RDKit Namespace Reference

Std stuff. More...

Namespaces
namespace	Abbreviations
namespace	AtomPair
namespace	AtomPairs
namespace	Atropisomers
namespace	Canon
namespace	Chirality
namespace	CIPLabeler
namespace	CIPLabeler_detail
namespace	common_properties
namespace	constants
namespace	Deprotect
namespace	Descriptors
namespace	detail
namespace	details
namespace	DGeomHelpers
namespace	DTags
namespace	EnumerationStrategyPickler
namespace	EnumerationTypes
namespace	FileParserUtils
namespace	FilterMatchOps
namespace	FMCS
namespace	ForceFieldsHelper
namespace	GeneralizedSubstruct
namespace	GeneralMolSupplier
namespace	GenericGroups
namespace	Local
namespace	MACCSFingerprints
namespace	MHFPFingerprints
namespace	MMFF
namespace	MMPA
namespace	MolAlign
namespace	MolDraw2D_detail
namespace	MolDraw2DUtils
namespace	MolEnumerator
namespace	MolFragmenter
namespace	MolHash
namespace	MolInterchange
namespace	MolOps
	Groups a variety of molecular query and transformation operations.
namespace	MolShapes
namespace	MolStandardize
namespace	MorganFingerprint
namespace	MorganFingerprints
namespace	PicklerOps
namespace	PNGData
	Tags used for PNG metadata.
namespace	QueryOps
namespace	RascalMCES
namespace	RDKitFP
namespace	RDKitFPUtils
namespace	RDTypeTag
namespace	ReactionRunnerUtils
namespace	ReducedGraphs
namespace	RxnOps
namespace	ScaffoldNetwork
namespace	SGroupParsing
namespace	SGroupWriting
namespace	SLNParse
namespace	SmartsWrite
namespace	SmilesParse
namespace	SmilesWrite
namespace	StructureCheck
namespace	Subgraphs
namespace	SubstanceGroupChecks
namespace	TopologicalTorsion
namespace	UFF
namespace	Utils
namespace	v1
namespace	v2

Classes
struct	AdditionalOutput
class	AromaticAtomIterator_
	Iterate over aromatic atoms, this is bidirectional. More...
class	Atom
	The class for representing atoms. More...
class	AtomEnvironment
	abstract base class that holds atom-environments that will be hashed to generate the fingerprint More...
class	AtomEnvironmentGenerator
	abstract base class that generates atom-environments from a molecule More...
class	atomicData
class	AtomInvariantsGenerator
	abstract base class for atom invariants generators More...
class	AtomIterator_
	A general random access iterator. More...
class	AtomKekulizeException
class	AtomMonomerInfo
	The abstract base class for atom-level monomer info. More...
class	AtomPDBResidueInfo
	Captures atom-level information about peptide residues. More...
class	AtomRingQuery
class	AtomSanitizeException
class	AtomValenceException
class	BadFileException
	used by various file parsing classes to indicate a bad file More...
class	Bond
	class for representing a bond More...
class	BondInvariantsGenerator
	abstract base class for bond invariants generators More...
class	BondIterator_
	iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More...
class	CachedMolHolder
	Concrete class that holds binary cached molecules in memory. More...
class	CachedSmilesMolHolder
	Concrete class that holds smiles strings in memory. More...
class	CachedTrustedSmilesMolHolder
	Concrete class that holds trusted smiles strings in memory. More...
struct	CartesianProduct
	iterate through all possible permutations of the rgroups More...
class	CartesianProductStrategy
struct	charptr_functor
	functor for comparing two strings More...
class	ChemicalReaction
	This is a class for storing and applying general chemical reactions. More...
class	ChemicalReactionException
	used to indicate an error in the chemical reaction engine More...
class	ChemicalReactionParserException
	used to indicate an error in parsing reaction data More...
class	Conformer
	The class for representing 2D or 3D conformation of a molecule. More...
class	ConformerException
	used to indicate errors from incorrect conformer access More...
class	ConstBondIterator_
	const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More...
class	CustomPropHandler
struct	CXXAtomIterator
struct	CXXBondIterator
class	DataStructsExplicitBitVecPropHandler
class	Dict
	The Dict class can be used to store objects of arbitrary type keyed by strings. More...
class	DiscreteDistMat
class	DiscreteValueVect
	a class for efficiently storing vectors of discrete values More...
