Chemical Data Processing Library C++ API - Version 1.1.1
Namespaces | Classes | Typedefs | Functions
CDPL::Chem Namespace Reference

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

Namespaces

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

Classes

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

Typedefs

typedef std::function< const Math::Vector3D &(const Chem::Atom &)> Atom3DCoordinatesFunction
 A generic wrapper class used to store a user-defined Chem::Atom 3D-coordinates function. More...
 
typedef std::function< bool(const Chem::Atom &, const Chem::Atom &)> AtomCompareFunction
 A generic wrapper class used to store a user-defined atom compare function. More...
 
typedef std::function< bool(const Chem::Atom &)> AtomPredicate
 A generic wrapper class used to store a user-defined atom predicate. More...
 
typedef std::function< std::size_t(const Chem::Atom &)> AtomPriorityFunction
 A generic wrapper class used to store a user-defined atom priority function. More...
 
typedef std::function< bool(const Chem::Bond &, const Chem::Bond &)> BondCompareFunction
 A generic wrapper class used to store a user-defined bond compare function. More...
 
typedef std::function< bool(const Chem::Bond &)> BondPredicate
 A generic wrapper class used to store a user-defined bond predicate. More...
 
typedef Util::DefaultDataOutputHandler< CDFBZ2MolecularGraphWriter, DataFormat::CDF_BZ2CDFBZ2MolecularGraphOutputHandler
 A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More...
 
typedef Util::CompressedDataWriter< CDFMolecularGraphWriter, Util::BZip2OStreamCDFBZ2MolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< CDFBZ2MoleculeReader, DataFormat::CDF_BZ2CDFBZ2MoleculeInputHandler
 A handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL. More...
 
typedef Util::CompressedDataReader< CDFMoleculeReader, Util::BZip2IStreamCDFBZ2MoleculeReader
 
typedef Util::DefaultDataInputHandler< CDFBZ2ReactionReader, DataFormat::CDF_BZ2CDFBZ2ReactionInputHandler
 A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More...
 
typedef Util::DefaultDataOutputHandler< CDFBZ2ReactionWriter, DataFormat::CDF_BZ2CDFBZ2ReactionOutputHandler
 A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More...
 
typedef Util::CompressedDataReader< CDFReactionReader, Util::BZip2IStreamCDFBZ2ReactionReader
 
typedef Util::CompressedDataWriter< CDFReactionWriter, Util::BZip2OStreamCDFBZ2ReactionWriter
 
typedef Util::DefaultDataOutputHandler< CDFGZMolecularGraphWriter, DataFormat::CDF_GZCDFGZMolecularGraphOutputHandler
 A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More...
 
typedef Util::CompressedDataWriter< CDFMolecularGraphWriter, Util::GZipOStreamCDFGZMolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< CDFGZMoleculeReader, DataFormat::CDF_GZCDFGZMoleculeInputHandler
 A handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL. More...
 
typedef Util::CompressedDataReader< CDFMoleculeReader, Util::GZipIStreamCDFGZMoleculeReader
 
typedef Util::DefaultDataInputHandler< CDFGZReactionReader, DataFormat::CDF_GZCDFGZReactionInputHandler
 A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More...
 
typedef Util::DefaultDataOutputHandler< CDFGZReactionWriter, DataFormat::CDF_GZCDFGZReactionOutputHandler
 A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More...
 
typedef Util::CompressedDataReader< CDFReactionReader, Util::GZipIStreamCDFGZReactionReader
 
typedef Util::CompressedDataWriter< CDFReactionWriter, Util::GZipOStreamCDFGZReactionWriter
 
typedef Util::DefaultDataOutputHandler< CDFMolecularGraphWriter, DataFormat::CDFCDFMolecularGraphOutputHandler
 A handler for the output of molecular graph data in the native I/O format of the CDPL. More...
 
typedef Util::DefaultDataInputHandler< CDFMoleculeReader, DataFormat::CDFCDFMoleculeInputHandler
 A handler for the input of molecule data in the native I/O format of the CDPL. More...
 
typedef Util::DefaultDataInputHandler< CDFReactionReader, DataFormat::CDFCDFReactionInputHandler
 A handler for the input of reaction data in the native I/O format of the CDPL. More...
 
typedef Util::DefaultDataOutputHandler< CDFReactionWriter, DataFormat::CDFCDFReactionOutputHandler
 A handler for the output of reaction data in the native I/O format of the CDPL. More...
 
typedef std::function< const Math::Vector3D &(const Chem::Entity &)> Entity3DCoordinatesFunction
 A generic wrapper class used to store a user-defined Chem::Entity3D coordinates function. More...
 
typedef Util::DefaultDataOutputHandler< INCHIMolecularGraphWriter, DataFormat::INCHIINCHIMolecularGraphOutputHandler
 A handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
 
typedef Util::DefaultDataInputHandler< INCHIMoleculeReader, DataFormat::INCHIINCHIMoleculeInputHandler
 A handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
 
typedef Util::DefaultDataOutputHandler< JMEMolecularGraphWriter, DataFormat::JMEJMEMolecularGraphOutputHandler
 A handler for the output of molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
 
typedef Util::DefaultDataInputHandler< JMEMoleculeReader, DataFormat::JMEJMEMoleculeInputHandler
 A handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
 
typedef Util::DefaultDataInputHandler< JMEReactionReader, DataFormat::JMEJMEReactionInputHandler
 A handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
 
typedef Util::DefaultDataOutputHandler< JMEReactionWriter, DataFormat::JMEJMEReactionOutputHandler
 A handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
 
typedef Util::DefaultDataOutputHandler< MOL2BZ2MolecularGraphWriter, DataFormat::MOL2_BZ2MOL2BZ2MolecularGraphOutputHandler
 A handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format. More...
 
typedef Util::CompressedDataWriter< MOL2MolecularGraphWriter, Util::BZip2OStreamMOL2BZ2MolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< MOL2BZ2MoleculeReader, DataFormat::MOL2_BZ2MOL2BZ2MoleculeInputHandler
 A handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format. More...
 
typedef Util::CompressedDataReader< MOL2MoleculeReader, Util::BZip2IStreamMOL2BZ2MoleculeReader
 
typedef Util::DefaultDataOutputHandler< MOL2GZMolecularGraphWriter, DataFormat::MOL2_GZMOL2GZMolecularGraphOutputHandler
 A handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format. More...
 
typedef Util::CompressedDataWriter< MOL2MolecularGraphWriter, Util::GZipOStreamMOL2GZMolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< MOL2GZMoleculeReader, DataFormat::MOL2_GZMOL2GZMoleculeInputHandler
 A handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format. More...
 
typedef Util::CompressedDataReader< MOL2MoleculeReader, Util::GZipIStreamMOL2GZMoleculeReader
 
typedef Util::DefaultDataOutputHandler< MOL2MolecularGraphWriter, DataFormat::MOL2MOL2MolecularGraphOutputHandler
 A handler for the output of molecular graph data in the Sybyl MOL2 format. More...
 
typedef Util::DefaultDataInputHandler< MOL2MoleculeReader, DataFormat::MOL2MOL2MoleculeInputHandler
 A handler for the input of molecule data in the Sybyl MOL2 format. More...
 
typedef Util::MultiFormatDataWriter< MolecularGraphMolecularGraphWriter
 Writer for molecule data in any supported format. More...
 
typedef Util::MultiFormatDataReader< MoleculeMoleculeReader
 Reader for molecule data in any supported format. More...
 
typedef Util::DefaultDataOutputHandler< MOLMolecularGraphWriter, DataFormat::MOLMOLMolecularGraphOutputHandler
 A handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format. More...
 
typedef Util::DefaultDataInputHandler< MOLMoleculeReader, DataFormat::MOLMOLMoleculeInputHandler
 A handler for the input of molecule data in the MDL Mol-File [CTFILE] format. More...
 
typedef Util::DefaultDataInputHandler< RDFBZ2ReactionReader, DataFormat::RDF_BZ2RDFBZ2ReactionInputHandler
 A handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
 
typedef Util::DefaultDataOutputHandler< RDFBZ2ReactionWriter, DataFormat::RDF_BZ2RDFBZ2ReactionOutputHandler
 A handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
 
typedef Util::CompressedDataReader< RDFReactionReader, Util::BZip2IStreamRDFBZ2ReactionReader
 
typedef Util::CompressedDataWriter< RDFReactionWriter, Util::BZip2OStreamRDFBZ2ReactionWriter
 
typedef Util::DefaultDataInputHandler< RDFGZReactionReader, DataFormat::RDF_GZRDFGZReactionInputHandler
 A handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
 
typedef Util::DefaultDataOutputHandler< RDFGZReactionWriter, DataFormat::RDF_GZRDFGZReactionOutputHandler
 A handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
 
typedef Util::CompressedDataReader< RDFReactionReader, Util::GZipIStreamRDFGZReactionReader
 
typedef Util::CompressedDataWriter< RDFReactionWriter, Util::GZipOStreamRDFGZReactionWriter
 
typedef Util::DefaultDataInputHandler< RDFReactionReader, DataFormat::RDFRDFReactionInputHandler
 A handler for the input of reaction data in the MDL RD-File [CTFILE] format. More...
 
typedef Util::DefaultDataOutputHandler< RDFReactionWriter, DataFormat::RDFRDFReactionOutputHandler
 A handler for the output of reaction data in the MDL RD-File [CTFILE] format. More...
 
typedef Util::MultiFormatDataReader< ReactionReactionReader
 Reader for reaction data in any supported format. More...
 
typedef Util::MultiFormatDataWriter< ReactionReactionWriter
 Writer for reaction data in any supported format. More...
 
typedef Util::DefaultDataInputHandler< RXNReactionReader, DataFormat::RXNRXNReactionInputHandler
 A handler for the input of reaction data in the MDL Rxn-File [CTFILE] format. More...
 
typedef Util::DefaultDataOutputHandler< RXNReactionWriter, DataFormat::RXNRXNReactionOutputHandler
 A handler for the output of reaction data in the MDL Rxn-File [CTFILE] format. More...
 
typedef Util::DefaultDataOutputHandler< SDFBZ2MolecularGraphWriter, DataFormat::SDF_BZ2SDFBZ2MolecularGraphOutputHandler
 A handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
 
typedef Util::CompressedDataWriter< SDFMolecularGraphWriter, Util::BZip2OStreamSDFBZ2MolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< SDFBZ2MoleculeReader, DataFormat::SDF_BZ2SDFBZ2MoleculeInputHandler
 A handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format. More...
 
typedef Util::CompressedDataReader< SDFMoleculeReader, Util::BZip2IStreamSDFBZ2MoleculeReader
 
typedef Util::DefaultDataOutputHandler< SDFGZMolecularGraphWriter, DataFormat::SDF_GZSDFGZMolecularGraphOutputHandler
 A handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
 
typedef Util::CompressedDataWriter< SDFMolecularGraphWriter, Util::GZipOStreamSDFGZMolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< SDFGZMoleculeReader, DataFormat::SDF_GZSDFGZMoleculeInputHandler
 A handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format. More...
 
typedef Util::CompressedDataReader< SDFMoleculeReader, Util::GZipIStreamSDFGZMoleculeReader
 
typedef Util::DefaultDataOutputHandler< SDFMolecularGraphWriter, DataFormat::SDFSDFMolecularGraphOutputHandler
 A handler for the output of molecular graph data in the MDL SD-File [CTFILE] format. More...
 
typedef Util::DefaultDataInputHandler< SDFMoleculeReader, DataFormat::SDFSDFMoleculeInputHandler
 A handler for the input of molecule data in the MDL SD-File [CTFILE] format. More...
 
typedef Util::DefaultDataOutputHandler< SMARTSMolecularGraphWriter, DataFormat::SMARTSSMARTSMolecularGraphOutputHandler
 A handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format. More...
 
typedef Util::DefaultDataInputHandler< SMARTSMoleculeReader, DataFormat::SMARTSSMARTSMoleculeInputHandler
 A handler for the input of molecule data in the Daylight SMARTS [SMARTS] format. More...
 
typedef Util::DefaultDataInputHandler< SMARTSReactionReader, DataFormat::SMARTSSMARTSReactionInputHandler
 A handler for the input of reaction data in the Daylight SMARTS [SMARTS] format. More...
 
typedef Util::DefaultDataOutputHandler< SMARTSReactionWriter, DataFormat::SMARTSSMARTSReactionOutputHandler
 A handler for the output of reaction data in the Daylight SMARTS [SMARTS] format. More...
 
typedef Util::DefaultDataOutputHandler< SMILESBZ2MolecularGraphWriter, DataFormat::SMILES_BZ2SMILESBZ2MolecularGraphOutputHandler
 A handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::CompressedDataWriter< SMILESMolecularGraphWriter, Util::BZip2OStreamSMILESBZ2MolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< SMILESBZ2MoleculeReader, DataFormat::SMILES_BZ2SMILESBZ2MoleculeInputHandler
 A handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::CompressedDataReader< SMILESMoleculeReader, Util::BZip2IStreamSMILESBZ2MoleculeReader
 
typedef Util::DefaultDataInputHandler< SMILESBZ2ReactionReader, DataFormat::SMILES_BZ2SMILESBZ2ReactionInputHandler
 A handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::DefaultDataOutputHandler< SMILESBZ2ReactionWriter, DataFormat::SMILES_BZ2SMILESBZ2ReactionOutputHandler
 A handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::CompressedDataReader< SMILESReactionReader, Util::BZip2IStreamSMILESBZ2ReactionReader
 
typedef Util::CompressedDataWriter< SMILESReactionWriter, Util::BZip2OStreamSMILESBZ2ReactionWriter
 
typedef Util::DefaultDataOutputHandler< SMILESGZMolecularGraphWriter, DataFormat::SMILES_GZSMILESGZMolecularGraphOutputHandler
 A handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::CompressedDataWriter< SMILESMolecularGraphWriter, Util::GZipOStreamSMILESGZMolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< SMILESGZMoleculeReader, DataFormat::SMILES_GZSMILESGZMoleculeInputHandler
 A handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format. More...
 
typedef Util::CompressedDataReader< SMILESMoleculeReader, Util::GZipIStreamSMILESGZMoleculeReader
 
typedef Util::DefaultDataInputHandler< SMILESGZReactionReader, DataFormat::SMILES_GZSMILESGZReactionInputHandler
 A handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::DefaultDataOutputHandler< SMILESGZReactionWriter, DataFormat::SMILES_GZSMILESGZReactionOutputHandler
 A handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::CompressedDataReader< SMILESReactionReader, Util::GZipIStreamSMILESGZReactionReader
 
typedef Util::CompressedDataWriter< SMILESReactionWriter, Util::GZipOStreamSMILESGZReactionWriter
 
typedef Util::DefaultDataOutputHandler< SMILESMolecularGraphWriter, DataFormat::SMILESSMILESMolecularGraphOutputHandler
 A handler for the output of molecular graph data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::DefaultDataInputHandler< SMILESMoleculeReader, DataFormat::SMILESSMILESMoleculeInputHandler
 A handler for the input of molecule data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::DefaultDataInputHandler< SMILESReactionReader, DataFormat::SMILESSMILESReactionInputHandler
 A handler for the input of reaction data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::DefaultDataOutputHandler< SMILESReactionWriter, DataFormat::SMILESSMILESReactionOutputHandler
 A handler for the output of reaction data in the Daylight SMILES [SMILES] format. More...
 
typedef Util::DefaultDataOutputHandler< XYZBZ2MolecularGraphWriter, DataFormat::XYZ_BZ2XYZBZ2MolecularGraphOutputHandler
 A handler for the output of bzip2-compressed molecular graph data in the XYZ format. More...
 
typedef Util::CompressedDataWriter< XYZMolecularGraphWriter, Util::BZip2OStreamXYZBZ2MolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< XYZBZ2MoleculeReader, DataFormat::XYZ_BZ2XYZBZ2MoleculeInputHandler
 A handler for the input of bzip2-compressed molecule data in the XYZ format. More...
 
typedef Util::CompressedDataReader< XYZMoleculeReader, Util::BZip2IStreamXYZBZ2MoleculeReader
 
typedef Util::DefaultDataOutputHandler< XYZGZMolecularGraphWriter, DataFormat::XYZ_GZXYZGZMolecularGraphOutputHandler
 A handler for the output of gzip-compressed molecular graph data in the XYZ format. More...
 
typedef Util::CompressedDataWriter< XYZMolecularGraphWriter, Util::GZipOStreamXYZGZMolecularGraphWriter
 
typedef Util::DefaultDataInputHandler< XYZGZMoleculeReader, DataFormat::XYZ_GZXYZGZMoleculeInputHandler
 A handler for the input of gzip-compressed molecule data in the XYZ format. More...
 
typedef Util::CompressedDataReader< XYZMoleculeReader, Util::GZipIStreamXYZGZMoleculeReader
 
typedef Util::DefaultDataOutputHandler< XYZMolecularGraphWriter, DataFormat::XYZXYZMolecularGraphOutputHandler
 A handler for the output of molecular graph data in the XYZ format. More...
 
typedef Util::DefaultDataInputHandler< XYZMoleculeReader, DataFormat::XYZXYZMoleculeInputHandler
 A handler for the input of molecule data in the XYZ format. More...
 

