph molgraph is set. More...
CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer	generateMatchExpression (const MolecularGraph &molgraph)
	Builds a match expression from the match constraints currently attached to the molecular graph molgraph. More...
CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer	generateMatchExpression (MolecularGraph &molgraph, bool overwrite)
	Builds and stores the match expression of the molecular graph molgraph. More...
CDPL_CHEM_API const FragmentList::SharedPointer &	getRings (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::RINGS property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setRings (MolecularGraph &molgraph, const FragmentList::SharedPointer &rings)
	Sets the value of the Chem::MolecularGraphProperty::RINGS property of the molecular graph molgraph to rings. More...
CDPL_CHEM_API void	clearRings (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::RINGS property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasRings (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::RINGS property of the molecular graph molgraph is set. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveRings (const MolecularGraph &molgraph)
	Perceives the full set of rings of the molecular graph molgraph. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveRings (MolecularGraph &molgraph, bool overwrite)
	Perceives and stores the full set of rings of the molecular graph molgraph. More...
CDPL_CHEM_API const FragmentList::SharedPointer &	getSSSR (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::SSSR property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setSSSR (MolecularGraph &molgraph, const FragmentList::SharedPointer &sssr)
	Sets the value of the Chem::MolecularGraphProperty::SSSR property of the molecular graph molgraph to sssr. More...
CDPL_CHEM_API void	clearSSSR (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::SSSR property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasSSSR (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::SSSR property of the molecular graph molgraph is set. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveSSSR (const MolecularGraph &molgraph)
	Perceives the SSSR of the molecular graph molgraph. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveSSSR (MolecularGraph &molgraph, bool overwrite)
	Perceives and stores the SSSR of the molecular graph molgraph. More...
CDPL_CHEM_API FragmentList::SharedPointer	extractSSSRSubset (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph)
	Extracts the SSSR subset of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph. More...
CDPL_CHEM_API FragmentList::SharedPointer	extractSSSRSubset (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite)
	Extracts the SSSR subset of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph and stores it on the latter. More...
CDPL_CHEM_API const Fragment::SharedPointer &	getCyclicSubstructure (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setCyclicSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct)
	Sets the value of the Chem::MolecularGraphProperty::CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct. More...
CDPL_CHEM_API void	clearCyclicSubstructure (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasCyclicSubstructure (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph is set. More...
CDPL_CHEM_API Fragment::SharedPointer	perceiveCyclicSubstructure (const MolecularGraph &molgraph)
	Perceives the cyclic substructure (union of all rings) of the molecular graph molgraph. More...
CDPL_CHEM_API Fragment::SharedPointer	perceiveCyclicSubstructure (MolecularGraph &molgraph, bool overwrite)
	Perceives and stores the cyclic substructure (union of all rings) of the molecular graph molgraph. More...
CDPL_CHEM_API const FragmentList::SharedPointer &	getComponents (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::COMPONENTS property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setComponents (MolecularGraph &molgraph, const FragmentList::SharedPointer &comps)
	Sets the value of the Chem::MolecularGraphProperty::COMPONENTS property of the molecular graph molgraph to comps. More...
CDPL_CHEM_API void	clearComponents (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::COMPONENTS property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasComponents (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::COMPONENTS property of the molecular graph molgraph is set. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponents (const MolecularGraph &molgraph)
	Perceives the connected components of the molecular graph molgraph. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponents (MolecularGraph &molgraph, bool overwrite)
	Perceives and stores the connected components of the molecular graph molgraph. More...
CDPL_CHEM_API const FragmentList::SharedPointer &	getComponentGroups (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::COMPONENT_GROUPS property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setComponentGroups (MolecularGraph &molgraph, const FragmentList::SharedPointer &comp_groups)
	Sets the value of the Chem::MolecularGraphProperty::COMPONENT_GROUPS property of the molecular graph molgraph to comp_groups. More...
CDPL_CHEM_API void	clearComponentGroups (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::COMPONENT_GROUPS property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasComponentGroups (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::COMPONENT_GROUPS property of the molecular graph molgraph is set. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponentGroups (const MolecularGraph &molgraph)
	Perceives the component groups of the molecular graph molgraph. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponentGroups (MolecularGraph &molgraph, bool overwrite)
	Perceives and optionally stores the component groups of the molecular graph molgraph. More...
CDPL_CHEM_API std::size_t	getConformationIndex (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::CONFORMATION_INDEX property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setConformationIndex (MolecularGraph &molgraph, std::size_t index)
	Sets the value of the Chem::MolecularGraphProperty::CONFORMATION_INDEX property of the molecular graph molgraph to index. More...
CDPL_CHEM_API void	clearConformationIndex (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::CONFORMATION_INDEX property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasConformationIndex (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::CONFORMATION_INDEX property of the molecular graph molgraph is set. More...
CDPL_CHEM_API const Util::DArray::SharedPointer &	getConformerEnergies (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::CONFORMER_ENERGIES property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setConformerEnergies (MolecularGraph &molgraph, const Util::DArray::SharedPointer &energies)
	Sets the value of the Chem::MolecularGraphProperty::CONFORMER_ENERGIES property of the molecular graph molgraph to energies. More...
CDPL_CHEM_API void	clearConformerEnergies (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::CONFORMER_ENERGIES property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasConformerEnergies (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::CONFORMER_ENERGIES property of the molecular graph molgraph is set. More...
CDPL_CHEM_API void	setConformation (MolecularGraph &molgraph, std::size_t conf_idx, const Math::Vector3DArray &coords, double energy)
	Overwrites the conformation at index conf_idx with the supplied coordinates and energy. More...
CDPL_CHEM_API void	addConformation (MolecularGraph &molgraph, const Math::Vector3DArray &coords, double energy)
	Appends a new conformation built from the supplied coordinates and energy. More...
CDPL_CHEM_API double	getConformationEnergy (const MolecularGraph &molgraph, std::size_t conf_idx)
	Returns the energy of the conformation at index conf_idx. More...
CDPL_CHEM_API std::uint64_t	getHashCode (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::HASH_CODE property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setHashCode (MolecularGraph &molgraph, std::uint64_t hash_code)
	Sets the value of the Chem::MolecularGraphProperty::HASH_CODE property of the molecular graph molgraph to hash_code. More...
CDPL_CHEM_API void	clearHashCode (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::HASH_CODE property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasHashCode (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::HASH_CODE property of the molecular graph molgraph is set. More...
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)
	Computes a 64-bit hash code for the molecular graph molgraph taking into account the specified atom and bond properties. More...
CDPL_CHEM_API void	extractReactionCenter (const MolecularGraph &molgraph, Fragment &rxn_center)
	Collects every atom and bond of the molecular graph molgraph that carries a reaction-center flag into the fragment rxn_center. More...
CDPL_CHEM_API double	getStoichiometricNumber (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::STOICHIOMETRIC_NUMBER property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setStoichiometricNumber (MolecularGraph &molgraph, double num)
	Sets the value of the Chem::MolecularGraphProperty::STOICHIOMETRIC_NUMBER property of the molecular graph molgraph to num. More...
CDPL_CHEM_API void	clearStoichiometricNumber (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::STOICHIOMETRIC_NUMBER property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasStoichiometricNumber (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::STOICHIOMETRIC_NUMBER property of the molecular graph molgraph is set. More...
CDPL_CHEM_API const std::string &	getMDLUserInitials (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MDL_USER_INITIALS property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMDLUserInitials (MolecularGraph &molgraph, const std::string &initials)
	Sets the value of the Chem::MolecularGraphProperty::MDL_USER_INITIALS property of the molecular graph molgraph to initials. More...
CDPL_CHEM_API void	clearMDLUserInitials (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MDL_USER_INITIALS property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMDLUserInitials (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MDL_USER_INITIALS property of the molecular graph molgraph is set. More...
CDPL_CHEM_API const std::string &	getMDLProgramName (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MDL_PROGRAM_NAME property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMDLProgramName (MolecularGraph &molgraph, const std::string &name)
	Sets the value of the Chem::MolecularGraphProperty::MDL_PROGRAM_NAME property of the molecular graph molgraph to name. More...
CDPL_CHEM_API void	clearMDLProgramName (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MDL_PROGRAM_NAME property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMDLProgramName (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MDL_PROGRAM_NAME property of the molecular graph molgraph is set. More...
CDPL_CHEM_API std::size_t	getMDLRegistryNumber (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MDL_REGISTRY_NUMBER property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMDLRegistryNumber (MolecularGraph &molgraph, std::size_t reg_no)
	Sets the value of the Chem::MolecularGraphProperty::MDL_REGISTRY_NUMBER property of the molecular graph molgraph to reg_no. More...
CDPL_CHEM_API void	clearMDLRegistryNumber (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MDL_REGISTRY_NUMBER property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMDLRegistryNumber (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MDL_REGISTRY_NUMBER property of the molecular graph molgraph is set. More...
CDPL_CHEM_API unsigned int	getMDLCTABVersion (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMDLCTABVersion (MolecularGraph &molgraph, unsigned int version)
	Sets the value of the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property of the molecular graph molgraph to version. More...
CDPL_CHEM_API void	clearMDLCTABVersion (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMDLCTABVersion (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property of the molecular graph molgraph is set. More...
CDPL_CHEM_API const StringDataBlock::SharedPointer &	getStructureData (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::STRUCTURE_DATA property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setStructureData (MolecularGraph &molgraph, const StringDataBlock::SharedPointer &data)
	Sets the value of the Chem::MolecularGraphProperty::STRUCTURE_DATA property of the molecular graph molgraph to data. More...
CDPL_CHEM_API void	clearStructureData (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::STRUCTURE_DATA property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasStructureData (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::STRUCTURE_DATA property of the molecular graph molgraph is set. More...
CDPL_CHEM_API std::size_t	getMDLDimensionality (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MDL_DIMENSIONALITY property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMDLDimensionality (MolecularGraph &molgraph, std::size_t dim)
	Sets the value of the Chem::MolecularGraphProperty::MDL_DIMENSIONALITY property of the molecular graph molgraph to dim. More...
CDPL_CHEM_API void	clearMDLDimensionality (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MDL_DIMENSIONALITY property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMDLDimensionality (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MDL_DIMENSIONALITY property of the molecular graph molgraph is set. More...
CDPL_CHEM_API long	getMDLScalingFactor1 (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR1 property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMDLScalingFactor1 (MolecularGraph &molgraph, long factor)
	Sets the value of the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR1 property of the molecular graph molgraph to factor. More...
CDPL_CHEM_API void	clearMDLScalingFactor1 (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR1 property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMDLScalingFactor1 (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR1 property of the molecular graph molgraph is set. More...
CDPL_CHEM_API double	getMDLScalingFactor2 (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR2 property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMDLScalingFactor2 (MolecularGraph &molgraph, double factor)
	Sets the value of the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR2 property of the molecular graph molgraph to factor. More...
CDPL_CHEM_API void	clearMDLScalingFactor2 (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR2 property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMDLScalingFactor2 (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR2 property of the molecular graph molgraph is set. More...
CDPL_CHEM_API double	getMDLEnergy (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MDL_ENERGY property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMDLEnergy (MolecularGraph &molgraph, double energy)
	Sets the value of the Chem::MolecularGraphProperty::MDL_ENERGY property of the molecular graph molgraph to energy. More...
CDPL_CHEM_API void	clearMDLEnergy (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MDL_ENERGY property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMDLEnergy (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MDL_ENERGY property of the molecular graph molgraph is set. More...
CDPL_CHEM_API bool	getMDLChiralFlag (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MDL_CHIRAL_FLAG property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMDLChiralFlag (MolecularGraph &molgraph, bool flag)
	Sets the value of the Chem::MolecularGraphProperty::MDL_CHIRAL_FLAG property of the molecular graph molgraph to flag. More...
CDPL_CHEM_API void	clearMDLChiralFlag (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MDL_CHIRAL_FLAG property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMDLChiralFlag (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MDL_CHIRAL_FLAG property of the molecular graph molgraph is set. More...
CDPL_CHEM_API unsigned int	getMOL2MoleculeType (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMOL2MoleculeType (MolecularGraph &molgraph, unsigned int type)
	Sets the value of the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property of the molecular graph molgraph to type. More...
CDPL_CHEM_API void	clearMOL2MoleculeType (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMOL2MoleculeType (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property of the molecular graph molgraph is set. More...
CDPL_CHEM_API unsigned int	getMOL2ChargeType (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setMOL2ChargeType (MolecularGraph &molgraph, unsigned int type)
	Sets the value of the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property of the molecular graph molgraph to type. More...
CDPL_CHEM_API void	clearMOL2ChargeType (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasMOL2ChargeType (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property of the molecular graph molgraph is set. More...
CDPL_CHEM_API void	generateAdjacencyMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
	Builds the adjacency matrix of the molecular graph molgraph. More...
CDPL_CHEM_API void	generateIncidenceMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
	Builds the atom/bond incidence matrix of the molecular graph molgraph. More...
CDPL_CHEM_API void	generateBondMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
	Builds the bond order matrix of the molecular graph molgraph. More...
CDPL_CHEM_API void	generateBondElectronMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
	Builds the bond-electron matrix of the molecular graph molgraph. More...
CDPL_CHEM_API void	generateBondAtomTypeMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
	Builds a matrix combining bond order and atom type information of the endpoints of every bond in molgraph. More...
CDPL_CHEM_API const Math::ULMatrix::SharedPointer &	getTopologicalDistanceMatrix (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setTopologicalDistanceMatrix (MolecularGraph &molgraph, const Math::ULMatrix::SharedPointer &mtx)
	Sets the value of the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx. More...
CDPL_CHEM_API void	clearTopologicalDistanceMatrix (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasTopologicalDistanceMatrix (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set. More...
CDPL_CHEM_API Math::ULMatrix::SharedPointer	calcTopologicalDistanceMatrix (MolecularGraph &molgraph, bool overwrite)
	Computes and stores the topological distance matrix of the molecular graph molgraph. More...
CDPL_CHEM_API void	calcTopologicalDistanceMatrix (const MolecularGraph &molgraph, Math::ULMatrix &mtx)
	Computes the topological distance matrix of the molecular graph molgraph into the supplied matrix mtx. More...
CDPL_CHEM_API Math::ULMatrix::SharedPointer	extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite)
	Extracts the topological distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph and stores it on the latter. More...
CDPL_CHEM_API void	extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph, Math::ULMatrix &mtx)
	Extracts the topological distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph into the supplied matrix mtx. More...
CDPL_CHEM_API const Math::DMatrix::SharedPointer &	getGeometricalDistanceMatrix (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setGeometricalDistanceMatrix (MolecularGraph &molgraph, const Math::DMatrix::SharedPointer &mtx)
	Sets the value of the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx. More...
CDPL_CHEM_API void	clearGeometricalDistanceMatrix (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasGeometricalDistanceMatrix (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set. More...
CDPL_CHEM_API Math::DMatrix::SharedPointer	calcGeometricalDistanceMatrix (MolecularGraph &molgraph, bool overwrite)
	Computes and stores the geometrical distance matrix of the molecular graph molgraph from its 3D coordinates. More...
CDPL_CHEM_API const Fragment::SharedPointer &	getAromaticSubstructure (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setAromaticSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct)
	Sets the value of the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct. More...
CDPL_CHEM_API void	clearAromaticSubstructure (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasAromaticSubstructure (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph is set. More...
CDPL_CHEM_API Fragment::SharedPointer	perceiveAromaticSubstructure (const MolecularGraph &molgraph)
	Perceives the aromatic substructure (union of all aromatic atoms/bonds) of the molecular graph molgraph. More...
CDPL_CHEM_API Fragment::SharedPointer	perceiveAromaticSubstructure (MolecularGraph &molgraph, bool overwrite)
	Perceives and stores the aromatic substructure of the molecular graph molgraph. More...
CDPL_CHEM_API const ElectronSystemList::SharedPointer &	getPiElectronSystems (const MolecularGraph &molgraph)
	Returns the value of the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of the molecular graph molgraph. More...
CDPL_CHEM_API void	setPiElectronSystems (MolecularGraph &molgraph, const ElectronSystemList::SharedPointer &pi_systems)
	Sets the value of the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of the molecular graph molgraph to pi_systems. More...
CDPL_CHEM_API void	clearPiElectronSystems (MolecularGraph &molgraph)
	Clears the value of the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of the molecular graph molgraph. More...
CDPL_CHEM_API bool	hasPiElectronSystems (const MolecularGraph &molgraph)
	Tells whether the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of the molecular graph molgraph is set. More...
CDPL_CHEM_API ElectronSystemList::SharedPointer	perceivePiElectronSystems (const MolecularGraph &molgraph)
	Perceives the π-electron systems of the molecular graph molgraph. More...
CDPL_CHEM_API ElectronSystemList::SharedPointer	perceivePiElectronSystems (MolecularGraph &molgraph, bool overwrite)
	Perceives and stores the π-electron systems of the molecular graph molgraph. More...
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)
	Generates a SMILES string for the molecular graph molgraph. More...
CDPL_CHEM_API int	generateINCHI (const MolecularGraph &molgraph, std::string &inchi, const std::string &options=ControlParameterDefault::INCHI_OUTPUT_OPTIONS, std::size_t dim=0)
	Generates an InChI string for the molecular graph molgraph using the InChI C-API. More...
CDPL_CHEM_API int	generateINCHIKey (const MolecularGraph &molgraph, std::string &inchi_key)
	Generates an InChIKey for the molecular graph molgraph using the InChI C-API. More...
CDPL_CHEM_API void	canonicalize (MolecularGraph &molgraph, const AtomCompareFunction &func, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false)
	Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to a user-supplied comparator. More...
CDPL_CHEM_API void	canonicalize (MolecularGraph &molgraph, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false)
	Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to the canonical number property value of its atoms. More...
CDPL_CHEM_API void	calc2DCoordinates (MolecularGraph &molgraph, bool overwrite)
	Computes 2D atom coordinates for the molecular graph molgraph and stores them as corresponding atom properties. More...
CDPL_CHEM_API bool	align2DCoordinates (MolecularGraph &molgraph, const AtomContainer &atoms, const Math::Vector2DArray &ref_coords, bool fix_bond_stereo=true)
	Transforms the 2D atom coordinates of molgraph so that the 2D coordinates of atoms are aligned with the reference coordinates ref_coords. More...
CDPL_CHEM_API bool	align2DCoordinates (MolecularGraph &molgraph, const AtomMapping &ref_atom_mpg, bool fix_bond_stereo=true)
	Transforms the 2D atom coordinates of molgraph so that the 2D coordinates of the mapped atoms are aligned. More...
CDPL_CHEM_API bool	align2DCoordinates (MolecularGraph &molgraph, const MolecularGraph &ref_molgraph, bool use_mcss, bool fix_bond_stereo=true)
	Aligns the 2D atom coordinates of molgraph with those of ref_molgraph, using either a maximum-common-substructure search or substructure matching. More...
CDPL_CHEM_API bool	align2DCoordinates (MolecularGraph &molgraph, const MolecularGraph &ref_molgraph, const MolecularGraph &substr_ptn, bool fix_bond_stereo=true)
	Aligns the 2D atom coordinates of molgraph with those of ref_molgraph, using substr_ptn as the explicit substructure search pattern. More...
CDPL_CHEM_API void	calcHydrogen3DCoordinates (MolecularGraph &molgraph, bool undef_only=true)
	Computes 3D coordinates for the hydrogen atoms of the molecular graph molgraph from the 3D coordinates of their non-hydrogen neighbors. More...
CDPL_CHEM_API void	calcBond2DStereoFlags (MolecularGraph &molgraph, bool overwrite)
	Derives 2D wedge/hash bond stereo flags for the bonds of the molecular graph molgraph from the atoms' stereo descriptors and 2D coordinates. More...
CDPL_CHEM_API void	calcCIPPriorities (MolecularGraph &molgraph, bool overwrite)
	Computes and stores topological CIP priorities for the atoms of the molecular graph molgraph. More...
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)
	Computes and stores topological symmetry classes for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API void	calcCanonicalNumbering (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT)
	Computes and stores canonical atom numbers for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API void	calcMorganNumbering (MolecularGraph &molgraph, bool overwrite)
	Computes and stores Morgan numbers for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API void	calcImplicitHydrogenCounts (MolecularGraph &molgraph, bool overwrite)
	Computes and stores implicit hydrogen counts for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API void	calcFormalCharges (MolecularGraph &molgraph, bool overwrite)
	Computes and stores formal charges for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API void	perceiveHybridizationStates (MolecularGraph &molgraph, bool overwrite)
	Computes and stores hybridization states for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API void	perceiveBondOrders (MolecularGraph &molgraph, bool overwrite)
	Perceives bond orders for the bonds of the molecular graph molgraph. More...
CDPL_CHEM_API void	kekulizeBonds (MolecularGraph &molgraph)
	Assigns Kekulé bond orders to the aromatic bonds of the molecular graph molgraph. More...
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)
	Flags the atoms of the molecular graph molgraph that qualify as stereo centers under the supplied criteria. More...
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)
	Flags the bonds of the molecular graph molgraph that qualify as stereo centers under the supplied criteria. More...
CDPL_CHEM_API void	calcMDLParities (MolecularGraph &molgraph, bool overwrite)
	Computes and stores MDL parities for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API void	calcAtomStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true)
	Computes and stores stereo descriptors for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API void	calcAtomStereoDescriptorsFromMDLParities (MolecularGraph &molgraph, bool overwrite)
	Derives atom stereo descriptors of the molecular graph molgraph from previously-assigned MDL parities. More...
CDPL_CHEM_API void	calcBondStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true)
	Computes and stores stereo descriptors for the bonds of the molecular graph molgraph. More...
CDPL_CHEM_API void	calcAtomCIPConfigurations (MolecularGraph &molgraph, bool overwrite)
	Computes and stores CIP configuration labels for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API void	calcBondCIPConfigurations (MolecularGraph &molgraph, bool overwrite)
	Computes and stores CIP configuration labels for the bonds of the molecular graph molgraph. More...
CDPL_CHEM_API void	setAtomMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite)
	Sets the match constraint list constr on every atom of the molecular graph molgraph. More...
CDPL_CHEM_API void	setBondMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite)
	Sets the match constraint list constr on every bond of the molecular graph molgraph. More...
CDPL_CHEM_API void	generateMatchExpressions (MolecularGraph &molgraph, bool overwrite)
	Generates and stores match expressions for every atom, bond and the molecular graph molgraph itself. More...
CDPL_CHEM_API void	generateMatchExpressionStrings (MolecularGraph &molgraph, bool overwrite)
	Generates and stores textual representations of the atom/bond match expressions of the molecular graph molgraph. More...
CDPL_CHEM_API void	initSubstructureSearchQuery (MolecularGraph &molgraph, bool overwrite)
	Prepares the molecular graph molgraph for use as a substructure search query. More...
CDPL_CHEM_API void	initSubstructureSearchTarget (MolecularGraph &molgraph, bool overwrite)
	Prepares the molecular graph molgraph for use as a substructure search target. More...
CDPL_CHEM_API void	setAromaticityFlags (MolecularGraph &molgraph, bool overwrite)
	Perceives aromaticity and sets the corresponding atom/bond aromaticity flags on the molecular graph molgraph. More...
CDPL_CHEM_API void	setRingFlags (MolecularGraph &molgraph, bool overwrite)
	Perceives ring membership and sets the corresponding atom/bond ring flags on the molecular graph molgraph. More...
CDPL_CHEM_API void	setAtomTypesFromSymbols (MolecularGraph &molgraph, bool overwrite)
	Sets the atom types of the molecular graph molgraph from their element symbols. More...
CDPL_CHEM_API void	setAtomSymbolsFromTypes (MolecularGraph &molgraph, bool overwrite)
	Sets the atom symbols of the molecular graph molgraph from their atom types. More...
CDPL_CHEM_API void	perceiveSybylAtomTypes (MolecularGraph &molgraph, bool overwrite)
	Perceives and assigns Sybyl MOL2 atom types for the atoms of the molecular graph molgraph. More...
CDPL_CHEM_API FragmentList::SharedPointer	getAromaticRings (const MolecularGraph &molgraph)
	Returns the subset of the aromatic rings of the molecular graph molgraph. More...
CDPL_CHEM_API FragmentList::SharedPointer	getAromaticSSSRSubset (const MolecularGraph &molgraph)
	Returns the subset of the SSSR of the molecular graph molgraph that contains only aromatic rings,. More...
CDPL_CHEM_API bool	containsMolecularGraph (const MolecularGraph &molgraph, const MolecularGraph &sub_molgraph, bool atoms=true, bool bonds=true)
	Tells whether the molecular graph molgraph contains the atoms and/or bonds of sub_molgraph. More...
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)
	Collects the fragments in frag_list that are fully contained in the molecular graph molgraph into cont_frag_list. More...
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)
	Collects the fragments in frag_list that contain the molecular graph molgraph into cont_frag_list. More...
CDPL_CHEM_API void	translateFragment (const MolecularGraph &src_molgraph, const Fragment &src_frag, const MolecularGraph &tgt_molgraph, Fragment &tgt_frag, bool append=false)
	Translates the atoms/bonds of src_frag to the corresponding atoms/bonds of tgt_molgraph and stores them in tgt_frag. More...
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)
	Translates every fragment in src_frag_list to the corresponding fragments on tgt_molgraph. More...
CDPL_CHEM_API void	splitIntoFragments (const MolecularGraph &molgraph, FragmentList &frag_list, const Util::BitSet &split_bond_mask, bool append=false)
	Splits the molecular graph molgraph into connected fragments by removing the bonds flagged in split_bond_mask. More...
CDPL_CHEM_API std::size_t	getCompleteBondCount (const MolecularGraph &molgraph)
	Returns the number of bonds of the molecular graph molgraph whose connected atoms are likewise contained in molgraph. More...
CDPL_CHEM_API void	calcBasicProperties (MolecularGraph &molgraph, bool overwrite)
	Computes basic atom/bond/molecular graph properties (aromaticity, SSSR, etc.) of the molecular graph molgraph. More...
CDPL_CHEM_API std::size_t	editSubstructures (const MolecularGraph &molgraph, Molecule &result_mol, const std::string &search_ptns, const std::string &result_ptn, const std::string &exclude_ptns=std::string())
	Builds the molecule result_mol from the molecular graph molgraph by replacing all substructures matching the SMARTS patterns in search_ptns with result_ptn. More...
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)
	Adds bonds between atoms of the molecule mol whose 3D distance falls within the covalent-radii sum plus dist_tol. More...
CDPL_CHEM_API void	connectAtoms (Molecule &mol, const Atom3DCoordinatesFunction &coords_func, double dist_tol=0.3, std::size_t atom_idx_offs=0)
	Adds bonds between atoms of the molecule mol whose 3D distance (obtained via coords_func) falls within the covalent-radii sum plus dist_tol. More...
CDPL_CHEM_API void	removeAtomsIf (Molecule &mol, const AtomPredicate &pred)
	Removes all atoms of the molecule mol for which the predicate pred returns true. More...
CDPL_CHEM_API void	removeAtomsIfNot (Molecule &mol, const AtomPredicate &pred)
	Removes all atoms of the molecule mol for which the predicate pred returns false. More...
CDPL_CHEM_API std::size_t	editSubstructures (Molecule &mol, const std::string &search_ptns, const std::string &result_ptn, const std::string &exclude_ptns=std::string())
	Edits the molecule mol by replacing all substructures matching the SMARTS search patterns in search_ptns with the SMILES replacement pattern result_ptn, optionally skipping matches that also match exclude_ptns. More...
CDPL_CHEM_API const std::string &	getName (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::NAME property of the reaction rxn. More...
CDPL_CHEM_API void	setName (Reaction &rxn, const std::string &name)
	Sets the value of the Chem::ReactionProperty::NAME property of the reaction rxn to name. More...
CDPL_CHEM_API void	clearName (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::NAME property of the reaction rxn. More...
CDPL_CHEM_API bool	hasName (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::NAME property of the reaction rxn is set. More...
CDPL_CHEM_API std::time_t	getTimestamp (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::TIMESTAMP property of the reaction rxn. More...
CDPL_CHEM_API void	setTimestamp (Reaction &rxn, std::time_t time)
	Sets the value of the Chem::ReactionProperty::TIMESTAMP property of the reaction rxn to time. More...
CDPL_CHEM_API void	clearTimestamp (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::TIMESTAMP property of the reaction rxn. More...
CDPL_CHEM_API bool	hasTimestamp (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::TIMESTAMP property of the reaction rxn is set. More...
CDPL_CHEM_API const std::string &	getComment (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::COMMENT property of the reaction rxn. More...
CDPL_CHEM_API void	setComment (Reaction &rxn, const std::string &comment)
	Sets the value of the Chem::ReactionProperty::COMMENT property of the reaction rxn to comment. More...
CDPL_CHEM_API void	clearComment (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::COMMENT property of the reaction rxn. More...
CDPL_CHEM_API bool	hasComment (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::COMMENT property of the reaction rxn is set. More...
CDPL_CHEM_API const MatchExpression< Reaction >::SharedPointer &	getMatchExpression (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::MATCH_EXPRESSION property of the reaction rxn. More...
CDPL_CHEM_API void	setMatchExpression (Reaction &rxn, const MatchExpression< Reaction >::SharedPointer &expr)
	Sets the value of the Chem::ReactionProperty::MATCH_EXPRESSION property of the reaction rxn to expr. More...
CDPL_CHEM_API void	clearMatchExpression (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::MATCH_EXPRESSION property of the reaction rxn. More...
CDPL_CHEM_API bool	hasMatchExpression (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::MATCH_EXPRESSION property of the reaction rxn is set. More...
CDPL_CHEM_API MatchExpression< Reaction >::SharedPointer	generateMatchExpression (const Reaction &rxn)
	Builds a match expression from the match constraints currently attached to the reaction rxn. More...
CDPL_CHEM_API MatchExpression< Reaction >::SharedPointer	generateMatchExpression (Reaction &rxn, bool overwrite)
	Builds and stores the match expression of the reaction rxn. More...
CDPL_CHEM_API const MatchConstraintList::SharedPointer &	getMatchConstraints (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::MATCH_CONSTRAINTS property of the reaction rxn. More...
CDPL_CHEM_API void	setMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr)
	Sets the value of the Chem::ReactionProperty::MATCH_CONSTRAINTS property of the reaction rxn to constr. More...
CDPL_CHEM_API void	clearMatchConstraints (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::MATCH_CONSTRAINTS property of the reaction rxn. More...
CDPL_CHEM_API bool	hasMatchConstraints (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::MATCH_CONSTRAINTS property of the reaction rxn is set. More...
CDPL_CHEM_API const FragmentList::SharedPointer &	getComponentGroups (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::COMPONENT_GROUPS property of the reaction rxn. More...
CDPL_CHEM_API void	setComponentGroups (Reaction &rxn, const FragmentList::SharedPointer &comp_groups)
	Sets the value of the Chem::ReactionProperty::COMPONENT_GROUPS property of the reaction rxn to comp_groups. More...
CDPL_CHEM_API void	clearComponentGroups (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::COMPONENT_GROUPS property of the reaction rxn. More...
CDPL_CHEM_API bool	hasComponentGroups (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::COMPONENT_GROUPS property of the reaction rxn is set. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponentGroups (const Reaction &rxn)
	Perceives the component groups of the reaction rxn. More...
CDPL_CHEM_API FragmentList::SharedPointer	perceiveComponentGroups (Reaction &rxn, bool overwrite)
	Perceives and stores the component groups of the reaction rxn. More...
CDPL_CHEM_API const AtomMapping::SharedPointer &	getAtomMapping (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::ATOM_MAPPING property of the reaction rxn. More...
CDPL_CHEM_API void	setAtomMapping (Reaction &rxn, const AtomMapping::SharedPointer &mapping)
	Sets the value of the Chem::ReactionProperty::ATOM_MAPPING property of the reaction rxn to mapping. More...
CDPL_CHEM_API void	clearAtomMapping (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::ATOM_MAPPING property of the reaction rxn. More...
CDPL_CHEM_API bool	hasAtomMapping (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::ATOM_MAPPING property of the reaction rxn is set. More...
CDPL_CHEM_API AtomMapping::SharedPointer	perceiveAtomMapping (const Reaction &rxn)
	Derives the reactant-to-product atom mapping from the atom mapping IDs of the reaction rxn. More...
CDPL_CHEM_API AtomMapping::SharedPointer	perceiveAtomMapping (Reaction &rxn, bool overwrite)
	Derives and stores the reactant-to-product atom mapping of the reaction rxn. More...
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)
	Generates a reaction SMILES string for the reaction rxn. More...
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)
	Computes a 64-bit hash code for the reaction rxn taking into account the specified reaction roles and atom/bond properties. More...
CDPL_CHEM_API const std::string &	getMDLUserInitials (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::MDL_USER_INITIALS property of the reaction rxn. More...
CDPL_CHEM_API void	setMDLUserInitials (Reaction &rxn, const std::string &initials)
	Sets the value of the Chem::ReactionProperty::MDL_USER_INITIALS property of the reaction rxn to initials. More...
CDPL_CHEM_API void	clearMDLUserInitials (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::MDL_USER_INITIALS property of the reaction rxn. More...
CDPL_CHEM_API bool	hasMDLUserInitials (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::MDL_USER_INITIALS property of the reaction rxn is set. More...
CDPL_CHEM_API const std::string &	getMDLProgramName (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::MDL_PROGRAM_NAME property of the reaction rxn. More...
CDPL_CHEM_API void	setMDLProgramName (Reaction &rxn, const std::string &name)
	Sets the value of the Chem::ReactionProperty::MDL_PROGRAM_NAME property of the reaction rxn to name. More...
CDPL_CHEM_API void	clearMDLProgramName (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::MDL_PROGRAM_NAME property of the reaction rxn. More...
CDPL_CHEM_API bool	hasMDLProgramName (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::MDL_PROGRAM_NAME property of the reaction rxn is set. More...
CDPL_CHEM_API std::size_t	getMDLRegistryNumber (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::MDL_REGISTRY_NUMBER property of the reaction rxn. More...
CDPL_CHEM_API void	setMDLRegistryNumber (Reaction &rxn, std::size_t reg_no)
	Sets the value of the Chem::ReactionProperty::MDL_REGISTRY_NUMBER property of the reaction rxn to reg_no. More...
CDPL_CHEM_API void	clearMDLRegistryNumber (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::MDL_REGISTRY_NUMBER property of the reaction rxn. More...
CDPL_CHEM_API bool	hasMDLRegistryNumber (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::MDL_REGISTRY_NUMBER property of the reaction rxn is set. More...
CDPL_CHEM_API const StringDataBlock::SharedPointer &	getReactionData (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::REACTION_DATA property of the reaction rxn. More...
CDPL_CHEM_API void	setReactionData (Reaction &rxn, const StringDataBlock::SharedPointer &data)
	Sets the value of the Chem::ReactionProperty::REACTION_DATA property of the reaction rxn to data. More...
CDPL_CHEM_API void	clearReactionData (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::REACTION_DATA property of the reaction rxn. More...
CDPL_CHEM_API bool	hasReactionData (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::REACTION_DATA property of the reaction rxn is set. More...
CDPL_CHEM_API const Molecule::SharedPointer &	getMDLMoleculeRecord (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::MDL_MOLECULE_RECORD property of the reaction rxn. More...
CDPL_CHEM_API void	setMDLMoleculeRecord (Reaction &rxn, const Molecule::SharedPointer &mol_rec)
	Sets the value of the Chem::ReactionProperty::MDL_MOLECULE_RECORD property of the reaction rxn to mol_rec. More...
CDPL_CHEM_API void	clearMDLMoleculeRecord (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::MDL_MOLECULE_RECORD property of the reaction rxn. More...
CDPL_CHEM_API bool	hasMDLMoleculeRecord (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::MDL_MOLECULE_RECORD property of the reaction rxn is set. More...
CDPL_CHEM_API const std::string &	getMDLInternalRegistryNumber (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn. More...
CDPL_CHEM_API void	setMDLInternalRegistryNumber (Reaction &rxn, const std::string &reg_no)
	Sets the value of the Chem::ReactionProperty::MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no. More...
CDPL_CHEM_API void	clearMDLInternalRegistryNumber (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn. More...
CDPL_CHEM_API bool	hasMDLInternalRegistryNumber (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn is set. More...
CDPL_CHEM_API const std::string &	getMDLExternalRegistryNumber (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn. More...
CDPL_CHEM_API void	setMDLExternalRegistryNumber (Reaction &rxn, const std::string &reg_no)
	Sets the value of the Chem::ReactionProperty::MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no. More...
CDPL_CHEM_API void	clearMDLExternalRegistryNumber (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn. More...
CDPL_CHEM_API bool	hasMDLExternalRegistryNumber (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn is set. More...
CDPL_CHEM_API unsigned int	getMDLRXNFileVersion (const Reaction &rxn)
	Returns the value of the Chem::ReactionProperty::MDL_RXN_FILE_VERSION property of the reaction rxn. More...
CDPL_CHEM_API void	setMDLRXNFileVersion (Reaction &rxn, unsigned int version)
	Sets the value of the Chem::ReactionProperty::MDL_RXN_FILE_VERSION property of the reaction rxn to version. More...
CDPL_CHEM_API void	clearMDLRXNFileVersion (Reaction &rxn)
	Clears the value of the Chem::ReactionProperty::MDL_RXN_FILE_VERSION property of the reaction rxn. More...
CDPL_CHEM_API bool	hasMDLRXNFileVersion (const Reaction &rxn)
	Tells whether the Chem::ReactionProperty::MDL_RXN_FILE_VERSION property of the reaction rxn is set. More...
CDPL_CHEM_API std::size_t	getMaxComponentGroupID (const Reaction &rxn)
	Returns the largest component group ID found for any of the atoms of the components of the reaction rxn. More...
CDPL_CHEM_API std::size_t	getMaxAtomMappingID (const Reaction &rxn)
	Returns the largest atom mapping ID found for any of the atoms of the components of the reaction rxn. More...
CDPL_CHEM_API void	setAtomMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite)
	Sets the atom-level match constraint list constr on every atom of every component of the reaction rxn. More...
CDPL_CHEM_API void	setBondMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite)
	Sets the bond-level match constraint list constr on every bond of every component of the reaction rxn. More...
CDPL_CHEM_API void	setComponentMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite)
	Sets the molecular graph-level match constraint list constr on every component of the reaction rxn. More...
CDPL_CHEM_API void	generateMatchExpressions (Reaction &rxn, bool overwrite)
	Generates and stores match expressions for the atoms, bonds, components, and the reaction rxn itself. More...
CDPL_CHEM_API void	initSubstructureSearchQuery (Reaction &rxn, bool overwrite)
	Prepares the reaction rxn for use as a reaction substructure search query. More...
CDPL_CHEM_API void	initSubstructureSearchTarget (Reaction &rxn, bool overwrite)
	Prepares the reaction rxn for use as a reaction substructure search target. More...
CDPL_CHEM_API void	calcBasicProperties (Reaction &rxn, bool overwrite)
	Computes basic atom/bond/molecular graph properties (aromaticity, ring info, etc.) for every component of the reaction rxn. More...
CDPL_CHEM_API Molecule::SharedPointer	parseSMARTS (const std::string &smarts, bool init_qry=true)
	Parses the SMARTS string smarts into a freshly allocated query Chem::Molecule. More...
CDPL_CHEM_API bool	parseSMARTS (const std::string &smarts, Molecule &mol, bool init_qry=true)
	Parses the SMARTS string smarts into the supplied molecule mol. More...
CDPL_CHEM_API Molecule::SharedPointer	parseSMILES (const std::string &smiles)
	Parses the SMILES string smiles into a freshly allocated Chem::Molecule. More...
CDPL_CHEM_API bool	parseSMILES (const std::string &smiles, Molecule &mol)
	Parses the SMILES string smiles into the supplied molecule mol. More...
CDPL_CHEM_API void	extendBoundingBox (Math::Vector3D &min, Math::Vector3D &max, const Math::Vector3D &coords, bool reset=false)
	Extends the axis-aligned bounding box defined by min and max so that it contains the point coords. More...
CDPL_CHEM_API bool	insideBoundingBox (const Math::Vector3D &min, const Math::Vector3D &max, const Math::Vector3D &coords)
	Tells whether the point coords lies inside the axis-aligned bounding box defined by min and max. More...
CDPL_CHEM_API bool	isAromatic (const Fragment &ring, const MolecularGraph &molgraph, const Util::BitSet &arom_bond_mask)
	Tells whether ring fulfills the Hückel (4n+2)π-electron criterion within molgraph. More...
CDPL_CHEM_API bool	isNotAromatic (const Fragment &ring, const MolecularGraph &molgraph)
	Tells whether ring is guaranteed not to be aromatic (based on quick geometric/topological criteria). More...
CDPL_CHEM_API bool	containsFragmentWithBond (const FragmentList &frag_list, const Bond &bond)
	Tells whether any fragment in frag_list contains the bond bond. More...
CDPL_CHEM_API bool	containsFragmentWithMinSize (const FragmentList &frag_list, std::size_t min_size)
	Tells whether frag_list contains at least one fragment with at least min_size atoms. More...
CDPL_CHEM_API bool	atomTypesMatch (unsigned int qry_type, unsigned int tgt_type)
	Tells whether the target atom type tgt_type matches the query atom type qry_type (taking generic atom type classes like Chem::AtomType::HET into account). More...
CDPL_CHEM_API unsigned int	sybylToAtomType (unsigned int sybyl_type)
	Translates a Sybyl atom type identifier to the corresponding generic Chem::AtomType value. More...
CDPL_CHEM_API const std::string &	getSybylAtomTypeString (unsigned int sybyl_type)
	Returns the canonical textual representation of the Sybyl atom type sybyl_type. More...
CDPL_CHEM_API const std::string &	getSybylBondTypeString (unsigned int sybyl_type)
	Returns the canonical textual representation of the Sybyl bond type sybyl_type. More...