struct	DrawColour
class	EnumerateLibrary
	This is a class for running reactions on sets of reagents. More...
class	EnumerateLibraryBase
struct	EnumerationParams
class	EnumerationStrategyBase
class	EnumerationStrategyException
	class for flagging enumeration strategy errors More...
class	EvenSamplePairsStrategy
	EvenSamplePairsStrategy. More...
class	ExclusionList
class	FeatureFileParseException
	class used to indicate errors in parsing feature definition files. More...
class	FileParseException
	used by various file parsing classes to indicate a parse error More...
class	FilterCatalog
class	FilterCatalogEntry
class	FilterCatalogParams
struct	FilterData_t
class	FilterHierarchyMatcher
struct	FilterMatch
	Holds the atomPairs matched by the underlying matcher. More...
class	FilterMatcherBase
struct	FilterProperty_t
class	FingerprintArguments
	Abstract base class that holds molecule independent arguments that are common amongst all fingerprint types and classes inherited from this would hold fingerprint type specific arguments. More...
struct	FingerprintFuncArguments
	struct that makes calling the fingerprint generation functions easier More...
class	FingerprintGenerator
	class that generates same fingerprint style for different output formats More...
struct	FingerprintVarianceScoreData
class	FixedMolSizeMolBundle
class	ForwardSDMolSupplier
class	FPBReader
	class for reading and searching FPB files More...
class	FPHolderBase
	Base FPI for the fingerprinter used to rule out impossible matches. More...
class	FragCatalogEntry
class	FragCatGenerator
class	FragCatParams
	container for user parameters used to create a fragment catalog More...
class	FragFPGenerator
struct	GaResult
class	GasteigerParams
class	HasPropQuery
class	HasPropWithValueQuery
class	HasPropWithValueQuery< TargetPtr, ExplicitBitVect >
class	HasPropWithValueQuery< TargetPtr, std::string >
class	HeteroatomIterator_
	Iterate over heteroatoms, this is bidirectional. More...
class	KekulizeException
class	KeyFromPropHolder
class	KeyHolderBase
struct	larger_of
	functor for returning the larger of two values More...
struct	ltDouble
	functor to compare two doubles with a tolerance More...
class	MarvinArrow
class	MarvinAtom
class	MarvinAttachmentPoint
class	MarvinBond
class	MarvinBondStereo
class	MarvinCondition
class	MarvinDataSgroup
class	MarvinGenericSgroup
class	MarvinMol
class	MarvinMolBase
class	MarvinMonomerSgroup
class	MarvinMulticenterSgroup
class	MarvinMultipleSgroup
class	MarvinPlus
class	MarvinReaction
class	MarvinRectangle
class	MarvinSruCoModSgroup
class	MarvinStereoGroup
class	MarvinSuperatomSgroup
class	MarvinSuperatomSgroupExpanded
class	MarvinWriterException
class	MatchingAtomIterator_
	Iterate over atoms matching a query function. This is bidirectional. More...
struct	MCSAtomCompareParameters
struct	MCSBondCompareParameters
struct	MCSParameters
struct	MCSProgressData
struct	MCSResult
class	MolBundle
	MolBundle contains a collection of related ROMols. More...
class	MolCatalogEntry
	This class is used to store ROMol objects in a MolCatalog. More...
class	MolCatalogParams
	container for user parameters used to create a mol catalog More...
class	MolChemicalFeature
class	MolChemicalFeatureDef
class	MolChemicalFeatureFactory
	The class for finding chemical features in molecules. More...
class	MolDraw2D
	MolDraw2D is the base class for doing 2D renderings of molecules. More...
class	MolDraw2DCairo
class	MolDraw2DJS
class	MolDraw2DQt
class	MolDraw2DSVG
class	MolDraw2Dwx
struct	MolDrawOptions
class	MolHolder
	Concrete class that holds molecules in memory. More...
class	MolHolderBase
	Base class API for holding molecules to substructure search. More...
class	MolMatchFinalCheckFunctor
class	MolPickler
	handles pickling (serializing) molecules More...
class	MolPicklerException
	used to indicate exceptions whilst pickling (serializing) molecules More...
class	MolSanitizeException
	class for flagging sanitization errors More...
class	MolSupplier
class	MolWriter
struct	MolWriterParams
struct	MolzipParams
struct	MrvWriterParams
class	MultiFPBReader
	class for reading and searching multiple FPB files More...