Functions

CDPL_CHEM_API bool hasCoordinates (const AtomContainer &cntnr, std::size_t dim)
 
CDPL_CHEM_API void get2DCoordinates (const AtomContainer &cntnr, Math::Vector2DArray &coords, bool append=false)
 
CDPL_CHEM_API void set2DCoordinates (AtomContainer &cntnr, const Math::Vector2DArray &coords)
 
CDPL_CHEM_API void transform2DCoordinates (AtomContainer &cntnr, const Math::Matrix3D &mtx)
 
CDPL_CHEM_API void get3DCoordinates (const AtomContainer &cntnr, Math::Vector3DArray &coords, const Atom3DCoordinatesFunction &coords_func, bool append=false)
 
CDPL_CHEM_API void clearConformations (AtomContainer &cntnr)
 
CDPL_CHEM_API std::size_t getNumConformations (const AtomContainer &cntnr)
 
CDPL_CHEM_API void applyConformation (AtomContainer &cntnr, std::size_t conf_idx)
 
CDPL_CHEM_API void getConformation (const AtomContainer &cntnr, std::size_t conf_idx, Math::Vector3DArray &coords, bool append=false)
 
CDPL_CHEM_API void setConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Vector3DArray &coords)
 
CDPL_CHEM_API void addConformation (AtomContainer &cntnr, const Math::Vector3DArray &coords)
 
CDPL_CHEM_API void transformConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Matrix4D &mtx)
 
CDPL_CHEM_API void transformConformations (AtomContainer &cntnr, const Math::Matrix4D &mtx)
 
CDPL_CHEM_API bool alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms, const Math::Vector3DArray &ref_coords)
 
CDPL_CHEM_API bool alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms, const Math::Vector3DArray &ref_coords)
 
CDPL_CHEM_API bool alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms)
 
CDPL_CHEM_API bool alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms)
 
CDPL_CHEM_API std::size_t getMaxComponentGroupID (const AtomContainer &cntnr)
 
CDPL_CHEM_API std::size_t getMaxAtomMappingID (const AtomContainer &cntnr)
 
CDPL_CHEM_API std::size_t createAtomTypeMask (const AtomContainer &cntnr, Util::BitSet &mask, unsigned int type, bool reset=true, bool strict=true)
 
CDPL_CHEM_API void copyAtomsIf (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false)
 
CDPL_CHEM_API void copyAtomsIf (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false)
 
CDPL_CHEM_API void copyAtomsIfNot (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false)
 
CDPL_CHEM_API void copyAtomsIfNot (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false)
 
CDPL_CHEM_API bool calcCenterOfMass (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr)
 
CDPL_CHEM_API bool calcCentroid (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr)
 
CDPL_CHEM_API void calcBoundingBox (const AtomContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func, bool reset=true)
 
CDPL_CHEM_API bool insideBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func)
 
CDPL_CHEM_API bool intersectsBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func)
 
CDPL_CHEM_API const std::string & getName (const Atom &atom)
 
CDPL_CHEM_API void setName (Atom &atom, const std::string &name)
 
CDPL_CHEM_API void clearName (Atom &atom)
 
CDPL_CHEM_API bool hasName (const Atom &atom)
 
CDPL_CHEM_API const std::string & getSymbol (const Atom &atom)
 
CDPL_CHEM_API void setSymbol (Atom &atom, const std::string &symbol)
 
CDPL_CHEM_API void clearSymbol (Atom &atom)
 
CDPL_CHEM_API bool hasSymbol (const Atom &atom)
 
CDPL_CHEM_API const std::string & getSymbolForType (const Atom &atom)
 
CDPL_CHEM_API unsigned int getType (const Atom &atom)
 
CDPL_CHEM_API void setType (Atom &atom, unsigned int type)
 
CDPL_CHEM_API void clearType (Atom &atom)
 
CDPL_CHEM_API bool hasType (const Atom &atom)
 
CDPL_CHEM_API unsigned int getTypeForSymbol (const Atom &atom)
 
CDPL_CHEM_API unsigned int getGenericType (const Atom &atom)
 
CDPL_CHEM_API long getFormalCharge (const Atom &atom)
 
CDPL_CHEM_API void setFormalCharge (Atom &atom, long charge)
 
CDPL_CHEM_API void clearFormalCharge (Atom &atom)
 
CDPL_CHEM_API bool hasFormalCharge (const Atom &atom)
 
CDPL_CHEM_API long calcFormalCharge (const Atom &atom, const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::size_t getIsotope (const Atom &atom)
 
CDPL_CHEM_API void setIsotope (Atom &atom, std::size_t isotope)
 
CDPL_CHEM_API void clearIsotope (Atom &atom)
 
CDPL_CHEM_API bool hasIsotope (const Atom &atom)
 
CDPL_CHEM_API unsigned int getRadicalType (const Atom &atom)
 
CDPL_CHEM_API void setRadicalType (Atom &atom, unsigned int type)
 
CDPL_CHEM_API void clearRadicalType (Atom &atom)
 
CDPL_CHEM_API bool hasRadicalType (const Atom &atom)
 
CDPL_CHEM_API unsigned int getHybridizationState (const Atom &atom)
 
CDPL_CHEM_API void setHybridizationState (Atom &atom, unsigned int state)
 
CDPL_CHEM_API void clearHybridizationState (Atom &atom)
 
CDPL_CHEM_API bool hasHybridizationState (const Atom &atom)
 
CDPL_CHEM_API unsigned int perceiveHybridizationState (const Atom &atom, const MolecularGraph &molgraph)
 
CDPL_CHEM_API bool getRingFlag (const Atom &atom)
 
CDPL_CHEM_API void setRingFlag (Atom &atom, bool in_ring)
 
CDPL_CHEM_API void clearRingFlag (Atom &atom)
 
CDPL_CHEM_API bool hasRingFlag (const Atom &atom)
 
CDPL_CHEM_API bool isInFragmentOfSize (const Atom &atom, const FragmentList &frag_list, std::size_t size)
 
CDPL_CHEM_API std::size_t getSizeOfSmallestContainingFragment (const Atom &atom, const FragmentList &frag_list)
 
CDPL_CHEM_API std::size_t getSizeOfLargestContainingFragment (const Atom &atom, const FragmentList &frag_list)
 
CDPL_CHEM_API std::size_t getNumContainingFragments (const Atom &atom, const FragmentList &frag_list)
 
CDPL_CHEM_API void getContainingFragments (const Atom &atom, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false)
 
CDPL_CHEM_API bool getAromaticityFlag (const Atom &atom)
 
CDPL_CHEM_API void setAromaticityFlag (Atom &atom, bool aromatic)
 
CDPL_CHEM_API void clearAromaticityFlag (Atom &atom)
 
CDPL_CHEM_API bool hasAromaticityFlag (const Atom &atom)
 
CDPL_CHEM_API std::size_t getUnpairedElectronCount (const Atom &atom)
 
CDPL_CHEM_API void setUnpairedElectronCount (Atom &atom, std::size_t count)
 
CDPL_CHEM_API void clearUnpairedElectronCount (Atom &atom)
 
CDPL_CHEM_API bool hasUnpairedElectronCount (const Atom &atom)
 
CDPL_CHEM_API std::size_t getImplicitHydrogenCount (const Atom &atom)
 
CDPL_CHEM_API void setImplicitHydrogenCount (Atom &atom, std::size_t count)
 
CDPL_CHEM_API void clearImplicitHydrogenCount (Atom &atom)
 
CDPL_CHEM_API bool hasImplicitHydrogenCount (const Atom &atom)
 
CDPL_CHEM_API std::size_t calcImplicitHydrogenCount (const Atom &atom, const MolecularGraph &molgraph)
 
CDPL_CHEM_API const Math::Vector2Dget2DCoordinates (const Atom &atom)
 
CDPL_CHEM_API void set2DCoordinates (Atom &atom, const Math::Vector2D &coords)
 
CDPL_CHEM_API void clear2DCoordinates (Atom &atom)
 
CDPL_CHEM_API bool has2DCoordinates (const Atom &atom)
 
CDPL_CHEM_API const Math::Vector3DgetConformer3DCoordinates (const Atom &atom, std::size_t conf_idx)
 
CDPL_CHEM_API const Math::Vector3DArray::SharedPointer & get3DCoordinatesArray (const Atom &atom)
 
CDPL_CHEM_API void set3DCoordinatesArray (Atom &atom, const Math::Vector3DArray::SharedPointer &coords_array)
 
CDPL_CHEM_API void clear3DCoordinatesArray (Atom &atom)
 
CDPL_CHEM_API bool has3DCoordinatesArray (const Atom &atom)
 
CDPL_CHEM_API std::size_t getMorganNumber (const Atom &atom)
 
CDPL_CHEM_API void setMorganNumber (Atom &atom, std::size_t num)
 
CDPL_CHEM_API void clearMorganNumber (Atom &atom)
 
CDPL_CHEM_API bool hasMorganNumber (const Atom &atom)
 
CDPL_CHEM_API std::size_t getCanonicalNumber (const Atom &atom)
 
CDPL_CHEM_API void setCanonicalNumber (Atom &atom, std::size_t num)
 
CDPL_CHEM_API void clearCanonicalNumber (Atom &atom)
 
CDPL_CHEM_API bool hasCanonicalNumber (const Atom &atom)
 
CDPL_CHEM_API std::size_t getCIPPriority (const Atom &atom)
 
CDPL_CHEM_API void setCIPPriority (Atom &atom, std::size_t priority)
 
CDPL_CHEM_API void clearCIPPriority (Atom &atom)
 
CDPL_CHEM_API bool hasCIPPriority (const Atom &atom)
 
CDPL_CHEM_API std::size_t getSymmetryClass (const Atom &atom)
 
CDPL_CHEM_API void setSymmetryClass (Atom &atom, std::size_t class_id)
 
CDPL_CHEM_API void clearSymmetryClass (Atom &atom)
 
CDPL_CHEM_API bool hasSymmetryClass (const Atom &atom)
 
CDPL_CHEM_API unsigned int getCIPConfiguration (const Atom &atom)
 
CDPL_CHEM_API void setCIPConfiguration (Atom &atom, unsigned int config)
 
CDPL_CHEM_API void clearCIPConfiguration (Atom &atom)
 
CDPL_CHEM_API bool hasCIPConfiguration (const Atom &atom)
 
CDPL_CHEM_API const StereoDescriptorgetStereoDescriptor (const Atom &atom)
 
CDPL_CHEM_API void setStereoDescriptor (Atom &atom, const StereoDescriptor &descr)
 
CDPL_CHEM_API void clearStereoDescriptor (Atom &atom)
 
CDPL_CHEM_API bool hasStereoDescriptor (const Atom &atom)
 
CDPL_CHEM_API StereoDescriptor calcStereoDescriptor (const Atom &atom, const MolecularGraph &molgraph, std::size_t dim=1)
 
CDPL_CHEM_API StereoDescriptor calcStereoDescriptorFromMDLParity (const Atom &atom, const MolecularGraph &molgraph)
 
CDPL_CHEM_API unsigned int calcConfiguration (const Atom &atom, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords)
 
CDPL_CHEM_API bool getStereoCenterFlag (const Atom &atom)
 
CDPL_CHEM_API void setStereoCenterFlag (Atom &atom, bool is_center)
 
CDPL_CHEM_API void clearStereoCenterFlag (Atom &atom)
 
CDPL_CHEM_API bool hasStereoCenterFlag (const Atom &atom)
 
CDPL_CHEM_API bool isStereoCenter (const Atom &atom, const MolecularGraph &molgraph, bool check_asym=true, bool check_inv_n=true, bool check_quart_n=true, bool check_plan_n=true, bool check_amide_n=true, bool check_res_ctrs=true)
 
CDPL_CHEM_API unsigned int getSybylType (const Atom &atom)
 
CDPL_CHEM_API void setSybylType (Atom &atom, unsigned int type)
 
CDPL_CHEM_API void clearSybylType (Atom &atom)
 
CDPL_CHEM_API bool hasSybylType (const Atom &atom)
 
CDPL_CHEM_API unsigned int perceiveSybylType (const Atom &atom, const MolecularGraph &molgraph)
 
CDPL_CHEM_API const std::string & getMOL2Name (const Atom &atom)
 
CDPL_CHEM_API void setMOL2Name (Atom &atom, const std::string &name)
 
CDPL_CHEM_API void clearMOL2Name (Atom &atom)
 
CDPL_CHEM_API bool hasMOL2Name (const Atom &atom)
 
CDPL_CHEM_API double getMOL2Charge (const Atom &atom)
 
CDPL_CHEM_API void setMOL2Charge (Atom &atom, double charge)
 
CDPL_CHEM_API void clearMOL2Charge (Atom &atom)
 
CDPL_CHEM_API bool hasMOL2Charge (const Atom &atom)
 
CDPL_CHEM_API std::size_t getMOL2SubstructureID (const Atom &atom)
 
CDPL_CHEM_API void setMOL2SubstructureID (Atom &atom, std::size_t id)
 
CDPL_CHEM_API void clearMOL2SubstructureID (Atom &atom)
 
CDPL_CHEM_API bool hasMOL2SubstructureID (const Atom &atom)
 
CDPL_CHEM_API const std::string & getMOL2SubstructureName (const Atom &atom)
 
CDPL_CHEM_API void setMOL2SubstructureName (Atom &atom, const std::string &id)
 
CDPL_CHEM_API void clearMOL2SubstructureName (Atom &atom)
 
CDPL_CHEM_API bool hasMOL2SubstructureName (const Atom &atom)
 
CDPL_CHEM_API const std::string & getMOL2SubstructureSubtype (const Atom &atom)
 
CDPL_CHEM_API void setMOL2SubstructureSubtype (Atom &atom, const std::string &subtype)
 
CDPL_CHEM_API void clearMOL2SubstructureSubtype (Atom &atom)
 
CDPL_CHEM_API bool hasMOL2SubstructureSubtype (const Atom &atom)
 
CDPL_CHEM_API const std::string & getMOL2SubstructureChain (const Atom &atom)
 
CDPL_CHEM_API void setMOL2SubstructureChain (Atom &atom, const std::string &chain)
 
CDPL_CHEM_API void clearMOL2SubstructureChain (Atom &atom)
 
CDPL_CHEM_API bool hasMOL2SubstructureChain (const Atom &atom)
 
CDPL_CHEM_API unsigned int getMDLParity (const Atom &atom)
 
CDPL_CHEM_API void setMDLParity (Atom &atom, unsigned int parity)
 
CDPL_CHEM_API void clearMDLParity (Atom &atom)
 
CDPL_CHEM_API bool hasMDLParity (const Atom &atom)
 
CDPL_CHEM_API unsigned int calcMDLParity (const Atom &atom, const MolecularGraph &molgraph)
 
CDPL_CHEM_API bool getMDLStereoCareFlag (const Atom &atom)
 
CDPL_CHEM_API void setMDLStereoCareFlag (Atom &atom, bool flag)
 
CDPL_CHEM_API void clearMDLStereoCareFlag (Atom &atom)
 
CDPL_CHEM_API bool hasMDLStereoCareFlag (const Atom &atom)
 
CDPL_CHEM_API unsigned int getReactionCenterStatus (const Atom &atom)
 
CDPL_CHEM_API void setReactionCenterStatus (Atom &atom, unsigned int status)
 
CDPL_CHEM_API void clearReactionCenterStatus (Atom &atom)
 
CDPL_CHEM_API bool hasReactionCenterStatus (const Atom &atom)
 
CDPL_CHEM_API std::size_t getAtomMappingID (const Atom &atom)
 
CDPL_CHEM_API void setAtomMappingID (Atom &atom, std::size_t id)
 
CDPL_CHEM_API void clearAtomMappingID (Atom &atom)
 
CDPL_CHEM_API bool hasAtomMappingID (const Atom &atom)
 
CDPL_CHEM_API std::size_t getComponentGroupID (const Atom &atom)
 
CDPL_CHEM_API void setComponentGroupID (Atom &atom, std::size_t id)
 
CDPL_CHEM_API void clearComponentGroupID (Atom &atom)
 
CDPL_CHEM_API bool hasComponentGroupID (const Atom &atom)
 
CDPL_CHEM_API const MatchConstraintList::SharedPointergetMatchConstraints (const Atom &atom)
 
CDPL_CHEM_API void setMatchConstraints (Atom &atom, const MatchConstraintList::SharedPointer &constr)
 
CDPL_CHEM_API void clearMatchConstraints (Atom &atom)
 
CDPL_CHEM_API bool hasMatchConstraints (const Atom &atom)
 
CDPL_CHEM_API const MatchExpression< Atom, MolecularGraph >::SharedPointergetMatchExpression (const Atom &atom)
 
CDPL_CHEM_API void setMatchExpression (Atom &atom, const MatchExpression< Atom, MolecularGraph >::SharedPointer &expr)
 
CDPL_CHEM_API void clearMatchExpression (Atom &atom)
 
CDPL_CHEM_API bool hasMatchExpression (const Atom &atom)
 
CDPL_CHEM_API MatchExpression< Atom, MolecularGraph >::SharedPointer generateMatchExpression (const Atom &atom, const MolecularGraph &molgraph)
 
CDPL_CHEM_API const std::string & getMatchExpressionString (const Atom &atom)
 
CDPL_CHEM_API void setMatchExpressionString (Atom &atom, const std::string &expr_str)
 
CDPL_CHEM_API void clearMatchExpressionString (Atom &atom)
 
CDPL_CHEM_API bool hasMatchExpressionString (const Atom &atom)
 
CDPL_CHEM_API void generateMatchExpressionString (const Atom &atom, const MolecularGraph &molgraph, std::string &expr_str)
 
CDPL_CHEM_API void markReachableAtoms (const Atom &atom, const MolecularGraph &molgraph, Util::BitSet &atom_mask, bool reset=true)
 
CDPL_CHEM_API std::size_t getTopologicalDistance (const Atom &atom1, const Atom &atom2, const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::size_t getEnvironment (const Atom &atom, const MolecularGraph &molgraph, std::size_t max_dist, Fragment &env, bool append=false)
 
template<typename AtomType , typename OutputIterator >
std::size_t getConnectedAtoms (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0)
 
template<typename AtomType , typename OutputIterator >
std::size_t getIncidentBonds (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0)
 
template<typename AtomType , typename AtomOutputIterator , typename BondOutputIterator >
std::size_t getConnectedAtomsAndBonds (AtomType &atom, const MolecularGraph &molgraph, AtomOutputIterator ao_it, BondOutputIterator bo_it, AtomType *excl_atom=0)
 
CDPL_CHEM_API std::size_t getOrder (const Bond &bond)
 
CDPL_CHEM_API void setOrder (Bond &bond, std::size_t order)
 
CDPL_CHEM_API void clearOrder (Bond &bond)
 
CDPL_CHEM_API bool hasOrder (const Bond &bond)
 
CDPL_CHEM_API bool getRingFlag (const Bond &bond)
 
CDPL_CHEM_API void setRingFlag (Bond &bond, bool in_ring)
 
CDPL_CHEM_API void clearRingFlag (Bond &bond)
 
CDPL_CHEM_API bool hasRingFlag (const Bond &bond)
 
CDPL_CHEM_API bool isInFragmentOfSize (const Bond &bond, const FragmentList &frag_list, std::size_t size)
 
CDPL_CHEM_API std::size_t getSizeOfSmallestContainingFragment (const Bond &bond, const FragmentList &frag_list)
 
CDPL_CHEM_API std::size_t getSizeOfLargestContainingFragment (const Bond &bond, const FragmentList &frag_list)
 
CDPL_CHEM_API std::size_t getNumContainingFragments (const Bond &bond, const FragmentList &frag_list)
 
CDPL_CHEM_API void getContainingFragments (const Bond &bond, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false)
 
CDPL_CHEM_API bool getAromaticityFlag (const Bond &bond)
 
CDPL_CHEM_API void setAromaticityFlag (Bond &bond, bool aromatic)
 
CDPL_CHEM_API void clearAromaticityFlag (Bond &bond)
 
CDPL_CHEM_API bool hasAromaticityFlag (const Bond &bond)
 
CDPL_CHEM_API unsigned int get2DStereoFlag (const Bond &bond)
 
CDPL_CHEM_API void set2DStereoFlag (Bond &bond, unsigned int flag)
 
CDPL_CHEM_API void clear2DStereoFlag (Bond &bond)
 
CDPL_CHEM_API bool has2DStereoFlag (const Bond &bond)
 
CDPL_CHEM_API unsigned int getCIPConfiguration (const Bond &bond)
 
CDPL_CHEM_API void setCIPConfiguration (Bond &bond, unsigned int config)
 
CDPL_CHEM_API void clearCIPConfiguration (Bond &bond)
 
CDPL_CHEM_API bool hasCIPConfiguration (const Bond &bond)
 