Detailed Description

Contains classes and functions related to chemistry.

Typedef Documentation

Atom3DCoordinatesFunction

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

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

AtomCompareFunction

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

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

AtomPredicate

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

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

AtomPriorityFunction

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

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

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

BondPredicate

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

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

CDFBZ2MolecularGraphOutputHandler

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

Handler for the output of bzip2-compressed molecular graph data in the native I/O format of the CDPL.

CDFBZ2MolecularGraphWriter

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

Writer for molecular graph data in the bzip2-compressed native I/O format of the CDPL.

CDFBZ2MoleculeInputHandler

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

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

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

CDFBZ2ReactionInputHandler

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

Handler for the input of bzip2-compressed reaction data in the native I/O format of the CDPL.

CDFBZ2ReactionOutputHandler

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

Handler for the output of bzip2-compressed reaction data in the native I/O format of the CDPL.

CDFBZ2ReactionReader

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

Reader for reaction data in the bzip2-compressed native I/O format of the CDPL.

CDFBZ2ReactionWriter

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

Writer for reaction data in the bzip2-compressed native I/O format of the CDPL.

CDFGZMolecularGraphOutputHandler

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

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

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

CDFGZMoleculeInputHandler

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

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

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

CDFGZReactionInputHandler

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

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

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

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

CDFGZReactionWriter

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

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

CDFMolecularGraphOutputHandler

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

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

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

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

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

CMLBZ2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<CMLBZ2MolecularGraphWriter, DataFormat::CML_BZ2> CDPL::Chem::CMLBZ2MolecularGraphOutputHandler

Handler for the output of bzip2-compressed molecular graph data in the Chemical Markup Language [CML] format.

Since

1.2

CMLBZ2MolecularGraphWriter

typedef Util::CompressedDataWriter<CMLMolecularGraphWriter, Util::BZip2OStream> CDPL::Chem::CMLBZ2MolecularGraphWriter

Writer for molecular graph data in the bzip2-compressed Chemical Markup Language [CML] format.

Since

1.2

CMLBZ2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<CMLBZ2MoleculeReader, DataFormat::CML_BZ2> CDPL::Chem::CMLBZ2MoleculeInputHandler

Handler for the input of bzip2-compressed molecule data in the Chemical Markup Language [CML] format.

Since

1.2

CMLBZ2MoleculeReader

typedef Util::CompressedDataReader<CMLMoleculeReader, Util::BZip2IStream> CDPL::Chem::CMLBZ2MoleculeReader

Reader for molecule data in the bzip2-compressed Chemical Markup Language [CML] format.

Since

1.2

CMLGZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<CMLGZMolecularGraphWriter, DataFormat::CML_GZ> CDPL::Chem::CMLGZMolecularGraphOutputHandler

Handler for the output of gzip-compressed molecular graph data in the Chemical Markup Language [CML] format.

Since

1.2

CMLGZMolecularGraphWriter

typedef Util::CompressedDataWriter<CMLMolecularGraphWriter, Util::GZipOStream> CDPL::Chem::CMLGZMolecularGraphWriter

Writer for molecular graph data in the gzip-compressed Chemical Markup Language [CML] format.

Since

1.2

CMLGZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<CMLGZMoleculeReader, DataFormat::CML_GZ> CDPL::Chem::CMLGZMoleculeInputHandler

Handler for the input of gzip-compressed molecule data in the Chemical Markup Language [CML] format.

Since

1.2

CMLGZMoleculeReader

typedef Util::CompressedDataReader<CMLMoleculeReader, Util::GZipIStream> CDPL::Chem::CMLGZMoleculeReader

Reader for molecule data in the gzip-compressed Chemical Markup Language [CML] format.

Since

1.2

CMLMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<CMLMolecularGraphWriter, DataFormat::CML> CDPL::Chem::CMLMolecularGraphOutputHandler

Handler for the output of molecular graph data in the Chemical Markup Language [CML] format.

Since

1.2

CMLMoleculeInputHandler

typedef Util::DefaultDataInputHandler<CMLMoleculeReader, DataFormat::CML> CDPL::Chem::CMLMoleculeInputHandler

Handler for the input of molecule data in the Chemical Markup Language [CML] format.

Since

1.2

Entity3DCoordinatesFunction

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

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

INCHIMolecularGraphOutputHandler

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

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

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

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

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

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

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

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

Writer for molecular graph data in the bzip2-compressed Sybyl MOL2 format.

MOL2BZ2MoleculeInputHandler

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

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

MOL2BZ2MoleculeReader

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

Reader for molecule data in the bzip2-compressed Sybyl MOL2 format.