class	PatternHolder
class	PDBMolSupplier
	Deprecated, will be removed in 2024.09 release. More...
class	PDBWriter
class	PeriodicTable
	singleton class for retrieving information about atoms More...
class	QueryAtom
	Class for storing atomic queries. More...
class	QueryAtomIterator_
	Iterate over atoms matching a query. This is bidirectional. More...
class	QueryBond
	Class for storing Bond queries. More...
class	RandomSampleAllBBsStrategy
class	RandomSampleStrategy
struct	RCore
	RCore is the core common to a series of molecules. More...
struct	RDAny
class	RDProps
struct	RDValue
struct	ReactionFingerprintParams
class	ReactionPickler
	handles pickling (serializing) reactions More...
class	ReactionPicklerException
	used to indicate exceptions whilst pickling (serializing) reactions More...
class	RecursiveStructureQuery
	allows use of recursive structure queries (e.g. recursive SMARTS) More...
class	ResonanceMolSupplier
class	ResonanceMolSupplierCallback
struct	RGroupData
	A single rgroup attached to a given core. More...
struct	RGroupDecompData
class	RGroupDecomposition
class	RGroupDecompositionChromosome
struct	RGroupDecompositionParameters
struct	RGroupDecompositionProcessResult
class	RGroupGa
struct	RGroupMatch
	RGroupMatch is the decomposition for a single molecule. More...
class	RGroupScorer
class	RingInfo
class	ROMol
class	RWMol
	RWMol is a molecule class that is intended to be edited. More...
class	RxnSanitizeException
	class for flagging sanitization errors More...
class	SDMolSupplier
class	SDWriter
class	SLNParseException
class	SmartsMatcher
struct	SmartsParserParams
class	SmilesMolSupplier
	lazy file parser for Smiles tables More...
struct	SmilesParserParams
struct	SmilesWriteParams
class	SmilesWriter
class	Snapshot
class	SparseIntVect
	a class for efficiently storing sparse vectors of ints More...
struct	StereoBondThresholds
class	StereoGroup
class	SubstanceGroup
	The class for representing SubstanceGroups. More...
class	SubstanceGroupException
	used to indicate errors from incorrect sgroup access More...
class	SubstructLibrary
	Substructure Search a library of molecules. More...
struct	SubstructMatchParameters
class	TautomerPatternHolder
class	TautomerQuery
class	TDTMolSupplier
	lazy file parser for TDT files More...
class	TDTWriter
class	Trajectory
class	UnimplementedFPException
class	UsedLabelMap
struct	VarianceDataForLabel

Typedefs
typedef boost::shared_ptr< Conformer >	CONFORMER_SPTR
typedef std::uint32_t	atomindex_t
typedef RDCatalog::Catalog< FilterCatalogEntry, FilterCatalogParams >	FCatalog
typedef std::map< std::string, std::string >	STRING_PROPS
typedef bool(*	MCSAtomCompareFunction) (const MCSAtomCompareParameters &, const ROMol &, unsigned int, const ROMol &, unsigned int, void *)
typedef bool(*	MCSBondCompareFunction) (const MCSBondCompareParameters &, const ROMol &, unsigned int, const ROMol &, unsigned int, void *)
typedef bool(*	MCSAcceptanceFunction) (const ROMol &, const ROMol &, const std::vector< std::pair< int, int > > &, const std::vector< std::pair< int, int > > &, const MCSParameters *)
typedef bool(*	MCSFinalMatchCheckFunction) (const std::uint32_t[], const std::uint32_t[], const ROMol &, const FMCS::Graph &, const ROMol &, const FMCS::Graph &, const MCSParameters *)
typedef bool(*	MCSProgressCallback) (const MCSProgressData &stat, const MCSParameters &params, void *userData)
typedef RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >	FragCatalog
typedef std::vector< std::pair< int, int > >	MatchVectType
	used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)
typedef RDCatalog::HierarchCatalog< MolCatalogEntry, MolCatalogParams, int >	MolCatalog