CDPL_CHEM_API const StereoDescriptorgetStereoDescriptor (const Bond &bond)
 
CDPL_CHEM_API void setStereoDescriptor (Bond &bond, const StereoDescriptor &descr)
 
CDPL_CHEM_API void clearStereoDescriptor (Bond &bond)
 
CDPL_CHEM_API bool hasStereoDescriptor (const Bond &bond)
 
CDPL_CHEM_API StereoDescriptor calcStereoDescriptor (const Bond &bond, const MolecularGraph &molgraph, std::size_t dim=1)
 
CDPL_CHEM_API unsigned int calcConfiguration (const Bond &bond, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords)
 
CDPL_CHEM_API bool getStereoCenterFlag (const Bond &bond)
 
CDPL_CHEM_API void setStereoCenterFlag (Bond &bond, bool is_center)
 
CDPL_CHEM_API void clearStereoCenterFlag (Bond &bond)
 
CDPL_CHEM_API bool hasStereoCenterFlag (const Bond &bond)
 
CDPL_CHEM_API bool isStereoCenter (const Bond &bond, const MolecularGraph &molgraph, bool check_asym=true, bool check_term_n=true, bool check_order=true, std::size_t min_ring_size=8)
 
CDPL_CHEM_API unsigned int getDirection (const Bond &bond)
 
CDPL_CHEM_API void setDirection (Bond &bond, unsigned int dir)
 
CDPL_CHEM_API void clearDirection (Bond &bond)
 
CDPL_CHEM_API bool hasDirection (const Bond &bond)
 
CDPL_CHEM_API unsigned int getReactionCenterStatus (const Bond &bond)
 
CDPL_CHEM_API void setReactionCenterStatus (Bond &bond, unsigned int status)
 
CDPL_CHEM_API void clearReactionCenterStatus (Bond &bond)
 
CDPL_CHEM_API bool hasReactionCenterStatus (const Bond &bond)
 
CDPL_CHEM_API const MatchConstraintList::SharedPointergetMatchConstraints (const Bond &bond)
 
CDPL_CHEM_API void setMatchConstraints (Bond &bond, const MatchConstraintList::SharedPointer &constr)
 
CDPL_CHEM_API void clearMatchConstraints (Bond &bond)
 
CDPL_CHEM_API bool hasMatchConstraints (const Bond &bond)
 
CDPL_CHEM_API const MatchExpression< Bond, MolecularGraph >::SharedPointergetMatchExpression (const Bond &bond)
 
CDPL_CHEM_API void setMatchExpression (Bond &bond, const MatchExpression< Bond, MolecularGraph >::SharedPointer &expr)
 
CDPL_CHEM_API void clearMatchExpression (Bond &bond)
 
CDPL_CHEM_API bool hasMatchExpression (const Bond &bond)
 
CDPL_CHEM_API MatchExpression< Bond, MolecularGraph >::SharedPointer generateMatchExpression (const Bond &bond, const MolecularGraph &molgraph)
 
CDPL_CHEM_API const std::string & getMatchExpressionString (const Bond &bond)
 
CDPL_CHEM_API void setMatchExpressionString (Bond &bond, const std::string &expr_str)
 
CDPL_CHEM_API void clearMatchExpressionString (Bond &bond)
 
CDPL_CHEM_API bool hasMatchExpressionString (const Bond &bond)
 
CDPL_CHEM_API void generateMatchExpressionString (const Bond &bond, const MolecularGraph &molgraph, std::string &str)
 
CDPL_CHEM_API unsigned int getSybylType (const Bond &bond)
 
CDPL_CHEM_API void setSybylType (Bond &bond, unsigned int type)
 
CDPL_CHEM_API void clearSybylType (Bond &bond)
 
CDPL_CHEM_API bool hasSybylType (const Bond &bond)
 
CDPL_CHEM_API unsigned int perceiveSybylType (const Bond &bond, const MolecularGraph &molgraph)
 
CDPL_CHEM_API bool getOrdinaryHydrogenDepleteParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setOrdinaryHydrogenDepleteParameter (Base::ControlParameterContainer &cntnr, bool deplete)
 
CDPL_CHEM_API bool hasOrdinaryHydrogenDepleteParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearOrdinaryHydrogenDepleteParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API std::size_t getCoordinatesDimensionParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setCoordinatesDimensionParameter (Base::ControlParameterContainer &cntnr, std::size_t dim)
 
CDPL_CHEM_API bool hasCoordinatesDimensionParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearCoordinatesDimensionParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict)
 
CDPL_CHEM_API bool hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API const std::string & getRecordSeparatorParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setRecordSeparatorParameter (Base::ControlParameterContainer &cntnr, const std::string &sep)
 
CDPL_CHEM_API bool hasRecordSeparatorParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearRecordSeparatorParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getBondMemberSwapStereoFixParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setBondMemberSwapStereoFixParameter (Base::ControlParameterContainer &cntnr, bool fix)
 
CDPL_CHEM_API bool hasBondMemberSwapStereoFixParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearBondMemberSwapStereoFixParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setCheckLineLengthParameter (Base::ControlParameterContainer &cntnr, bool check)
 
CDPL_CHEM_API bool hasCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearCheckLineLengthParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API unsigned int getMDLCTABVersionParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLCTABVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int version)
 
CDPL_CHEM_API bool hasMDLCTABVersionParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLCTABVersionParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMDLIgnoreParityParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLIgnoreParityParameter (Base::ControlParameterContainer &cntnr, bool ignore)
 
CDPL_CHEM_API bool hasMDLIgnoreParityParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLIgnoreParityParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMDLUpdateTimestampParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLUpdateTimestampParameter (Base::ControlParameterContainer &cntnr, bool update)
 
CDPL_CHEM_API bool hasMDLUpdateTimestampParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLUpdateTimestampParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMDLTrimStringsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLTrimStringsParameter (Base::ControlParameterContainer &cntnr, bool trim)
 
CDPL_CHEM_API bool hasMDLTrimStringsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLTrimStringsParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMDLTrimLinesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLTrimLinesParameter (Base::ControlParameterContainer &cntnr, bool trim)
 
CDPL_CHEM_API bool hasMDLTrimLinesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLTrimLinesParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMDLTruncateStringsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLTruncateStringsParameter (Base::ControlParameterContainer &cntnr, bool trunc)
 
CDPL_CHEM_API bool hasMDLTruncateStringsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLTruncateStringsParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMDLTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLTruncateLinesParameter (Base::ControlParameterContainer &cntnr, bool trunc)
 
CDPL_CHEM_API bool hasMDLTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLTruncateLinesParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API unsigned int getMDLRXNFileVersionParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLRXNFileVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int version)
 
CDPL_CHEM_API bool hasMDLRXNFileVersionParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLRXNFileVersionParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMDLOutputConfEnergyToEnergyFieldParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLOutputConfEnergyToEnergyFieldParameter (Base::ControlParameterContainer &cntnr, bool output)
 
CDPL_CHEM_API bool hasMDLOutputConfEnergyToEnergyFieldParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLOutputConfEnergyToEnergyFieldParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMDLOutputConfEnergyAsSDEntryParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLOutputConfEnergyAsSDEntryParameter (Base::ControlParameterContainer &cntnr, bool output)
 
CDPL_CHEM_API bool hasMDLOutputConfEnergyAsSDEntryParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLOutputConfEnergyAsSDEntryParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API const std::string & getMDLConfEnergySDTagParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMDLConfEnergySDTagParameter (Base::ControlParameterContainer &cntnr, const std::string &tag)
 
CDPL_CHEM_API bool hasMDLConfEnergySDTagParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMDLConfEnergySDTagParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getJMESeparateComponentsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setJMESeparateComponentsParameter (Base::ControlParameterContainer &cntnr, bool separate)
 
CDPL_CHEM_API bool hasJMESeparateComponentsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearJMESeparateComponentsParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API const std::string & getSMILESRecordFormatParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESRecordFormatParameter (Base::ControlParameterContainer &cntnr, const std::string &format)
 
CDPL_CHEM_API bool hasSMILESRecordFormatParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESRecordFormatParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESWriteCanonicalFormParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESWriteCanonicalFormParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESWriteCanonicalFormParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESWriteCanonicalFormParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESWriteKekuleFormParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESWriteKekuleFormParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESWriteKekuleFormParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESWriteKekuleFormParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESWriteAtomStereoParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESWriteAtomStereoParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESWriteAtomStereoParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESWriteAtomStereoParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESWriteBondStereoParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESWriteBondStereoParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESWriteBondStereoParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESWriteBondStereoParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESWriteRingBondStereoParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESWriteRingBondStereoParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESWriteRingBondStereoParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESWriteRingBondStereoParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API std::size_t getSMILESMinStereoBondRingSizeParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESMinStereoBondRingSizeParameter (Base::ControlParameterContainer &cntnr, std::size_t min_size)
 
CDPL_CHEM_API bool hasSMILESMinStereoBondRingSizeParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESMinStereoBondRingSizeParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESWriteIsotopeParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESWriteIsotopeParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESWriteIsotopeParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESWriteIsotopeParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESMolWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESMolWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESMolWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESMolWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESRxnWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESRxnWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESRxnWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESRxnWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESWriteSingleBondsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESWriteSingleBondsParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESWriteSingleBondsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESWriteSingleBondsParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESWriteAromaticBondsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESWriteAromaticBondsParameter (Base::ControlParameterContainer &cntnr, bool write)
 
CDPL_CHEM_API bool hasSMILESWriteAromaticBondsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESWriteAromaticBondsParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getSMILESNoOrganicSubsetParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setSMILESNoOrganicSubsetParameter (Base::ControlParameterContainer &cntnr, bool no_subset)
 
CDPL_CHEM_API bool hasSMILESNoOrganicSubsetParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearSMILESNoOrganicSubsetParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API const std::string & getINCHIInputOptionsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setINCHIInputOptionsParameter (Base::ControlParameterContainer &cntnr, const std::string &opts)
 
CDPL_CHEM_API bool hasINCHIInputOptionsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearINCHIInputOptionsParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API const std::string & getINCHIOutputOptionsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setINCHIOutputOptionsParameter (Base::ControlParameterContainer &cntnr, const std::string &opts)
 
CDPL_CHEM_API bool hasINCHIOutputOptionsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearINCHIOutputOptionsParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMultiConfImportParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMultiConfImportParameter (Base::ControlParameterContainer &cntnr, bool multi_conf)
 
CDPL_CHEM_API bool hasMultiConfImportParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMultiConfImportParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMultiConfExportParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMultiConfExportParameter (Base::ControlParameterContainer &cntnr, bool multi_conf)
 
CDPL_CHEM_API bool hasMultiConfExportParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMultiConfExportParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getOutputConfEnergyAsCommentParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setOutputConfEnergyAsCommentParameter (Base::ControlParameterContainer &cntnr, bool output)
 
CDPL_CHEM_API bool hasOutputConfEnergyAsCommentParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearOutputConfEnergyAsCommentParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API const std::string & getConfIndexNameSuffixPatternParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setConfIndexNameSuffixPatternParameter (Base::ControlParameterContainer &cntnr, const std::string &pattern)
 
CDPL_CHEM_API bool hasConfIndexNameSuffixPatternParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearConfIndexNameSuffixPatternParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API const MultiConfMoleculeInputProcessor::SharedPointergetMultiConfInputProcessorParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMultiConfInputProcessorParameter (Base::ControlParameterContainer &cntnr, const MultiConfMoleculeInputProcessor::SharedPointer &proc)
 
CDPL_CHEM_API bool hasMultiConfInputProcessorParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMultiConfInputProcessorParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr, bool single_prec)
 
CDPL_CHEM_API bool hasCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMOL2EnableExtendedAtomTypesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMOL2EnableExtendedAtomTypesParameter (Base::ControlParameterContainer &cntnr, bool enable)
 
CDPL_CHEM_API bool hasMOL2EnableExtendedAtomTypesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMOL2EnableExtendedAtomTypesParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMOL2EnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMOL2EnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr, bool enable)
 
CDPL_CHEM_API bool hasMOL2EnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMOL2EnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMOL2CalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMOL2CalcFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc)
 
CDPL_CHEM_API bool hasMOL2CalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMOL2CalcFormalChargesParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API unsigned int getMOL2ChargeTypeParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMOL2ChargeTypeParameter (Base::ControlParameterContainer &cntnr, unsigned int type)
 
CDPL_CHEM_API bool hasMOL2ChargeTypeParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMOL2ChargeTypeParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API unsigned int getMOL2MoleculeTypeParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMOL2MoleculeTypeParameter (Base::ControlParameterContainer &cntnr, unsigned int type)
 
CDPL_CHEM_API bool hasMOL2MoleculeTypeParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMOL2MoleculeTypeParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getMOL2OutputSubstructuresParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setMOL2OutputSubstructuresParameter (Base::ControlParameterContainer &cntnr, bool output)
 
CDPL_CHEM_API bool hasMOL2OutputSubstructuresParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearMOL2OutputSubstructuresParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getXYZCommentIsNameParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setXYZCommentIsNameParameter (Base::ControlParameterContainer &cntnr, bool is_name)
 
CDPL_CHEM_API bool hasXYZCommentIsNameParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearXYZCommentIsNameParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getXYZPerceiveConnectivityParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setXYZPerceiveConnectivityParameter (Base::ControlParameterContainer &cntnr, bool perceive)
 
CDPL_CHEM_API bool hasXYZPerceiveConnectivityParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearXYZPerceiveConnectivityParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getXYZPerceiveBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setXYZPerceiveBondOrdersParameter (Base::ControlParameterContainer &cntnr, bool perceive)
 
CDPL_CHEM_API bool hasXYZPerceiveBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearXYZPerceiveBondOrdersParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API bool getXYZCalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void setXYZCalcFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc)
 
CDPL_CHEM_API bool hasXYZCalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void clearXYZCalcFormalChargesParameter (Base::ControlParameterContainer &cntnr)
 
CDPL_CHEM_API void calcGeometricalDistanceMatrix (const Entity3DContainer &cntnr, Math::DMatrix &mtx)
 
CDPL_CHEM_API void get3DCoordinates (const Entity3DContainer &cntnr, Math::Vector3DArray &coords, bool append=false)
 
CDPL_CHEM_API void set3DCoordinates (Entity3DContainer &cntnr, const Math::Vector3DArray &coords)
 
CDPL_CHEM_API void transform3DCoordinates (Entity3DContainer &cntnr, const Math::Matrix4D &mtx)
 
CDPL_CHEM_API bool align3DCoordinates (Entity3DContainer &cntnr, const Entity3DContainer &ref_entities, const Math::Vector3DArray &ref_coords)
 
CDPL_CHEM_API bool calcCentroid (const Entity3DContainer &cntnr, Math::Vector3D &ctr)
 
CDPL_CHEM_API void calcBoundingBox (const Entity3DContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, bool reset=true)
 
CDPL_CHEM_API bool insideBoundingBox (const Entity3DContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max)
 
CDPL_CHEM_API bool intersectsBoundingBox (const Entity3DContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max)
 
CDPL_CHEM_API const Math::Vector3Dget3DCoordinates (const Entity3D &entity)
 
CDPL_CHEM_API void set3DCoordinates (Entity3D &entity, const Math::Vector3D &coords)
 
CDPL_CHEM_API void clear3DCoordinates (Entity3D &entity)
 
CDPL_CHEM_API bool has3DCoordinates (const Entity3D &entity)
 
CDPL_CHEM_API bool makeHydrogenDeplete (Fragment &frag)
 Removes all explicit hydrogen atoms from the fragment frag. More...
 
CDPL_CHEM_API bool makeOrdinaryHydrogenDeplete (Fragment &frag, unsigned int flags)
 Removes all explicit ordinary hydrogen atoms from the fragment frag. More...
 
CDPL_CHEM_API void removeAtomsIf (Fragment &frag, const AtomPredicate &pred)
 
CDPL_CHEM_API void removeAtomsIfNot (Fragment &frag, const AtomPredicate &pred)
 
CDPL_CHEM_API const std::string & getName (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setName (MolecularGraph &molgraph, const std::string &name)
 
CDPL_CHEM_API void clearName (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasName (const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::time_t getTimestamp (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setTimestamp (MolecularGraph &molgraph, std::time_t time)
 
CDPL_CHEM_API void clearTimestamp (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasTimestamp (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const std::string & getComment (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setComment (MolecularGraph &molgraph, const std::string &comment)
 
CDPL_CHEM_API void clearComment (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasComment (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const MatchConstraintList::SharedPointergetMatchConstraints (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr)
 
CDPL_CHEM_API void clearMatchConstraints (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMatchConstraints (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const MatchExpression< MolecularGraph >::SharedPointergetMatchExpression (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMatchExpression (MolecularGraph &molgraph, const MatchExpression< MolecularGraph >::SharedPointer &expr)
 
CDPL_CHEM_API void clearMatchExpression (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMatchExpression (const MolecularGraph &molgraph)
 
CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer generateMatchExpression (const MolecularGraph &molgraph)
 
CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer generateMatchExpression (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const FragmentList::SharedPointergetRings (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setRings (MolecularGraph &molgraph, const FragmentList::SharedPointer &rings)
 
CDPL_CHEM_API void clearRings (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasRings (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveRings (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveRings (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const FragmentList::SharedPointergetSSSR (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setSSSR (MolecularGraph &molgraph, const FragmentList::SharedPointer &sssr)
 
CDPL_CHEM_API void clearSSSR (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasSSSR (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveSSSR (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveSSSR (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API FragmentList::SharedPointer extractSSSRSubset (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer extractSSSRSubset (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite)
 
CDPL_CHEM_API const Fragment::SharedPointergetCyclicSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setCyclicSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct)
 
CDPL_CHEM_API void clearCyclicSubstructure (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasCyclicSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Fragment::SharedPointer perceiveCyclicSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Fragment::SharedPointer perceiveCyclicSubstructure (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const FragmentList::SharedPointergetComponents (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setComponents (MolecularGraph &molgraph, const FragmentList::SharedPointer &comps)
 
CDPL_CHEM_API void clearComponents (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasComponents (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveComponents (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveComponents (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const FragmentList::SharedPointergetComponentGroups (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setComponentGroups (MolecularGraph &molgraph, const FragmentList::SharedPointer &comp_groups)
 
CDPL_CHEM_API void clearComponentGroups (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasComponentGroups (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveComponentGroups (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveComponentGroups (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API std::size_t getConformationIndex (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setConformationIndex (MolecularGraph &molgraph, std::size_t index)
 
CDPL_CHEM_API void clearConformationIndex (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasConformationIndex (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const Util::DArray::SharedPointer & getConformerEnergies (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setConformerEnergies (MolecularGraph &molgraph, const Util::DArray::SharedPointer &energies)
 