MOL2GZMolecularGraphOutputHandler

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

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

Writer for molecular graph data in the gzip-compressed Sybyl MOL2 format.

MOL2GZMoleculeInputHandler

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

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

MOL2GZMoleculeReader

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

Reader for molecule data in the gzip-compressed Sybyl MOL2 format.

MOL2MolecularGraphOutputHandler

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

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

MOL2MoleculeInputHandler

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

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

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

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

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

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

Reader for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format.

RDFBZ2ReactionWriter

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

Writer for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format.

RDFGZReactionInputHandler

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

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

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

Reader for reaction data in the gzip-compressed MDL RD-File [CTFILE] format.

RDFGZReactionWriter

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

Writer for reaction data in the gzip-compressed MDL RD-File [CTFILE] format.

RDFReactionInputHandler

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

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

RDFReactionOutputHandler

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

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

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

RXNReactionOutputHandler

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

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

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

Writer for molecular graph data in the bzip2-compressed MDL SD-File [CTFILE] format.

SDFBZ2MoleculeInputHandler

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

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

Reader for molecule data in the bzip2-compressed MDL SD-File [CTFILE] format.

SDFGZMolecularGraphOutputHandler

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

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

Writer for molecular graph data in the gzip-compressed MDL SD-File [CTFILE] format.

SDFGZMoleculeInputHandler

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

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

Reader for molecule data in the gzip-compressed MDL SD-File [CTFILE] format.

SDFMolecularGraphOutputHandler

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

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

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

SMARTSMolecularGraphOutputHandler

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

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

SMARTSMoleculeInputHandler

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

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

SMARTSReactionInputHandler

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

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

SMARTSReactionOutputHandler

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

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

SMILESBZ2MolecularGraphOutputHandler

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

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

Writer for molecular graph data in the bzip2-compressed Daylight SMILES [SMILES] format.

SMILESBZ2MoleculeInputHandler

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

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

Reader for molecule data in the bzip2-compressed Daylight SMILES [SMILES] format.

SMILESBZ2ReactionInputHandler

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

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

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

Reader for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format.

SMILESBZ2ReactionWriter

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

Writer for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format.

SMILESGZMolecularGraphOutputHandler

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

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

Writer for molecular graph data in the gzip-compressed Daylight SMILES [SMILES] format.

SMILESGZMoleculeInputHandler

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

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

SMILESGZMoleculeReader

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

Reader for molecule data in the gzip-compressed Daylight SMILES [SMILES] format.

SMILESGZReactionInputHandler

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

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

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

Reader for reaction data in the gzip-compressed Daylight SMILES [SMILES] format.

SMILESGZReactionWriter

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

Writer for reaction data in the gzip-compressed Daylight SMILES [SMILES] format.

SMILESMolecularGraphOutputHandler

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

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

SMILESMoleculeInputHandler

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

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

SMILESReactionInputHandler

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

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

SMILESReactionOutputHandler

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

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

XYZBZ2MolecularGraphOutputHandler

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

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

Since

1.1

XYZBZ2MolecularGraphWriter

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

Writer for molecular graph data in the bzip2-compressed XYZ format.

Since

1.1

XYZBZ2MoleculeInputHandler

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

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

Since

1.1

XYZBZ2MoleculeReader

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

Reader for molecule data in the bzip2-compressed XYZ format.

Since

1.1

XYZGZMolecularGraphOutputHandler

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

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

Since

1.1

XYZGZMolecularGraphWriter

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

Writer for molecular graph data in the gzip-compressed XYZ format.

Since

1.1

XYZGZMoleculeInputHandler

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

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

Since

1.1

XYZGZMoleculeReader

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

Reader for molecule data in the gzip-compressed XYZ format.

Since

1.1

XYZMolecularGraphOutputHandler

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

Handler for the output of molecular graph data in the XYZ format.

Since

1.1

XYZMoleculeInputHandler

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

Handler for the input of molecule data in the XYZ format.

Since

1.1

Function Documentation

hasCoordinates()

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

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

Parameters

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

Returns

true if all atoms have the requested coordinates, and false otherwise.

get2DCoordinates() [1/2]

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

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

Parameters

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

set2DCoordinates() [1/2]

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

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

Parameters

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

transform2DCoordinates()

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

Transforms the 2D coordinates of all atoms in cntnr by the affine 3×3 matrix mtx.

Parameters

cntnr	The atom container.
mtx	The 2D affine transformation matrix.

get3DCoordinates() [1/3]

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

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

Parameters

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

clearConformations()

CDPL_CHEM_API void CDPL::Chem::clearConformations

(

AtomContainer &

cntnr

)

Removes all stored conformations from the atoms of cntnr.

Parameters

cntnr

The atom container.

getNumConformations()

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

(

const AtomContainer &

cntnr

)

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

Parameters

cntnr

The atom container.

Returns

The conformation count.

applyConformation()

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

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

Parameters

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

getConformation()

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

Extracts the conformation at index conf_idx into coords.

Parameters

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

setConformation() [1/2]

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

Overwrites the conformation at index conf_idx with the supplied 3D coordinates.

Parameters

cntnr	The atom container.
conf_idx	The zero-based conformation index.
coords	The 3D coordinates of the conformation.

addConformation() [1/2]

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

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

Parameters

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

transformConformation()

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

Transforms the conformation at index conf_idx by the homogeneous 4×4 matrix mtx.

Parameters

cntnr	The atom container.
conf_idx	The zero-based conformation index.
mtx	The homogeneous 4×4 transformation matrix.

transformConformations()

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

Transforms every stored conformation of the atoms in cntnr by the homogeneous 4×4 matrix mtx.

Parameters

cntnr	The atom container.
mtx	The homogeneous 4×4 transformation matrix.

alignConformations() [1/4]

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

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

Parameters

cntnr	The atom container holding the conformations to be aligned.
ref_atoms	Bit mask selecting the atoms of cntnr used as alignment anchors.
ref_coords	Reference 3D coordinates of the alignment-anchor atoms.

Returns

true if the alignment succeeded for every conformation, and false otherwise.

Since

1.1

alignConformations() [2/4]

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

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

Parameters

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

Returns

true if the alignment succeeded for every conformation, and false otherwise.

Since

1.1

alignConformations() [3/4]

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

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

Parameters

cntnr	The atom container holding the conformations to be aligned.
ref_atoms	Bit mask selecting the atoms of cntnr used as alignment anchors.

Returns

true if the alignment succeeded for every conformation, and false otherwise.

Since

1.1

alignConformations() [4/4]

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

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

Parameters

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

Returns

true if the alignment succeeded for every conformation, and false otherwise.

Since

1.1

getMaxComponentGroupID() [1/2]

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

(

const AtomContainer &

cntnr

)

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

Parameters

cntnr

The atom container.

Returns

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

getMaxAtomMappingID() [1/2]

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

(

const AtomContainer &

cntnr

)

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

Parameters

cntnr

The atom container.

Returns

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

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
	)

Sets bits in mask corresponding to atoms of cntnr whose atom type matches type.

Parameters

cntnr	The atom container.
mask	The output bit mask (bit i is set if atom i of cntnr has the requested type).
type	The query atom type (Chem::AtomType value, possibly a generic class such as Chem::AtomType::HET).
reset	If true, mask is reset before processing. Otherwise, existing bits are preserved.
strict	If true, only exact type matches are accepted. If false, generic-class matches also set the bit.

Returns

The number of atoms whose bit was set.

copyAtomsIf() [1/2]

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

Copies every atom of cntnr that satisfies pred into the molecule mol.

Parameters

cntnr	The source atom container.
mol	The target molecule.
pred	The predicate evaluated for each atom. Only atoms for which it returns true are copied.
append	If true, atoms are appended to mol. Otherwise, mol is cleared first.

copyAtomsIf() [2/2]

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

Copies every atom of cntnr that satisfies pred into the fragment frag.

Parameters

cntnr	The source atom container.
frag	The target fragment.
pred	The predicate evaluated for each atom. Only atoms for which it returns true are copied.
append	If true, atoms are appended to frag. Otherwise, frag is cleared first.

copyAtomsIfNot() [1/2]

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

Copies every atom of cntnr that does not satisfy pred into the molecule mol.

Parameters

cntnr	The source atom container.
mol	The target molecule.
pred	The predicate evaluated for each atom. Only atoms for which it returns false are copied.
append	If true, atoms are appended to mol. Otherwise, mol is cleared first.

copyAtomsIfNot() [2/2]

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

Copies every atom of cntnr that does not satisfy pred into the fragment frag.

Parameters

cntnr	The source atom container.
frag	The target fragment.
pred	The predicate evaluated for each atom. Only atoms for which it returns false are copied.
append	If true, atoms are appended to frag. Otherwise, frag is cleared first.

calcCenterOfMass()

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

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

Parameters

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

Returns

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

calcCentroid() [1/2]

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

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

Parameters

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

Returns

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

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
	)

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

Parameters

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

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
	)

Tells whether every atom of cntnr lies inside the axis-aligned bounding box defined by min and max.

Parameters

cntnr	The atom container.
min	The lower-left corner of the bounding box.
max	The upper-right corner of the bounding box.
coords_func	The function returning the 3D coordinates of an atom.

Returns

true if all atoms are inside the box, and false otherwise.

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
	)

Tells whether at least one atom of cntnr lies inside the axis-aligned bounding box defined by min and max.

Parameters

cntnr	The atom container.
min	The lower-left corner of the bounding box.
max	The upper-right corner of the bounding box.
coords_func	The function returning the 3D coordinates of an atom.

Returns

true if at least one atom is inside the box, and false otherwise.

getName() [1/3]

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored atom name.

setName() [1/3]

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

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

Parameters

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

clearName() [1/3]

CDPL_CHEM_API void CDPL::Chem::clearName

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasName() [1/3]

CDPL_CHEM_API bool CDPL::Chem::hasName

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getSymbol()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored element symbol.

setSymbol()

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

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

Parameters

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

clearSymbol()

CDPL_CHEM_API void CDPL::Chem::clearSymbol

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasSymbol()

CDPL_CHEM_API bool CDPL::Chem::hasSymbol

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getSymbolForType()

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

(

const Atom &

atom

)

Returns the symbol that corresponds to the numeric type property of the atom atom.

Parameters

atom	The atom to query.

Returns

The symbol associated with the numeric type (see namespace Chem::AtomType).

getType()

CDPL_CHEM_API unsigned int CDPL::Chem::getType

(

const Atom &

atom

)

Returns the value of the Chem::AtomProperty::TYPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored atom type (see namespace Chem::AtomType).

setType()

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

Sets the value of the Chem::AtomProperty::TYPE property of the atom atom to type.

Parameters

atom	The atom for which to set the property value.
type	The new atom type (see namespace Chem::AtomType).

clearType()

CDPL_CHEM_API void CDPL::Chem::clearType

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasType()

CDPL_CHEM_API bool CDPL::Chem::hasType

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getTypeForSymbol()

CDPL_CHEM_API unsigned int CDPL::Chem::getTypeForSymbol

(

const Atom &

atom

)

Returns the numeric atom type that corresponds to the symbol property of the atom atom.

Parameters

atom	The atom to query.

Returns

The numeric atom type (see namespace Chem::AtomType) associated with the symbol.

getGenericType()

CDPL_CHEM_API unsigned int CDPL::Chem::getGenericType

(

const Atom &

atom

)

Returns the generic atom type associated with numeric type property of the atom atom.

Parameters

atom	The atom to query.

Returns

The generic atom type (see namespace Chem::AtomType).

getFormalCharge()

CDPL_CHEM_API long CDPL::Chem::getFormalCharge

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored formal charge.

setFormalCharge()

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

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

Parameters

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

clearFormalCharge()

CDPL_CHEM_API void CDPL::Chem::clearFormalCharge

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasFormalCharge()

CDPL_CHEM_API bool CDPL::Chem::hasFormalCharge

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

calcFormalCharge()

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

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

Parameters

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

Returns

The computed formal charge.

getIsotope()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

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

setIsotope()

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

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

Parameters

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

clearIsotope()

CDPL_CHEM_API void CDPL::Chem::clearIsotope

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasIsotope()

CDPL_CHEM_API bool CDPL::Chem::hasIsotope

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getRadicalType()

CDPL_CHEM_API unsigned int CDPL::Chem::getRadicalType

(

const Atom &

atom

)

Returns the value of the Chem::AtomProperty::RADICAL_TYPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored radical type (see namespace Chem::RadicalType).

setRadicalType()

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

Sets the value of the Chem::AtomProperty::RADICAL_TYPE property of the atom atom to type.

Parameters

atom	The atom for which to set the property value.
type	The new radical type (see namespace Chem::RadicalType).

clearRadicalType()

CDPL_CHEM_API void CDPL::Chem::clearRadicalType

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasRadicalType()

CDPL_CHEM_API bool CDPL::Chem::hasRadicalType

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getHybridizationState()

CDPL_CHEM_API unsigned int CDPL::Chem::getHybridizationState

(

const Atom &

atom

)

Returns the value of the Chem::AtomProperty::HYBRIDIZATION property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored hybridization state (see namespace Chem::HybridizationState).

setHybridizationState()

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

Sets the value of the Chem::AtomProperty::HYBRIDIZATION property of the atom atom to state.

Parameters

atom	The atom for which to set the property value.
state	The new hybridization state (see namespace Chem::HybridizationState).

clearHybridizationState()

CDPL_CHEM_API void CDPL::Chem::clearHybridizationState

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasHybridizationState()

CDPL_CHEM_API bool CDPL::Chem::hasHybridizationState

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveHybridizationState()

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

Derives the hybridization state of the atom atom from its connectivity in the molecular graph molgraph.

Parameters

atom	The atom for which to perceive the hybridzation state.
molgraph	The molecular graph providing the structural context.

Returns

The perceived hybridization state (see namespace Chem::HybridizationState).

getRingFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::getRingFlag

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

true if the atom is flagged as part of any ring, and false otherwise.

setRingFlag() [1/2]

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

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

Parameters

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

clearRingFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearRingFlag

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasRingFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasRingFlag

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

isInFragmentOfSize() [1/2]

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

Tells whether the atom atom is a member of any fragment in frag_list whose size matches size.

Parameters

atom	The atom to query.
frag_list	The list of fragments to search.
size	The required fragment size (in number of atoms).

Returns

true if at least one matching fragment contains the atom atom, and false otherwise.

getSizeOfSmallestContainingFragment() [1/2]

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

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

Parameters

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

Returns

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

getSizeOfLargestContainingFragment() [1/2]

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

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

Parameters

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

Returns

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

getNumContainingFragments() [1/2]

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

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

Parameters

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

Returns

The number of containing fragments.

getContainingFragments() [1/3]

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

Collects the fragments in frag_list that contain the atom atom into cont_frag_list.

Parameters

atom	The atom to query.
frag_list	The list of fragments to search.
cont_frag_list	The output fragment list receiving the matches.
append	If true, matches are appended to cont_frag_list. Otherwise, it is cleared first.

getAromaticityFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::getAromaticityFlag

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

true if the atom is flagged as aromatic, and false otherwise.

setAromaticityFlag() [1/2]

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

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

Parameters

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

clearAromaticityFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearAromaticityFlag

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasAromaticityFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasAromaticityFlag

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getUnpairedElectronCount()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored unpaired electron count.

setUnpairedElectronCount()

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

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

Parameters

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

clearUnpairedElectronCount()

CDPL_CHEM_API void CDPL::Chem::clearUnpairedElectronCount

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasUnpairedElectronCount()

CDPL_CHEM_API bool CDPL::Chem::hasUnpairedElectronCount

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getImplicitHydrogenCount()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored implicit hydrogen count.

setImplicitHydrogenCount()

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

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

Parameters

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

clearImplicitHydrogenCount()

CDPL_CHEM_API void CDPL::Chem::clearImplicitHydrogenCount

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasImplicitHydrogenCount()

CDPL_CHEM_API bool CDPL::Chem::hasImplicitHydrogenCount

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

calcImplicitHydrogenCount()

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

Computes the implicit hydrogen count of the atom atom from its connectivity in the molecular graph molgraph.

Parameters

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

Returns

The computed implicit hydrogen count.

get2DCoordinates() [2/2]

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored 2D coordinates.

set2DCoordinates() [2/2]

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

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

Parameters

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

clear2DCoordinates()

CDPL_CHEM_API void CDPL::Chem::clear2DCoordinates

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

has2DCoordinates()

CDPL_CHEM_API bool CDPL::Chem::has2DCoordinates

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getConformer3DCoordinates()

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

Returns the 3D coordinates of the atom atom in the conformer with index conf_idx.

Parameters

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

Returns

The 3D coordinates of the specified conformer.

Exceptions

Base::IndexError

if conf_idx is out of the valid range.

get3DCoordinatesArray()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored 3D conformer-coordinates array.

set3DCoordinatesArray()

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

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

Parameters

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

clear3DCoordinatesArray()

CDPL_CHEM_API void CDPL::Chem::clear3DCoordinatesArray

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

has3DCoordinatesArray()

CDPL_CHEM_API bool CDPL::Chem::has3DCoordinatesArray

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMorganNumber()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored Morgan number.

setMorganNumber()

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

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

Parameters

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

clearMorganNumber()

CDPL_CHEM_API void CDPL::Chem::clearMorganNumber

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMorganNumber()

CDPL_CHEM_API bool CDPL::Chem::hasMorganNumber

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getCanonicalNumber()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored canonical number.

setCanonicalNumber()

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

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

Parameters

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

clearCanonicalNumber()

CDPL_CHEM_API void CDPL::Chem::clearCanonicalNumber

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasCanonicalNumber()

CDPL_CHEM_API bool CDPL::Chem::hasCanonicalNumber

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getCIPPriority()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored topological CIP priority.

setCIPPriority()

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

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

Parameters

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

clearCIPPriority()

CDPL_CHEM_API void CDPL::Chem::clearCIPPriority

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasCIPPriority()

CDPL_CHEM_API bool CDPL::Chem::hasCIPPriority

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getSymmetryClass()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored topological-symmetry class ID.

setSymmetryClass()

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

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

Parameters

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

clearSymmetryClass()

CDPL_CHEM_API void CDPL::Chem::clearSymmetryClass

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasSymmetryClass()

CDPL_CHEM_API bool CDPL::Chem::hasSymmetryClass

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getCIPConfiguration() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getCIPConfiguration

(

const Atom &

atom

)

Returns the value of the Chem::AtomProperty::CIP_CONFIGURATION property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored CIP configuration label (see namespace Chem::CIPDescriptor).

setCIPConfiguration() [1/2]

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

Sets the value of the Chem::AtomProperty::CIP_CONFIGURATION property of the atom atom to config.

Parameters

atom	The atom for which to set the property value.
config	The new CIP configuration label (see namespace Chem::CIPDescriptor).

clearCIPConfiguration() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearCIPConfiguration

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasCIPConfiguration() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasCIPConfiguration

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getStereoDescriptor() [1/2]

CDPL_CHEM_API const StereoDescriptor& CDPL::Chem::getStereoDescriptor

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored stereo descriptor.

setStereoDescriptor() [1/2]

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

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

Parameters

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

clearStereoDescriptor() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoDescriptor

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasStereoDescriptor() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoDescriptor

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

calcStereoDescriptor() [1/2]

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

Computes the stereo descriptor for the atom atom in the molecular graph molgraph.

Parameters

atom	The atom for which to calculate the stereo descriptor.
molgraph	The molecular graph providing the structural context.
dim	The dimensionality of the atomic coordinates to use (2 = 2D, 3 = 3D, 0 = recalc. existing descriptor, other values = use any information available).

Returns

The computed stereo descriptor.

calcStereoDescriptorFromMDLParity()

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

Calculates the stereo descriptor of the atom atom from its MDL parity in the molecular graph molgraph.

Parameters

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

Returns

The calculated stereo descriptor.

calcConfiguration() [1/2]

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

Calculates the atom configuration from the supplied descriptor and reference atom 3D coordinates.

Parameters

atom	The atom for which to calculate the configuration.
molgraph	The molecular graph providing the structural context.
descr	The stereo descriptor providing the reference atoms.
coords	The atom 3D coordinates to use for the calculation.

Returns

The calculated configuration (see namespace Chem::AtomConfiguration).

getStereoCenterFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::getStereoCenterFlag

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

true if the atom is flagged as a stereo center, and false otherwise.

setStereoCenterFlag() [1/2]

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

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

Parameters

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

clearStereoCenterFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoCenterFlag

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasStereoCenterFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoCenterFlag

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

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
	)

Tells whether the atom atom qualifies as a stereo center in the context of the molecular graph molgraph.

Parameters

atom	The atom to evaluate.
molgraph	The molecular graph providing the structural context.
check_asym	true to consider only topologically non-equivalent ligand environments.
check_inv_n	true to reject inversion-prone nitrogen centers (umbrella inversion).
check_quart_n	true to accept positively charged quaternary nitrogen centers.
check_plan_n	true to reject planar nitrogen centers.
check_amide_n	true to reject amide nitrogen centers.
check_res_ctrs	true to reject centers participating in resonance.

Returns

true if the atom qualifies as a stereo center under the given conditions, and false otherwise.

getSybylType() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getSybylType

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

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

setSybylType() [1/2]

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

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

Parameters

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

clearSybylType() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearSybylType

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasSybylType() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasSybylType

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveSybylType() [1/2]

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

Derives the Sybyl MOL2 atom type of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom for which to perceive the type.
molgraph	The molecular graph providing the structural context.

Returns

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

getMOL2Name()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 atom name.

setMOL2Name()

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

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

Parameters

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

clearMOL2Name()

CDPL_CHEM_API void CDPL::Chem::clearMOL2Name

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMOL2Name()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2Name

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMOL2Charge()

CDPL_CHEM_API double CDPL::Chem::getMOL2Charge

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 partial charge.

setMOL2Charge()

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

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

Parameters

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

clearMOL2Charge()

CDPL_CHEM_API void CDPL::Chem::clearMOL2Charge

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMOL2Charge()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2Charge

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMOL2SubstructureID()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 substructure ID.

setMOL2SubstructureID()

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

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

Parameters

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

clearMOL2SubstructureID()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureID

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMOL2SubstructureID()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureID

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMOL2SubstructureName()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 substructure name.

setMOL2SubstructureName()

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

Sets the value of the Chem::AtomProperty::MOL2_SUBSTRUCTURE_NAME property of the atom atom to id.

Parameters

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

clearMOL2SubstructureName()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureName

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMOL2SubstructureName()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureName

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMOL2SubstructureSubtype()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 substructure subtype string.

setMOL2SubstructureSubtype()

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

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

Parameters

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

clearMOL2SubstructureSubtype()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureSubtype

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMOL2SubstructureSubtype()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureSubtype

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMOL2SubstructureChain()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored Sybyl MOL2 substructure chain identifier.

setMOL2SubstructureChain()

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

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

Parameters

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

clearMOL2SubstructureChain()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureChain

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMOL2SubstructureChain()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureChain

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLParity()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLParity

(

const Atom &

atom

)

Returns the value of the Chem::AtomProperty::MDL_PARITY property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

The stored MDL stereo parity (see namespace Chem::MDLParity).

setMDLParity()

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

Sets the value of the Chem::AtomProperty::MDL_PARITY property of the atom atom to parity.