	a hierarchical catalog for holding molecules
typedef boost::shared_ptr< MolChemicalFeature >	FeatSPtr
typedef std::list< FeatSPtr >	FeatSPtrList
typedef FeatSPtrList::iterator	FeatSPtrList_I
typedef std::map< int, DrawColour >	ColourPalette
typedef std::vector< double >	DashPattern
typedef std::vector< double >	INVAR_VECT
typedef INVAR_VECT::iterator	INVAR_VECT_I
typedef INVAR_VECT::const_iterator	INVAR_VECT_CI
typedef Queries::Query< bool, Atom const *, true >	ATOM_BOOL_QUERY
typedef Queries::Query< bool, Bond const *, true >	BOND_BOOL_QUERY
typedef Queries::AndQuery< int, Atom const *, true >	ATOM_AND_QUERY
typedef Queries::AndQuery< int, Bond const *, true >	BOND_AND_QUERY
typedef Queries::OrQuery< int, Atom const *, true >	ATOM_OR_QUERY
typedef Queries::OrQuery< int, Bond const *, true >	BOND_OR_QUERY
typedef Queries::XOrQuery< int, Atom const *, true >	ATOM_XOR_QUERY
typedef Queries::XOrQuery< int, Bond const *, true >	BOND_XOR_QUERY
typedef Queries::EqualityQuery< int, Atom const *, true >	ATOM_EQUALS_QUERY
typedef Queries::EqualityQuery< int, Bond const *, true >	BOND_EQUALS_QUERY
typedef Queries::GreaterQuery< int, Atom const *, true >	ATOM_GREATER_QUERY
typedef Queries::GreaterQuery< int, Bond const *, true >	BOND_GREATER_QUERY
typedef Queries::GreaterEqualQuery< int, Atom const *, true >	ATOM_GREATEREQUAL_QUERY
typedef Queries::GreaterEqualQuery< int, Bond const *, true >	BOND_GREATEREQUAL_QUERY
typedef Queries::LessQuery< int, Atom const *, true >	ATOM_LESS_QUERY
typedef Queries::LessQuery< int, Bond const *, true >	BOND_LESS_QUERY
typedef Queries::LessEqualQuery< int, Atom const *, true >	ATOM_LESSEQUAL_QUERY
typedef Queries::LessEqualQuery< int, Bond const *, true >	BOND_LESSEQUAL_QUERY
typedef Queries::RangeQuery< int, Atom const *, true >	ATOM_RANGE_QUERY
typedef Queries::RangeQuery< int, Bond const *, true >	BOND_RANGE_QUERY
typedef Queries::SetQuery< int, Atom const *, true >	ATOM_SET_QUERY
typedef Queries::SetQuery< int, Bond const *, true >	BOND_SET_QUERY
typedef Queries::Query< int, Bond const *, true >	BOND_NULL_QUERY
typedef Queries::Query< int, Atom const *, true >	ATOM_NULL_QUERY
typedef Atom const *	ConstAtomPtr
typedef Bond const *	ConstBondPtr
typedef Queries::EqualityQuery< int, Atom const *, true >	ATOM_PROP_QUERY
typedef Queries::EqualityQuery< int, Bond const *, true >	BOND_PROP_QUERY
typedef std::map< unsigned int, BondElectrons * >	ConjBondMap
typedef std::map< unsigned int, AtomElectrons * >	ConjAtomMap
typedef std::vector< ConjElectrons * >	CEVect
typedef std::vector< CEVect2 * >	CEVect3
typedef std::vector< std::uint8_t >	ConjFP
typedef std::unordered_map< std::size_t, ConjElectrons * >	CEMap
typedef std::map< std::string, ROMOL_SPTR >	RGroupRow
typedef std::vector< ROMOL_SPTR >	RGroupColumn
typedef std::vector< RGroupRow >	RGroupRows
typedef std::map< std::string, RGroupColumn >	RGroupColumns
typedef LinkedPopLinearSel< RGroupDecompositionChromosome, RGroupGa >	RGroupGaPopulation
typedef boost::shared_ptr< RGroupData >	RData
typedef std::map< int, RData >	R_DECOMP
typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, Atom *, Bond * >	MolGraph
	This is the BGL type used to store the topology:
typedef boost::shared_ptr< RWMol >	RWMOL_SPTR
typedef std::vector< RWMOL_SPTR >	RWMOL_SPTR_VECT
typedef std::vector< int >	PATH_TYPE
typedef std::list< PATH_TYPE >	PATH_LIST
typedef PATH_LIST::const_iterator	PATH_LIST_CI
typedef std::map< int, PATH_LIST >	INT_PATH_LIST_MAP
typedef INT_PATH_LIST_MAP::const_iterator	INT_PATH_LIST_MAP_CI
typedef INT_PATH_LIST_MAP::iterator	INT_PATH_LIST_MAP_I