CDPL_CHEM_API void clearConformerEnergies (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasConformerEnergies (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setConformation (MolecularGraph &molgraph, std::size_t conf_idx, const Math::Vector3DArray &coords, double energy)
 
CDPL_CHEM_API void addConformation (MolecularGraph &molgraph, const Math::Vector3DArray &coords, double energy)
 
CDPL_CHEM_API double getConformationEnergy (const MolecularGraph &molgraph, std::size_t conf_idx)
 
CDPL_CHEM_API std::uint64_t getHashCode (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setHashCode (MolecularGraph &molgraph, std::uint64_t hash_code)
 
CDPL_CHEM_API void clearHashCode (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasHashCode (const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::uint64_t calcHashCode (const MolecularGraph &molgraph, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool ord_h_deplete=true)
 
CDPL_CHEM_API void extractReactionCenter (const MolecularGraph &molgraph, Fragment &rxn_center)
 
CDPL_CHEM_API double getStoichiometricNumber (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setStoichiometricNumber (MolecularGraph &molgraph, double num)
 
CDPL_CHEM_API void clearStoichiometricNumber (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasStoichiometricNumber (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const std::string & getMDLUserInitials (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMDLUserInitials (MolecularGraph &molgraph, const std::string &initials)
 
CDPL_CHEM_API void clearMDLUserInitials (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMDLUserInitials (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const std::string & getMDLProgramName (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMDLProgramName (MolecularGraph &molgraph, const std::string &name)
 
CDPL_CHEM_API void clearMDLProgramName (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMDLProgramName (const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::size_t getMDLRegistryNumber (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMDLRegistryNumber (MolecularGraph &molgraph, std::size_t reg_no)
 
CDPL_CHEM_API void clearMDLRegistryNumber (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMDLRegistryNumber (const MolecularGraph &molgraph)
 
CDPL_CHEM_API unsigned int getMDLCTABVersion (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMDLCTABVersion (MolecularGraph &molgraph, unsigned int version)
 
CDPL_CHEM_API void clearMDLCTABVersion (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMDLCTABVersion (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const StringDataBlock::SharedPointergetStructureData (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setStructureData (MolecularGraph &molgraph, const StringDataBlock::SharedPointer &data)
 
CDPL_CHEM_API void clearStructureData (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasStructureData (const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::size_t getMDLDimensionality (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMDLDimensionality (MolecularGraph &molgraph, std::size_t dim)
 
CDPL_CHEM_API void clearMDLDimensionality (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMDLDimensionality (const MolecularGraph &molgraph)
 
CDPL_CHEM_API long getMDLScalingFactor1 (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMDLScalingFactor1 (MolecularGraph &molgraph, long factor)
 
CDPL_CHEM_API void clearMDLScalingFactor1 (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMDLScalingFactor1 (const MolecularGraph &molgraph)
 
CDPL_CHEM_API double getMDLScalingFactor2 (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMDLScalingFactor2 (MolecularGraph &molgraph, double factor)
 
CDPL_CHEM_API void clearMDLScalingFactor2 (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMDLScalingFactor2 (const MolecularGraph &molgraph)
 
CDPL_CHEM_API double getMDLEnergy (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMDLEnergy (MolecularGraph &molgraph, double energy)
 
CDPL_CHEM_API void clearMDLEnergy (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMDLEnergy (const MolecularGraph &molgraph)
 
CDPL_CHEM_API bool getMDLChiralFlag (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMDLChiralFlag (MolecularGraph &molgraph, bool flag)
 
CDPL_CHEM_API void clearMDLChiralFlag (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMDLChiralFlag (const MolecularGraph &molgraph)
 
CDPL_CHEM_API unsigned int getMOL2MoleculeType (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMOL2MoleculeType (MolecularGraph &molgraph, unsigned int type)
 
CDPL_CHEM_API void clearMOL2MoleculeType (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMOL2MoleculeType (const MolecularGraph &molgraph)
 
CDPL_CHEM_API unsigned int getMOL2ChargeType (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setMOL2ChargeType (MolecularGraph &molgraph, unsigned int type)
 
CDPL_CHEM_API void clearMOL2ChargeType (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasMOL2ChargeType (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void generateAdjacencyMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API void generateIncidenceMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API void generateBondMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API void generateBondElectronMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API void generateBondAtomTypeMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API const Math::ULMatrix::SharedPointergetTopologicalDistanceMatrix (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setTopologicalDistanceMatrix (MolecularGraph &molgraph, const Math::ULMatrix::SharedPointer &mtx)
 
CDPL_CHEM_API void clearTopologicalDistanceMatrix (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasTopologicalDistanceMatrix (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Math::ULMatrix::SharedPointer calcTopologicalDistanceMatrix (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void calcTopologicalDistanceMatrix (const MolecularGraph &molgraph, Math::ULMatrix &mtx)
 
CDPL_CHEM_API Math::ULMatrix::SharedPointer extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite)
 
CDPL_CHEM_API void extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph, Math::ULMatrix &mtx)
 
CDPL_CHEM_API const Math::DMatrix::SharedPointergetGeometricalDistanceMatrix (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setGeometricalDistanceMatrix (MolecularGraph &molgraph, const Math::DMatrix::SharedPointer &mtx)
 
CDPL_CHEM_API void clearGeometricalDistanceMatrix (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasGeometricalDistanceMatrix (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Math::DMatrix::SharedPointer calcGeometricalDistanceMatrix (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const Fragment::SharedPointergetAromaticSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setAromaticSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct)
 
CDPL_CHEM_API void clearAromaticSubstructure (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasAromaticSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Fragment::SharedPointer perceiveAromaticSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Fragment::SharedPointer perceiveAromaticSubstructure (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const ElectronSystemList::SharedPointergetPiElectronSystems (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void setPiElectronSystems (MolecularGraph &molgraph, const ElectronSystemList::SharedPointer &pi_systems)
 
CDPL_CHEM_API void clearPiElectronSystems (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool hasPiElectronSystems (const MolecularGraph &molgraph)
 
CDPL_CHEM_API ElectronSystemList::SharedPointer perceivePiElectronSystems (const MolecularGraph &molgraph)
 
CDPL_CHEM_API ElectronSystemList::SharedPointer perceivePiElectronSystems (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API bool generateSMILES (const MolecularGraph &molgraph, std::string &smiles, bool canonical=false, bool ord_h_deplete=true, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT)
 
CDPL_CHEM_API int generateINCHI (const MolecularGraph &molgraph, std::string &inchi, const std::string &options=ControlParameterDefault::INCHI_OUTPUT_OPTIONS, std::size_t dim=0)
 
CDPL_CHEM_API int generateINCHIKey (const MolecularGraph &molgraph, std::string &inchi_key)
 
CDPL_CHEM_API void canonicalize (MolecularGraph &molgraph, const AtomCompareFunction &func, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false)
 
CDPL_CHEM_API void canonicalize (MolecularGraph &molgraph, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false)
 
CDPL_CHEM_API void calc2DCoordinates (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void calcHydrogen3DCoordinates (MolecularGraph &molgraph, bool undef_only=true)
 
CDPL_CHEM_API void calcBond2DStereoFlags (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void calcCIPPriorities (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void perceiveSymmetryClasses (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool inc_impl_h=true)
 
CDPL_CHEM_API void calcCanonicalNumbering (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT)
 
CDPL_CHEM_API void calcMorganNumbering (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void calcImplicitHydrogenCounts (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void calcFormalCharges (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void perceiveHybridizationStates (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void perceiveBondOrders (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void kekulizeBonds (MolecularGraph &molgraph)
 
CDPL_CHEM_API void perceiveAtomStereoCenters (MolecularGraph &molgraph, bool overwrite, bool check_asym=true, bool check_inv_n=true, bool check_quart_n=true, bool check_plan_n=true, bool check_amide_n=true, bool check_res_ctrs=true)
 
CDPL_CHEM_API void perceiveBondStereoCenters (MolecularGraph &molgraph, bool overwrite, bool check_asym=true, bool check_term_n=true, bool check_order=true, std::size_t min_ring_size=8)
 
CDPL_CHEM_API void calcMDLParities (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void calcAtomStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true)
 
CDPL_CHEM_API void calcAtomStereoDescriptorsFromMDLParities (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void calcBondStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true)
 
CDPL_CHEM_API void calcAtomCIPConfigurations (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void calcBondCIPConfigurations (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void setAtomMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite)
 
CDPL_CHEM_API void setBondMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite)
 
CDPL_CHEM_API void generateMatchExpressions (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void generateMatchExpressionStrings (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void initSubstructureSearchQuery (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void initSubstructureSearchTarget (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void setAromaticityFlags (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void setRingFlags (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void setAtomTypesFromSymbols (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void setAtomSymbolsFromTypes (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void perceiveSybylAtomTypes (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API FragmentList::SharedPointer getAromaticRings (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer getAromaticSSSRSubset (const MolecularGraph &molgraph)
 
CDPL_CHEM_API bool containsMolecularGraph (const MolecularGraph &molgraph, const MolecularGraph &sub_molgraph, bool atoms=true, bool bonds=true)
 
CDPL_CHEM_API void getContainedFragments (const MolecularGraph &molgraph, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false, bool atoms=true, bool bonds=true)
 
CDPL_CHEM_API void getContainingFragments (const MolecularGraph &molgraph, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false, bool atoms=true, bool bonds=true)
 
CDPL_CHEM_API void translateFragment (const MolecularGraph &src_molgraph, const Fragment &src_frag, const MolecularGraph &tgt_molgraph, Fragment &tgt_frag, bool append=false)
 
CDPL_CHEM_API void translateFragments (const MolecularGraph &src_molgraph, const FragmentList &src_frag_list, const MolecularGraph &tgt_molgraph, FragmentList &tgt_frag_list, bool append=false)
 
CDPL_CHEM_API void splitIntoFragments (const MolecularGraph &molgraph, FragmentList &frag_list, const Util::BitSet &split_bond_mask, bool append=false)
 
CDPL_CHEM_API std::size_t getCompleteBondCount (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void calcBasicProperties (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API bool makeHydrogenDeplete (Molecule &mol, bool corr_impl_h_count=true)
 Removes all explicit hydrogen atoms from the molecule mol. More...
 
CDPL_CHEM_API bool makeOrdinaryHydrogenDeplete (Molecule &mol, unsigned int flags, bool corr_impl_h_count=true)
 Removes all explicit ordinary hydrogen atoms from the molecule mol. More...
 
CDPL_CHEM_API bool makeHydrogenComplete (Molecule &mol, bool corr_impl_h_count=true)
 Converts all implicit hydrogens of the molecule mol to explicit hydrogen atoms. More...
 
CDPL_CHEM_API void connectAtoms (Molecule &mol, double dist_tol=0.3, std::size_t atom_idx_offs=0)
 
CDPL_CHEM_API void connectAtoms (Molecule &mol, const Atom3DCoordinatesFunction &coords_func, double dist_tol=0.3, std::size_t atom_idx_offs=0)
 
CDPL_CHEM_API void removeAtomsIf (Molecule &mol, const AtomPredicate &pred)
 
CDPL_CHEM_API void removeAtomsIfNot (Molecule &mol, const AtomPredicate &pred)
 
CDPL_CHEM_API const std::string & getName (const Reaction &rxn)
 
CDPL_CHEM_API void setName (Reaction &rxn, const std::string &name)
 
CDPL_CHEM_API void clearName (Reaction &rxn)
 
CDPL_CHEM_API bool hasName (const Reaction &rxn)
 
CDPL_CHEM_API std::time_t getTimestamp (const Reaction &rxn)
 
CDPL_CHEM_API void setTimestamp (Reaction &rxn, std::time_t time)
 
CDPL_CHEM_API void clearTimestamp (Reaction &rxn)
 
CDPL_CHEM_API bool hasTimestamp (const Reaction &rxn)
 
CDPL_CHEM_API const std::string & getComment (const Reaction &rxn)
 
CDPL_CHEM_API void setComment (Reaction &rxn, const std::string &comment)
 
CDPL_CHEM_API void clearComment (Reaction &rxn)
 
CDPL_CHEM_API bool hasComment (const Reaction &rxn)
 
CDPL_CHEM_API const MatchExpression< Reaction >::SharedPointergetMatchExpression (const Reaction &rxn)
 
CDPL_CHEM_API void setMatchExpression (Reaction &rxn, const MatchExpression< Reaction >::SharedPointer &expr)
 
CDPL_CHEM_API void clearMatchExpression (Reaction &rxn)
 
CDPL_CHEM_API bool hasMatchExpression (const Reaction &rxn)
 
CDPL_CHEM_API MatchExpression< Reaction >::SharedPointer generateMatchExpression (const Reaction &rxn)
 
CDPL_CHEM_API MatchExpression< Reaction >::SharedPointer generateMatchExpression (Reaction &rxn, bool overwrite)
 
CDPL_CHEM_API const MatchConstraintList::SharedPointergetMatchConstraints (const Reaction &rxn)
 
CDPL_CHEM_API void setMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr)
 
CDPL_CHEM_API void clearMatchConstraints (Reaction &rxn)
 
CDPL_CHEM_API bool hasMatchConstraints (const Reaction &rxn)
 
CDPL_CHEM_API const FragmentList::SharedPointergetComponentGroups (const Reaction &rxn)
 
CDPL_CHEM_API void setComponentGroups (Reaction &rxn, const FragmentList::SharedPointer &comp_groups)
 
CDPL_CHEM_API void clearComponentGroups (Reaction &rxn)
 
CDPL_CHEM_API bool hasComponentGroups (const Reaction &rxn)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveComponentGroups (const Reaction &rxn)
 
CDPL_CHEM_API FragmentList::SharedPointer perceiveComponentGroups (Reaction &rxn, bool overwrite)
 
CDPL_CHEM_API const AtomMapping::SharedPointergetAtomMapping (const Reaction &rxn)
 
CDPL_CHEM_API void setAtomMapping (Reaction &rxn, const AtomMapping::SharedPointer &mapping)
 
CDPL_CHEM_API void clearAtomMapping (Reaction &rxn)
 
CDPL_CHEM_API bool hasAtomMapping (const Reaction &rxn)
 
CDPL_CHEM_API AtomMapping::SharedPointer perceiveAtomMapping (const Reaction &rxn)
 
CDPL_CHEM_API AtomMapping::SharedPointer perceiveAtomMapping (Reaction &rxn, bool overwrite)
 
CDPL_CHEM_API bool generateSMILES (const Reaction &rxn, std::string &smiles, bool canonical=false, bool ord_h_deplete=true, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT)
 
CDPL_CHEM_API std::uint64_t calcHashCode (const Reaction &rxn, unsigned int role_mask=ReactionRole::ALL, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool ord_h_deplete=true)
 
CDPL_CHEM_API const std::string & getMDLUserInitials (const Reaction &rxn)
 
CDPL_CHEM_API void setMDLUserInitials (Reaction &rxn, const std::string &initials)
 
CDPL_CHEM_API void clearMDLUserInitials (Reaction &rxn)
 
CDPL_CHEM_API bool hasMDLUserInitials (const Reaction &rxn)
 
CDPL_CHEM_API const std::string & getMDLProgramName (const Reaction &rxn)
 
CDPL_CHEM_API void setMDLProgramName (Reaction &rxn, const std::string &name)
 
CDPL_CHEM_API void clearMDLProgramName (Reaction &rxn)
 
CDPL_CHEM_API bool hasMDLProgramName (const Reaction &rxn)
 
CDPL_CHEM_API std::size_t getMDLRegistryNumber (const Reaction &rxn)
 
CDPL_CHEM_API void setMDLRegistryNumber (Reaction &rxn, std::size_t reg_no)
 
CDPL_CHEM_API void clearMDLRegistryNumber (Reaction &rxn)
 
CDPL_CHEM_API bool hasMDLRegistryNumber (const Reaction &rxn)
 
CDPL_CHEM_API const StringDataBlock::SharedPointergetReactionData (const Reaction &rxn)
 
CDPL_CHEM_API void setReactionData (Reaction &rxn, const StringDataBlock::SharedPointer &data)
 
CDPL_CHEM_API void clearReactionData (Reaction &rxn)
 
CDPL_CHEM_API bool hasReactionData (const Reaction &rxn)
 
CDPL_CHEM_API const Molecule::SharedPointergetMDLMoleculeRecord (const Reaction &rxn)
 
CDPL_CHEM_API void setMDLMoleculeRecord (Reaction &rxn, const Molecule::SharedPointer &mol_rec)
 
CDPL_CHEM_API void clearMDLMoleculeRecord (Reaction &rxn)
 
CDPL_CHEM_API bool hasMDLMoleculeRecord (const Reaction &rxn)
 
CDPL_CHEM_API const std::string & getMDLInternalRegistryNumber (const Reaction &rxn)
 
CDPL_CHEM_API void setMDLInternalRegistryNumber (Reaction &rxn, const std::string &reg_no)
 
CDPL_CHEM_API void clearMDLInternalRegistryNumber (Reaction &rxn)
 
CDPL_CHEM_API bool hasMDLInternalRegistryNumber (const Reaction &rxn)
 
CDPL_CHEM_API const std::string & getMDLExternalRegistryNumber (const Reaction &rxn)
 
CDPL_CHEM_API void setMDLExternalRegistryNumber (Reaction &rxn, const std::string &reg_no)
 
CDPL_CHEM_API void clearMDLExternalRegistryNumber (Reaction &rxn)
 
CDPL_CHEM_API bool hasMDLExternalRegistryNumber (const Reaction &rxn)
 
CDPL_CHEM_API unsigned int getMDLRXNFileVersion (const Reaction &rxn)
 
CDPL_CHEM_API void setMDLRXNFileVersion (Reaction &rxn, unsigned int version)
 
CDPL_CHEM_API void clearMDLRXNFileVersion (Reaction &rxn)
 
CDPL_CHEM_API bool hasMDLRXNFileVersion (const Reaction &rxn)
 
CDPL_CHEM_API std::size_t getMaxComponentGroupID (const Reaction &rxn)
 
CDPL_CHEM_API std::size_t getMaxAtomMappingID (const Reaction &rxn)
 
CDPL_CHEM_API void setAtomMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite)
 
CDPL_CHEM_API void setBondMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite)
 
CDPL_CHEM_API void setComponentMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite)
 
CDPL_CHEM_API void generateMatchExpressions (Reaction &rxn, bool overwrite)
 
CDPL_CHEM_API void initSubstructureSearchQuery (Reaction &rxn, bool overwrite)
 
CDPL_CHEM_API void initSubstructureSearchTarget (Reaction &rxn, bool overwrite)
 
CDPL_CHEM_API void calcBasicProperties (Reaction &rxn, bool overwrite)
 
CDPL_CHEM_API Molecule::SharedPointer parseSMARTS (const std::string &smarts, bool init_qry=true)
 
CDPL_CHEM_API bool parseSMARTS (const std::string &smarts, Molecule &mol, bool init_qry=true)
 
CDPL_CHEM_API Molecule::SharedPointer parseSMILES (const std::string &smiles)
 
CDPL_CHEM_API bool parseSMILES (const std::string &smiles, Molecule &mol)
 
CDPL_CHEM_API void extendBoundingBox (Math::Vector3D &min, Math::Vector3D &max, const Math::Vector3D &coords, bool reset=false)
 
CDPL_CHEM_API bool insideBoundingBox (const Math::Vector3D &min, const Math::Vector3D &max, const Math::Vector3D &coords)
 
CDPL_CHEM_API bool isAromatic (const Fragment &ring, const MolecularGraph &molgraph, const Util::BitSet &arom_bond_mask)
 
CDPL_CHEM_API bool isNotAromatic (const Fragment &ring, const MolecularGraph &molgraph)
 
CDPL_CHEM_API bool containsFragmentWithBond (const FragmentList &frag_list, const Bond &bond)
 
CDPL_CHEM_API bool containsFragmentWithMinSize (const FragmentList &frag_list, std::size_t min_size)
 
CDPL_CHEM_API bool atomTypesMatch (unsigned int qry_type, unsigned int tgt_type)
 
CDPL_CHEM_API unsigned int sybylToAtomType (unsigned int sybyl_type)
 
CDPL_CHEM_API const std::string & getSybylAtomTypeString (unsigned int sybyl_type)
 
CDPL_CHEM_API const std::string & getSybylBondTypeString (unsigned int sybyl_type)
 

Detailed Description

Contains classes and functions related to chemistry.