Parameters

atom	The atom for which to set the property value.
parity	The new MDL stereo parity (see namespace Chem::MDLParity).

clearMDLParity()

CDPL_CHEM_API void CDPL::Chem::clearMDLParity

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMDLParity()

CDPL_CHEM_API bool CDPL::Chem::hasMDLParity

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

calcMDLParity()

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

Calculates the MDL parity of the atom atom in the molecular graph molgraph.

Parameters

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

Returns

The calculated MDL parity (see namespace Chem::MDLParity).

getMDLStereoCareFlag()

CDPL_CHEM_API bool CDPL::Chem::getMDLStereoCareFlag

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored MDL stereo-care flag.

setMDLStereoCareFlag()

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

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

Parameters

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

clearMDLStereoCareFlag()

CDPL_CHEM_API void CDPL::Chem::clearMDLStereoCareFlag

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMDLStereoCareFlag()

CDPL_CHEM_API bool CDPL::Chem::hasMDLStereoCareFlag

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getReactionCenterStatus() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getReactionCenterStatus

(

const Atom &

atom

)

Returns the value of the Chem::AtomProperty::REACTION_CENTER_STATUS property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns

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

setReactionCenterStatus() [1/2]

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

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

Parameters

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

clearReactionCenterStatus() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearReactionCenterStatus

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasReactionCenterStatus() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasReactionCenterStatus

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getAtomMappingID()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored reactant-to-product atom mapping ID.

setAtomMappingID()

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

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

Parameters

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

clearAtomMappingID()

CDPL_CHEM_API void CDPL::Chem::clearAtomMappingID

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasAtomMappingID()

CDPL_CHEM_API bool CDPL::Chem::hasAtomMappingID

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getComponentGroupID()

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored component-group ID.

setComponentGroupID()

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

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

Parameters

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

clearComponentGroupID()

CDPL_CHEM_API void CDPL::Chem::clearComponentGroupID

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasComponentGroupID()

CDPL_CHEM_API bool CDPL::Chem::hasComponentGroupID

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMatchConstraints() [1/4]

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored match constraint list.

setMatchConstraints() [1/4]

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

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

Parameters

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

clearMatchConstraints() [1/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMatchConstraints() [1/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMatchExpression() [1/4]

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored atom-level match expression.

setMatchExpression() [1/4]

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

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

Parameters

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

clearMatchExpression() [1/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMatchExpression() [1/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

generateMatchExpression() [1/6]

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

Builds an match expression from the match constraint list attached to the atom atom.

Parameters

atom	The atom for which to generate the expression.
molgraph	The molecular graph providing the structural context.

Returns

The generated match expression.

getMatchExpressionString() [1/2]

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

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The stored match expression string.

setMatchExpressionString() [1/2]

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

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

Parameters

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

clearMatchExpressionString() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpressionString

(

Atom &

atom

)

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

Parameters

atom	The atom for which to clear the property value.

hasMatchExpressionString() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpressionString

(

const Atom &

atom

)

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

Parameters

atom	The atom for which to query the property value.

Returns

true if the property is set, and false otherwise.

generateMatchExpressionString() [1/2]

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

Generates a textual representation of the match expression resulting from the match constraint list attached to the atom atom.

Parameters

atom	The atom for which to generate the match expression string.
molgraph	The molecular graph providing the structural context.
expr_str	Stores the generated match expression string.

markReachableAtoms()

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

Sets bits in atom_mask for every atom of the molecular graph molgraph that is reachable from the atom atom through the bonds of molgraph.

Parameters

atom	The seed atom.
molgraph	The molecular graph providing the structural context.
atom_mask	The output bit mask.
reset	If true, atom_mask is cleared first. Otherwise, existing bits are preserved.

getTopologicalDistance()

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

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

Parameters

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

Returns

The topological distance between atom1 and atom2.

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
	)

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

Parameters

atom	The seed atom.
molgraph	The molecular graph providing the structural context.
max_dist	The maximum topological distance.
env	The output fragment receiving the environment atoms and the bonds between them.
append	If false, env gets cleared before adding any atoms and bonds.

Returns

The number of atoms added to env.

getConnectedAtoms()

template<typename AtomType , typename OutputIterator >

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

Writes every neighbor of the atom atom that is connected by a bond belonging to the molecular graph molgraph into the output iterator it, skipping excl_atom.

Template Parameters

AtomType	The atom object type.
OutputIterator	The output iterator type receiving pointers to the connected atoms.

Parameters

atom	The atom whose connected neighbors in molgraph shall be retrieved.
molgraph	The molecular graph providing the structural context.
it	The output iterator receiving the connected atom pointers.
excl_atom	If non-null, a connected atom matching this pointer is skipped.

Returns

The number of connected atoms written to it.

getIncidentBonds()

template<typename AtomType , typename OutputIterator >

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

Writes every bond incident to the atom atom where the bond itself and both atoms are members of the molecular graph molgraph into the output iterator it, skipping bonds to excl_atom.

Template Parameters

AtomType	The atom object type.
OutputIterator	The output iterator type receiving pointers to the incident bonds.

Parameters

atom	The atom whose incident bonds in molgraph shall be retrieved.
molgraph	The molecular graph providing the structural context.
it	The output iterator receiving the incident bond pointers.
excl_atom	If non-null, a bond connecting to an atom matching this pointer is skipped.

Returns

The number of incident bonds written to it.

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
	)

Writes every connected neighbor of the atom atom and the corresponding incident bond that are both members of molecular graph molgraph into the supplied output iterators.

Template Parameters

AtomType	The atom object type.
AtomOutputIterator	The output iterator type receiving connected atom pointers.
BondOutputIterator	The output iterator type receiving incident bond pointers.

Parameters

atom	The atom for which connected atoms/bonds in molgraph shall be retrieved.
molgraph	The molecular graph providing the structural context.
ao_it	The output iterator receiving the neighbor atom pointers.
bo_it	The output iterator receiving the corresponding incident bond pointers.
excl_atom	If non-null, a connection to an atom matching this pointer is skipped.

Returns

The number of atom/bond pairs written to the iterators.

getOrder()

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

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

The stored bond order.

setOrder()

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

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

Parameters

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

clearOrder()

CDPL_CHEM_API void CDPL::Chem::clearOrder

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasOrder()

CDPL_CHEM_API bool CDPL::Chem::hasOrder

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

getRingFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::getRingFlag

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

true if the bond is flagged as part of any ring, and false otherwise.

setRingFlag() [2/2]

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

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

Parameters

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

clearRingFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearRingFlag

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasRingFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasRingFlag

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

isInFragmentOfSize() [2/2]

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

Tells whether the bond bond is a member of any fragment in frag_list whose size matches size.

Parameters

bond	The bond to query.
frag_list	The list of fragments to search.
size	The required fragment size (in number of atoms).

Returns

true if at least one matching fragment contains the bond bond, and false otherwise.

getSizeOfSmallestContainingFragment() [2/2]

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

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

Parameters

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

Returns

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

getSizeOfLargestContainingFragment() [2/2]

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

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

Parameters

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

Returns

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

getNumContainingFragments() [2/2]

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

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

Parameters

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

Returns

The number of containing fragments.

getContainingFragments() [2/3]

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

Collects the fragments in frag_list that contain the bond bond into cont_frag_list.

Parameters

bond	The bond to query.
frag_list	The list of fragments to search.
cont_frag_list	The output fragment list receiving the matches.
append	If true, matches are appended to cont_frag_list. Otherwise, it is cleared first.

getAromaticityFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::getAromaticityFlag

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

true if the bond is flagged as aromatic, and false otherwise.

setAromaticityFlag() [2/2]

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

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

Parameters

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

clearAromaticityFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearAromaticityFlag

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasAromaticityFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasAromaticityFlag

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

get2DStereoFlag()

CDPL_CHEM_API unsigned int CDPL::Chem::get2DStereoFlag

(

const Bond &

bond

)

Returns the value of the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored 2D stereo flag (see namespace Chem::BondStereoFlag).

set2DStereoFlag()

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

Sets the value of the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond to flag.

Parameters

bond	The bond for which to set the property value.
flag	The new 2D stereo flag value (see namespace Chem::BondStereoFlag).

clear2DStereoFlag()

CDPL_CHEM_API void CDPL::Chem::clear2DStereoFlag

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

has2DStereoFlag()

CDPL_CHEM_API bool CDPL::Chem::has2DStereoFlag

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

getCIPConfiguration() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getCIPConfiguration

(

const Bond &

bond

)

Returns the value of the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns

The stored CIP configuration label (see namespace Chem::CIPDescriptor).

setCIPConfiguration() [2/2]

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

Sets the value of the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond to config.

Parameters

bond	The bond for which to set the property value.
config	The new CIP configuration label (see namespace Chem::CIPDescriptor).

clearCIPConfiguration() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearCIPConfiguration

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasCIPConfiguration() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasCIPConfiguration

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

getStereoDescriptor() [2/2]

CDPL_CHEM_API const StereoDescriptor& CDPL::Chem::getStereoDescriptor

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

The stored stereo descriptor.

setStereoDescriptor() [2/2]

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

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

Parameters

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

clearStereoDescriptor() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoDescriptor

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasStereoDescriptor() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoDescriptor

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

calcStereoDescriptor() [2/2]

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

Computes the stereo descriptor for the bond bond in the molecular graph molgraph.

Parameters

bond	The bond for which to calculate the stereo descriptor.
molgraph	The molecular graph providing the structural context.
dim	The dimensionality of the atomic coordinates to use (2 = 2D, 3 = 3D, 0 = recalc. existing descriptor, other values = use any information available).

Returns

The computed stereo descriptor.

calcConfiguration() [2/2]

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

Calculates the bond configuration from the supplied descriptor and reference atom 3D coordinates.

Parameters

bond	The bond for which to calculate the configuration.
molgraph	The molecular graph providing the structural context.
descr	The stereo descriptor providing the reference atoms.
coords	The atom 3D coordinates to use for the calculation.

Returns

The calculated configuration (see namespace Chem::BondConfiguration).

getStereoCenterFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::getStereoCenterFlag

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

true if the bond is flagged as a stereo center, and false otherwise.

setStereoCenterFlag() [2/2]

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

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

Parameters

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

clearStereoCenterFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoCenterFlag

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasStereoCenterFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoCenterFlag

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

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
	)

Tells whether the bond bond qualifies as a stereo center in the context of the molecular graph molgraph.

Parameters

bond	The bond to evaluate.
molgraph	The molecular graph providing the structural context.
check_asym	true to consider only topologically non-equivalent ligand environments.
check_term_n	true to reject bonds to terminal nitrogen atoms.
check_order	true to require that the bond order matches a stereogenic pattern.
min_ring_size	If the bond bond is a ring bond, the containing ring must have at least this size to qualify.

Returns

true if the bond qualifies as a stereo center under the given conditions, and false otherwise.

getDirection()

CDPL_CHEM_API unsigned int CDPL::Chem::getDirection

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

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

setDirection()

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

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

Parameters

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

clearDirection()

CDPL_CHEM_API void CDPL::Chem::clearDirection

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasDirection()

CDPL_CHEM_API bool CDPL::Chem::hasDirection

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

getReactionCenterStatus() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getReactionCenterStatus

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

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

setReactionCenterStatus() [2/2]

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

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

Parameters

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

clearReactionCenterStatus() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearReactionCenterStatus

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasReactionCenterStatus() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasReactionCenterStatus

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMatchConstraints() [2/4]

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

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

The stored match constraint list.

setMatchConstraints() [2/4]

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

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

Parameters

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

clearMatchConstraints() [2/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasMatchConstraints() [2/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMatchExpression() [2/4]

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

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

The stored bond-level match expression.

setMatchExpression() [2/4]

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

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

Parameters

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

clearMatchExpression() [2/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasMatchExpression() [2/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

generateMatchExpression() [2/6]

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

Builds a match expression from the match constraint list attached to the bond bond.

Parameters

bond	The bond for which to generate the expression..
molgraph	The molecular graph providing the structural context.

Returns

The generated match expression.

getMatchExpressionString() [2/2]

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

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

The stored match expression string.

setMatchExpressionString() [2/2]

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

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

Parameters

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

clearMatchExpressionString() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpressionString

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasMatchExpressionString() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpressionString

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

generateMatchExpressionString() [2/2]

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

Generates a textual representation of the match expression resulting from the match constraint list attached to the bond bond.

Parameters

bond	The bond for which to generate the match expression string.
molgraph	The molecular graph providing the structural context.
str	Stores the generated match expression string.

getSybylType() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getSybylType

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to return the property value.

Returns

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

setSybylType() [2/2]

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

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

Parameters

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

clearSybylType() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearSybylType

(

Bond &

bond

)

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

Parameters

bond	The bond for which to clear the property value.

hasSybylType() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasSybylType

(

const Bond &

bond

)

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

Parameters

bond	The bond for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveSybylType() [2/2]

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

Derives the Sybyl MOL2 bond type of the bond bond in the molecular graph molgraph.

Parameters

bond	The bond for which to perceive the type..
molgraph	The molecular graph providing the structural context.

Returns

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

getOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API bool CDPL::Chem::getOrdinaryHydrogenDepleteParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setOrdinaryHydrogenDepleteParameter()

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

Sets the value of the Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE parameter of cntnr to deplete.

Parameters

cntnr	The control-parameter container.
deplete	The new parameter value.

hasOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API bool CDPL::Chem::hasOrdinaryHydrogenDepleteParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API void CDPL::Chem::clearOrdinaryHydrogenDepleteParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getCoordinatesDimensionParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::COORDINATES_DIMENSION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored coordinates dimensionality.

setCoordinatesDimensionParameter()

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

Sets the value of the Chem::ControlParameter::COORDINATES_DIMENSION parameter of cntnr to dim.

Parameters

cntnr	The control-parameter container.
dim	The new coordinates dimensionality.

hasCoordinatesDimensionParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCoordinatesDimensionParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::COORDINATES_DIMENSION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearCoordinatesDimensionParameter()

CDPL_CHEM_API void CDPL::Chem::clearCoordinatesDimensionParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::COORDINATES_DIMENSION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getStrictErrorCheckingParameter()

CDPL_CHEM_API bool CDPL::Chem::getStrictErrorCheckingParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::STRICT_ERROR_CHECKING parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setStrictErrorCheckingParameter()

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

Sets the value of the Chem::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr to strict.

Parameters

cntnr	The control-parameter container.
strict	The new parameter value.

hasStrictErrorCheckingParameter()

CDPL_CHEM_API bool CDPL::Chem::hasStrictErrorCheckingParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearStrictErrorCheckingParameter()

CDPL_CHEM_API void CDPL::Chem::clearStrictErrorCheckingParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::STRICT_ERROR_CHECKING parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getRecordSeparatorParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::RECORD_SEPARATOR parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored record separator string.

setRecordSeparatorParameter()

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

Sets the value of the Chem::ControlParameter::RECORD_SEPARATOR parameter of cntnr to sep.

Parameters

cntnr	The control-parameter container.
sep	The new record separator string.

hasRecordSeparatorParameter()

CDPL_CHEM_API bool CDPL::Chem::hasRecordSeparatorParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::RECORD_SEPARATOR parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearRecordSeparatorParameter()

CDPL_CHEM_API void CDPL::Chem::clearRecordSeparatorParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::RECORD_SEPARATOR parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getBondMemberSwapStereoFixParameter()

CDPL_CHEM_API bool CDPL::Chem::getBondMemberSwapStereoFixParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setBondMemberSwapStereoFixParameter()

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

Sets the value of the Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr to fix.

Parameters

cntnr	The control-parameter container.
fix	The new parameter value.

hasBondMemberSwapStereoFixParameter()

CDPL_CHEM_API bool CDPL::Chem::hasBondMemberSwapStereoFixParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearBondMemberSwapStereoFixParameter()

CDPL_CHEM_API void CDPL::Chem::clearBondMemberSwapStereoFixParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getCheckLineLengthParameter()

CDPL_CHEM_API bool CDPL::Chem::getCheckLineLengthParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CHECK_LINE_LENGTH parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setCheckLineLengthParameter()

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

Sets the value of the Chem::ControlParameter::CHECK_LINE_LENGTH parameter of cntnr to check.

Parameters

cntnr	The control-parameter container.
check	The new parameter value.

hasCheckLineLengthParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCheckLineLengthParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CHECK_LINE_LENGTH parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearCheckLineLengthParameter()

CDPL_CHEM_API void CDPL::Chem::clearCheckLineLengthParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CHECK_LINE_LENGTH parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLCTABVersionParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLCTABVersionParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_CTAB_VERSION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored CTAB version (see namespace Chem::MDLDataFormatVersion).

setMDLCTABVersionParameter()

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

Sets the value of the Chem::ControlParameter::MDL_CTAB_VERSION parameter of cntnr to version.

Parameters

cntnr	The control-parameter container.
version	The new CTAB version (see namespace Chem::MDLDataFormatVersion).

hasMDLCTABVersionParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLCTABVersionParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_CTAB_VERSION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLCTABVersionParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLCTABVersionParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_CTAB_VERSION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLIgnoreParityParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLIgnoreParityParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_IGNORE_PARITY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMDLIgnoreParityParameter()

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

Sets the value of the Chem::ControlParameter::MDL_IGNORE_PARITY parameter of cntnr to ignore.

Parameters

cntnr	The control-parameter container.
ignore	The new parameter value.

hasMDLIgnoreParityParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLIgnoreParityParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_IGNORE_PARITY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLIgnoreParityParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLIgnoreParityParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_IGNORE_PARITY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLUpdateTimestampParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLUpdateTimestampParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_UPDATE_TIMESTAMP parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMDLUpdateTimestampParameter()

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

Sets the value of the Chem::ControlParameter::MDL_UPDATE_TIMESTAMP parameter of cntnr to update.

Parameters

cntnr	The control-parameter container.
update	The new parameter value.

hasMDLUpdateTimestampParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLUpdateTimestampParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_UPDATE_TIMESTAMP parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLUpdateTimestampParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLUpdateTimestampParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_UPDATE_TIMESTAMP parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLTrimStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTrimStringsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_TRIM_STRINGS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMDLTrimStringsParameter()

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

Sets the value of the Chem::ControlParameter::MDL_TRIM_STRINGS parameter of cntnr to trim.

Parameters

cntnr	The control-parameter container.
trim	The new parameter value.

hasMDLTrimStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTrimStringsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_TRIM_STRINGS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLTrimStringsParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTrimStringsParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_TRIM_STRINGS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLTrimLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTrimLinesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_TRIM_LINES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMDLTrimLinesParameter()

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

Sets the value of the Chem::ControlParameter::MDL_TRIM_LINES parameter of cntnr to trim.

Parameters

cntnr	The control-parameter container.
trim	The new parameter value.

hasMDLTrimLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTrimLinesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_TRIM_LINES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLTrimLinesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTrimLinesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_TRIM_LINES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLTruncateStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTruncateStringsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_TRUNCATE_STRINGS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMDLTruncateStringsParameter()

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

Sets the value of the Chem::ControlParameter::MDL_TRUNCATE_STRINGS parameter of cntnr to trunc.

Parameters

cntnr	The control-parameter container.
trunc	The new parameter value.

hasMDLTruncateStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTruncateStringsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_TRUNCATE_STRINGS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLTruncateStringsParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTruncateStringsParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_TRUNCATE_STRINGS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLTruncateLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTruncateLinesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_TRUNCATE_LINES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMDLTruncateLinesParameter()

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

Sets the value of the Chem::ControlParameter::MDL_TRUNCATE_LINES parameter of cntnr to trunc.

Parameters

cntnr	The control-parameter container.
trunc	The new parameter value.

hasMDLTruncateLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTruncateLinesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_TRUNCATE_LINES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLTruncateLinesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTruncateLinesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_TRUNCATE_LINES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLRXNFileVersionParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLRXNFileVersionParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_RXN_FILE_VERSION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored MDL Rxn-File version (see namespace Chem::MDLDataFormatVersion).

setMDLRXNFileVersionParameter()

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

Sets the value of the Chem::ControlParameter::MDL_RXN_FILE_VERSION parameter of cntnr to version.

Parameters

cntnr	The control-parameter container.
version	The new MDL Rxn-File version (see namespace Chem::MDLDataFormatVersion).

hasMDLRXNFileVersionParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLRXNFileVersionParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_RXN_FILE_VERSION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLRXNFileVersionParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLRXNFileVersionParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_RXN_FILE_VERSION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLOutputConfEnergyToEnergyFieldParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMDLOutputConfEnergyToEnergyFieldParameter()

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

Sets the value of the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

hasMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLOutputConfEnergyToEnergyFieldParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLOutputConfEnergyToEnergyFieldParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLOutputConfEnergyAsSDEntryParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMDLOutputConfEnergyAsSDEntryParameter()

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

Sets the value of the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

hasMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLOutputConfEnergyAsSDEntryParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLOutputConfEnergyAsSDEntryParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMDLEnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLEnableAromaticBondTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.3

setMDLEnableAromaticBondTypesParameter()

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

Sets the value of the Chem::ControlParameter::MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable.

Parameters

cntnr	The control-parameter container.
enable	The new parameter value.

Since

1.3

hasMDLEnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLEnableAromaticBondTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.3

clearMDLEnableAromaticBondTypesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLEnableAromaticBondTypesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.3

getMDLConfEnergySDTagParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MDL_CONF_ENERGY_SD_TAG parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored MDL SD-File structure data record header string.

setMDLConfEnergySDTagParameter()

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

Sets the value of the Chem::ControlParameter::MDL_CONF_ENERGY_SD_TAG parameter of cntnr to tag.

Parameters

cntnr	The control-parameter container.
tag	The new MDL SD-File structure data record header string.

hasMDLConfEnergySDTagParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLConfEnergySDTagParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MDL_CONF_ENERGY_SD_TAG parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMDLConfEnergySDTagParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLConfEnergySDTagParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MDL_CONF_ENERGY_SD_TAG parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getJMESeparateComponentsParameter()

CDPL_CHEM_API bool CDPL::Chem::getJMESeparateComponentsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::JME_SEPARATE_COMPONENTS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setJMESeparateComponentsParameter()

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

Sets the value of the Chem::ControlParameter::JME_SEPARATE_COMPONENTS parameter of cntnr to separate.

Parameters

cntnr	The control-parameter container.
separate	The new parameter value.

hasJMESeparateComponentsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasJMESeparateComponentsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::JME_SEPARATE_COMPONENTS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearJMESeparateComponentsParameter()

CDPL_CHEM_API void CDPL::Chem::clearJMESeparateComponentsParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::JME_SEPARATE_COMPONENTS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getSMILESRecordFormatParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_RECORD_FORMAT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored record-format string.

setSMILESRecordFormatParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_RECORD_FORMAT parameter of cntnr to format.