typedef std::vector< Snapshot >	SnapshotVect
typedef std::vector< std::string >	STR_VECT
typedef RDValue	RDValue_cast_t
typedef std::vector< std::shared_ptr< const CustomPropHandler > >	CustomPropHandlerVec
typedef long long int	LONGINT
typedef unsigned int	UINT
typedef unsigned short	USHORT
typedef unsigned char	UCHAR
typedef std::vector< int >	INT_VECT
typedef INT_VECT::iterator	INT_VECT_I
typedef INT_VECT::const_iterator	INT_VECT_CI
typedef INT_VECT::reverse_iterator	INT_VECT_RI
typedef INT_VECT::const_reverse_iterator	INT_VECT_CRI
typedef std::list< int >	INT_LIST
typedef INT_LIST::iterator	INT_LIST_I
typedef INT_LIST::const_iterator	INT_LIST_CI
typedef std::list< INT_VECT >	LIST_INT_VECT
typedef LIST_INT_VECT::iterator	LIST_INT_VECT_I
typedef LIST_INT_VECT::const_iterator	LIST_INT_VECT_CI
typedef std::vector< INT_VECT >	VECT_INT_VECT
typedef VECT_INT_VECT::iterator	VECT_INT_VECT_I
typedef VECT_INT_VECT::const_iterator	VECT_INT_VECT_CI
typedef std::vector< UINT >::const_iterator	UINT_VECT_CI
typedef std::vector< UINT >	UINT_VECT
typedef std::vector< std::string >::const_iterator	STR_VECT_CI
typedef std::vector< std::string >::iterator	STR_VECT_I
typedef std::vector< double >	DOUBLE_VECT
typedef DOUBLE_VECT::iterator	DOUBLE_VECT_I
typedef DOUBLE_VECT::const_iterator	DOUBLE_VECT_CI
typedef std::vector< DOUBLE_VECT >	VECT_DOUBLE_VECT
typedef VECT_DOUBLE_VECT::iterator	VECT_DOUBLE_VECT_I
typedef VECT_DOUBLE_VECT::const_iterator	VECT_DOUBLE_VECT_CI
typedef std::map< std::string, UINT >	STR_UINT_MAP
typedef std::map< std::string, UINT >::const_iterator	STR_UINT_MAP_CI
typedef std::map< int, INT_VECT >	INT_INT_VECT_MAP
typedef INT_INT_VECT_MAP::const_iterator	INT_INT_VECT_MAP_CI
typedef std::map< int, int >	INT_MAP_INT
typedef INT_MAP_INT::iterator	INT_MAP_INT_I
typedef INT_MAP_INT::const_iterator	INT_MAP_INT_CI
typedef std::deque< int >	INT_DEQUE
typedef INT_DEQUE::iterator	INT_DEQUE_I
typedef INT_DEQUE::const_iterator	INT_DEQUE_CI
typedef std::map< int, INT_DEQUE >	INT_INT_DEQ_MAP
typedef INT_INT_DEQ_MAP::const_iterator	INT_INT_DEQ_MAP_CI
typedef std::set< int >	INT_SET
typedef INT_SET::iterator	INT_SET_I
typedef INT_SET::const_iterator	INT_SET_CI
typedef std::map< double, int, ltDouble >	DOUBLE_INT_MAP
	std::map from double to integer.
typedef boost::minstd_rand	rng_type
typedef boost::uniform_int	uniform_int
typedef boost::uniform_real	uniform_double
typedef boost::variate_generator< rng_type &, uniform_int >	int_source_type
typedef boost::variate_generator< rng_type &, uniform_double >	double_source_type
C++11 Iterators
ROMol is a molecule class that is intended to have a fixed topology This is the primary class for most molecule operations. If you need to be manipulating the molecule (e.g. adding or deleting atoms or bonds, use an RWMol instead. Notes: each ROMol maintains a Dict of properties: Each property is keyed by name and can store an arbitrary type. Properties can be marked as calculated, in which case they will be cleared when the clearComputedProps() method is called. Because they have no impact upon chemistry, all property operations are const, this allows extra flexibility for clients who need to store extra data on ROMol objects. each ROMol has collections of bookmarks for Atoms and Bonds: the Atom bookmarks and Bond bookmarks are stored separately from each other each bookmark, an integer, can map to more than one Atom or Bond these are currently used in molecule construction, but could also be useful for reaction mapping and the like information about rings (SSSR and the like) is stored in the molecule's RingInfo pointer.