Typedef Documentation

◆ Atom3DCoordinatesFunction

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

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

◆ AtomCompareFunction

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

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

◆ AtomPredicate

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

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

◆ AtomPriorityFunction

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

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

◆ BondCompareFunction

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

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

◆ BondPredicate

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

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

◆ CDFBZ2MolecularGraphOutputHandler

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

◆ CDFBZ2MolecularGraphWriter

◆ CDFBZ2MoleculeInputHandler

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

◆ CDFBZ2MoleculeReader

◆ CDFBZ2ReactionInputHandler

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

◆ CDFBZ2ReactionOutputHandler

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

◆ CDFBZ2ReactionReader

◆ CDFBZ2ReactionWriter

◆ CDFGZMolecularGraphOutputHandler

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

◆ CDFGZMolecularGraphWriter

◆ CDFGZMoleculeInputHandler

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

◆ CDFGZMoleculeReader

◆ CDFGZReactionInputHandler

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

◆ CDFGZReactionOutputHandler

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

◆ CDFGZReactionReader

◆ CDFGZReactionWriter

◆ CDFMolecularGraphOutputHandler

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

◆ CDFMoleculeInputHandler

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

◆ CDFReactionInputHandler

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

◆ CDFReactionOutputHandler

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

◆ Entity3DCoordinatesFunction

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

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

◆ INCHIMolecularGraphOutputHandler

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

◆ INCHIMoleculeInputHandler

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

◆ JMEMolecularGraphOutputHandler

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

◆ JMEMoleculeInputHandler

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

◆ JMEReactionInputHandler

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

◆ JMEReactionOutputHandler

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

◆ MOL2BZ2MolecularGraphOutputHandler

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

◆ MOL2BZ2MolecularGraphWriter

◆ MOL2BZ2MoleculeInputHandler

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

◆ MOL2BZ2MoleculeReader

◆ MOL2GZMolecularGraphOutputHandler

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

◆ MOL2GZMolecularGraphWriter

◆ MOL2GZMoleculeInputHandler

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

◆ MOL2GZMoleculeReader

◆ MOL2MolecularGraphOutputHandler

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

◆ MOL2MoleculeInputHandler

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

◆ MolecularGraphWriter

Writer for molecule data in any supported format.

◆ MoleculeReader

Reader for molecule data in any supported format.

◆ MOLMolecularGraphOutputHandler

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

◆ MOLMoleculeInputHandler

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

◆ RDFBZ2ReactionInputHandler

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

◆ RDFBZ2ReactionOutputHandler

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

◆ RDFBZ2ReactionReader

◆ RDFBZ2ReactionWriter

◆ RDFGZReactionInputHandler

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

◆ RDFGZReactionOutputHandler

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

◆ RDFGZReactionReader

◆ RDFGZReactionWriter

◆ RDFReactionInputHandler

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

◆ RDFReactionOutputHandler

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

◆ ReactionReader

Reader for reaction data in any supported format.

◆ ReactionWriter

Writer for reaction data in any supported format.

◆ RXNReactionInputHandler

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

◆ RXNReactionOutputHandler

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

◆ SDFBZ2MolecularGraphOutputHandler

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

◆ SDFBZ2MolecularGraphWriter

◆ SDFBZ2MoleculeInputHandler

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

◆ SDFBZ2MoleculeReader

◆ SDFGZMolecularGraphOutputHandler

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

◆ SDFGZMolecularGraphWriter

◆ SDFGZMoleculeInputHandler

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

◆ SDFGZMoleculeReader

◆ SDFMolecularGraphOutputHandler

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

◆ SDFMoleculeInputHandler

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

◆ SMARTSMolecularGraphOutputHandler

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

◆ SMARTSMoleculeInputHandler

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

◆ SMARTSReactionInputHandler

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

◆ SMARTSReactionOutputHandler

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

◆ SMILESBZ2MolecularGraphOutputHandler

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

◆ SMILESBZ2MolecularGraphWriter

◆ SMILESBZ2MoleculeInputHandler

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

◆ SMILESBZ2MoleculeReader

◆ SMILESBZ2ReactionInputHandler

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

◆ SMILESBZ2ReactionOutputHandler

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

◆ SMILESBZ2ReactionReader

◆ SMILESBZ2ReactionWriter

◆ SMILESGZMolecularGraphOutputHandler

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

◆ SMILESGZMolecularGraphWriter

◆ SMILESGZMoleculeInputHandler

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

◆ SMILESGZMoleculeReader

◆ SMILESGZReactionInputHandler

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

◆ SMILESGZReactionOutputHandler

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

◆ SMILESGZReactionReader

◆ SMILESGZReactionWriter

◆ SMILESMolecularGraphOutputHandler

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

◆ SMILESMoleculeInputHandler

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

◆ SMILESReactionInputHandler

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

◆ SMILESReactionOutputHandler

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

◆ XYZBZ2MolecularGraphOutputHandler

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

◆ XYZBZ2MolecularGraphWriter

◆ XYZBZ2MoleculeInputHandler

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

◆ XYZBZ2MoleculeReader

◆ XYZGZMolecularGraphOutputHandler

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

◆ XYZGZMolecularGraphWriter

◆ XYZGZMoleculeInputHandler

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

◆ XYZGZMoleculeReader

◆ XYZMolecularGraphOutputHandler

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

◆ XYZMoleculeInputHandler

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

Function Documentation

◆ hasCoordinates()

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

◆ get2DCoordinates() [1/2]

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

◆ set2DCoordinates() [1/2]

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

◆ transform2DCoordinates()

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

◆ get3DCoordinates() [1/3]

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

◆ clearConformations()

CDPL_CHEM_API void CDPL::Chem::clearConformations ( AtomContainer cntnr)

◆ getNumConformations()

CDPL_CHEM_API std::size_t CDPL::Chem::getNumConformations ( const AtomContainer cntnr)

◆ applyConformation()

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

◆ getConformation()

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

◆ setConformation() [1/2]

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

◆ addConformation() [1/2]

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

◆ transformConformation()

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

◆ transformConformations()

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

◆ alignConformations() [1/4]

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

◆ alignConformations() [2/4]

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

◆ alignConformations() [3/4]

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

◆ alignConformations() [4/4]

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

◆ getMaxComponentGroupID() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxComponentGroupID ( const AtomContainer cntnr)

◆ getMaxAtomMappingID() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxAtomMappingID ( const AtomContainer cntnr)

◆ createAtomTypeMask()

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

◆ copyAtomsIf() [1/2]

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

◆ copyAtomsIf() [2/2]

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

◆ copyAtomsIfNot() [1/2]

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

◆ copyAtomsIfNot() [2/2]

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

◆ calcCenterOfMass()

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

◆ calcCentroid() [1/2]

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

◆ calcBoundingBox() [1/2]

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

◆ insideBoundingBox() [1/3]

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

◆ intersectsBoundingBox() [1/2]

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

◆ getName() [1/3]

CDPL_CHEM_API const std::string& CDPL::Chem::getName ( const Atom atom)

◆ setName() [1/3]

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

◆ clearName() [1/3]

CDPL_CHEM_API void CDPL::Chem::clearName ( Atom atom)

◆ hasName() [1/3]

CDPL_CHEM_API bool CDPL::Chem::hasName ( const Atom atom)

◆ getSymbol()

CDPL_CHEM_API const std::string& CDPL::Chem::getSymbol ( const Atom atom)

◆ setSymbol()

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

◆ clearSymbol()

CDPL_CHEM_API void CDPL::Chem::clearSymbol ( Atom atom)

◆ hasSymbol()

CDPL_CHEM_API bool CDPL::Chem::hasSymbol ( const Atom atom)

◆ getSymbolForType()

CDPL_CHEM_API const std::string& CDPL::Chem::getSymbolForType ( const Atom atom)

◆ getType()

CDPL_CHEM_API unsigned int CDPL::Chem::getType ( const Atom atom)

◆ setType()

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

◆ clearType()

CDPL_CHEM_API void CDPL::Chem::clearType ( Atom atom)

◆ hasType()

CDPL_CHEM_API bool CDPL::Chem::hasType ( const Atom atom)

◆ getTypeForSymbol()

CDPL_CHEM_API unsigned int CDPL::Chem::getTypeForSymbol ( const Atom atom)

◆ getGenericType()

CDPL_CHEM_API unsigned int CDPL::Chem::getGenericType ( const Atom atom)

◆ getFormalCharge()

CDPL_CHEM_API long CDPL::Chem::getFormalCharge ( const Atom atom)

◆ setFormalCharge()

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

◆ clearFormalCharge()

CDPL_CHEM_API void CDPL::Chem::clearFormalCharge ( Atom atom)

◆ hasFormalCharge()

CDPL_CHEM_API bool CDPL::Chem::hasFormalCharge ( const Atom atom)

◆ calcFormalCharge()

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

◆ getIsotope()

CDPL_CHEM_API std::size_t CDPL::Chem::getIsotope ( const Atom atom)

◆ setIsotope()

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

◆ clearIsotope()

CDPL_CHEM_API void CDPL::Chem::clearIsotope ( Atom atom)

◆ hasIsotope()

CDPL_CHEM_API bool CDPL::Chem::hasIsotope ( const Atom atom)

◆ getRadicalType()

CDPL_CHEM_API unsigned int CDPL::Chem::getRadicalType ( const Atom atom)

◆ setRadicalType()

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

◆ clearRadicalType()

CDPL_CHEM_API void CDPL::Chem::clearRadicalType ( Atom atom)

◆ hasRadicalType()

CDPL_CHEM_API bool CDPL::Chem::hasRadicalType ( const Atom atom)

◆ getHybridizationState()

CDPL_CHEM_API unsigned int CDPL::Chem::getHybridizationState ( const Atom atom)

◆ setHybridizationState()

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

◆ clearHybridizationState()

CDPL_CHEM_API void CDPL::Chem::clearHybridizationState ( Atom atom)

◆ hasHybridizationState()

CDPL_CHEM_API bool CDPL::Chem::hasHybridizationState ( const Atom atom)

◆ perceiveHybridizationState()

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

◆ getRingFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::getRingFlag ( const Atom atom)

◆ setRingFlag() [1/2]

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

◆ clearRingFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearRingFlag ( Atom atom)

◆ hasRingFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasRingFlag ( const Atom atom)

◆ isInFragmentOfSize() [1/2]

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

◆ getSizeOfSmallestContainingFragment() [1/2]

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

◆ getSizeOfLargestContainingFragment() [1/2]

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

◆ getNumContainingFragments() [1/2]

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

◆ getContainingFragments() [1/3]

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

◆ getAromaticityFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::getAromaticityFlag ( const Atom atom)

◆ setAromaticityFlag() [1/2]

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

◆ clearAromaticityFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearAromaticityFlag ( Atom atom)

◆ hasAromaticityFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasAromaticityFlag ( const Atom atom)

◆ getUnpairedElectronCount()

CDPL_CHEM_API std::size_t CDPL::Chem::getUnpairedElectronCount ( const Atom atom)

◆ setUnpairedElectronCount()

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

◆ clearUnpairedElectronCount()

CDPL_CHEM_API void CDPL::Chem::clearUnpairedElectronCount ( Atom atom)

◆ hasUnpairedElectronCount()

CDPL_CHEM_API bool CDPL::Chem::hasUnpairedElectronCount ( const Atom atom)

◆ getImplicitHydrogenCount()

CDPL_CHEM_API std::size_t CDPL::Chem::getImplicitHydrogenCount ( const Atom atom)

◆ setImplicitHydrogenCount()

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

◆ clearImplicitHydrogenCount()

CDPL_CHEM_API void CDPL::Chem::clearImplicitHydrogenCount ( Atom atom)

◆ hasImplicitHydrogenCount()

CDPL_CHEM_API bool CDPL::Chem::hasImplicitHydrogenCount ( const Atom atom)

◆ calcImplicitHydrogenCount()

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

◆ get2DCoordinates() [2/2]

CDPL_CHEM_API const Math::Vector2D& CDPL::Chem::get2DCoordinates ( const Atom atom)

◆ set2DCoordinates() [2/2]

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

◆ clear2DCoordinates()

CDPL_CHEM_API void CDPL::Chem::clear2DCoordinates ( Atom atom)

◆ has2DCoordinates()

CDPL_CHEM_API bool CDPL::Chem::has2DCoordinates ( const Atom atom)

◆ getConformer3DCoordinates()

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

◆ get3DCoordinatesArray()

CDPL_CHEM_API const Math::Vector3DArray::SharedPointer& CDPL::Chem::get3DCoordinatesArray ( const Atom atom)

◆ set3DCoordinatesArray()

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

◆ clear3DCoordinatesArray()

CDPL_CHEM_API void CDPL::Chem::clear3DCoordinatesArray ( Atom atom)

◆ has3DCoordinatesArray()

CDPL_CHEM_API bool CDPL::Chem::has3DCoordinatesArray ( const Atom atom)

◆ getMorganNumber()

CDPL_CHEM_API std::size_t CDPL::Chem::getMorganNumber ( const Atom atom)

◆ setMorganNumber()

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

◆ clearMorganNumber()

CDPL_CHEM_API void CDPL::Chem::clearMorganNumber ( Atom atom)

◆ hasMorganNumber()

CDPL_CHEM_API bool CDPL::Chem::hasMorganNumber ( const Atom atom)

◆ getCanonicalNumber()

CDPL_CHEM_API std::size_t CDPL::Chem::getCanonicalNumber ( const Atom atom)

◆ setCanonicalNumber()

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

◆ clearCanonicalNumber()

CDPL_CHEM_API void CDPL::Chem::clearCanonicalNumber ( Atom atom)

◆ hasCanonicalNumber()

CDPL_CHEM_API bool CDPL::Chem::hasCanonicalNumber ( const Atom atom)

◆ getCIPPriority()

CDPL_CHEM_API std::size_t CDPL::Chem::getCIPPriority ( const Atom atom)

◆ setCIPPriority()

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

◆ clearCIPPriority()

CDPL_CHEM_API void CDPL::Chem::clearCIPPriority ( Atom atom)

◆ hasCIPPriority()

CDPL_CHEM_API bool CDPL::Chem::hasCIPPriority ( const Atom atom)

◆ getSymmetryClass()

CDPL_CHEM_API std::size_t CDPL::Chem::getSymmetryClass ( const Atom atom)

◆ setSymmetryClass()

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

◆ clearSymmetryClass()

CDPL_CHEM_API void CDPL::Chem::clearSymmetryClass ( Atom atom)

◆ hasSymmetryClass()

CDPL_CHEM_API bool CDPL::Chem::hasSymmetryClass ( const Atom atom)

◆ getCIPConfiguration() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getCIPConfiguration ( const Atom atom)

◆ setCIPConfiguration() [1/2]

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

◆ clearCIPConfiguration() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearCIPConfiguration ( Atom atom)

◆ hasCIPConfiguration() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasCIPConfiguration ( const Atom atom)

◆ getStereoDescriptor() [1/2]

CDPL_CHEM_API const StereoDescriptor& CDPL::Chem::getStereoDescriptor ( const Atom atom)

◆ setStereoDescriptor() [1/2]

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

◆ clearStereoDescriptor() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoDescriptor ( Atom atom)

◆ hasStereoDescriptor() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoDescriptor ( const Atom atom)

◆ calcStereoDescriptor() [1/2]

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

◆ calcStereoDescriptorFromMDLParity()

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

◆ calcConfiguration() [1/2]

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

◆ getStereoCenterFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::getStereoCenterFlag ( const Atom atom)

◆ setStereoCenterFlag() [1/2]

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

◆ clearStereoCenterFlag() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoCenterFlag ( Atom atom)

◆ hasStereoCenterFlag() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoCenterFlag ( const Atom atom)

◆ isStereoCenter() [1/2]

CDPL_CHEM_API bool CDPL::Chem::isStereoCenter ( const Atom atom,
const MolecularGraph molgraph,
bool  check_asym = true,
bool  check_inv_n = true,
bool  check_quart_n = true,
bool  check_plan_n = true,
bool  check_amide_n = true,
bool  check_res_ctrs = true 
)

◆ getSybylType() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getSybylType ( const Atom atom)

◆ setSybylType() [1/2]

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

◆ clearSybylType() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearSybylType ( Atom atom)

◆ hasSybylType() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasSybylType ( const Atom atom)

◆ perceiveSybylType() [1/2]

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

◆ getMOL2Name()

CDPL_CHEM_API const std::string& CDPL::Chem::getMOL2Name ( const Atom atom)

◆ setMOL2Name()

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

◆ clearMOL2Name()

CDPL_CHEM_API void CDPL::Chem::clearMOL2Name ( Atom atom)

◆ hasMOL2Name()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2Name ( const Atom atom)

◆ getMOL2Charge()

CDPL_CHEM_API double CDPL::Chem::getMOL2Charge ( const Atom atom)

◆ setMOL2Charge()

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

◆ clearMOL2Charge()

CDPL_CHEM_API void CDPL::Chem::clearMOL2Charge ( Atom atom)

◆ hasMOL2Charge()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2Charge ( const Atom atom)

◆ getMOL2SubstructureID()

CDPL_CHEM_API std::size_t CDPL::Chem::getMOL2SubstructureID ( const Atom atom)

◆ setMOL2SubstructureID()

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

◆ clearMOL2SubstructureID()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureID ( Atom atom)

◆ hasMOL2SubstructureID()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureID ( const Atom atom)

◆ getMOL2SubstructureName()

CDPL_CHEM_API const std::string& CDPL::Chem::getMOL2SubstructureName ( const Atom atom)

◆ setMOL2SubstructureName()

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

◆ clearMOL2SubstructureName()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureName ( Atom atom)

◆ hasMOL2SubstructureName()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureName ( const Atom atom)

◆ getMOL2SubstructureSubtype()