Parameters

cntnr	The control-parameter container.
format	The new record-format string.

hasSMILESRecordFormatParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESRecordFormatParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_RECORD_FORMAT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearSMILESRecordFormatParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESRecordFormatParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_RECORD_FORMAT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getSMILESOutputCanonicalFormParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESOutputCanonicalFormParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_CANONICAL_FORM parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESOutputCanonicalFormParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputCanonicalFormParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESOutputCanonicalFormParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESOutputCanonicalFormParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESOutputCanonicalFormParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_OUTPUT_CANONICAL_FORM parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESOutputKekuleFormParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESOutputKekuleFormParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_KEKULE_FORM parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESOutputKekuleFormParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_KEKULE_FORM parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputKekuleFormParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESOutputKekuleFormParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_OUTPUT_KEKULE_FORM parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESOutputKekuleFormParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESOutputKekuleFormParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_OUTPUT_KEKULE_FORM parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESOutputAtomStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESOutputAtomStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_ATOM_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESOutputAtomStereoParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_ATOM_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputAtomStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESOutputAtomStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_OUTPUT_ATOM_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESOutputAtomStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESOutputAtomStereoParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_OUTPUT_ATOM_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESOutputBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESOutputBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_BOND_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESOutputBondStereoParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_BOND_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESOutputBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_OUTPUT_BOND_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESOutputBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESOutputBondStereoParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_OUTPUT_BOND_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESOutputRingBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESOutputRingBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_RING_BOND_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESOutputRingBondStereoParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputRingBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESOutputRingBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESOutputRingBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESOutputRingBondStereoParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_OUTPUT_RING_BOND_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESMinStereoBondRingSizeParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored minimum ring size.

setSMILESMinStereoBondRingSizeParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr to min_size.

Parameters

cntnr	The control-parameter container.
min_size	The new minimum ring size.

hasSMILESMinStereoBondRingSizeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESMinStereoBondRingSizeParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearSMILESMinStereoBondRingSizeParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESMinStereoBondRingSizeParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getSMILESOutputIsotopeParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESOutputIsotopeParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_ISOTOPE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESOutputIsotopeParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_ISOTOPE parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputIsotopeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESOutputIsotopeParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_OUTPUT_ISOTOPE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESOutputIsotopeParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESOutputIsotopeParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_OUTPUT_ISOTOPE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESOutputHydrogenCountParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESOutputHydrogenCountParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_HYDROGEN_COUNT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.3

setSMILESOutputHydrogenCountParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.3

hasSMILESOutputHydrogenCountParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESOutputHydrogenCountParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.3

clearSMILESOutputHydrogenCountParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESOutputHydrogenCountParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_OUTPUT_HYDROGEN_COUNT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.3

getSMILESMolOutputAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESMolOutputAtomMappingIDParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESMolOutputAtomMappingIDParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESMolOutputAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESMolOutputAtomMappingIDParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESMolOutputAtomMappingIDParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESMolOutputAtomMappingIDParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESRxnOutputAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESRxnOutputAtomMappingIDParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESRxnOutputAtomMappingIDParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESRxnOutputAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESRxnOutputAtomMappingIDParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESRxnOutputAtomMappingIDParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESRxnOutputAtomMappingIDParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESOutputSingleBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESOutputSingleBondsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_SINGLE_BONDS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESOutputSingleBondsParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputSingleBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESOutputSingleBondsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESOutputSingleBondsParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESOutputSingleBondsParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_OUTPUT_SINGLE_BONDS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESOutputAromaticBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESOutputAromaticBondsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_OUTPUT_AROMATIC_BONDS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setSMILESOutputAromaticBondsParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasSMILESOutputAromaticBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESOutputAromaticBondsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearSMILESOutputAromaticBondsParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESOutputAromaticBondsParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_OUTPUT_AROMATIC_BONDS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESNoOrganicSubsetParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setSMILESNoOrganicSubsetParameter()

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

Sets the value of the Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET parameter of cntnr to no_subset.

Parameters

cntnr	The control-parameter container.
no_subset	The new parameter value.

hasSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESNoOrganicSubsetParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESNoOrganicSubsetParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getINCHIInputOptionsParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::INCHI_INPUT_OPTIONS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored InChI input-options string.

setINCHIInputOptionsParameter()

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

Sets the value of the Chem::ControlParameter::INCHI_INPUT_OPTIONS parameter of cntnr to opts.

Parameters

cntnr	The control-parameter container.
opts	The new InChI input-options string.

hasINCHIInputOptionsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasINCHIInputOptionsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::INCHI_INPUT_OPTIONS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearINCHIInputOptionsParameter()

CDPL_CHEM_API void CDPL::Chem::clearINCHIInputOptionsParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::INCHI_INPUT_OPTIONS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getINCHIOutputOptionsParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::INCHI_OUTPUT_OPTIONS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored InChI output-options string.

setINCHIOutputOptionsParameter()

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

Sets the value of the Chem::ControlParameter::INCHI_OUTPUT_OPTIONS parameter of cntnr to opts.

Parameters

cntnr	The control-parameter container.
opts	The new InChI output-options string.

hasINCHIOutputOptionsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasINCHIOutputOptionsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::INCHI_OUTPUT_OPTIONS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearINCHIOutputOptionsParameter()

CDPL_CHEM_API void CDPL::Chem::clearINCHIOutputOptionsParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::INCHI_OUTPUT_OPTIONS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMultiConfImportParameter()

CDPL_CHEM_API bool CDPL::Chem::getMultiConfImportParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MULTI_CONF_IMPORT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMultiConfImportParameter()

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

Sets the value of the Chem::ControlParameter::MULTI_CONF_IMPORT parameter of cntnr to multi_conf.

Parameters

cntnr	The control-parameter container.
multi_conf	The new parameter value.

hasMultiConfImportParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMultiConfImportParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MULTI_CONF_IMPORT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMultiConfImportParameter()

CDPL_CHEM_API void CDPL::Chem::clearMultiConfImportParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MULTI_CONF_IMPORT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMultiConfExportParameter()

CDPL_CHEM_API bool CDPL::Chem::getMultiConfExportParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MULTI_CONF_EXPORT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMultiConfExportParameter()

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

Sets the value of the Chem::ControlParameter::MULTI_CONF_EXPORT parameter of cntnr to multi_conf.

Parameters

cntnr	The control-parameter container.
multi_conf	The new parameter value.

hasMultiConfExportParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMultiConfExportParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MULTI_CONF_EXPORT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMultiConfExportParameter()

CDPL_CHEM_API void CDPL::Chem::clearMultiConfExportParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MULTI_CONF_EXPORT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API bool CDPL::Chem::getOutputConfEnergyAsCommentParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COMMENT parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setOutputConfEnergyAsCommentParameter()

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

Sets the value of the Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

hasOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API bool CDPL::Chem::hasOutputConfEnergyAsCommentParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API void CDPL::Chem::clearOutputConfEnergyAsCommentParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COMMENT parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getConfIndexNameSuffixPatternParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CONF_INDEX_NAME_SUFFIX_PATTERN parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored suffix pattern string.

setConfIndexNameSuffixPatternParameter()

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

Sets the value of the Chem::ControlParameter::CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr to pattern.

Parameters

cntnr	The control-parameter container.
pattern	The new suffix pattern string.

hasConfIndexNameSuffixPatternParameter()

CDPL_CHEM_API bool CDPL::Chem::hasConfIndexNameSuffixPatternParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearConfIndexNameSuffixPatternParameter()

CDPL_CHEM_API void CDPL::Chem::clearConfIndexNameSuffixPatternParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CONF_INDEX_NAME_SUFFIX_PATTERN parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMultiConfInputProcessorParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored Chem::MultiConfMoleculeInputProcessor implementation pointer.

setMultiConfInputProcessorParameter()

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

Sets the value of the Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR parameter of cntnr to proc.

Parameters

cntnr	The control-parameter container.
proc	The new Chem::MultiConfMoleculeInputProcessor implementation pointer.

hasMultiConfInputProcessorParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMultiConfInputProcessorParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMultiConfInputProcessorParameter()

CDPL_CHEM_API void CDPL::Chem::clearMultiConfInputProcessorParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getCDFOutputSinglePrecisionFloatsParameter()

CDPL_CHEM_API bool CDPL::Chem::getCDFOutputSinglePrecisionFloatsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCDFOutputSinglePrecisionFloatsParameter()

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

Sets the value of the Chem::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr to single_prec.

Parameters

cntnr	The control-parameter container.
single_prec	The new parameter value.

Since

1.2

hasCDFOutputSinglePrecisionFloatsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCDFOutputSinglePrecisionFloatsParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCDFOutputSinglePrecisionFloatsParameter()

CDPL_CHEM_API void CDPL::Chem::clearCDFOutputSinglePrecisionFloatsParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2EnableExtendedAtomTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMOL2EnableExtendedAtomTypesParameter()

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

Sets the value of the Chem::ControlParameter::MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr to enable.

Parameters

cntnr	The control-parameter container.
enable	The new parameter value.

hasMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2EnableExtendedAtomTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2EnableExtendedAtomTypesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2EnableAromaticBondTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MOL2_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMOL2EnableAromaticBondTypesParameter()

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

Sets the value of the Chem::ControlParameter::MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable.

Parameters

cntnr	The control-parameter container.
enable	The new parameter value.

hasMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2EnableAromaticBondTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2EnableAromaticBondTypesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MOL2_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMOL2ReadPartialAsFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2ReadPartialAsFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2.3

setMOL2ReadPartialAsFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::setMOL2ReadPartialAsFormalChargesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	read
	)

Sets the value of the Chem::ControlParameter::MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr to read.

Parameters

cntnr	The control-parameter container.
read	The new parameter value.

Since

1.2.3

hasMOL2ReadPartialAsFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2ReadPartialAsFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2.3

clearMOL2ReadPartialAsFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2ReadPartialAsFormalChargesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2.3

getMOL2CalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2CalcFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MOL2_CALC_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMOL2CalcFormalChargesParameter()

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

Sets the value of the Chem::ControlParameter::MOL2_CALC_FORMAL_CHARGES parameter of cntnr to calc.

Parameters

cntnr	The control-parameter container.
calc	The new parameter value.

hasMOL2CalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2CalcFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MOL2_CALC_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMOL2CalcFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2CalcFormalChargesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MOL2_CALC_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMOL2ChargeTypeParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2ChargeTypeParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MOL2_CHARGE_TYPE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored Sybyl MOL2 charge type (see namespace Chem::MOL2ChargeType).

setMOL2ChargeTypeParameter()

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

Sets the value of the Chem::ControlParameter::MOL2_CHARGE_TYPE parameter of cntnr to type.

Parameters

cntnr	The control-parameter container.
type	The new Sybyl MOL2 charge type (see namespace Chem::MOL2ChargeType).

hasMOL2ChargeTypeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2ChargeTypeParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MOL2_CHARGE_TYPE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMOL2ChargeTypeParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2ChargeTypeParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MOL2_CHARGE_TYPE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMOL2MoleculeTypeParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2MoleculeTypeParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MOL2_MOLECULE_TYPE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored Sybyl MOL2 molecule type (see namespace Chem::MOL2MoleculeType).

setMOL2MoleculeTypeParameter()

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

Sets the value of the Chem::ControlParameter::MOL2_MOLECULE_TYPE parameter of cntnr to type.

Parameters

cntnr	The control-parameter container.
type	The new Sybyl MOL2 molecule type (see namespace Chem::MOL2MoleculeType).

hasMOL2MoleculeTypeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2MoleculeTypeParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MOL2_MOLECULE_TYPE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMOL2MoleculeTypeParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2MoleculeTypeParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MOL2_MOLECULE_TYPE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMOL2OutputSubstructuresParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2OutputSubstructuresParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MOL2_OUTPUT_SUBSTRUCTURES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

setMOL2OutputSubstructuresParameter()

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

Sets the value of the Chem::ControlParameter::MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

hasMOL2OutputSubstructuresParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2OutputSubstructuresParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

clearMOL2OutputSubstructuresParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2OutputSubstructuresParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MOL2_OUTPUT_SUBSTRUCTURES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

getMOL2OutputFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2OutputFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::MOL2_OUTPUT_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2.3

setMOL2OutputFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::setMOL2OutputFormalChargesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	output
	)

Sets the value of the Chem::ControlParameter::MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2.3

hasMOL2OutputFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2OutputFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2.3

clearMOL2OutputFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2OutputFormalChargesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::MOL2_OUTPUT_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2.3

getXYZCommentIsNameParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZCommentIsNameParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::XYZ_COMMENT_IS_NAME parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.1

setXYZCommentIsNameParameter()

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

Sets the value of the Chem::ControlParameter::XYZ_COMMENT_IS_NAME parameter of cntnr to is_name.

Parameters

cntnr	The control-parameter container.
is_name	The new parameter value.

Since

1.1

hasXYZCommentIsNameParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZCommentIsNameParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::XYZ_COMMENT_IS_NAME parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.1

clearXYZCommentIsNameParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZCommentIsNameParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::XYZ_COMMENT_IS_NAME parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.1

getXYZPerceiveConnectivityParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZPerceiveConnectivityParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::XYZ_PERCEIVE_CONNECTIVITY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.1

setXYZPerceiveConnectivityParameter()

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

Sets the value of the Chem::ControlParameter::XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr to perceive.

Parameters

cntnr	The control-parameter container.
perceive	The new parameter value.

Since

1.1

hasXYZPerceiveConnectivityParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZPerceiveConnectivityParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.1

clearXYZPerceiveConnectivityParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZPerceiveConnectivityParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::XYZ_PERCEIVE_CONNECTIVITY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.1

getXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZPerceiveBondOrdersParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::XYZ_PERCEIVE_BOND_ORDERS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.1

setXYZPerceiveBondOrdersParameter()

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

Sets the value of the Chem::ControlParameter::XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr to perceive.

Parameters

cntnr	The control-parameter container.
perceive	The new parameter value.

Since

1.1

hasXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZPerceiveBondOrdersParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.1

clearXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZPerceiveBondOrdersParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::XYZ_PERCEIVE_BOND_ORDERS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.1

getXYZCalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZCalcFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::XYZ_CALC_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.1

setXYZCalcFormalChargesParameter()

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

Sets the value of the Chem::ControlParameter::XYZ_CALC_FORMAL_CHARGES parameter of cntnr to calc.

Parameters

cntnr	The control-parameter container.
calc	The new parameter value.

Since

1.1

hasXYZCalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZCalcFormalChargesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::XYZ_CALC_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.1

clearXYZCalcFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZCalcFormalChargesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::XYZ_CALC_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.1

getCMLOutputXMLDeclarationParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputXMLDeclarationParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_XML_DECLARATION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputXMLDeclarationParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_XML_DECLARATION parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputXMLDeclarationParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputXMLDeclarationParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_XML_DECLARATION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputXMLDeclarationParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputXMLDeclarationParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_XML_DECLARATION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLOutputElementNamespaceParameter()

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

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_ELEMENT_NAMESPACE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The stored XML-namespace string.

Since

1.2

setCMLOutputElementNamespaceParameter()

CDPL_CHEM_API void CDPL::Chem::setCMLOutputElementNamespaceParameter	(	Base::ControlParameterContainer &	cntnr,
		const std::string &	ns
	)

Sets the value of the Chem::ControlParameter::CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr to ns.

Parameters

cntnr	The control-parameter container.
ns	The new XML-namespace string.

Since

1.2

hasCMLOutputElementNamespaceParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputElementNamespaceParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputElementNamespaceParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputElementNamespaceParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_ELEMENT_NAMESPACE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLOutputAtomParityParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputAtomParityParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_ATOM_PARITY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputAtomParityParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_ATOM_PARITY parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputAtomParityParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputAtomParityParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_ATOM_PARITY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputAtomParityParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputAtomParityParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_ATOM_PARITY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLOutputSingleBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputSingleBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_SINGLE_BOND_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputSingleBondStereoParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputSingleBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputSingleBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputSingleBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputSingleBondStereoParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_SINGLE_BOND_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLOutputDoubleBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputDoubleBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_DOUBLE_BOND_STEREO parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputDoubleBondStereoParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputDoubleBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputDoubleBondStereoParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputDoubleBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputDoubleBondStereoParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_DOUBLE_BOND_STEREO parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLEnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLEnableAromaticBondTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.3

setCMLEnableAromaticBondTypesParameter()

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

Sets the value of the Chem::ControlParameter::CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable.

Parameters

cntnr	The control-parameter container.
enable	The new parameter value.

Since

1.3

hasCMLEnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLEnableAromaticBondTypesParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.3

clearCMLEnableAromaticBondTypesParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLEnableAromaticBondTypesParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.3

getCMLOutputMoleculeNameParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputMoleculeNameParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_MOLECULE_NAME parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputMoleculeNameParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_MOLECULE_NAME parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputMoleculeNameParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputMoleculeNameParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_MOLECULE_NAME parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputMoleculeNameParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputMoleculeNameParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_MOLECULE_NAME parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLOutputStructureDataParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputStructureDataParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_STRUCTURE_DATA parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputStructureDataParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_STRUCTURE_DATA parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputStructureDataParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputStructureDataParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_STRUCTURE_DATA parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputStructureDataParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputStructureDataParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_STRUCTURE_DATA parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLOutputIsotopeParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputIsotopeParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_ISOTOPE parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputIsotopeParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_ISOTOPE parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputIsotopeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputIsotopeParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_ISOTOPE parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputIsotopeParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputIsotopeParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_ISOTOPE parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLOutputSpinMultiplicityParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputSpinMultiplicityParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_SPIN_MULTIPLICITY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputSpinMultiplicityParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputSpinMultiplicityParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputSpinMultiplicityParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputSpinMultiplicityParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputSpinMultiplicityParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_SPIN_MULTIPLICITY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLOutputCompactAtomDataParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputCompactAtomDataParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_COMPACT_ATOM_DATA parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputCompactAtomDataParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputCompactAtomDataParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputCompactAtomDataParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputCompactAtomDataParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputCompactAtomDataParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_COMPACT_ATOM_DATA parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

getCMLOutputCompactBondDataParameter()

CDPL_CHEM_API bool CDPL::Chem::getCMLOutputCompactBondDataParameter

(

const Base::ControlParameterContainer &

cntnr

)

Returns the value of the Chem::ControlParameter::CML_OUTPUT_COMPACT_BOND_DATA parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

setCMLOutputCompactBondDataParameter()

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

Sets the value of the Chem::ControlParameter::CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	The new parameter value.

Since

1.2

hasCMLOutputCompactBondDataParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCMLOutputCompactBondDataParameter

(

const Base::ControlParameterContainer &

cntnr

)

Tells whether the Chem::ControlParameter::CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

true if the parameter is set, and false otherwise.

Since

1.2

clearCMLOutputCompactBondDataParameter()

CDPL_CHEM_API void CDPL::Chem::clearCMLOutputCompactBondDataParameter

(

Base::ControlParameterContainer &

cntnr

)

Removes the Chem::ControlParameter::CML_OUTPUT_COMPACT_BOND_DATA parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

calcGeometricalDistanceMatrix() [1/2]

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

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

Parameters

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

get3DCoordinates() [2/3]

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

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

Parameters

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

set3DCoordinates() [1/2]

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

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

Parameters

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

transform3DCoordinates()

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

Transforms the 3D coordinates of the entities of cntnr by the affine matrix mtx.

Parameters

cntnr	The entity 3D container whose coordinates are to be transformed.
mtx	The 4×4 affine transformation matrix.

align3DCoordinates()

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

Transforms the 3D coordinates of the entities of cntnr by the affine matrix that is calculated for the rigid-body alignment of the 3D coordinates of the entities of ref_entities with the given reference coordinates ref_coords.

Parameters

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

Returns

true if the alignment succeeded, and false otherwise.

Since

1.1

calcCentroid() [2/2]

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

Calculates the geometric centroid of the 3D coordinates of the entities of cntnr.

Parameters

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

Returns

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

calcBoundingBox() [2/2]

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

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

Parameters

cntnr	The entity 3D container.
min	The output vector receiving the per-axis minimum coordinates.
max	The output vector receiving the per-axis maximum coordinates.
reset	If true, min and max are reset before the calculation. If false, the given bounding box is extended.

insideBoundingBox() [2/3]

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

Tells whether all 3D coordinates of the entities of cntnr lie within the axis-aligned bounding box defined by min and max.

Parameters

cntnr	The entity 3D container.
min	The per-axis minimum coordinates of the box.
max	The per-axis maximum coordinates of the box.

Returns

true if every entity coordinate is inside the bounding box, and false otherwise.

intersectsBoundingBox() [2/2]

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

Tells whether at least one entity of cntnr lies within the axis-aligned bounding box defined by min and max.

Parameters

cntnr	The entity 3D container.
min	The per-axis minimum coordinates of the box.
max	The per-axis maximum coordinates of the box.

Returns

true if any entity coordinate is inside the bounding box, and false otherwise.

get3DCoordinates() [3/3]

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

(

const Entity3D &

entity

)

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

Parameters

entity

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

Returns

The stored 3D coordinates.

Exceptions

Base::ItemNotFound

if the property has not been set.

set3DCoordinates() [2/2]

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

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

Parameters

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

clear3DCoordinates()

CDPL_CHEM_API void CDPL::Chem::clear3DCoordinates

(

Entity3D &

entity

)

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

Parameters

entity

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

has3DCoordinates()

CDPL_CHEM_API bool CDPL::Chem::has3DCoordinates

(

const Entity3D &

entity

)

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

Parameters

entity

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

Returns

true if the property is set, and false otherwise.

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

MolProp::isOrdinaryHydrogen

removeAtomsIf() [1/2]

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

Removes all atoms of the fragment frag for which the predicate pred returns true.

Parameters

frag	The fragment to filter in place.
pred	The atom predicate to evaluate.

removeAtomsIfNot() [1/2]

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

Removes all atoms of the fragment frag for which the predicate pred returns false.

Parameters

frag	The fragment to filter in place.
pred	The atom predicate to evaluate.

getName() [2/3]

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored name.

setName() [2/3]

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

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

Parameters

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

clearName() [2/3]

CDPL_CHEM_API void CDPL::Chem::clearName

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasName() [2/3]

CDPL_CHEM_API bool CDPL::Chem::hasName

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getTimestamp() [1/2]

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored timestamp.

setTimestamp() [1/2]

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

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

Parameters

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

clearTimestamp() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearTimestamp

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasTimestamp() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasTimestamp

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getComment() [1/2]

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored comment.

setComment() [1/2]

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

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

Parameters

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

clearComment() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearComment

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasComment() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasComment

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMatchConstraints() [3/4]

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored match constraint list.

setMatchConstraints() [3/4]

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

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

Parameters

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

clearMatchConstraints() [3/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMatchConstraints() [3/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMatchExpression() [3/4]

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored match expression.

setMatchExpression() [3/4]

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

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

Parameters

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

clearMatchExpression() [3/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMatchExpression() [3/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

generateMatchExpression() [3/6]

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

(

const MolecularGraph &

molgraph

)

Builds a match expression from the match constraints currently attached to the molecular graph molgraph.

Parameters

molgraph

The molecular graph.