typedef boost::shared_ptr< ROMol >	ROMOL_SPTR
typedef std::vector< boost::shared_ptr< ROMol > >	MOL_SPTR_VECT
typedef std::vector< ROMol >	MOL_VECT
typedef std::vector< ROMol * >	MOL_PTR_VECT
typedef MOL_PTR_VECT::const_iterator	MOL_PTR_VECT_CI
typedef MOL_PTR_VECT::iterator	MOL_PTR_VECT_I

Enumerations
enum	FingerprintType {   AtomPairFP = 1 , TopologicalTorsion , MorganFP , RDKitFP ,   PatternFP }
enum	ReactionMoleculeType { Reactant , Product , Agent }
enum class	MolzipLabel {   AtomMapNumber , Isotope , FragmentOnBonds , AtomType ,   AtomProperty }
enum class	FPType { AtomPairFP , MorganFP , RDKitFP , TopologicalTorsionFP }
enum	AtomComparator { AtomCompareAny , AtomCompareElements , AtomCompareIsotopes , AtomCompareAnyHeavyAtom }
enum	BondComparator { BondCompareAny , BondCompareOrder , BondCompareOrderExact }
enum	RingComparator { IgnoreRingFusion , PermissiveRingFusion , StrictRingFusion }
enum	IsSgroupInAtomSetResult { SgroupInAtomSet , SgroupNotInAtomSet , SgroupBothInAndNotInAtomSet }
enum class	MultiColourHighlightStyle { CIRCLEANDLINE , LASSO }
enum	RGroupLabels {   IsotopeLabels = 0x01 , AtomMapLabels = 0x02 , AtomIndexLabels = 0x04 , RelabelDuplicateLabels = 0x08 ,   MDLRGroupLabels = 0x10 , DummyAtomLabels = 0x20 , AutoDetect = 0xFF }
enum	RGroupMatching {   Greedy = 0x01 , GreedyChunks = 0x02 , Exhaustive = 0x04 , NoSymmetrization = 0x08 ,   GA = 0x10 }
enum	RGroupLabelling { AtomMap = 0x01 , Isotope = 0x02 , MDLRGroup = 0x04 }
enum	RGroupCoreAlignment { None = 0x0 , NoAlignment = 0x0 , MCS = 0x01 }
enum	RGroupScore { Match = 0x1 , FingerprintVariance = 0x4 }
enum	OperationName { RgroupMutate = 0x01 , Crossover = 0x02 , Create = 0x04 }
enum class	Labelling {   RGROUP_LABELS , ISOTOPE_LABELS , ATOMMAP_LABELS , INDEX_LABELS ,   DUMMY_LABELS , INTERNAL_LABELS }
enum	FIND_RING_TYPE { FIND_RING_TYPE_FAST , FIND_RING_TYPE_SSSR , FIND_RING_TYPE_SYMM_SSSR , FIND_RING_TYPE_OTHER_OR_UNKNOWN }
	A class to store information about a molecule's rings. More...