CDPL_CHEM_API const std::string& CDPL::Chem::getMOL2SubstructureSubtype ( const Atom atom)

◆ setMOL2SubstructureSubtype()

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

◆ clearMOL2SubstructureSubtype()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureSubtype ( Atom atom)

◆ hasMOL2SubstructureSubtype()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureSubtype ( const Atom atom)

◆ getMOL2SubstructureChain()

CDPL_CHEM_API const std::string& CDPL::Chem::getMOL2SubstructureChain ( const Atom atom)

◆ setMOL2SubstructureChain()

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

◆ clearMOL2SubstructureChain()

CDPL_CHEM_API void CDPL::Chem::clearMOL2SubstructureChain ( Atom atom)

◆ hasMOL2SubstructureChain()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2SubstructureChain ( const Atom atom)

◆ getMDLParity()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLParity ( const Atom atom)

◆ setMDLParity()

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

◆ clearMDLParity()

CDPL_CHEM_API void CDPL::Chem::clearMDLParity ( Atom atom)

◆ hasMDLParity()

CDPL_CHEM_API bool CDPL::Chem::hasMDLParity ( const Atom atom)

◆ calcMDLParity()

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

◆ getMDLStereoCareFlag()

CDPL_CHEM_API bool CDPL::Chem::getMDLStereoCareFlag ( const Atom atom)

◆ setMDLStereoCareFlag()

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

◆ clearMDLStereoCareFlag()

CDPL_CHEM_API void CDPL::Chem::clearMDLStereoCareFlag ( Atom atom)

◆ hasMDLStereoCareFlag()

CDPL_CHEM_API bool CDPL::Chem::hasMDLStereoCareFlag ( const Atom atom)

◆ getReactionCenterStatus() [1/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getReactionCenterStatus ( const Atom atom)

◆ setReactionCenterStatus() [1/2]

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

◆ clearReactionCenterStatus() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearReactionCenterStatus ( Atom atom)

◆ hasReactionCenterStatus() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasReactionCenterStatus ( const Atom atom)

◆ getAtomMappingID()

CDPL_CHEM_API std::size_t CDPL::Chem::getAtomMappingID ( const Atom atom)

◆ setAtomMappingID()

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

◆ clearAtomMappingID()

CDPL_CHEM_API void CDPL::Chem::clearAtomMappingID ( Atom atom)

◆ hasAtomMappingID()

CDPL_CHEM_API bool CDPL::Chem::hasAtomMappingID ( const Atom atom)

◆ getComponentGroupID()

CDPL_CHEM_API std::size_t CDPL::Chem::getComponentGroupID ( const Atom atom)

◆ setComponentGroupID()

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

◆ clearComponentGroupID()

CDPL_CHEM_API void CDPL::Chem::clearComponentGroupID ( Atom atom)

◆ hasComponentGroupID()

CDPL_CHEM_API bool CDPL::Chem::hasComponentGroupID ( const Atom atom)

◆ getMatchConstraints() [1/4]

CDPL_CHEM_API const MatchConstraintList::SharedPointer& CDPL::Chem::getMatchConstraints ( const Atom atom)

◆ setMatchConstraints() [1/4]

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

◆ clearMatchConstraints() [1/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints ( Atom atom)

◆ hasMatchConstraints() [1/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints ( const Atom atom)

◆ getMatchExpression() [1/4]

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

◆ setMatchExpression() [1/4]

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

◆ clearMatchExpression() [1/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression ( Atom atom)

◆ hasMatchExpression() [1/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression ( const Atom atom)

◆ generateMatchExpression() [1/6]

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

◆ getMatchExpressionString() [1/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMatchExpressionString ( const Atom atom)

◆ setMatchExpressionString() [1/2]

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

◆ clearMatchExpressionString() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpressionString ( Atom atom)

◆ hasMatchExpressionString() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpressionString ( const Atom atom)

◆ generateMatchExpressionString() [1/2]

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

◆ markReachableAtoms()

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

◆ getTopologicalDistance()

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

◆ getEnvironment()

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

◆ getConnectedAtoms()

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

◆ getIncidentBonds()

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

◆ getConnectedAtomsAndBonds()

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

◆ getOrder()

CDPL_CHEM_API std::size_t CDPL::Chem::getOrder ( const Bond bond)

◆ setOrder()

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

◆ clearOrder()

CDPL_CHEM_API void CDPL::Chem::clearOrder ( Bond bond)

◆ hasOrder()

CDPL_CHEM_API bool CDPL::Chem::hasOrder ( const Bond bond)

◆ getRingFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::getRingFlag ( const Bond bond)

◆ setRingFlag() [2/2]

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

◆ clearRingFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearRingFlag ( Bond bond)

◆ hasRingFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasRingFlag ( const Bond bond)

◆ isInFragmentOfSize() [2/2]

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

◆ getSizeOfSmallestContainingFragment() [2/2]

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

◆ getSizeOfLargestContainingFragment() [2/2]

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

◆ getNumContainingFragments() [2/2]

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

◆ getContainingFragments() [2/3]

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

◆ getAromaticityFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::getAromaticityFlag ( const Bond bond)

◆ setAromaticityFlag() [2/2]

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

◆ clearAromaticityFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearAromaticityFlag ( Bond bond)

◆ hasAromaticityFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasAromaticityFlag ( const Bond bond)

◆ get2DStereoFlag()

CDPL_CHEM_API unsigned int CDPL::Chem::get2DStereoFlag ( const Bond bond)

◆ set2DStereoFlag()

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

◆ clear2DStereoFlag()

CDPL_CHEM_API void CDPL::Chem::clear2DStereoFlag ( Bond bond)

◆ has2DStereoFlag()

CDPL_CHEM_API bool CDPL::Chem::has2DStereoFlag ( const Bond bond)

◆ getCIPConfiguration() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getCIPConfiguration ( const Bond bond)

◆ setCIPConfiguration() [2/2]

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

◆ clearCIPConfiguration() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearCIPConfiguration ( Bond bond)

◆ hasCIPConfiguration() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasCIPConfiguration ( const Bond bond)

◆ getStereoDescriptor() [2/2]

CDPL_CHEM_API const StereoDescriptor& CDPL::Chem::getStereoDescriptor ( const Bond bond)

◆ setStereoDescriptor() [2/2]

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

◆ clearStereoDescriptor() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoDescriptor ( Bond bond)

◆ hasStereoDescriptor() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoDescriptor ( const Bond bond)

◆ calcStereoDescriptor() [2/2]

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

◆ calcConfiguration() [2/2]

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

◆ getStereoCenterFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::getStereoCenterFlag ( const Bond bond)

◆ setStereoCenterFlag() [2/2]

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

◆ clearStereoCenterFlag() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearStereoCenterFlag ( Bond bond)

◆ hasStereoCenterFlag() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasStereoCenterFlag ( const Bond bond)

◆ isStereoCenter() [2/2]

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

◆ getDirection()

CDPL_CHEM_API unsigned int CDPL::Chem::getDirection ( const Bond bond)

◆ setDirection()

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

◆ clearDirection()

CDPL_CHEM_API void CDPL::Chem::clearDirection ( Bond bond)

◆ hasDirection()

CDPL_CHEM_API bool CDPL::Chem::hasDirection ( const Bond bond)

◆ getReactionCenterStatus() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getReactionCenterStatus ( const Bond bond)

◆ setReactionCenterStatus() [2/2]

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

◆ clearReactionCenterStatus() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearReactionCenterStatus ( Bond bond)

◆ hasReactionCenterStatus() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasReactionCenterStatus ( const Bond bond)

◆ getMatchConstraints() [2/4]

CDPL_CHEM_API const MatchConstraintList::SharedPointer& CDPL::Chem::getMatchConstraints ( const Bond bond)

◆ setMatchConstraints() [2/4]

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

◆ clearMatchConstraints() [2/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints ( Bond bond)

◆ hasMatchConstraints() [2/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints ( const Bond bond)

◆ getMatchExpression() [2/4]

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

◆ setMatchExpression() [2/4]

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

◆ clearMatchExpression() [2/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression ( Bond bond)

◆ hasMatchExpression() [2/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression ( const Bond bond)

◆ generateMatchExpression() [2/6]

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

◆ getMatchExpressionString() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMatchExpressionString ( const Bond bond)

◆ setMatchExpressionString() [2/2]

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

◆ clearMatchExpressionString() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpressionString ( Bond bond)

◆ hasMatchExpressionString() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpressionString ( const Bond bond)

◆ generateMatchExpressionString() [2/2]

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

◆ getSybylType() [2/2]

CDPL_CHEM_API unsigned int CDPL::Chem::getSybylType ( const Bond bond)

◆ setSybylType() [2/2]

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

◆ clearSybylType() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearSybylType ( Bond bond)

◆ hasSybylType() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasSybylType ( const Bond bond)

◆ perceiveSybylType() [2/2]

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

◆ getOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API bool CDPL::Chem::getOrdinaryHydrogenDepleteParameter ( const Base::ControlParameterContainer cntnr)

◆ setOrdinaryHydrogenDepleteParameter()

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

◆ hasOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API bool CDPL::Chem::hasOrdinaryHydrogenDepleteParameter ( const Base::ControlParameterContainer cntnr)

◆ clearOrdinaryHydrogenDepleteParameter()

CDPL_CHEM_API void CDPL::Chem::clearOrdinaryHydrogenDepleteParameter ( Base::ControlParameterContainer cntnr)

◆ getCoordinatesDimensionParameter()

CDPL_CHEM_API std::size_t CDPL::Chem::getCoordinatesDimensionParameter ( const Base::ControlParameterContainer cntnr)

◆ setCoordinatesDimensionParameter()

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

◆ hasCoordinatesDimensionParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCoordinatesDimensionParameter ( const Base::ControlParameterContainer cntnr)

◆ clearCoordinatesDimensionParameter()

CDPL_CHEM_API void CDPL::Chem::clearCoordinatesDimensionParameter ( Base::ControlParameterContainer cntnr)

◆ getStrictErrorCheckingParameter()

CDPL_CHEM_API bool CDPL::Chem::getStrictErrorCheckingParameter ( const Base::ControlParameterContainer cntnr)

◆ setStrictErrorCheckingParameter()

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

◆ hasStrictErrorCheckingParameter()

CDPL_CHEM_API bool CDPL::Chem::hasStrictErrorCheckingParameter ( const Base::ControlParameterContainer cntnr)

◆ clearStrictErrorCheckingParameter()

CDPL_CHEM_API void CDPL::Chem::clearStrictErrorCheckingParameter ( Base::ControlParameterContainer cntnr)

◆ getRecordSeparatorParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getRecordSeparatorParameter ( const Base::ControlParameterContainer cntnr)

◆ setRecordSeparatorParameter()

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

◆ hasRecordSeparatorParameter()

CDPL_CHEM_API bool CDPL::Chem::hasRecordSeparatorParameter ( const Base::ControlParameterContainer cntnr)

◆ clearRecordSeparatorParameter()

CDPL_CHEM_API void CDPL::Chem::clearRecordSeparatorParameter ( Base::ControlParameterContainer cntnr)

◆ getBondMemberSwapStereoFixParameter()

CDPL_CHEM_API bool CDPL::Chem::getBondMemberSwapStereoFixParameter ( const Base::ControlParameterContainer cntnr)

◆ setBondMemberSwapStereoFixParameter()

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

◆ hasBondMemberSwapStereoFixParameter()

CDPL_CHEM_API bool CDPL::Chem::hasBondMemberSwapStereoFixParameter ( const Base::ControlParameterContainer cntnr)

◆ clearBondMemberSwapStereoFixParameter()

CDPL_CHEM_API void CDPL::Chem::clearBondMemberSwapStereoFixParameter ( Base::ControlParameterContainer cntnr)

◆ getCheckLineLengthParameter()

CDPL_CHEM_API bool CDPL::Chem::getCheckLineLengthParameter ( const Base::ControlParameterContainer cntnr)

◆ setCheckLineLengthParameter()

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

◆ hasCheckLineLengthParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCheckLineLengthParameter ( const Base::ControlParameterContainer cntnr)

◆ clearCheckLineLengthParameter()

CDPL_CHEM_API void CDPL::Chem::clearCheckLineLengthParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLCTABVersionParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLCTABVersionParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLCTABVersionParameter()

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

◆ hasMDLCTABVersionParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLCTABVersionParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLCTABVersionParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLCTABVersionParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLIgnoreParityParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLIgnoreParityParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLIgnoreParityParameter()

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

◆ hasMDLIgnoreParityParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLIgnoreParityParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLIgnoreParityParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLIgnoreParityParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLUpdateTimestampParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLUpdateTimestampParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLUpdateTimestampParameter()

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

◆ hasMDLUpdateTimestampParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLUpdateTimestampParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLUpdateTimestampParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLUpdateTimestampParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLTrimStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTrimStringsParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLTrimStringsParameter()

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

◆ hasMDLTrimStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTrimStringsParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLTrimStringsParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTrimStringsParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLTrimLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTrimLinesParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLTrimLinesParameter()

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

◆ hasMDLTrimLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTrimLinesParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLTrimLinesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTrimLinesParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLTruncateStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTruncateStringsParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLTruncateStringsParameter()

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

◆ hasMDLTruncateStringsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTruncateStringsParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLTruncateStringsParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTruncateStringsParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLTruncateLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLTruncateLinesParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLTruncateLinesParameter()

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

◆ hasMDLTruncateLinesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLTruncateLinesParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLTruncateLinesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLTruncateLinesParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLRXNFileVersionParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLRXNFileVersionParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLRXNFileVersionParameter()

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

◆ hasMDLRXNFileVersionParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLRXNFileVersionParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLRXNFileVersionParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLRXNFileVersionParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLOutputConfEnergyToEnergyFieldParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLOutputConfEnergyToEnergyFieldParameter()

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

◆ hasMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLOutputConfEnergyToEnergyFieldParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLOutputConfEnergyToEnergyFieldParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLOutputConfEnergyToEnergyFieldParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API bool CDPL::Chem::getMDLOutputConfEnergyAsSDEntryParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLOutputConfEnergyAsSDEntryParameter()

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

◆ hasMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLOutputConfEnergyAsSDEntryParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLOutputConfEnergyAsSDEntryParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLOutputConfEnergyAsSDEntryParameter ( Base::ControlParameterContainer cntnr)

◆ getMDLConfEnergySDTagParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLConfEnergySDTagParameter ( const Base::ControlParameterContainer cntnr)

◆ setMDLConfEnergySDTagParameter()

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

◆ hasMDLConfEnergySDTagParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMDLConfEnergySDTagParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMDLConfEnergySDTagParameter()

CDPL_CHEM_API void CDPL::Chem::clearMDLConfEnergySDTagParameter ( Base::ControlParameterContainer cntnr)

◆ getJMESeparateComponentsParameter()

CDPL_CHEM_API bool CDPL::Chem::getJMESeparateComponentsParameter ( const Base::ControlParameterContainer cntnr)

◆ setJMESeparateComponentsParameter()

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

◆ hasJMESeparateComponentsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasJMESeparateComponentsParameter ( const Base::ControlParameterContainer cntnr)

◆ clearJMESeparateComponentsParameter()

CDPL_CHEM_API void CDPL::Chem::clearJMESeparateComponentsParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESRecordFormatParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getSMILESRecordFormatParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESRecordFormatParameter()

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

◆ hasSMILESRecordFormatParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESRecordFormatParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESRecordFormatParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESRecordFormatParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESWriteCanonicalFormParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteCanonicalFormParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESWriteCanonicalFormParameter()

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

◆ hasSMILESWriteCanonicalFormParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteCanonicalFormParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESWriteCanonicalFormParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteCanonicalFormParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESWriteKekuleFormParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteKekuleFormParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESWriteKekuleFormParameter()

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

◆ hasSMILESWriteKekuleFormParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteKekuleFormParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESWriteKekuleFormParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteKekuleFormParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESWriteAtomStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteAtomStereoParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESWriteAtomStereoParameter()

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

◆ hasSMILESWriteAtomStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteAtomStereoParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESWriteAtomStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteAtomStereoParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESWriteBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteBondStereoParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESWriteBondStereoParameter()

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

◆ hasSMILESWriteBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteBondStereoParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESWriteBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteBondStereoParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESWriteRingBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteRingBondStereoParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESWriteRingBondStereoParameter()

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

◆ hasSMILESWriteRingBondStereoParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteRingBondStereoParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESWriteRingBondStereoParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteRingBondStereoParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESMinStereoBondRingSizeParameter()

CDPL_CHEM_API std::size_t CDPL::Chem::getSMILESMinStereoBondRingSizeParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESMinStereoBondRingSizeParameter()

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

◆ hasSMILESMinStereoBondRingSizeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESMinStereoBondRingSizeParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESMinStereoBondRingSizeParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESMinStereoBondRingSizeParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESWriteIsotopeParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteIsotopeParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESWriteIsotopeParameter()

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

◆ hasSMILESWriteIsotopeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteIsotopeParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESWriteIsotopeParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteIsotopeParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESMolWriteAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESMolWriteAtomMappingIDParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESMolWriteAtomMappingIDParameter()

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

◆ hasSMILESMolWriteAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESMolWriteAtomMappingIDParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESMolWriteAtomMappingIDParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESMolWriteAtomMappingIDParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESRxnWriteAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESRxnWriteAtomMappingIDParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESRxnWriteAtomMappingIDParameter()

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

◆ hasSMILESRxnWriteAtomMappingIDParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESRxnWriteAtomMappingIDParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESRxnWriteAtomMappingIDParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESRxnWriteAtomMappingIDParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESWriteSingleBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteSingleBondsParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESWriteSingleBondsParameter()

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

◆ hasSMILESWriteSingleBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteSingleBondsParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESWriteSingleBondsParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteSingleBondsParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESWriteAromaticBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESWriteAromaticBondsParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESWriteAromaticBondsParameter()

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

◆ hasSMILESWriteAromaticBondsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESWriteAromaticBondsParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESWriteAromaticBondsParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESWriteAromaticBondsParameter ( Base::ControlParameterContainer cntnr)

◆ getSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API bool CDPL::Chem::getSMILESNoOrganicSubsetParameter ( const Base::ControlParameterContainer cntnr)

◆ setSMILESNoOrganicSubsetParameter()

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

◆ hasSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API bool CDPL::Chem::hasSMILESNoOrganicSubsetParameter ( const Base::ControlParameterContainer cntnr)

◆ clearSMILESNoOrganicSubsetParameter()

CDPL_CHEM_API void CDPL::Chem::clearSMILESNoOrganicSubsetParameter ( Base::ControlParameterContainer cntnr)

◆ getINCHIInputOptionsParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getINCHIInputOptionsParameter ( const Base::ControlParameterContainer cntnr)