Returns

The generated match expression.

generateMatchExpression() [4/6]

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

Builds and stores the match expression of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing match expression property should be replaced.

Returns

The generated (or pre-existing) match expression.

getRings()

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored full ring set.

setRings()

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

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

Parameters

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

clearRings()

CDPL_CHEM_API void CDPL::Chem::clearRings

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasRings()

CDPL_CHEM_API bool CDPL::Chem::hasRings

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveRings() [1/2]

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

(

const MolecularGraph &

molgraph

)

Perceives the full set of rings of the molecular graph molgraph.

Parameters

molgraph

The molecular graph.

Returns

The perceived ring set.

perceiveRings() [2/2]

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

Perceives and stores the full set of rings of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing ring set property should be replaced.

Returns

The perceived (or pre-existing) ring set.

getSSSR()

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored Smallest Set of Smallest Rings.

setSSSR()

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

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

Parameters

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

clearSSSR()

CDPL_CHEM_API void CDPL::Chem::clearSSSR

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasSSSR()

CDPL_CHEM_API bool CDPL::Chem::hasSSSR

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveSSSR() [1/2]

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

(

const MolecularGraph &

molgraph

)

Perceives the SSSR of the molecular graph molgraph.

Parameters

molgraph

The molecular graph.

Returns

A shared pointer to the perceived SSSR.

perceiveSSSR() [2/2]

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

Perceives and stores the SSSR of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing SSSR property should be replaced.

Returns

The perceived (or pre-existing) SSSR.

extractSSSRSubset() [1/2]

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

Extracts the SSSR subset of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph.

Parameters

src_molgraph	The source molecular graph whose SSSR is to be projected.
tgt_molgraph	The target molecular graph acting as filter.

Returns

The extracted SSSR subset.

extractSSSRSubset() [2/2]

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

Extracts the SSSR subset of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph and stores it on the latter.

Parameters

src_molgraph	The source molecular graph whose SSSR is to be projected.
tgt_molgraph	The target molecular graph which receives the projected SSSR and acts as filter.
overwrite	Specifies whether an already existing tgt_molgraph SSSR property should be replaced.

Returns

The extracted (or pre-existing) SSSR subset.

getCyclicSubstructure()

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored cyclic substructure.

setCyclicSubstructure()

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

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

Parameters

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

clearCyclicSubstructure()

CDPL_CHEM_API void CDPL::Chem::clearCyclicSubstructure

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasCyclicSubstructure()

CDPL_CHEM_API bool CDPL::Chem::hasCyclicSubstructure

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveCyclicSubstructure() [1/2]

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

(

const MolecularGraph &

molgraph

)

Perceives the cyclic substructure (union of all rings) of the molecular graph molgraph.

Parameters

molgraph

The molecular graph.

Returns

The perceived cyclic substructure.

perceiveCyclicSubstructure() [2/2]

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

Perceives and stores the cyclic substructure (union of all rings) of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing cyclic substructure property should be replaced.

Returns

The perceived (or pre-existing) cyclic substructure.

getComponents()

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored connected-component list.

setComponents()

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

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

Parameters

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

clearComponents()

CDPL_CHEM_API void CDPL::Chem::clearComponents

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasComponents()

CDPL_CHEM_API bool CDPL::Chem::hasComponents

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveComponents() [1/2]

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

(

const MolecularGraph &

molgraph

)

Perceives the connected components of the molecular graph molgraph.

Parameters

molgraph

The molecular graph.

Returns

The perceived component list.

perceiveComponents() [2/2]

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

Perceives and stores the connected components of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing component list property should be replaced.

Returns

The perceived (or pre-existing) component list.

getComponentGroups() [1/2]

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored component-group fragment list.

setComponentGroups() [1/2]

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

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

Parameters

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

clearComponentGroups() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearComponentGroups

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasComponentGroups() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasComponentGroups

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveComponentGroups() [1/4]

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

(

const MolecularGraph &

molgraph

)

Perceives the component groups of the molecular graph molgraph.

Component groups are generated by merging components whose atoms have the same Chem::AtomProperty::COMPONENT_GROUP_ID property value.

Parameters

molgraph

The molecular graph.

Returns

The perceived component group fragment list.

perceiveComponentGroups() [2/4]

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

Perceives and optionally stores the component groups of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing component groups property should be replaced.

Returns

The perceived (or pre-existing) component group fragment list.

getConformationIndex()

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored zero-based conformation index.

setConformationIndex()

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

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

Parameters

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

clearConformationIndex()

CDPL_CHEM_API void CDPL::Chem::clearConformationIndex

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasConformationIndex()

CDPL_CHEM_API bool CDPL::Chem::hasConformationIndex

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getConformerEnergies()

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored conformer energy array.

setConformerEnergies()

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

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

Parameters

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

clearConformerEnergies()

CDPL_CHEM_API void CDPL::Chem::clearConformerEnergies

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasConformerEnergies()

CDPL_CHEM_API bool CDPL::Chem::hasConformerEnergies

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

setConformation() [2/2]

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

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

Parameters

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

Exceptions

Base::IndexError

if conf_idx is out of the valid range.

addConformation() [2/2]

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

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

Parameters

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

getConformationEnergy()

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

Returns the energy of the conformation at index conf_idx.

Parameters

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

Returns

The energy of the requested conformation.

Exceptions

Base::IndexError

if conf_idx is out of the valid range.

getHashCode()

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored 64-bit hash code.

setHashCode()

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

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

Parameters

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

clearHashCode()

CDPL_CHEM_API void CDPL::Chem::clearHashCode

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasHashCode()

CDPL_CHEM_API bool CDPL::Chem::hasHashCode

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

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
	)

Computes a 64-bit hash code for the molecular graph molgraph taking into account the specified atom and bond properties.

Parameters

molgraph	The molecular graph.
atom_flags	A bitmask of Chem::AtomPropertyFlag flags controlling which atomic properties contribute to the hash.
bond_flags	A bitmask of Chem::BondPropertyFlag flags controlling which bond properties contribute to the hash.
ord_h_deplete	true to suppress ordinary hydrogens before hashing.

Returns

The computed hash code.

extractReactionCenter()

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

Collects every atom and bond of the molecular graph molgraph that carries a reaction-center flag into the fragment rxn_center.

Parameters

molgraph	The molecular graph.
rxn_center	The output fragment receiving the reaction-center atoms and bonds.

getStoichiometricNumber()

CDPL_CHEM_API double CDPL::Chem::getStoichiometricNumber

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored stoichiometric number.

setStoichiometricNumber()

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

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

Parameters

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

clearStoichiometricNumber()

CDPL_CHEM_API void CDPL::Chem::clearStoichiometricNumber

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasStoichiometricNumber()

CDPL_CHEM_API bool CDPL::Chem::hasStoichiometricNumber

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLUserInitials() [1/2]

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL user initials.

setMDLUserInitials() [1/2]

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

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

Parameters

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

clearMDLUserInitials() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLUserInitials

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMDLUserInitials() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLUserInitials

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLProgramName() [1/2]

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL program name.

setMDLProgramName() [1/2]

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

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

Parameters

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

clearMDLProgramName() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLProgramName

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMDLProgramName() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLProgramName

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLRegistryNumber() [1/2]

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL registry number.

setMDLRegistryNumber() [1/2]

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

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

Parameters

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

clearMDLRegistryNumber() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLRegistryNumber

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMDLRegistryNumber() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLRegistryNumber

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLCTABVersion()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLCTABVersion

(

const MolecularGraph &

molgraph

)

Returns the value of the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored CTAB version (see namespace Chem::MDLDataFormatVersion).

setMDLCTABVersion()

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

Sets the value of the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property of the molecular graph molgraph to version.

Parameters

molgraph	The molecular graph for which to set the property value.
version	The new CTAB version (see namespace Chem::MDLDataFormatVersion).

clearMDLCTABVersion()

CDPL_CHEM_API void CDPL::Chem::clearMDLCTABVersion

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMDLCTABVersion()

CDPL_CHEM_API bool CDPL::Chem::hasMDLCTABVersion

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getStructureData()

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored structure data block.

setStructureData()

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

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

Parameters

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

clearStructureData()

CDPL_CHEM_API void CDPL::Chem::clearStructureData

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasStructureData()

CDPL_CHEM_API bool CDPL::Chem::hasStructureData

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLDimensionality()

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

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL coordinate dimensionality.

setMDLDimensionality()

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

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

Parameters

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

clearMDLDimensionality()

CDPL_CHEM_API void CDPL::Chem::clearMDLDimensionality

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMDLDimensionality()

CDPL_CHEM_API bool CDPL::Chem::hasMDLDimensionality

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLScalingFactor1()

CDPL_CHEM_API long CDPL::Chem::getMDLScalingFactor1

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL scaling factor 1.

setMDLScalingFactor1()

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

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

Parameters

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

clearMDLScalingFactor1()

CDPL_CHEM_API void CDPL::Chem::clearMDLScalingFactor1

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMDLScalingFactor1()

CDPL_CHEM_API bool CDPL::Chem::hasMDLScalingFactor1

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLScalingFactor2()

CDPL_CHEM_API double CDPL::Chem::getMDLScalingFactor2

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL scaling factor 2.

setMDLScalingFactor2()

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

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

Parameters

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

clearMDLScalingFactor2()

CDPL_CHEM_API void CDPL::Chem::clearMDLScalingFactor2

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMDLScalingFactor2()

CDPL_CHEM_API bool CDPL::Chem::hasMDLScalingFactor2

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLEnergy()

CDPL_CHEM_API double CDPL::Chem::getMDLEnergy

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL energy.

setMDLEnergy()

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

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

Parameters

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

clearMDLEnergy()

CDPL_CHEM_API void CDPL::Chem::clearMDLEnergy

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMDLEnergy()

CDPL_CHEM_API bool CDPL::Chem::hasMDLEnergy

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLChiralFlag()

CDPL_CHEM_API bool CDPL::Chem::getMDLChiralFlag

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored MDL chiral flag.

setMDLChiralFlag()

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

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

Parameters

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

clearMDLChiralFlag()

CDPL_CHEM_API void CDPL::Chem::clearMDLChiralFlag

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMDLChiralFlag()

CDPL_CHEM_API bool CDPL::Chem::hasMDLChiralFlag

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMOL2MoleculeType()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2MoleculeType

(

const MolecularGraph &

molgraph

)

Returns the value of the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored Sybyl MOL2 molecule type (see namespace Chem::MOL2MoleculeType).

setMOL2MoleculeType()

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

Sets the value of the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property of the molecular graph molgraph to type.

Parameters

molgraph	The molecular graph for which to set the property value.
type	The new Sybyl MOL2 molecule type (see namespace Chem::MOL2MoleculeType).

clearMOL2MoleculeType()

CDPL_CHEM_API void CDPL::Chem::clearMOL2MoleculeType

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMOL2MoleculeType()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2MoleculeType

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMOL2ChargeType()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2ChargeType

(

const MolecularGraph &

molgraph

)

Returns the value of the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored Sybyl MOL2 charge type (see namespace Chem::MOL2ChargeType).

setMOL2ChargeType()

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

Sets the value of the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property of the molecular graph molgraph to type.

Parameters

molgraph	The molecular graph for which to set the property value.
type	The new Sybyl MOL2 charge type (see namespace Chem::MOL2ChargeType).

clearMOL2ChargeType()

CDPL_CHEM_API void CDPL::Chem::clearMOL2ChargeType

(

MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to clear the property value.

hasMOL2ChargeType()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2ChargeType

(

const MolecularGraph &

molgraph

)

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

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

generateAdjacencyMatrix()

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

Builds the adjacency matrix of the molecular graph molgraph.

Entry (i,j) is 1 if atoms i and j are connected by a bond and 0 if there is no bond.

Parameters

molgraph	The molecular graph.
mtx	The output adjacency matrix.

generateIncidenceMatrix()

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

Builds the atom/bond incidence matrix of the molecular graph molgraph.

Entry (i,j) is 1 if atom i is an endpoint of bond j.

Parameters

molgraph	The molecular graph.
mtx	The output incidence matrix.

generateBondMatrix()

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

Builds the bond order matrix of the molecular graph molgraph.

Entry (i,j) is the order of the bond between atoms i and j and 0 if there is no bond.

Parameters

molgraph	The molecular graph.
mtx	The output bond matrix.

generateBondElectronMatrix()

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

Builds the bond-electron matrix of the molecular graph molgraph.

Entry (i,j) is the order of the bond between atoms i and j and 0 if there is no bond. Diagonal entries (i,i) store the free valence electron count of each atom i.

Parameters

molgraph	The molecular graph.
mtx	The output bond-electron matrix.

generateBondAtomTypeMatrix()

CDPL_CHEM_API void CDPL::Chem::generateBondAtomTypeMatrix	(	const MolecularGraph &	molgraph,
		Math::SparseULMatrix &	mtx
	)

Builds a matrix combining bond order and atom type information of the endpoints of every bond in molgraph.

Entry (i,j) is the order of the bond between atoms i and j and 0 if there is no bond. Diagonal entries (i,i) store the type of each atom i.

Parameters

molgraph	The molecular graph.
mtx	The output bond and atom type matrix.

getTopologicalDistanceMatrix()

CDPL_CHEM_API const Math::ULMatrix::SharedPointer& CDPL::Chem::getTopologicalDistanceMatrix

(

const MolecularGraph &

molgraph

)

Returns the value of the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored topological distance matrix.

setTopologicalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::setTopologicalDistanceMatrix	(	MolecularGraph &	molgraph,
		const Math::ULMatrix::SharedPointer &	mtx
	)

Sets the value of the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx.

Parameters

molgraph	The molecular graph for which to set the property value.
mtx	The new topological distance matrix.

clearTopologicalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::clearTopologicalDistanceMatrix

(

MolecularGraph &

molgraph

)

Clears the value of the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

hasTopologicalDistanceMatrix()

CDPL_CHEM_API bool CDPL::Chem::hasTopologicalDistanceMatrix

(

const MolecularGraph &

molgraph

)

Tells whether the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

calcTopologicalDistanceMatrix() [1/2]

CDPL_CHEM_API Math::ULMatrix::SharedPointer CDPL::Chem::calcTopologicalDistanceMatrix	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores the topological distance matrix of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing distance matrix property should be replaced.

Returns

The computed (or pre-existing) topological distance matrix.

calcTopologicalDistanceMatrix() [2/2]

CDPL_CHEM_API void CDPL::Chem::calcTopologicalDistanceMatrix	(	const MolecularGraph &	molgraph,
		Math::ULMatrix &	mtx
	)

Computes the topological distance matrix of the molecular graph molgraph into the supplied matrix mtx.

Parameters

molgraph	The molecular graph.
mtx	The output topological distance matrix.

extractTopologicalDistanceSubMatrix() [1/2]

CDPL_CHEM_API Math::ULMatrix::SharedPointer CDPL::Chem::extractTopologicalDistanceSubMatrix	(	const MolecularGraph &	src_molgraph,
		MolecularGraph &	tgt_molgraph,
		bool	overwrite
	)

Extracts the topological distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph and stores it on the latter.

Parameters

src_molgraph	The source molecular graph providing the full matrix.
tgt_molgraph	The target molecular graph providing the atom subset and (optionally) receiving the sub-matrix.
overwrite	Specifies whether an already existing distance matrix property should be replaced.

Returns

The extracted (or pre-existing) topological distance matrix.

extractTopologicalDistanceSubMatrix() [2/2]

CDPL_CHEM_API void CDPL::Chem::extractTopologicalDistanceSubMatrix	(	const MolecularGraph &	src_molgraph,
		const MolecularGraph &	tgt_molgraph,
		Math::ULMatrix &	mtx
	)

Extracts the topological distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph into the supplied matrix mtx.

Parameters

src_molgraph	The source molecular graph providing the full matrix.
tgt_molgraph	The target molecular graph providing the atom subset.
mtx	The output topological distance matrix.

getGeometricalDistanceMatrix()

CDPL_CHEM_API const Math::DMatrix::SharedPointer& CDPL::Chem::getGeometricalDistanceMatrix

(

const MolecularGraph &

molgraph

)

Returns the value of the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored geometrical distance matrix.

setGeometricalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::setGeometricalDistanceMatrix	(	MolecularGraph &	molgraph,
		const Math::DMatrix::SharedPointer &	mtx
	)

Sets the value of the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx.

Parameters

molgraph	The molecular graph for which to set the property value.
mtx	The new geometrical distance matrix.

clearGeometricalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::clearGeometricalDistanceMatrix

(

MolecularGraph &

molgraph

)

Clears the value of the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

hasGeometricalDistanceMatrix()

CDPL_CHEM_API bool CDPL::Chem::hasGeometricalDistanceMatrix

(

const MolecularGraph &

molgraph

)

Tells whether the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

calcGeometricalDistanceMatrix() [2/2]

CDPL_CHEM_API Math::DMatrix::SharedPointer CDPL::Chem::calcGeometricalDistanceMatrix	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores the geometrical distance matrix of the molecular graph molgraph from its 3D coordinates.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing distance matrix property should be replaced.

Returns

The computed (or pre-existing) geometrical distance matrix.

getAromaticSubstructure()

CDPL_CHEM_API const Fragment::SharedPointer& CDPL::Chem::getAromaticSubstructure

(

const MolecularGraph &

molgraph

)

Returns the value of the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored aromatic substructure.

setAromaticSubstructure()

CDPL_CHEM_API void CDPL::Chem::setAromaticSubstructure	(	MolecularGraph &	molgraph,
		const Fragment::SharedPointer &	substruct
	)

Sets the value of the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct.

Parameters

molgraph	The molecular graph for which to set the property value.
substruct	The new aromatic substructure.

clearAromaticSubstructure()

CDPL_CHEM_API void CDPL::Chem::clearAromaticSubstructure

(

MolecularGraph &

molgraph

)

Clears the value of the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

hasAromaticSubstructure()

CDPL_CHEM_API bool CDPL::Chem::hasAromaticSubstructure

(

const MolecularGraph &

molgraph

)

Tells whether the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveAromaticSubstructure() [1/2]

CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveAromaticSubstructure

(

const MolecularGraph &

molgraph

)

Perceives the aromatic substructure (union of all aromatic atoms/bonds) of the molecular graph molgraph.

Parameters

molgraph

The molecular graph.

Returns

The perceived aromatic substructure.

perceiveAromaticSubstructure() [2/2]

CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveAromaticSubstructure	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Perceives and stores the aromatic substructure of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing aromatic substructure property should be replaced.

Returns

The perceived (or pre-existing) aromatic substructure.

getPiElectronSystems()

CDPL_CHEM_API const ElectronSystemList::SharedPointer& CDPL::Chem::getPiElectronSystems

(

const MolecularGraph &

molgraph

)

Returns the value of the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The stored π-electron system list.

setPiElectronSystems()

CDPL_CHEM_API void CDPL::Chem::setPiElectronSystems	(	MolecularGraph &	molgraph,
		const ElectronSystemList::SharedPointer &	pi_systems
	)

Sets the value of the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of the molecular graph molgraph to pi_systems.

Parameters

molgraph	The molecular graph for which to set the property value.
pi_systems	The new π-electron system list.

clearPiElectronSystems()

CDPL_CHEM_API void CDPL::Chem::clearPiElectronSystems

(

MolecularGraph &

molgraph

)

Clears the value of the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

hasPiElectronSystems()

CDPL_CHEM_API bool CDPL::Chem::hasPiElectronSystems

(

const MolecularGraph &

molgraph

)

Tells whether the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceivePiElectronSystems() [1/2]

CDPL_CHEM_API ElectronSystemList::SharedPointer CDPL::Chem::perceivePiElectronSystems

(

const MolecularGraph &

molgraph

)

Perceives the π-electron systems of the molecular graph molgraph.

Parameters

molgraph

The molecular graph.

Returns

The perceived π-electron system list.

perceivePiElectronSystems() [2/2]

CDPL_CHEM_API ElectronSystemList::SharedPointer CDPL::Chem::perceivePiElectronSystems	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Perceives and stores the π-electron systems of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether an already existing electron system property should be replaced.

Returns

The perceived (or pre-existing) π-electron system list.

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
	)

Generates a SMILES string for the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
smiles	The string receiving the generated SMILES.
canonical	true to emit a canonical SMILES.
ord_h_deplete	true to suppress the output of ordinary hydrogens.
atom_flags	A bitmask of Chem::AtomPropertyFlag flags controlling which atomic properties to encode.
bond_flags	A bitmask of Chem::BondPropertyFlag flags controlling which bond properties to encode.

Returns

true on success, and false if an unrecoverable error was encountered.

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
	)

Generates an InChI string for the molecular graph molgraph using the InChI C-API.

Parameters

molgraph	The molecular graph.
inchi	The string receiving the generated InChI.
options	The InChI C-API option string (see Chem::ControlParameter::INCHI_OUTPUT_OPTIONS).
dim	The dimensionality of the output atomic coordinates (see Chem::INCHIMolecularGraphWriter).

Returns

The InChI return code (see namespace Chem::INCHIReturnCode).

generateINCHIKey()

CDPL_CHEM_API int CDPL::Chem::generateINCHIKey	(	const MolecularGraph &	molgraph,
		std::string &	inchi_key
	)

Generates an InChIKey for the molecular graph molgraph using the InChI C-API.

Parameters

molgraph	The molecular graph.
inchi_key	The string receiving the generated InChIKey.

Returns

The InChI return code (see namespace Chem::INCHIReturnCode).

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
	)

Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to a user-supplied comparator.

Parameters

molgraph	The molecular graph.
func	The atom comparator that defines the canonical ordering.
atoms	true to sort atoms.
atom_nbrs	true to sort each atom's neighbor list.
bonds	true to sort bonds.
bond_atoms	true to reorder the start/end atoms of each bond according to the comparator.

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
	)

Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to the canonical number property value of its atoms.

Parameters

molgraph	The molecular graph.
atoms	true to sort atoms.
atom_nbrs	true to sort each atom's neighbor list.
bonds	true to sort bonds.
bond_atoms	true to reorder the start/end atoms of each bond.

calc2DCoordinates()

CDPL_CHEM_API void CDPL::Chem::calc2DCoordinates	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes 2D atom coordinates for the molecular graph molgraph and stores them as corresponding atom properties.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing 2D coordinates properties should be replaced.

align2DCoordinates() [1/4]

CDPL_CHEM_API bool CDPL::Chem::align2DCoordinates	(	MolecularGraph &	molgraph,
		const AtomContainer &	atoms,
		const Math::Vector2DArray &	ref_coords,
		bool	fix_bond_stereo = true
	)

Transforms the 2D atom coordinates of molgraph so that the 2D coordinates of atoms are aligned with the reference coordinates ref_coords.

Parameters

molgraph	The molecular graph to align.
atoms	The atoms used as alignment anchors.
ref_coords	Reference 2D coordinates of the alignment anchor atoms.
fix_bond_stereo	If true, postprocess 2D bond stereo flags so that they remain consistent with the aligned coordinates.

Returns

true if the alignment succeeded, and false otherwise.

Since

1.3

align2DCoordinates() [2/4]

CDPL_CHEM_API bool CDPL::Chem::align2DCoordinates	(	MolecularGraph &	molgraph,
		const AtomMapping &	ref_atom_mpg,
		bool	fix_bond_stereo = true
	)

Transforms the 2D atom coordinates of molgraph so that the 2D coordinates of the mapped atoms are aligned.