enum	RestoreBondDirOption { RestoreBondDirOptionTrue = 0 , RestoreBondDirOptionClear = 1 }
enum class	StereoGroupType { STEREO_ABSOLUTE = 0 , STEREO_OR = 1 , STEREO_AND = 2 }
enum	EEndian { LITTLE_ENDIAN_ORDER , BIG_ENDIAN_ORDER }

Functions
RDKIT_GRAPHMOL_EXPORT void	setAtomRLabel (Atom *atm, int rlabel)
RDKIT_GRAPHMOL_EXPORT int	getAtomRLabel (const Atom *atm)
RDKIT_GRAPHMOL_EXPORT void	setAtomAlias (Atom *atom, const std::string &alias)
RDKIT_GRAPHMOL_EXPORT std::string	getAtomAlias (const Atom *atom)
RDKIT_GRAPHMOL_EXPORT void	setAtomValue (Atom *atom, const std::string &value)
RDKIT_GRAPHMOL_EXPORT std::string	getAtomValue (const Atom *atom)
RDKIT_GRAPHMOL_EXPORT void	setSupplementalSmilesLabel (Atom *atom, const std::string &label)
RDKIT_GRAPHMOL_EXPORT std::string	getSupplementalSmilesLabel (const Atom *atom)
RDKIT_GRAPHMOL_EXPORT bool	isEarlyAtom (int atomicNum)
	returns true if the atom is to the left of C
RDKIT_GRAPHMOL_EXPORT bool	isAromaticAtom (const Atom &atom)
	returns true if the atom is aromatic or has an aromatic bond
bool	isDative (const Bond &bond)
bool	canSetDoubleBondStereo (const Bond &bond)
bool	canHaveDirection (const Bond &bond)
RDKIT_GRAPHMOL_EXPORT uint8_t	getTwiceBondType (const RDKit::Bond &b)
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::BBS	removeNonmatchingReagents (const ChemicalReaction &rxn, EnumerationTypes::BBS bbs, const EnumerationParams &params=EnumerationParams())
RDKIT_CHEMREACTIONS_EXPORT bool	EnumerateLibraryCanSerialize ()
template<class T >
EnumerationTypes::RGROUPS	getSizesFromBBs (const std::vector< std::vector< T > > &bbs)
	Return the number of elements per input vector.
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::RGROUPS	getSizesFromReactants (const std::vector< MOL_SPTR_VECT > &bbs)
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT	getReactantsFromRGroups (const std::vector< MOL_SPTR_VECT > &bbs, const EnumerationTypes::RGROUPS &rgroups)
RDKIT_CHEMREACTIONS_EXPORT boost::uint64_t	computeNumProducts (const EnumerationTypes::RGROUPS &sizes)
RDKIT_CHEMREACTIONS_EXPORT bool	preprocessReaction (ChemicalReaction &rxn, const std::string &propName=common_properties::molFileValue)
RDKIT_CHEMREACTIONS_EXPORT bool	preprocessReaction (ChemicalReaction &rxn, unsigned int &numWarnings, unsigned int &numErrors, std::vector< std::vector< std::pair< unsigned int, std::string > > > &reactantLabels, const std::string &propName=common_properties::molFileValue)
RDKIT_CHEMREACTIONS_EXPORT bool	preprocessReaction (ChemicalReaction &rxn, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName=common_properties::molFileValue)
RDKIT_CHEMREACTIONS_EXPORT bool	preprocessReaction (ChemicalReaction &rxn, unsigned int &numWarnings, unsigned int &numErrors, std::vector< std::vector< std::pair< unsigned int, std::string > > > &reactantLabels, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName=common_properties::molFileValue)
RDKIT_CHEMREACTIONS_EXPORT bool	isMoleculeReactantOfReaction (const ChemicalReaction &rxn, const ROMol &mol, std::vector< unsigned int > &which, bool stopAtFirstMatch=false)
RDKIT_CHEMREACTIONS_EXPORT bool	isMoleculeReactantOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_CHEMREACTIONS_EXPORT bool	isMoleculeReactantOfReaction (const ChemicalReaction &rxn, const ROMol &mol)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_CHEMREACTIONS_EXPORT bool	isMoleculeProductOfReaction (const ChemicalReaction &rxn, const ROMol &mol, std::vector< unsigned int > &which, bool stopAtFirstMatch=false)
RDKIT_CHEMREACTIONS_EXPORT bool	isMoleculeProductOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_CHEMREACTIONS_EXPORT bool	isMoleculeProductOfReaction (const ChemicalReaction &rxn, const ROMol &mol)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_CHEMREACTIONS_EXPORT bool	isMoleculeAgentOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which)
RDKIT_CHEMREACTIONS_EXPORT bool	isMoleculeAgentOfReaction (const ChemicalReaction &rxn, const ROMol &mol)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_CHEMREACTIONS_EXPORT VECT_INT_VECT	getReactingAtoms (const ChemicalReaction &rxn, bool mappedAtomsOnly=false)
RDKIT_CHEMREACTIONS_EXPORT void	addRecursiveQueriesToReaction (ChemicalReaction &rxn, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName, std::vector< std::vector< std::pair< unsigned int, std::string > > > *reactantLabels=nullptr)
	add the recursive queries to the reactants of a reaction
RDKIT_CHEMREACTIONS_EXPORT ExplicitBitVect *	StructuralFingerprintChemReaction (const ChemicalReaction &rxn, const ReactionFingerprintParams &params=DefaultStructuralFPParams)
RDKIT_CHEMREACTIONS_EXPORT SparseIntVect< std::uint32_t > *	DifferenceFingerprintChemReaction (const ChemicalReaction &rxn, const ReactionFingerprintParams &params=DefaultDifferenceFPParams)
RDKIT_CHEMREACTIONS_EXPORT std::string	ChemicalReactionToRxnSmarts (const ChemicalReaction &rxn)
	returns the reaction SMARTS for a reaction
RDKIT_CHEMREACTIONS_EXPORT std::string	ChemicalReactionToRxnSmiles (const ChemicalReaction &rxn, bool canonical=true)
	returns the reaction SMILES for a reaction
ChemicalReaction *	RxnBlockToChemicalReaction (const std::string &rxnBlock, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
	Parse a text block in MDL rxn format into a ChemicalReaction.