◆ setINCHIInputOptionsParameter()

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

◆ hasINCHIInputOptionsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasINCHIInputOptionsParameter ( const Base::ControlParameterContainer cntnr)

◆ clearINCHIInputOptionsParameter()

CDPL_CHEM_API void CDPL::Chem::clearINCHIInputOptionsParameter ( Base::ControlParameterContainer cntnr)

◆ getINCHIOutputOptionsParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getINCHIOutputOptionsParameter ( const Base::ControlParameterContainer cntnr)

◆ setINCHIOutputOptionsParameter()

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

◆ hasINCHIOutputOptionsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasINCHIOutputOptionsParameter ( const Base::ControlParameterContainer cntnr)

◆ clearINCHIOutputOptionsParameter()

CDPL_CHEM_API void CDPL::Chem::clearINCHIOutputOptionsParameter ( Base::ControlParameterContainer cntnr)

◆ getMultiConfImportParameter()

CDPL_CHEM_API bool CDPL::Chem::getMultiConfImportParameter ( const Base::ControlParameterContainer cntnr)

◆ setMultiConfImportParameter()

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

◆ hasMultiConfImportParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMultiConfImportParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMultiConfImportParameter()

CDPL_CHEM_API void CDPL::Chem::clearMultiConfImportParameter ( Base::ControlParameterContainer cntnr)

◆ getMultiConfExportParameter()

CDPL_CHEM_API bool CDPL::Chem::getMultiConfExportParameter ( const Base::ControlParameterContainer cntnr)

◆ setMultiConfExportParameter()

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

◆ hasMultiConfExportParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMultiConfExportParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMultiConfExportParameter()

CDPL_CHEM_API void CDPL::Chem::clearMultiConfExportParameter ( Base::ControlParameterContainer cntnr)

◆ getOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API bool CDPL::Chem::getOutputConfEnergyAsCommentParameter ( const Base::ControlParameterContainer cntnr)

◆ setOutputConfEnergyAsCommentParameter()

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

◆ hasOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API bool CDPL::Chem::hasOutputConfEnergyAsCommentParameter ( const Base::ControlParameterContainer cntnr)

◆ clearOutputConfEnergyAsCommentParameter()

CDPL_CHEM_API void CDPL::Chem::clearOutputConfEnergyAsCommentParameter ( Base::ControlParameterContainer cntnr)

◆ getConfIndexNameSuffixPatternParameter()

CDPL_CHEM_API const std::string& CDPL::Chem::getConfIndexNameSuffixPatternParameter ( const Base::ControlParameterContainer cntnr)

◆ setConfIndexNameSuffixPatternParameter()

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

◆ hasConfIndexNameSuffixPatternParameter()

CDPL_CHEM_API bool CDPL::Chem::hasConfIndexNameSuffixPatternParameter ( const Base::ControlParameterContainer cntnr)

◆ clearConfIndexNameSuffixPatternParameter()

CDPL_CHEM_API void CDPL::Chem::clearConfIndexNameSuffixPatternParameter ( Base::ControlParameterContainer cntnr)

◆ getMultiConfInputProcessorParameter()

CDPL_CHEM_API const MultiConfMoleculeInputProcessor::SharedPointer& CDPL::Chem::getMultiConfInputProcessorParameter ( const Base::ControlParameterContainer cntnr)

◆ setMultiConfInputProcessorParameter()

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

◆ hasMultiConfInputProcessorParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMultiConfInputProcessorParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMultiConfInputProcessorParameter()

CDPL_CHEM_API void CDPL::Chem::clearMultiConfInputProcessorParameter ( Base::ControlParameterContainer cntnr)

◆ getCDFWriteSinglePrecisionFloatsParameter()

CDPL_CHEM_API bool CDPL::Chem::getCDFWriteSinglePrecisionFloatsParameter ( const Base::ControlParameterContainer cntnr)

◆ setCDFWriteSinglePrecisionFloatsParameter()

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

◆ hasCDFWriteSinglePrecisionFloatsParameter()

CDPL_CHEM_API bool CDPL::Chem::hasCDFWriteSinglePrecisionFloatsParameter ( const Base::ControlParameterContainer cntnr)

◆ clearCDFWriteSinglePrecisionFloatsParameter()

CDPL_CHEM_API void CDPL::Chem::clearCDFWriteSinglePrecisionFloatsParameter ( Base::ControlParameterContainer cntnr)

◆ getMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2EnableExtendedAtomTypesParameter ( const Base::ControlParameterContainer cntnr)

◆ setMOL2EnableExtendedAtomTypesParameter()

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

◆ hasMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2EnableExtendedAtomTypesParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMOL2EnableExtendedAtomTypesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2EnableExtendedAtomTypesParameter ( Base::ControlParameterContainer cntnr)

◆ getMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2EnableAromaticBondTypesParameter ( const Base::ControlParameterContainer cntnr)

◆ setMOL2EnableAromaticBondTypesParameter()

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

◆ hasMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2EnableAromaticBondTypesParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMOL2EnableAromaticBondTypesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2EnableAromaticBondTypesParameter ( Base::ControlParameterContainer cntnr)

◆ getMOL2CalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2CalcFormalChargesParameter ( const Base::ControlParameterContainer cntnr)

◆ setMOL2CalcFormalChargesParameter()

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

◆ hasMOL2CalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2CalcFormalChargesParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMOL2CalcFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2CalcFormalChargesParameter ( Base::ControlParameterContainer cntnr)

◆ getMOL2ChargeTypeParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2ChargeTypeParameter ( const Base::ControlParameterContainer cntnr)

◆ setMOL2ChargeTypeParameter()

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

◆ hasMOL2ChargeTypeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2ChargeTypeParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMOL2ChargeTypeParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2ChargeTypeParameter ( Base::ControlParameterContainer cntnr)

◆ getMOL2MoleculeTypeParameter()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2MoleculeTypeParameter ( const Base::ControlParameterContainer cntnr)

◆ setMOL2MoleculeTypeParameter()

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

◆ hasMOL2MoleculeTypeParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2MoleculeTypeParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMOL2MoleculeTypeParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2MoleculeTypeParameter ( Base::ControlParameterContainer cntnr)

◆ getMOL2OutputSubstructuresParameter()

CDPL_CHEM_API bool CDPL::Chem::getMOL2OutputSubstructuresParameter ( const Base::ControlParameterContainer cntnr)

◆ setMOL2OutputSubstructuresParameter()

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

◆ hasMOL2OutputSubstructuresParameter()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2OutputSubstructuresParameter ( const Base::ControlParameterContainer cntnr)

◆ clearMOL2OutputSubstructuresParameter()

CDPL_CHEM_API void CDPL::Chem::clearMOL2OutputSubstructuresParameter ( Base::ControlParameterContainer cntnr)

◆ getXYZCommentIsNameParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZCommentIsNameParameter ( const Base::ControlParameterContainer cntnr)

◆ setXYZCommentIsNameParameter()

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

◆ hasXYZCommentIsNameParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZCommentIsNameParameter ( const Base::ControlParameterContainer cntnr)

◆ clearXYZCommentIsNameParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZCommentIsNameParameter ( Base::ControlParameterContainer cntnr)

◆ getXYZPerceiveConnectivityParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZPerceiveConnectivityParameter ( const Base::ControlParameterContainer cntnr)

◆ setXYZPerceiveConnectivityParameter()

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

◆ hasXYZPerceiveConnectivityParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZPerceiveConnectivityParameter ( const Base::ControlParameterContainer cntnr)

◆ clearXYZPerceiveConnectivityParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZPerceiveConnectivityParameter ( Base::ControlParameterContainer cntnr)

◆ getXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZPerceiveBondOrdersParameter ( const Base::ControlParameterContainer cntnr)

◆ setXYZPerceiveBondOrdersParameter()

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

◆ hasXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZPerceiveBondOrdersParameter ( const Base::ControlParameterContainer cntnr)

◆ clearXYZPerceiveBondOrdersParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZPerceiveBondOrdersParameter ( Base::ControlParameterContainer cntnr)

◆ getXYZCalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::getXYZCalcFormalChargesParameter ( const Base::ControlParameterContainer cntnr)

◆ setXYZCalcFormalChargesParameter()

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

◆ hasXYZCalcFormalChargesParameter()

CDPL_CHEM_API bool CDPL::Chem::hasXYZCalcFormalChargesParameter ( const Base::ControlParameterContainer cntnr)

◆ clearXYZCalcFormalChargesParameter()

CDPL_CHEM_API void CDPL::Chem::clearXYZCalcFormalChargesParameter ( Base::ControlParameterContainer cntnr)

◆ calcGeometricalDistanceMatrix() [1/2]

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

◆ get3DCoordinates() [2/3]

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

◆ set3DCoordinates() [1/2]

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

◆ transform3DCoordinates()

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

◆ align3DCoordinates()

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

◆ calcCentroid() [2/2]

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

◆ calcBoundingBox() [2/2]

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

◆ insideBoundingBox() [2/3]

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

◆ intersectsBoundingBox() [2/2]

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

◆ get3DCoordinates() [3/3]

CDPL_CHEM_API const Math::Vector3D& CDPL::Chem::get3DCoordinates ( const Entity3D entity)

◆ set3DCoordinates() [2/2]

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

◆ clear3DCoordinates()

CDPL_CHEM_API void CDPL::Chem::clear3DCoordinates ( Entity3D entity)

◆ has3DCoordinates()

CDPL_CHEM_API bool CDPL::Chem::has3DCoordinates ( const Entity3D entity)

◆ makeHydrogenDeplete() [1/2]

CDPL_CHEM_API bool CDPL::Chem::makeHydrogenDeplete ( Fragment frag)

Removes all explicit hydrogen atoms from the fragment frag.

Parameters
fragThe 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
fragThe fragment for which to remove all explicit ordinary hydrogen atoms.
flagsSpecifies the set of atom properties to check (see namespace Chem::AtomPropertyFlag).
Returns
false if frag was not altered, true otherwise.
See also
Chem::isOrdinaryHydrogen

◆ removeAtomsIf() [1/2]

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

◆ removeAtomsIfNot() [1/2]

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

◆ getName() [2/3]

CDPL_CHEM_API const std::string& CDPL::Chem::getName ( const MolecularGraph molgraph)

◆ setName() [2/3]

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

◆ clearName() [2/3]

CDPL_CHEM_API void CDPL::Chem::clearName ( MolecularGraph molgraph)

◆ hasName() [2/3]

CDPL_CHEM_API bool CDPL::Chem::hasName ( const MolecularGraph molgraph)

◆ getTimestamp() [1/2]

CDPL_CHEM_API std::time_t CDPL::Chem::getTimestamp ( const MolecularGraph molgraph)

◆ setTimestamp() [1/2]

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

◆ clearTimestamp() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearTimestamp ( MolecularGraph molgraph)

◆ hasTimestamp() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasTimestamp ( const MolecularGraph molgraph)

◆ getComment() [1/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getComment ( const MolecularGraph molgraph)

◆ setComment() [1/2]

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

◆ clearComment() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearComment ( MolecularGraph molgraph)

◆ hasComment() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasComment ( const MolecularGraph molgraph)

◆ getMatchConstraints() [3/4]

CDPL_CHEM_API const MatchConstraintList::SharedPointer& CDPL::Chem::getMatchConstraints ( const MolecularGraph molgraph)

◆ setMatchConstraints() [3/4]

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

◆ clearMatchConstraints() [3/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints ( MolecularGraph molgraph)

◆ hasMatchConstraints() [3/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints ( const MolecularGraph molgraph)

◆ getMatchExpression() [3/4]

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

◆ setMatchExpression() [3/4]

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

◆ clearMatchExpression() [3/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression ( MolecularGraph molgraph)

◆ hasMatchExpression() [3/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression ( const MolecularGraph molgraph)

◆ generateMatchExpression() [3/6]

CDPL_CHEM_API MatchExpression<MolecularGraph>::SharedPointer CDPL::Chem::generateMatchExpression ( const MolecularGraph molgraph)

◆ generateMatchExpression() [4/6]

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

◆ getRings()

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getRings ( const MolecularGraph molgraph)

◆ setRings()

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

◆ clearRings()

CDPL_CHEM_API void CDPL::Chem::clearRings ( MolecularGraph molgraph)

◆ hasRings()

CDPL_CHEM_API bool CDPL::Chem::hasRings ( const MolecularGraph molgraph)

◆ perceiveRings() [1/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveRings ( const MolecularGraph molgraph)

◆ perceiveRings() [2/2]

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

◆ getSSSR()

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getSSSR ( const MolecularGraph molgraph)

◆ setSSSR()

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

◆ clearSSSR()

CDPL_CHEM_API void CDPL::Chem::clearSSSR ( MolecularGraph molgraph)

◆ hasSSSR()

CDPL_CHEM_API bool CDPL::Chem::hasSSSR ( const MolecularGraph molgraph)

◆ perceiveSSSR() [1/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveSSSR ( const MolecularGraph molgraph)

◆ perceiveSSSR() [2/2]

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

◆ extractSSSRSubset() [1/2]

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

◆ extractSSSRSubset() [2/2]

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

◆ getCyclicSubstructure()

CDPL_CHEM_API const Fragment::SharedPointer& CDPL::Chem::getCyclicSubstructure ( const MolecularGraph molgraph)

◆ setCyclicSubstructure()

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

◆ clearCyclicSubstructure()

CDPL_CHEM_API void CDPL::Chem::clearCyclicSubstructure ( MolecularGraph molgraph)

◆ hasCyclicSubstructure()

CDPL_CHEM_API bool CDPL::Chem::hasCyclicSubstructure ( const MolecularGraph molgraph)

◆ perceiveCyclicSubstructure() [1/2]

CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveCyclicSubstructure ( const MolecularGraph molgraph)

◆ perceiveCyclicSubstructure() [2/2]

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

◆ getComponents()

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getComponents ( const MolecularGraph molgraph)

◆ setComponents()

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

◆ clearComponents()

CDPL_CHEM_API void CDPL::Chem::clearComponents ( MolecularGraph molgraph)

◆ hasComponents()

CDPL_CHEM_API bool CDPL::Chem::hasComponents ( const MolecularGraph molgraph)

◆ perceiveComponents() [1/2]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponents ( const MolecularGraph molgraph)

◆ perceiveComponents() [2/2]

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

◆ getComponentGroups() [1/2]

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getComponentGroups ( const MolecularGraph molgraph)

◆ setComponentGroups() [1/2]

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

◆ clearComponentGroups() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearComponentGroups ( MolecularGraph molgraph)

◆ hasComponentGroups() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasComponentGroups ( const MolecularGraph molgraph)

◆ perceiveComponentGroups() [1/4]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups ( const MolecularGraph molgraph)

◆ perceiveComponentGroups() [2/4]

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

◆ getConformationIndex()

CDPL_CHEM_API std::size_t CDPL::Chem::getConformationIndex ( const MolecularGraph molgraph)

◆ setConformationIndex()

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

◆ clearConformationIndex()

CDPL_CHEM_API void CDPL::Chem::clearConformationIndex ( MolecularGraph molgraph)

◆ hasConformationIndex()

CDPL_CHEM_API bool CDPL::Chem::hasConformationIndex ( const MolecularGraph molgraph)

◆ getConformerEnergies()

CDPL_CHEM_API const Util::DArray::SharedPointer& CDPL::Chem::getConformerEnergies ( const MolecularGraph molgraph)

◆ setConformerEnergies()

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

◆ clearConformerEnergies()

CDPL_CHEM_API void CDPL::Chem::clearConformerEnergies ( MolecularGraph molgraph)

◆ hasConformerEnergies()

CDPL_CHEM_API bool CDPL::Chem::hasConformerEnergies ( const MolecularGraph molgraph)

◆ setConformation() [2/2]

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

◆ addConformation() [2/2]

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

◆ getConformationEnergy()

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

◆ getHashCode()

CDPL_CHEM_API std::uint64_t CDPL::Chem::getHashCode ( const MolecularGraph molgraph)

◆ setHashCode()

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

◆ clearHashCode()

CDPL_CHEM_API void CDPL::Chem::clearHashCode ( MolecularGraph molgraph)

◆ hasHashCode()

CDPL_CHEM_API bool CDPL::Chem::hasHashCode ( const MolecularGraph molgraph)

◆ calcHashCode() [1/2]

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

◆ extractReactionCenter()

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

◆ getStoichiometricNumber()

CDPL_CHEM_API double CDPL::Chem::getStoichiometricNumber ( const MolecularGraph molgraph)

◆ setStoichiometricNumber()

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

◆ clearStoichiometricNumber()

CDPL_CHEM_API void CDPL::Chem::clearStoichiometricNumber ( MolecularGraph molgraph)

◆ hasStoichiometricNumber()

CDPL_CHEM_API bool CDPL::Chem::hasStoichiometricNumber ( const MolecularGraph molgraph)

◆ getMDLUserInitials() [1/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLUserInitials ( const MolecularGraph molgraph)

◆ setMDLUserInitials() [1/2]

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

◆ clearMDLUserInitials() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLUserInitials ( MolecularGraph molgraph)

◆ hasMDLUserInitials() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLUserInitials ( const MolecularGraph molgraph)

◆ getMDLProgramName() [1/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLProgramName ( const MolecularGraph molgraph)

◆ setMDLProgramName() [1/2]

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

◆ clearMDLProgramName() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLProgramName ( MolecularGraph molgraph)

◆ hasMDLProgramName() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLProgramName ( const MolecularGraph molgraph)

◆ getMDLRegistryNumber() [1/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMDLRegistryNumber ( const MolecularGraph molgraph)

◆ setMDLRegistryNumber() [1/2]

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

◆ clearMDLRegistryNumber() [1/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLRegistryNumber ( MolecularGraph molgraph)

◆ hasMDLRegistryNumber() [1/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLRegistryNumber ( const MolecularGraph molgraph)

◆ getMDLCTABVersion()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLCTABVersion ( const MolecularGraph molgraph)

◆ setMDLCTABVersion()

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

◆ clearMDLCTABVersion()

CDPL_CHEM_API void CDPL::Chem::clearMDLCTABVersion ( MolecularGraph molgraph)

◆ hasMDLCTABVersion()

CDPL_CHEM_API bool CDPL::Chem::hasMDLCTABVersion ( const MolecularGraph molgraph)

◆ getStructureData()

CDPL_CHEM_API const StringDataBlock::SharedPointer& CDPL::Chem::getStructureData ( const MolecularGraph molgraph)

◆ setStructureData()

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

◆ clearStructureData()

CDPL_CHEM_API void CDPL::Chem::clearStructureData ( MolecularGraph molgraph)

◆ hasStructureData()

CDPL_CHEM_API bool CDPL::Chem::hasStructureData ( const MolecularGraph molgraph)

◆ getMDLDimensionality()

CDPL_CHEM_API std::size_t CDPL::Chem::getMDLDimensionality ( const MolecularGraph molgraph)

◆ setMDLDimensionality()

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

◆ clearMDLDimensionality()