Parameters

molgraph	The molecular graph to align.
ref_atom_mpg	The atom mapping providing the target atom→atom correspondence.
fix_bond_stereo	If true, postprocess 2D bond stereo flags so that they remain consistent with the aligned coordinates.

Returns

true if the alignment succeeded, and false otherwise.

Since

1.3

align2DCoordinates() [3/4]

CDPL_CHEM_API bool CDPL::Chem::align2DCoordinates	(	MolecularGraph &	molgraph,
		const MolecularGraph &	ref_molgraph,
		bool	use_mcss,
		bool	fix_bond_stereo = true
	)

Aligns the 2D atom coordinates of molgraph with those of ref_molgraph, using either a maximum-common-substructure search or substructure matching.

Parameters

molgraph	The molecular graph to align.
ref_molgraph	The reference molecular graph providing the target coordinates.
use_mcss	If true, the atom correspondence is found by maximum common substructure search. Otherwise, by substructure matching.
fix_bond_stereo	If true, postprocess 2D bond stereo flags so that they remain consistent with the aligned coordinates.

Returns

true if the alignment succeeded, and false otherwise.

Since

1.3

align2DCoordinates() [4/4]

CDPL_CHEM_API bool CDPL::Chem::align2DCoordinates	(	MolecularGraph &	molgraph,
		const MolecularGraph &	ref_molgraph,
		const MolecularGraph &	substr_ptn,
		bool	fix_bond_stereo = true
	)

Aligns the 2D atom coordinates of molgraph with those of ref_molgraph, using substr_ptn as the explicit substructure search pattern.

Parameters

molgraph	The molecular graph to align.
ref_molgraph	The reference molecular graph providing the target coordinates.
substr_ptn	The substructure search pattern that defines the atoms to align.
fix_bond_stereo	If true, postprocess 2D bond stereo flags so that they remain consistent with the aligned coordinates.

Returns

true if the alignment succeeded, and false otherwise.

Since

1.3

calcHydrogen3DCoordinates()

CDPL_CHEM_API void CDPL::Chem::calcHydrogen3DCoordinates	(	MolecularGraph &	molgraph,
		bool	undef_only = true
	)

Computes 3D coordinates for the hydrogen atoms of the molecular graph molgraph from the 3D coordinates of their non-hydrogen neighbors.

Parameters

molgraph	The molecular graph.
undef_only	If true, only hydrogens without prior 3D coordinates are placed. If false, all hydrogen coordinates are recomputed.

calcBond2DStereoFlags()

CDPL_CHEM_API void CDPL::Chem::calcBond2DStereoFlags	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Derives 2D wedge/hash bond stereo flags for the bonds of the molecular graph molgraph from the atoms' stereo descriptors and 2D coordinates.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing 2D bond stereo flag properties should be replaced.

calcCIPPriorities()

CDPL_CHEM_API void CDPL::Chem::calcCIPPriorities	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores topological CIP priorities for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing CIP priority properties should be replaced.

See also

[TCIP]

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
	)

Computes and stores topological symmetry classes for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing symmetry class ID properties should be replaced.
atom_flags	A bitmask of Chem::AtomPropertyFlag flags controlling which atomic properties affect the perception.
bond_flags	A bitmask of Chem::BondPropertyFlag flags controlling which bond properties affect the perception.
inc_impl_h	If true, implicit hydrogens are treated as if they were explicit. Otherwise, they are ignored.

calcCanonicalNumbering()

CDPL_CHEM_API void CDPL::Chem::calcCanonicalNumbering	(	MolecularGraph &	molgraph,
		bool	overwrite,
		unsigned int	atom_flags = AtomPropertyFlag::DEFAULT,
		unsigned int	bond_flags = BondPropertyFlag::DEFAULT
	)

Computes and stores canonical atom numbers for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing canonical number properties should be replaced.
atom_flags	A bitmask of Chem::AtomPropertyFlag flags controlling which atomic properties affect the numbering.
bond_flags	A bitmask of Chem::BondPropertyFlag flags controlling which bond properties affect the numbering.

calcMorganNumbering()

CDPL_CHEM_API void CDPL::Chem::calcMorganNumbering	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores Morgan numbers for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing morgan number properties should be replaced.

calcImplicitHydrogenCounts()

CDPL_CHEM_API void CDPL::Chem::calcImplicitHydrogenCounts	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores implicit hydrogen counts for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing hydrogen count properties should be replaced.

calcFormalCharges()

CDPL_CHEM_API void CDPL::Chem::calcFormalCharges	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores formal charges for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing formal charge properties should be replaced.

perceiveHybridizationStates()

CDPL_CHEM_API void CDPL::Chem::perceiveHybridizationStates	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores hybridization states for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing hybridization state properties should be replaced.

perceiveBondOrders()

CDPL_CHEM_API void CDPL::Chem::perceiveBondOrders	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Perceives bond orders for the bonds of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing bond order properties should be replaced.

kekulizeBonds()

CDPL_CHEM_API void CDPL::Chem::kekulizeBonds

(

MolecularGraph &

molgraph

)

Assigns Kekulé bond orders to the aromatic bonds of the molecular graph molgraph.

Parameters

molgraph

The molecular graph.

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
	)

Flags the atoms of the molecular graph molgraph that qualify as stereo centers under the supplied criteria.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing stereo center flag properties should be replaced.
check_asym	true to enforce non-equivalent ligand environments.
check_inv_n	true to reject inversion-prone nitrogen centers.
check_quart_n	true to accept positively charged quaternary nitrogen centers.
check_plan_n	true to reject planar nitrogen centers.
check_amide_n	true to reject amide nitrogen centers.
check_res_ctrs	true to reject centers participating in resonance.

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
	)

Flags the bonds of the molecular graph molgraph that qualify as stereo centers under the supplied criteria.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing bond order properties should be replaced.
check_asym	true to enforce non-equivalent ligand environments.
check_term_n	true to reject bonds to terminal nitrogen atoms.
check_order	true to require that the bond order matches a stereogenic pattern.
min_ring_size	The minimum ring size required for ring bonds to qualify.

calcMDLParities()

CDPL_CHEM_API void CDPL::Chem::calcMDLParities	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores MDL parities for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing MDL parity properties should be replaced.

calcAtomStereoDescriptors()

CDPL_CHEM_API void CDPL::Chem::calcAtomStereoDescriptors	(	MolecularGraph &	molgraph,
		bool	overwrite,
		std::size_t	dim = 1,
		bool	check_stc_flag = true
	)

Computes and stores stereo descriptors for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing stereo descriptor properties should be replaced.
dim	The dimensionality of the atomic coordinates to use (2 = 2D, 3 = 3D, 0 = recalc. existing descriptor, other values = use any information available).
check_stc_flag	If true, descriptors are only computed for atoms whose Chem::AtomProperty::STEREO_CENTER_FLAG property is true.

calcAtomStereoDescriptorsFromMDLParities()

CDPL_CHEM_API void CDPL::Chem::calcAtomStereoDescriptorsFromMDLParities	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Derives atom stereo descriptors of the molecular graph molgraph from previously-assigned MDL parities.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing stereo descriptor properties should be replaced.

calcBondStereoDescriptors()

CDPL_CHEM_API void CDPL::Chem::calcBondStereoDescriptors	(	MolecularGraph &	molgraph,
		bool	overwrite,
		std::size_t	dim = 1,
		bool	check_stc_flag = true
	)

Computes and stores stereo descriptors for the bonds of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing stereo descriptor properties should be replaced.
dim	The dimensionality of the atomic coordinates to use (2 = 2D, 3 = 3D, 0 = recalc. existing descriptor, other values = use any information available).
check_stc_flag	If true, descriptors are only computed for bonds whose Chem::BondProperty::STEREO_CENTER_FLAG property is true.

calcAtomCIPConfigurations()

CDPL_CHEM_API void CDPL::Chem::calcAtomCIPConfigurations	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores CIP configuration labels for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing CIP configuration properties should be replaced.

calcBondCIPConfigurations()

CDPL_CHEM_API void CDPL::Chem::calcBondCIPConfigurations	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes and stores CIP configuration labels for the bonds of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing CIP configuration properties should be replaced.

setAtomMatchConstraints() [1/2]

CDPL_CHEM_API void CDPL::Chem::setAtomMatchConstraints	(	MolecularGraph &	molgraph,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

Sets the match constraint list constr on every atom of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
constr	The match constraint list to assign.
overwrite	Specifies whether already existing match constraint properties should be replaced.

setBondMatchConstraints() [1/2]

CDPL_CHEM_API void CDPL::Chem::setBondMatchConstraints	(	MolecularGraph &	molgraph,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

Sets the match constraint list constr on every bond of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
constr	The match constraint list to assign.
overwrite	Specifies whether already existing match constraint properties should be replaced.

generateMatchExpressions() [1/2]

CDPL_CHEM_API void CDPL::Chem::generateMatchExpressions	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Generates and stores match expressions for every atom, bond and the molecular graph molgraph itself.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing match expression properties should be replaced.

generateMatchExpressionStrings()

CDPL_CHEM_API void CDPL::Chem::generateMatchExpressionStrings	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Generates and stores textual representations of the atom/bond match expressions of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing match expression string properties should be replaced.

initSubstructureSearchQuery() [1/2]

CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchQuery	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Prepares the molecular graph molgraph for use as a substructure search query.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing property values should be replaced.

initSubstructureSearchTarget() [1/2]

CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchTarget	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Prepares the molecular graph molgraph for use as a substructure search target.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing property values should be replaced.

setAromaticityFlags()

CDPL_CHEM_API void CDPL::Chem::setAromaticityFlags	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Perceives aromaticity and sets the corresponding atom/bond aromaticity flags on the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing aromaticity flag properties should be replaced.

setRingFlags()

CDPL_CHEM_API void CDPL::Chem::setRingFlags	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Perceives ring membership and sets the corresponding atom/bond ring flags on the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing ring flag properties should be replaced.

setAtomTypesFromSymbols()

CDPL_CHEM_API void CDPL::Chem::setAtomTypesFromSymbols	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Sets the atom types of the molecular graph molgraph from their element symbols.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing atom type properties should be replaced.

setAtomSymbolsFromTypes()

CDPL_CHEM_API void CDPL::Chem::setAtomSymbolsFromTypes	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Sets the atom symbols of the molecular graph molgraph from their atom types.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing atom symbol properties should be replaced.

perceiveSybylAtomTypes()

CDPL_CHEM_API void CDPL::Chem::perceiveSybylAtomTypes	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Perceives and assigns Sybyl MOL2 atom types for the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing atom type properties should be replaced.

getAromaticRings()

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::getAromaticRings

(

const MolecularGraph &

molgraph

)

Returns the subset of the aromatic rings of the molecular graph molgraph.

Parameters

molgraph

The molecular graph.

Returns

The aromatic rings.

getAromaticSSSRSubset()

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::getAromaticSSSRSubset

(

const MolecularGraph &

molgraph

)

Returns the subset of the SSSR of the molecular graph molgraph that contains only aromatic rings,.

Parameters

molgraph

The molecular graph.

Returns

The aromatic SSSR subset.

containsMolecularGraph()

CDPL_CHEM_API bool CDPL::Chem::containsMolecularGraph	(	const MolecularGraph &	molgraph,
		const MolecularGraph &	sub_molgraph,
		bool	atoms = true,
		bool	bonds = true
	)

Tells whether the molecular graph molgraph contains the atoms and/or bonds of sub_molgraph.

Parameters

molgraph	The host molecular graph.
sub_molgraph	The candidate sub-graph.
atoms	If true, every atom of sub_molgraph must be a member of the molecular graph molgraph.
bonds	If true, every bond of sub_molgraph must be a member of the molecular graph molgraph.

Returns

true if the requested containment relations all hold, and false otherwise.

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
	)

Collects the fragments in frag_list that are fully contained in the molecular graph molgraph into cont_frag_list.

Parameters

molgraph	The host molecular graph.
frag_list	The candidate fragment list.
cont_frag_list	The output fragment list receiving the matches.
append	If true, matches are appended to cont_frag_list. Otherwise, it is cleared first.
atoms	If true, atom membership is required for a match.
bonds	If true, bond membership is required for a match.

getContainingFragments() [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
	)

Collects the fragments in frag_list that contain the molecular graph molgraph into cont_frag_list.

Parameters

molgraph	The query molecular graph.
frag_list	The candidate fragment list.
cont_frag_list	The output fragment list receiving the matches.
append	If true, matches are appended to cont_frag_list. Otherwise, it is cleared first.
atoms	If true, atom membership is required for a match.
bonds	If true, bond membership is required for a match.

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
	)

Translates the atoms/bonds of src_frag to the corresponding atoms/bonds of tgt_molgraph and stores them in tgt_frag.

Parameters

src_molgraph	The source molecular graph providing the original atoms/bonds.
src_frag	The fragment defining the atom/bond subset to translate (a fragment of the molecular graph src_molgraph).
tgt_molgraph	The target molecular graph providing the translated atoms/bonds.
tgt_frag	The output fragment receiving the translated atoms/bonds.
append	If true, atoms/bonds are appended to tgt_frag. Otherwise, it is cleared first.

translateFragments()

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
	)

Translates every fragment in src_frag_list to the corresponding fragments on tgt_molgraph.

Parameters

src_molgraph	The source molecular graph providing the original atoms/bonds.
src_frag_list	The fragments to translate (fragments of the molecular graph src_molgraph).
tgt_molgraph	The target molecular graph providing the translated atoms/bonds.
tgt_frag_list	The output fragment list receiving the translated fragments.
append	If true, fragments are appended to tgt_frag_list. Otherwise, it is cleared first.

splitIntoFragments()

CDPL_CHEM_API void CDPL::Chem::splitIntoFragments	(	const MolecularGraph &	molgraph,
		FragmentList &	frag_list,
		const Util::BitSet &	split_bond_mask,
		bool	append = false
	)

Splits the molecular graph molgraph into connected fragments by removing the bonds flagged in split_bond_mask.

Parameters

molgraph	The molecular graph to split.
frag_list	The output fragment list receiving the resulting fragments.
split_bond_mask	Bit mask selecting the bonds to be virtually removed before fragmentation (bit i corresponds to the bond at index i in molgraph).
append	If true, fragments are appended to frag_list. Otherwise, it is cleared first.

getCompleteBondCount()

CDPL_CHEM_API std::size_t CDPL::Chem::getCompleteBondCount

(

const MolecularGraph &

molgraph

)

Returns the number of bonds of the molecular graph molgraph whose connected atoms are likewise contained in molgraph.

Parameters

molgraph

The molecular graph.

Returns

The count of non-dangling bonds.

calcBasicProperties() [1/2]

CDPL_CHEM_API void CDPL::Chem::calcBasicProperties	(	MolecularGraph &	molgraph,
		bool	overwrite
	)

Computes basic atom/bond/molecular graph properties (aromaticity, SSSR, etc.) of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
overwrite	Specifies whether already existing property values should be replaced.

Since

1.1

editSubstructures() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::editSubstructures	(	const MolecularGraph &	molgraph,
		Molecule &	result_mol,
		const std::string &	search_ptns,
		const std::string &	result_ptn,
		const std::string &	exclude_ptns = std::string()
	)

Builds the molecule result_mol from the molecular graph molgraph by replacing all substructures matching the SMARTS patterns in search_ptns with result_ptn.

A molecule editing operation is specified via a string of one or more SMARTS patterns (search_ptns) describing the substructures to edit, optional substructure exclude patterns (exclude_ptns) and a SMILES string (result_ptn) encoding the specific atom and bond modifications to perform. If multiple search and/or exclude patterns are specified then they need to be separated by a whitespace character.

In the substructure search pattern(s), any atoms to be edited and/or atoms connected by bonds to be modified must be labeled by a unique non-zero integer number (by means of a colon followed the integer number at the end of the SMARTS atom specification). These numeric ids are used to establish an unambiguous mapping between the atoms/bonds of the search pattern and the SMILES string encoding the editing instructions. As mentioned above, the atom/bond editing operations are all specified by means of a simple SMILES string. For the purpose of substructure editing, the SMILES format has been extended by additional atom type and bond order symbols that allow to mark atom/bonds for deletion or act as a 'do not change' marker for atom type or bond order.

Editing result SMILES strings have to be composed according to the following rules:

• Atoms of the molecule matching labeled search pattern atoms are referenced by their numeric id (likewise specified by means of a colon followed by the integer number at the end of the SMILES atom specification)
• A bond between two labeled atoms in the result SMILES string will be mapped to the bond of the molecule that matched the corresponding bond of the search pattern
• If such a bond of the molecule does not exist it will be created with the specified bond order
• A molecule bond connecting two atoms that match labeled search pattern atoms which is not occurring in the result SMILES string will be left unchanged
• A molecule atom matching a labeled search pattern atom which is not occurring in the result SMILES string will be left unchanged
• A labeled atom in the result SMILES string with a numeric id that does not occur in the search pattern will be created with specified properties (symbol, form. charge, isotope, chirality, ...)
• Any unlabeled atoms in the result SMILES string will be created with the specified properties (symbol, form. charge, isotope, chirality, ...)
• Bonds to/between unlabeled result SMILES string atoms will be created with the specified bond order
• For a mapped molecule atom only those properties (symbol, form. charge, isotope, chirality, ...) that were specified for the corresponding result SMILES string atom will be modified
• The special result SMILES string atom type symbol x (only valid in brackets) results in the removal of the mapped molecule atom including any incident bonds
• The special result SMILES string atom type symbol ~ (only valid in brackets) indicates that the type of the mapped molecule atom shall be left unchanged
• The special result SMILES string bond order symbol x results in the removal of the mapped molecule bond
• The special result SMILES string bond order symbol ~ indicates that the order of the mapped molecule bond shall be left unchanged

Parameters

molgraph	The source molecular graph.
result_mol	The molecule receiving the edited result.
search_ptns	A whitespace-separated list of SMARTS patterns specifying the substructures to replace.
result_ptn	The SMARTS replacement pattern.
exclude_ptns	A whitespace-separated list of SMARTS patterns specifying substructures that shall be retained even if they also match search_ptns.

Returns

The number of performed substructure replacements.

Since

1.3

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 affected remaining 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 affected remaining atoms shall be corrected, false if the property shall be left unchanged.

Returns

false if mol was not altered, true otherwise.

See also

MolProp::isOrdinaryHydrogen

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 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
	)

Adds bonds between atoms of the molecule mol whose 3D distance falls within the covalent-radii sum plus dist_tol.

Parameters

mol	The molecule whose atoms shall be connected.
dist_tol	The tolerance added to the sum of the two atoms' covalent radii.
atom_idx_offs	Bonds are only added when at least one of the two atom indices is greater than or equal to atom_idx_offs.

Note

The minimum atom pair distance is 0.5 Å.

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
	)

Adds bonds between atoms of the molecule mol whose 3D distance (obtained via coords_func) falls within the covalent-radii sum plus dist_tol.

Parameters

mol	The molecule whose atoms are to be connected.
coords_func	The function used to retrieve the 3D coordinates of an atom.
dist_tol	The tolerance added to the sum of the two atoms' covalent radii.
atom_idx_offs	Bonds are only added when at least one of the two atom indices is greater than or equal to atom_idx_offs.

Note

The minimum atom pair distance is 0.5 Å.

removeAtomsIf() [2/2]

CDPL_CHEM_API void CDPL::Chem::removeAtomsIf	(	Molecule &	mol,
		const AtomPredicate &	pred
	)

Removes all atoms of the molecule mol for which the predicate pred returns true.

Parameters

mol	The molecule to filter in place.
pred	The atom predicate to evaluate.

removeAtomsIfNot() [2/2]

CDPL_CHEM_API void CDPL::Chem::removeAtomsIfNot	(	Molecule &	mol,
		const AtomPredicate &	pred
	)

Removes all atoms of the molecule mol for which the predicate pred returns false.

Parameters

mol	The molecule to filter in place.
pred	The atom predicate to evaluate.

editSubstructures() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::editSubstructures	(	Molecule &	mol,
		const std::string &	search_ptns,
		const std::string &	result_ptn,
		const std::string &	exclude_ptns = std::string()
	)

Edits the molecule mol by replacing all substructures matching the SMARTS search patterns in search_ptns with the SMILES replacement pattern result_ptn, optionally skipping matches that also match exclude_ptns.

A molecule editing operation is specified via a string of one or more SMARTS patterns (search_ptns) describing the substructures to edit, optional substructure exclude patterns (exclude_ptns) and a SMILES string (result_ptn) encoding the specific atom and bond modifications to perform. If multiple search and/or exclude patterns are specified then they need to be separated by a whitespace character.

In the substructure search pattern(s), any atoms to be edited and/or atoms connected by bonds to be modified must be labeled by a unique non-zero integer number (by means of a colon followed the integer number at the end of the SMARTS atom specification). These numeric ids are used to establish an unambiguous mapping between the atoms/bonds of the search pattern and the SMILES string encoding the editing instructions. As mentioned above, the atom/bond editing operations are all specified by means of a simple SMILES string. For the purpose of substructure editing, the SMILES format has been extended by additional atom type and bond order symbols that allow to mark atom/bonds for deletion or act as a 'do not change' marker for atom type or bond order.

Editing result SMILES strings have to be composed according to the following rules:

• Atoms of the molecule matching labeled search pattern atoms are referenced by their numeric id (likewise specified by means of a colon followed by the integer number at the end of the SMILES atom specification)
• A bond between two labeled atoms in the result SMILES string will be mapped to the bond of the molecule that matched the corresponding bond of the search pattern
• If such a bond of the molecule does not exist it will be created with the specified bond order
• A molecule bond connecting two atoms that match labeled search pattern atoms which is not occurring in the result SMILES string will be left unchanged
• A molecule atom matching a labeled search pattern atom which is not occurring in the result SMILES string will be left unchanged
• A labeled atom in the result SMILES string with a numeric id that does not occur in the search pattern will be created with specified properties (symbol, form. charge, isotope, chirality, ...)
• Any unlabeled atoms in the result SMILES string will be created with the specified properties (symbol, form. charge, isotope, chirality, ...)
• Bonds to/between unlabeled result SMILES string atoms will be created with the specified bond order
• For a mapped molecule atom only those properties (symbol, form. charge, isotope, chirality, ...) that were specified for the corresponding result SMILES string atom will be modified
• The special result SMILES string atom type symbol x (only valid in brackets) results in the removal of the mapped molecule atom including any incident bonds
• The special result SMILES string atom type symbol ~ (only valid in brackets) indicates that the type of the mapped molecule atom shall be left unchanged
• The special result SMILES string bond order symbol x results in the removal of the mapped molecule bond
• The special result SMILES string bond order symbol ~ indicates that the order of the mapped molecule bond shall be left unchanged

Parameters

mol	The molecule to edit in place.
search_ptns	A whitespace-separated list of SMARTS patterns specifying the substructures to replace.
result_ptn	The SMARTS replacement pattern.
exclude_ptns	A whitespace-separated list of SMARTS patterns specifying substructures that shall be retained even if they match search_ptns.

Returns

The number of performed substructure replacements.