CDPL_CHEM_API void CDPL::Chem::clearMDLDimensionality ( MolecularGraph molgraph)

◆ hasMDLDimensionality()

CDPL_CHEM_API bool CDPL::Chem::hasMDLDimensionality ( const MolecularGraph molgraph)

◆ getMDLScalingFactor1()

CDPL_CHEM_API long CDPL::Chem::getMDLScalingFactor1 ( const MolecularGraph molgraph)

◆ setMDLScalingFactor1()

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

◆ clearMDLScalingFactor1()

CDPL_CHEM_API void CDPL::Chem::clearMDLScalingFactor1 ( MolecularGraph molgraph)

◆ hasMDLScalingFactor1()

CDPL_CHEM_API bool CDPL::Chem::hasMDLScalingFactor1 ( const MolecularGraph molgraph)

◆ getMDLScalingFactor2()

CDPL_CHEM_API double CDPL::Chem::getMDLScalingFactor2 ( const MolecularGraph molgraph)

◆ setMDLScalingFactor2()

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

◆ clearMDLScalingFactor2()

CDPL_CHEM_API void CDPL::Chem::clearMDLScalingFactor2 ( MolecularGraph molgraph)

◆ hasMDLScalingFactor2()

CDPL_CHEM_API bool CDPL::Chem::hasMDLScalingFactor2 ( const MolecularGraph molgraph)

◆ getMDLEnergy()

CDPL_CHEM_API double CDPL::Chem::getMDLEnergy ( const MolecularGraph molgraph)

◆ setMDLEnergy()

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

◆ clearMDLEnergy()

CDPL_CHEM_API void CDPL::Chem::clearMDLEnergy ( MolecularGraph molgraph)

◆ hasMDLEnergy()

CDPL_CHEM_API bool CDPL::Chem::hasMDLEnergy ( const MolecularGraph molgraph)

◆ getMDLChiralFlag()

CDPL_CHEM_API bool CDPL::Chem::getMDLChiralFlag ( const MolecularGraph molgraph)

◆ setMDLChiralFlag()

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

◆ clearMDLChiralFlag()

CDPL_CHEM_API void CDPL::Chem::clearMDLChiralFlag ( MolecularGraph molgraph)

◆ hasMDLChiralFlag()

CDPL_CHEM_API bool CDPL::Chem::hasMDLChiralFlag ( const MolecularGraph molgraph)

◆ getMOL2MoleculeType()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2MoleculeType ( const MolecularGraph molgraph)

◆ setMOL2MoleculeType()

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

◆ clearMOL2MoleculeType()

CDPL_CHEM_API void CDPL::Chem::clearMOL2MoleculeType ( MolecularGraph molgraph)

◆ hasMOL2MoleculeType()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2MoleculeType ( const MolecularGraph molgraph)

◆ getMOL2ChargeType()

CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2ChargeType ( const MolecularGraph molgraph)

◆ setMOL2ChargeType()

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

◆ clearMOL2ChargeType()

CDPL_CHEM_API void CDPL::Chem::clearMOL2ChargeType ( MolecularGraph molgraph)

◆ hasMOL2ChargeType()

CDPL_CHEM_API bool CDPL::Chem::hasMOL2ChargeType ( const MolecularGraph molgraph)

◆ generateAdjacencyMatrix()

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

◆ generateIncidenceMatrix()

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

◆ generateBondMatrix()

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

◆ generateBondElectronMatrix()

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

◆ generateBondAtomTypeMatrix()

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

◆ getTopologicalDistanceMatrix()

CDPL_CHEM_API const Math::ULMatrix::SharedPointer& CDPL::Chem::getTopologicalDistanceMatrix ( const MolecularGraph molgraph)

◆ setTopologicalDistanceMatrix()

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

◆ clearTopologicalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::clearTopologicalDistanceMatrix ( MolecularGraph molgraph)

◆ hasTopologicalDistanceMatrix()

CDPL_CHEM_API bool CDPL::Chem::hasTopologicalDistanceMatrix ( const MolecularGraph molgraph)

◆ calcTopologicalDistanceMatrix() [1/2]

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

◆ calcTopologicalDistanceMatrix() [2/2]

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

◆ extractTopologicalDistanceSubMatrix() [1/2]

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

◆ extractTopologicalDistanceSubMatrix() [2/2]

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

◆ getGeometricalDistanceMatrix()

CDPL_CHEM_API const Math::DMatrix::SharedPointer& CDPL::Chem::getGeometricalDistanceMatrix ( const MolecularGraph molgraph)

◆ setGeometricalDistanceMatrix()

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

◆ clearGeometricalDistanceMatrix()

CDPL_CHEM_API void CDPL::Chem::clearGeometricalDistanceMatrix ( MolecularGraph molgraph)

◆ hasGeometricalDistanceMatrix()

CDPL_CHEM_API bool CDPL::Chem::hasGeometricalDistanceMatrix ( const MolecularGraph molgraph)

◆ calcGeometricalDistanceMatrix() [2/2]

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

◆ getAromaticSubstructure()

CDPL_CHEM_API const Fragment::SharedPointer& CDPL::Chem::getAromaticSubstructure ( const MolecularGraph molgraph)

◆ setAromaticSubstructure()

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

◆ clearAromaticSubstructure()

CDPL_CHEM_API void CDPL::Chem::clearAromaticSubstructure ( MolecularGraph molgraph)

◆ hasAromaticSubstructure()

CDPL_CHEM_API bool CDPL::Chem::hasAromaticSubstructure ( const MolecularGraph molgraph)

◆ perceiveAromaticSubstructure() [1/2]

CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveAromaticSubstructure ( const MolecularGraph molgraph)

◆ perceiveAromaticSubstructure() [2/2]

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

◆ getPiElectronSystems()

CDPL_CHEM_API const ElectronSystemList::SharedPointer& CDPL::Chem::getPiElectronSystems ( const MolecularGraph molgraph)

◆ setPiElectronSystems()

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

◆ clearPiElectronSystems()

CDPL_CHEM_API void CDPL::Chem::clearPiElectronSystems ( MolecularGraph molgraph)

◆ hasPiElectronSystems()

CDPL_CHEM_API bool CDPL::Chem::hasPiElectronSystems ( const MolecularGraph molgraph)

◆ perceivePiElectronSystems() [1/2]

CDPL_CHEM_API ElectronSystemList::SharedPointer CDPL::Chem::perceivePiElectronSystems ( const MolecularGraph molgraph)

◆ perceivePiElectronSystems() [2/2]

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

◆ generateSMILES() [1/2]

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

◆ generateINCHI()

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

◆ generateINCHIKey()

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

◆ canonicalize() [1/2]

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

◆ canonicalize() [2/2]

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

◆ calc2DCoordinates()

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

◆ calcHydrogen3DCoordinates()

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

◆ calcBond2DStereoFlags()

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

◆ calcCIPPriorities()

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

◆ perceiveSymmetryClasses()

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

◆ calcCanonicalNumbering()

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

◆ calcMorganNumbering()

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

◆ calcImplicitHydrogenCounts()

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

◆ calcFormalCharges()

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

◆ perceiveHybridizationStates()

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

◆ perceiveBondOrders()

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

◆ kekulizeBonds()

CDPL_CHEM_API void CDPL::Chem::kekulizeBonds ( MolecularGraph molgraph)

◆ perceiveAtomStereoCenters()

CDPL_CHEM_API void CDPL::Chem::perceiveAtomStereoCenters ( MolecularGraph molgraph,
bool  overwrite,
bool  check_asym = true,
bool  check_inv_n = true,
bool  check_quart_n = true,
bool  check_plan_n = true,
bool  check_amide_n = true,
bool  check_res_ctrs = true 
)

◆ perceiveBondStereoCenters()

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

◆ calcMDLParities()

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

◆ calcAtomStereoDescriptors()

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

◆ calcAtomStereoDescriptorsFromMDLParities()

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

◆ calcBondStereoDescriptors()

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

◆ calcAtomCIPConfigurations()

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

◆ calcBondCIPConfigurations()

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

◆ setAtomMatchConstraints() [1/2]

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

◆ setBondMatchConstraints() [1/2]

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

◆ generateMatchExpressions() [1/2]

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

◆ generateMatchExpressionStrings()

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

◆ initSubstructureSearchQuery() [1/2]

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

◆ initSubstructureSearchTarget() [1/2]

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

◆ setAromaticityFlags()

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

◆ setRingFlags()

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

◆ setAtomTypesFromSymbols()

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

◆ setAtomSymbolsFromTypes()

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

◆ perceiveSybylAtomTypes()

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

◆ getAromaticRings()

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::getAromaticRings ( const MolecularGraph molgraph)

◆ getAromaticSSSRSubset()

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::getAromaticSSSRSubset ( const MolecularGraph molgraph)

◆ containsMolecularGraph()

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

◆ getContainedFragments()

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

◆ getContainingFragments() [3/3]

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

◆ translateFragment()

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

◆ translateFragments()

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

◆ splitIntoFragments()

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

◆ getCompleteBondCount()

CDPL_CHEM_API std::size_t CDPL::Chem::getCompleteBondCount ( const MolecularGraph molgraph)

◆ calcBasicProperties() [1/2]

CDPL_CHEM_API void CDPL::Chem::calcBasicProperties ( MolecularGraph molgraph,
bool  overwrite 
)
Since
1.1

◆ makeHydrogenDeplete() [2/2]

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

Removes all explicit hydrogen atoms from the molecule mol.

Parameters
molThe molecule for which to remove all explicit hydrogen atoms.
corr_impl_h_counttrue if the implicit hydrogen count property of the hydrogen completed atoms shall be corrected, false if the property shall be left unchanged.
Returns
false if mol was not altered, true otherwise.

◆ makeOrdinaryHydrogenDeplete() [2/2]

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

Removes all explicit ordinary hydrogen atoms from the molecule mol.

Parameters
molThe molecule for which to remove all explicit ordinary hydrogen atoms.
flagsSpecifies the set of atom properties to check (see namespace Chem::AtomPropertyFlag).
corr_impl_h_counttrue if the implicit hydrogen count property of the hydrogen completed atoms shall be corrected, false if the property shall be left unchanged.
Returns
false if mol was not altered, true otherwise.
See also
Chem::isOrdinaryHydrogen

◆ makeHydrogenComplete()

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

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

Parameters
molThe molecule that has to be made hydrogen complete.
corr_impl_h_counttrue if the implicit hydrogen count property of the hydrogen completed atoms shall be set to zero, false if the property shall be left unchanged.
Returns
false if mol was not altered, true otherwise.

◆ connectAtoms() [1/2]

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

◆ connectAtoms() [2/2]

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

◆ removeAtomsIf() [2/2]

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

◆ removeAtomsIfNot() [2/2]

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

◆ getName() [3/3]

CDPL_CHEM_API const std::string& CDPL::Chem::getName ( const Reaction rxn)

◆ setName() [3/3]

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

◆ clearName() [3/3]

CDPL_CHEM_API void CDPL::Chem::clearName ( Reaction rxn)

◆ hasName() [3/3]

CDPL_CHEM_API bool CDPL::Chem::hasName ( const Reaction rxn)

◆ getTimestamp() [2/2]

CDPL_CHEM_API std::time_t CDPL::Chem::getTimestamp ( const Reaction rxn)

◆ setTimestamp() [2/2]

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

◆ clearTimestamp() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearTimestamp ( Reaction rxn)

◆ hasTimestamp() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasTimestamp ( const Reaction rxn)

◆ getComment() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getComment ( const Reaction rxn)

◆ setComment() [2/2]

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

◆ clearComment() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearComment ( Reaction rxn)

◆ hasComment() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasComment ( const Reaction rxn)

◆ getMatchExpression() [4/4]

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

◆ setMatchExpression() [4/4]

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

◆ clearMatchExpression() [4/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchExpression ( Reaction rxn)

◆ hasMatchExpression() [4/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression ( const Reaction rxn)

◆ generateMatchExpression() [5/6]

CDPL_CHEM_API MatchExpression<Reaction>::SharedPointer CDPL::Chem::generateMatchExpression ( const Reaction rxn)

◆ generateMatchExpression() [6/6]

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

◆ getMatchConstraints() [4/4]

CDPL_CHEM_API const MatchConstraintList::SharedPointer& CDPL::Chem::getMatchConstraints ( const Reaction rxn)

◆ setMatchConstraints() [4/4]

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

◆ clearMatchConstraints() [4/4]

CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints ( Reaction rxn)

◆ hasMatchConstraints() [4/4]

CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints ( const Reaction rxn)

◆ getComponentGroups() [2/2]

CDPL_CHEM_API const FragmentList::SharedPointer& CDPL::Chem::getComponentGroups ( const Reaction rxn)

◆ setComponentGroups() [2/2]

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

◆ clearComponentGroups() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearComponentGroups ( Reaction rxn)

◆ hasComponentGroups() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasComponentGroups ( const Reaction rxn)

◆ perceiveComponentGroups() [3/4]

CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups ( const Reaction rxn)

◆ perceiveComponentGroups() [4/4]

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

◆ getAtomMapping()

CDPL_CHEM_API const AtomMapping::SharedPointer& CDPL::Chem::getAtomMapping ( const Reaction rxn)

◆ setAtomMapping()

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

◆ clearAtomMapping()

CDPL_CHEM_API void CDPL::Chem::clearAtomMapping ( Reaction rxn)

◆ hasAtomMapping()

CDPL_CHEM_API bool CDPL::Chem::hasAtomMapping ( const Reaction rxn)

◆ perceiveAtomMapping() [1/2]

CDPL_CHEM_API AtomMapping::SharedPointer CDPL::Chem::perceiveAtomMapping ( const Reaction rxn)

◆ perceiveAtomMapping() [2/2]

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

◆ generateSMILES() [2/2]

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

◆ calcHashCode() [2/2]

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

◆ getMDLUserInitials() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLUserInitials ( const Reaction rxn)

◆ setMDLUserInitials() [2/2]

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

◆ clearMDLUserInitials() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLUserInitials ( Reaction rxn)

◆ hasMDLUserInitials() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLUserInitials ( const Reaction rxn)

◆ getMDLProgramName() [2/2]

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLProgramName ( const Reaction rxn)

◆ setMDLProgramName() [2/2]

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

◆ clearMDLProgramName() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLProgramName ( Reaction rxn)

◆ hasMDLProgramName() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLProgramName ( const Reaction rxn)

◆ getMDLRegistryNumber() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMDLRegistryNumber ( const Reaction rxn)

◆ setMDLRegistryNumber() [2/2]

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

◆ clearMDLRegistryNumber() [2/2]

CDPL_CHEM_API void CDPL::Chem::clearMDLRegistryNumber ( Reaction rxn)

◆ hasMDLRegistryNumber() [2/2]

CDPL_CHEM_API bool CDPL::Chem::hasMDLRegistryNumber ( const Reaction rxn)

◆ getReactionData()

CDPL_CHEM_API const StringDataBlock::SharedPointer& CDPL::Chem::getReactionData ( const Reaction rxn)

◆ setReactionData()

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

◆ clearReactionData()

CDPL_CHEM_API void CDPL::Chem::clearReactionData ( Reaction rxn)

◆ hasReactionData()

CDPL_CHEM_API bool CDPL::Chem::hasReactionData ( const Reaction rxn)

◆ getMDLMoleculeRecord()

CDPL_CHEM_API const Molecule::SharedPointer& CDPL::Chem::getMDLMoleculeRecord ( const Reaction rxn)

◆ setMDLMoleculeRecord()

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

◆ clearMDLMoleculeRecord()

CDPL_CHEM_API void CDPL::Chem::clearMDLMoleculeRecord ( Reaction rxn)

◆ hasMDLMoleculeRecord()

CDPL_CHEM_API bool CDPL::Chem::hasMDLMoleculeRecord ( const Reaction rxn)

◆ getMDLInternalRegistryNumber()

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLInternalRegistryNumber ( const Reaction rxn)

◆ setMDLInternalRegistryNumber()

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

◆ clearMDLInternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::clearMDLInternalRegistryNumber ( Reaction rxn)

◆ hasMDLInternalRegistryNumber()

CDPL_CHEM_API bool CDPL::Chem::hasMDLInternalRegistryNumber ( const Reaction rxn)

◆ getMDLExternalRegistryNumber()

CDPL_CHEM_API const std::string& CDPL::Chem::getMDLExternalRegistryNumber ( const Reaction rxn)

◆ setMDLExternalRegistryNumber()

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

◆ clearMDLExternalRegistryNumber()

CDPL_CHEM_API void CDPL::Chem::clearMDLExternalRegistryNumber ( Reaction rxn)

◆ hasMDLExternalRegistryNumber()

CDPL_CHEM_API bool CDPL::Chem::hasMDLExternalRegistryNumber ( const Reaction rxn)

◆ getMDLRXNFileVersion()

CDPL_CHEM_API unsigned int CDPL::Chem::getMDLRXNFileVersion ( const Reaction rxn)

◆ setMDLRXNFileVersion()

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

◆ clearMDLRXNFileVersion()

CDPL_CHEM_API void CDPL::Chem::clearMDLRXNFileVersion ( Reaction rxn)

◆ hasMDLRXNFileVersion()

CDPL_CHEM_API bool CDPL::Chem::hasMDLRXNFileVersion ( const Reaction rxn)

◆ getMaxComponentGroupID() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxComponentGroupID ( const Reaction rxn)

◆ getMaxAtomMappingID() [2/2]

CDPL_CHEM_API std::size_t CDPL::Chem::getMaxAtomMappingID ( const Reaction rxn)

◆ setAtomMatchConstraints() [2/2]

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

◆ setBondMatchConstraints() [2/2]

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

◆ setComponentMatchConstraints()

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

◆ generateMatchExpressions() [2/2]

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

◆ initSubstructureSearchQuery() [2/2]

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

◆ initSubstructureSearchTarget() [2/2]

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

◆ calcBasicProperties() [2/2]

CDPL_CHEM_API void CDPL::Chem::calcBasicProperties ( Reaction rxn,
bool  overwrite 
)
Since
1.1

◆ parseSMARTS() [1/2]

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

◆ parseSMARTS() [2/2]

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

◆ parseSMILES() [1/2]

CDPL_CHEM_API Molecule::SharedPointer CDPL::Chem::parseSMILES ( const std::string &  smiles)

◆ parseSMILES() [2/2]

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

◆ extendBoundingBox()

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

◆ insideBoundingBox() [3/3]

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

◆ isAromatic()

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

◆ isNotAromatic()

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

◆ containsFragmentWithBond()

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

◆ containsFragmentWithMinSize()

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

◆ atomTypesMatch()

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

◆ sybylToAtomType()

CDPL_CHEM_API unsigned int CDPL::Chem::sybylToAtomType ( unsigned int  sybyl_type)

◆ getSybylAtomTypeString()

CDPL_CHEM_API const std::string& CDPL::Chem::getSybylAtomTypeString ( unsigned int  sybyl_type)

◆ getSybylBondTypeString()

CDPL_CHEM_API const std::string& CDPL::Chem::getSybylBondTypeString ( unsigned int  sybyl_type)