Since

1.3

getName() [3/3]

CDPL_CHEM_API const std::string& CDPL::Chem::getName

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::NAME property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored reaction name.

setName() [3/3]

CDPL_CHEM_API void CDPL::Chem::setName	(	Reaction &	rxn,
		const std::string &	name
	)

Sets the value of the Chem::ReactionProperty::NAME property of the reaction rxn to name.

Parameters

rxn	The reaction for which to set the property value.
name	The new reaction name.

clearName() [3/3]

CDPL_CHEM_API void CDPL::Chem::clearName

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::NAME property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasName() [3/3]

CDPL_CHEM_API bool CDPL::Chem::hasName

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::NAME property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getTimestamp() [2/2]

CDPL_CHEM_API std::time_t CDPL::Chem::getTimestamp

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::TIMESTAMP property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored timestamp.

setTimestamp() [2/2]

CDPL_CHEM_API void CDPL::Chem::setTimestamp	(	Reaction &	rxn,
		std::time_t	time
	)

Sets the value of the Chem::ReactionProperty::TIMESTAMP property of the reaction rxn to time.

Parameters

rxn	The reaction for which to set the property value.
time	The new timestamp value.

clearTimestamp() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearTimestamp

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::TIMESTAMP property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasTimestamp() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasTimestamp

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::TIMESTAMP property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getComment() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getComment

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::COMMENT property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored comment.

setComment() [2/2]

CDPL_CHEM_API void CDPL::Chem::setComment	(	Reaction &	rxn,
		const std::string &	comment
	)

Sets the value of the Chem::ReactionProperty::COMMENT property of the reaction rxn to comment.

Parameters

rxn	The reaction for which to set the property value.
comment	The new comment string.

clearComment() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearComment

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::COMMENT property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasComment() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasComment

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::COMMENT property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMatchExpression() [4/4]

CDPL_CHEM_API const MatchExpression<Reaction>::SharedPointer& CDPL::Chem::getMatchExpression

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::MATCH_EXPRESSION property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored reaction match expression.

setMatchExpression() [4/4]

CDPL_CHEM_API void CDPL::Chem::setMatchExpression	(	Reaction &	rxn,
		const MatchExpression< Reaction >::SharedPointer &	expr
	)

Sets the value of the Chem::ReactionProperty::MATCH_EXPRESSION property of the reaction rxn to expr.

Parameters

rxn	The reaction for which to set the property value.
expr	The new match expression to store.

clearMatchExpression() [4/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::MATCH_EXPRESSION property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasMatchExpression() [4/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::MATCH_EXPRESSION property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

generateMatchExpression() [5/6]

CDPL_CHEM_API MatchExpression<Reaction>::SharedPointer CDPL::Chem::generateMatchExpression

(

const Reaction &

rxn

)

Builds a match expression from the match constraints currently attached to the reaction rxn.

Parameters

rxn	The reaction.

Returns

The generated match expression.

generateMatchExpression() [6/6]

CDPL_CHEM_API MatchExpression<Reaction>::SharedPointer CDPL::Chem::generateMatchExpression	(	Reaction &	rxn,
		bool	overwrite
	)

Builds and stores the match expression of the reaction rxn.

Parameters

rxn	The reaction.
overwrite	Specifies whether an already existing match expression property should be replaced.

Returns

The generated (or pre-existing) match expression.

getMatchConstraints() [4/4]

CDPL_CHEM_API const MatchConstraintList::SharedPointer& CDPL::Chem::getMatchConstraints

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::MATCH_CONSTRAINTS property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored match constraint list.

setMatchConstraints() [4/4]

CDPL_CHEM_API void CDPL::Chem::setMatchConstraints	(	Reaction &	rxn,
		const MatchConstraintList::SharedPointer &	constr
	)

Sets the value of the Chem::ReactionProperty::MATCH_CONSTRAINTS property of the reaction rxn to constr.

Parameters

rxn	The reaction for which to set the property value.
constr	The new match constraint list to store.

clearMatchConstraints() [4/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::MATCH_CONSTRAINTS property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasMatchConstraints() [4/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::MATCH_CONSTRAINTS property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getComponentGroups() [2/2]

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getComponentGroups

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::COMPONENT_GROUPS property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored component-group fragment list.

setComponentGroups() [2/2]

CDPL_CHEM_API void CDPL::Chem::setComponentGroups	(	Reaction &	rxn,
		const FragmentList::SharedPointer &	comp_groups
	)

Sets the value of the Chem::ReactionProperty::COMPONENT_GROUPS property of the reaction rxn to comp_groups.

Parameters

rxn	The reaction for which to set the property value.
comp_groups	The new component-group fragment list.

clearComponentGroups() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearComponentGroups

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::COMPONENT_GROUPS property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasComponentGroups() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasComponentGroups

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::COMPONENT_GROUPS property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveComponentGroups() [3/4]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups

(

const Reaction &

rxn

)

Perceives the component groups of the reaction rxn.

Parameters

rxn	The reaction.

Returns

The perceived component group fragment list.

perceiveComponentGroups() [4/4]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups	(	Reaction &	rxn,
		bool	overwrite
	)

Perceives and stores the component groups of the reaction rxn.

Parameters

rxn	The reaction.
overwrite	Specifies whether an already existing component groups property should be replaced.

Returns

The perceived (or pre-existing) component group fragment list.

getAtomMapping()

CDPL_CHEM_API const AtomMapping::SharedPointer& CDPL::Chem::getAtomMapping

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::ATOM_MAPPING property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored reactant-to-product atom mapping.

setAtomMapping()

CDPL_CHEM_API void CDPL::Chem::setAtomMapping	(	Reaction &	rxn,
		const AtomMapping::SharedPointer &	mapping
	)

Sets the value of the Chem::ReactionProperty::ATOM_MAPPING property of the reaction rxn to mapping.

Parameters

rxn	The reaction for which to set the property value.
mapping	The new reactant-to-product atom mapping.

clearAtomMapping()

CDPL_CHEM_API void CDPL::Chem::clearAtomMapping

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::ATOM_MAPPING property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasAtomMapping()

CDPL_CHEM_API bool CDPL::Chem::hasAtomMapping

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::ATOM_MAPPING property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

perceiveAtomMapping() [1/2]

CDPL_CHEM_API AtomMapping::SharedPointer CDPL::Chem::perceiveAtomMapping

(

const Reaction &

rxn

)

Derives the reactant-to-product atom mapping from the atom mapping IDs of the reaction rxn.

Parameters

rxn	The reaction.

Returns

The perceived atom mapping.

perceiveAtomMapping() [2/2]

CDPL_CHEM_API AtomMapping::SharedPointer CDPL::Chem::perceiveAtomMapping	(	Reaction &	rxn,
		bool	overwrite
	)

Derives and stores the reactant-to-product atom mapping of the reaction rxn.

Parameters

rxn	The reaction.
overwrite	Specifies whether an already existing atom mapping property should be replaced.

Returns

The perceived (or pre-existing) atom mapping.

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
	)

Generates a reaction SMILES string for the reaction rxn.

Parameters

rxn	The reaction to encode.
smiles	The string to receiving the generated reaction SMILES.
canonical	true to emit a canonical reaction SMILES.
ord_h_deplete	true to suppress the output ordinary hydrogens.
atom_flags	A bitmask of Chem::AtomPropertyFlag flags controlling which atomic properties to encode.
bond_flags	A bitmask of Chem::BondPropertyFlag flags controlling which bond properties to encode.

Returns

true on success, and false if an unrecoverable error was encountered.

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
	)

Computes a 64-bit hash code for the reaction rxn taking into account the specified reaction roles and atom/bond properties.

Parameters

rxn	The reaction to hash.
role_mask	A bitmask of Chem::ReactionRole flags selecting the considered component sets.
atom_flags	A bitmask of Chem::AtomPropertyFlag flags controlling which atomic properties enter the hash.
bond_flags	A bitmask of Chem::BondPropertyFlag flags controlling which bond properties enter the hash.
ord_h_deplete	true to suppress ordinary hydrogens before hashing.

Returns

The computed hash code.

getMDLUserInitials() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLUserInitials

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::MDL_USER_INITIALS property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL user initials.

setMDLUserInitials() [2/2]

CDPL_CHEM_API void CDPL::Chem::setMDLUserInitials	(	Reaction &	rxn,
		const std::string &	initials
	)

Sets the value of the Chem::ReactionProperty::MDL_USER_INITIALS property of the reaction rxn to initials.

Parameters

rxn	The reaction for which to set the property value.
initials	The new MDL user initials.

clearMDLUserInitials() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLUserInitials

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::MDL_USER_INITIALS property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasMDLUserInitials() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLUserInitials

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::MDL_USER_INITIALS property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLProgramName() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLProgramName

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::MDL_PROGRAM_NAME property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL program name.

setMDLProgramName() [2/2]

CDPL_CHEM_API void CDPL::Chem::setMDLProgramName	(	Reaction &	rxn,
		const std::string &	name
	)

Sets the value of the Chem::ReactionProperty::MDL_PROGRAM_NAME property of the reaction rxn to name.

Parameters

rxn	The reaction for which to set the property value.
name	The new MDL program name.

clearMDLProgramName() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLProgramName

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::MDL_PROGRAM_NAME property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasMDLProgramName() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLProgramName

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::MDL_PROGRAM_NAME property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLRegistryNumber() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMDLRegistryNumber

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::MDL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL registry number.

setMDLRegistryNumber() [2/2]

CDPL_CHEM_API void CDPL::Chem::setMDLRegistryNumber	(	Reaction &	rxn,
		std::size_t	reg_no
	)

Sets the value of the Chem::ReactionProperty::MDL_REGISTRY_NUMBER property of the reaction rxn to reg_no.

Parameters

rxn	The reaction for which to set the property value.
reg_no	The new MDL registry number.

clearMDLRegistryNumber() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLRegistryNumber

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::MDL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasMDLRegistryNumber() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLRegistryNumber

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::MDL_REGISTRY_NUMBER property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getReactionData()

CDPL_CHEM_API const StringDataBlock::SharedPointer& CDPL::Chem::getReactionData

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::REACTION_DATA property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored reaction data block.

setReactionData()

CDPL_CHEM_API void CDPL::Chem::setReactionData	(	Reaction &	rxn,
		const StringDataBlock::SharedPointer &	data
	)

Sets the value of the Chem::ReactionProperty::REACTION_DATA property of the reaction rxn to data.

Parameters

rxn	The reaction for which to set the property value.
data	The new reaction data block.

clearReactionData()

CDPL_CHEM_API void CDPL::Chem::clearReactionData

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::REACTION_DATA property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasReactionData()

CDPL_CHEM_API bool CDPL::Chem::hasReactionData

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::REACTION_DATA property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLMoleculeRecord()

CDPL_CHEM_API const Molecule::SharedPointer& CDPL::Chem::getMDLMoleculeRecord

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::MDL_MOLECULE_RECORD property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL RD-File molecule record.

setMDLMoleculeRecord()

CDPL_CHEM_API void CDPL::Chem::setMDLMoleculeRecord	(	Reaction &	rxn,
		const Molecule::SharedPointer &	mol_rec
	)

Sets the value of the Chem::ReactionProperty::MDL_MOLECULE_RECORD property of the reaction rxn to mol_rec.

Parameters

rxn	The reaction for which to set the property value.
mol_rec	The new MDL RD-File molecule record.

clearMDLMoleculeRecord()

CDPL_CHEM_API void CDPL::Chem::clearMDLMoleculeRecord

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::MDL_MOLECULE_RECORD property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasMDLMoleculeRecord()

CDPL_CHEM_API bool CDPL::Chem::hasMDLMoleculeRecord

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::MDL_MOLECULE_RECORD property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLInternalRegistryNumber()

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLInternalRegistryNumber

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL internal registry number.

setMDLInternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::setMDLInternalRegistryNumber	(	Reaction &	rxn,
		const std::string &	reg_no
	)

Sets the value of the Chem::ReactionProperty::MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no.

Parameters

rxn	The reaction for which to set the property value.
reg_no	The new MDL internal registry number.

clearMDLInternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::clearMDLInternalRegistryNumber

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasMDLInternalRegistryNumber()

CDPL_CHEM_API bool CDPL::Chem::hasMDLInternalRegistryNumber

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLExternalRegistryNumber()

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLExternalRegistryNumber

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL external registry number.

setMDLExternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::setMDLExternalRegistryNumber	(	Reaction &	rxn,
		const std::string &	reg_no
	)

Sets the value of the Chem::ReactionProperty::MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no.

Parameters

rxn	The reaction for which to set the property value.
reg_no	The new MDL external registry number.

clearMDLExternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::clearMDLExternalRegistryNumber

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasMDLExternalRegistryNumber()

CDPL_CHEM_API bool CDPL::Chem::hasMDLExternalRegistryNumber

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMDLRXNFileVersion()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLRXNFileVersion

(

const Reaction &

rxn

)

Returns the value of the Chem::ReactionProperty::MDL_RXN_FILE_VERSION property of the reaction rxn.

Parameters

rxn	The reaction for which to return the property value.

Returns

The stored MDL Rxn-File version (see Chem::MDLDataFormatVersion).

setMDLRXNFileVersion()

CDPL_CHEM_API void CDPL::Chem::setMDLRXNFileVersion	(	Reaction &	rxn,
		unsigned int	version
	)

Sets the value of the Chem::ReactionProperty::MDL_RXN_FILE_VERSION property of the reaction rxn to version.

Parameters

rxn	The reaction for which to set the property value.
version	The new MDL Rxn-File version (see Chem::MDLDataFormatVersion).

clearMDLRXNFileVersion()

CDPL_CHEM_API void CDPL::Chem::clearMDLRXNFileVersion

(

Reaction &

rxn

)

Clears the value of the Chem::ReactionProperty::MDL_RXN_FILE_VERSION property of the reaction rxn.

Parameters

rxn	The reaction for which to clear the property value.

hasMDLRXNFileVersion()

CDPL_CHEM_API bool CDPL::Chem::hasMDLRXNFileVersion

(

const Reaction &

rxn

)

Tells whether the Chem::ReactionProperty::MDL_RXN_FILE_VERSION property of the reaction rxn is set.

Parameters

rxn	The reaction for which to query the property value.

Returns

true if the property is set, and false otherwise.

getMaxComponentGroupID() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxComponentGroupID

(

const Reaction &

rxn

)

Returns the largest component group ID found for any of the atoms of the components of the reaction rxn.

Parameters

rxn	The reaction to scan.

Returns

The largest component group ID, or zero if no IDs are assigned.

getMaxAtomMappingID() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxAtomMappingID

(

const Reaction &

rxn

)

Returns the largest atom mapping ID found for any of the atoms of the components of the reaction rxn.

Parameters

rxn	The reaction to scan.

Returns

The largest atom mapping ID, or zero if no IDs are assigned.

setAtomMatchConstraints() [2/2]

CDPL_CHEM_API void CDPL::Chem::setAtomMatchConstraints	(	Reaction &	rxn,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

Sets the atom-level match constraint list constr on every atom of every component of the reaction rxn.

Parameters

rxn	The reaction.
constr	The match constraint list to assign.
overwrite	Specifies whether already existing match constraints properties should be replaced.

setBondMatchConstraints() [2/2]

CDPL_CHEM_API void CDPL::Chem::setBondMatchConstraints	(	Reaction &	rxn,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

Sets the bond-level match constraint list constr on every bond of every component of the reaction rxn.

Parameters

rxn	The reaction.
constr	The match constraint list to assign.
overwrite	Specifies whether already existing match constraint properties should be replaced.

setComponentMatchConstraints()

CDPL_CHEM_API void CDPL::Chem::setComponentMatchConstraints	(	Reaction &	rxn,
		const MatchConstraintList::SharedPointer &	constr,
		bool	overwrite
	)

Sets the molecular graph-level match constraint list constr on every component of the reaction rxn.

Parameters

rxn	The reaction.
constr	The match constraint list to assign.
overwrite	Specifies whether already existing match constraint properties should be replaced.

generateMatchExpressions() [2/2]

CDPL_CHEM_API void CDPL::Chem::generateMatchExpressions	(	Reaction &	rxn,
		bool	overwrite
	)

Generates and stores match expressions for the atoms, bonds, components, and the reaction rxn itself.

Parameters

rxn	The reaction.
overwrite	Specifies whether already existing match expression properties should be replaced.

initSubstructureSearchQuery() [2/2]

CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchQuery	(	Reaction &	rxn,
		bool	overwrite
	)

Prepares the reaction rxn for use as a reaction substructure search query.

Parameters

rxn	The reaction.
overwrite	Specifies whether already existing property values should be replaced.

initSubstructureSearchTarget() [2/2]

CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchTarget	(	Reaction &	rxn,
		bool	overwrite
	)

Prepares the reaction rxn for use as a reaction substructure search target.

Parameters

rxn	The reaction.
overwrite	Specifies whether already existing property values should be replaced.

calcBasicProperties() [2/2]

CDPL_CHEM_API void CDPL::Chem::calcBasicProperties	(	Reaction &	rxn,
		bool	overwrite
	)

Computes basic atom/bond/molecular graph properties (aromaticity, ring info, etc.) for every component of the reaction rxn.

Parameters

rxn	The reaction.
overwrite	Specifies whether already existing property values should be replaced.

Since

1.1

parseSMARTS() [1/2]

CDPL_CHEM_API Molecule::SharedPointer CDPL::Chem::parseSMARTS	(	const std::string &	smarts,
		bool	init_qry = true
	)

Parses the SMARTS string smarts into a freshly allocated query Chem::Molecule.

Parameters

smarts	The SMARTS string to parse.
init_qry	If true, query-specific perception (e.g. ring-membership, aromaticity) is run on the parsed molecule.

Returns

A smart pointer to the parsed molecule, or an empty smart pointer if parsing failed.

parseSMARTS() [2/2]

CDPL_CHEM_API bool CDPL::Chem::parseSMARTS	(	const std::string &	smarts,
		Molecule &	mol,
		bool	init_qry = true
	)

Parses the SMARTS string smarts into the supplied molecule mol.

Parameters

smarts	The SMARTS string to parse.
mol	The molecule to populate (cleared before parsing).
init_qry	If true, query-specific perception is run on the parsed molecule.

Returns

true if parsing succeeded, and false otherwise.

parseSMILES() [1/2]

CDPL_CHEM_API Molecule::SharedPointer CDPL::Chem::parseSMILES

(

const std::string &

smiles

)

Parses the SMILES string smiles into a freshly allocated Chem::Molecule.

Parameters

smiles

The SMILES string to parse.

Returns

A smart pointer to the parsed molecule, or an empty smart pointer if parsing failed.

parseSMILES() [2/2]

CDPL_CHEM_API bool CDPL::Chem::parseSMILES	(	const std::string &	smiles,
		Molecule &	mol
	)

Parses the SMILES string smiles into the supplied molecule mol.

Parameters

smiles	The SMILES string to parse.
mol	The molecule to populate (cleared before parsing).

Returns

true if parsing succeeded, and false otherwise.

extendBoundingBox()

CDPL_CHEM_API void CDPL::Chem::extendBoundingBox	(	Math::Vector3D &	min,
		Math::Vector3D &	max,
		const Math::Vector3D &	coords,
		bool	reset = false
	)

Extends the axis-aligned bounding box defined by min and max so that it contains the point coords.

Parameters

min	The lower-left corner of the bounding box (updated in place).
max	The upper-right corner of the bounding box (updated in place).
coords	The 3D point to include.
reset	If true, the bounding box is first reset to coords (degenerate point box) before extension.

insideBoundingBox() [3/3]

CDPL_CHEM_API bool CDPL::Chem::insideBoundingBox	(	const Math::Vector3D &	min,
		const Math::Vector3D &	max,
		const Math::Vector3D &	coords
	)

Tells whether the point coords lies inside the axis-aligned bounding box defined by min and max.

Parameters

min	The lower-left corner of the bounding box.
max	The upper-right corner of the bounding box.
coords	The 3D point to test.

Returns

true if the point is inside (componentwise <= max and >= min), and false otherwise.

isAromatic()

CDPL_CHEM_API bool CDPL::Chem::isAromatic	(	const Fragment &	ring,
		const MolecularGraph &	molgraph,
		const Util::BitSet &	arom_bond_mask
	)

Tells whether ring fulfills the Hückel (4n+2)π-electron criterion within molgraph.

Parameters

ring	The candidate aromatic ring.
molgraph	The parent molecular graph.
arom_bond_mask	A bond bit mask flagging bonds already known to be aromatic.

Returns

true if ring satisfies the Hückel rule, and false otherwise.

isNotAromatic()

CDPL_CHEM_API bool CDPL::Chem::isNotAromatic	(	const Fragment &	ring,
		const MolecularGraph &	molgraph
	)

Tells whether ring is guaranteed not to be aromatic (based on quick geometric/topological criteria).

Parameters

ring	The ring to test.
molgraph	The parent molecular graph.

Returns

true if ring cannot be aromatic, and false if a more thorough test is required.

containsFragmentWithBond()

CDPL_CHEM_API bool CDPL::Chem::containsFragmentWithBond	(	const FragmentList &	frag_list,
		const Bond &	bond
	)

Tells whether any fragment in frag_list contains the bond bond.

Parameters

frag_list	The list of fragments to search.
bond	The queried bond.

Returns

true if at least one fragment contains bond, and false otherwise.

containsFragmentWithMinSize()

CDPL_CHEM_API bool CDPL::Chem::containsFragmentWithMinSize	(	const FragmentList &	frag_list,
		std::size_t	min_size
	)

Tells whether frag_list contains at least one fragment with at least min_size atoms.

Parameters

frag_list	The list of fragments to search.
min_size	The minimum required atom count.

Returns

true if such a fragment exists, and false otherwise.

atomTypesMatch()

CDPL_CHEM_API bool CDPL::Chem::atomTypesMatch	(	unsigned int	qry_type,
		unsigned int	tgt_type
	)

Tells whether the target atom type tgt_type matches the query atom type qry_type (taking generic atom type classes like Chem::AtomType::HET into account).

Parameters

qry_type	The query atom type (Chem::AtomType value).
tgt_type	The target atom type (Chem::AtomType value).

Returns

true if the target matches the query, and false otherwise.

sybylToAtomType()

CDPL_CHEM_API unsigned int CDPL::Chem::sybylToAtomType

(

unsigned int

sybyl_type

)

Translates a Sybyl atom type identifier to the corresponding generic Chem::AtomType value.

Parameters

sybyl_type

The Sybyl atom type identifier (Chem::SybylAtomType value).

Returns

The corresponding Chem::AtomType value.

getSybylAtomTypeString()

CDPL_CHEM_API const std::string& CDPL::Chem::getSybylAtomTypeString

(

unsigned int

sybyl_type

)

Returns the canonical textual representation of the Sybyl atom type sybyl_type.

Parameters

sybyl_type

The Sybyl atom type identifier (Chem::SybylAtomType value).

Returns

A const reference to the type-name string (empty for unknown types).

getSybylBondTypeString()

CDPL_CHEM_API const std::string& CDPL::Chem::getSybylBondTypeString

(

unsigned int

sybyl_type

)

Returns the canonical textual representation of the Sybyl bond type sybyl_type.

Parameters

sybyl_type

The Sybyl bond-type identifier (Chem::SybylBondType value).

Returns

A const reference to the type-name string (empty for unknown types).