ChemicalReaction *	RxnFileToChemicalReaction (const std::string &fileName, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
	Parse a file in MDL rxn format into a ChemicalReaction.
ChemicalReaction *	RxnDataStreamToChemicalReaction (std::istream &rxnStream, unsigned int &line, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
	Parse a text stream in MDL rxn format into a ChemicalReaction.
ChemicalReaction *	PNGStreamToChemicalReaction (std::istream &pngStream)
	constructs a ChemicalReaction from the metadata in a PNG stream
ChemicalReaction *	PNGStringToChemicalReaction (const std::string &data)
	constructs a ChemicalReaction from the metadata in a PNG string See PNGStreamToChemicalReaction() for more details
ChemicalReaction *	PNGFileToChemicalReaction (const std::string &fname)
	constructs a ChemicalReaction from the metadata in a PNG file See PNGStreamToChemicalReaction() for more details
std::unique_ptr< ChemicalReaction >	operator""_rxnsmarts (const char *text, size_t len)
std::unique_ptr< ChemicalReaction >	operator""_rxnsmiles (const char *text, size_t len)
RDKIT_CHEMREACTIONS_EXPORT std::vector< MOL_SPTR_VECT >	run_Reactants (const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants, unsigned int maxProducts=1000)
	Runs the reaction on a set of reactants.
RDKIT_CHEMREACTIONS_EXPORT std::vector< MOL_SPTR_VECT >	run_Reactant (const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx)
	Runs a single reactant against a single reactant template.
RDKIT_CHEMREACTIONS_EXPORT bool	run_Reactant (const ChemicalReaction &rxn, RWMol &reactant, bool removeUnmatchedAtoms=true)
RDKIT_CHEMREACTIONS_EXPORT ROMol *	reduceProductToSideChains (const ROMOL_SPTR &product, bool addDummyAtoms=true)
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT::const_iterator	getStartIterator (const ChemicalReaction &rxn, ReactionMoleculeType t)
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT::const_iterator	getEndIterator (const ChemicalReaction &rxn, ReactionMoleculeType t)
RDKIT_CHEMREACTIONS_EXPORT bool	hasReactantTemplateSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn)
RDKIT_CHEMREACTIONS_EXPORT bool	hasProductTemplateSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn)
RDKIT_CHEMREACTIONS_EXPORT bool	hasAgentTemplateSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn)
RDKIT_CHEMREACTIONS_EXPORT bool	hasReactionSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn, bool includeAgents=false)
RDKIT_CHEMREACTIONS_EXPORT bool	hasReactionAtomMapping (const ChemicalReaction &rxn)
RDKIT_CHEMREACTIONS_EXPORT bool	isReactionTemplateMoleculeAgent (const ROMol &mol, double agentThreshold)
RDKIT_CHEMREACTIONS_EXPORT void	updateProductsStereochem (ChemicalReaction *rxn)
RDKIT_CHEMREACTIONS_EXPORT void	removeMappingNumbersFromReactions (const ChemicalReaction &rxn)
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *	deleteSubstructs (const ROMol &mol, const ROMol &query, bool onlyFrags=false, bool useChirality=false)
	Returns a copy of an ROMol with the atoms and bonds that match a pattern removed.
RDKIT_CHEMTRANSFORMS_EXPORT std::vector< ROMOL_SPTR >	replaceSubstructs (const ROMol &mol, const ROMol &query, const ROMol &replacement, bool replaceAll=false, unsigned int replacementConnectionPoint=0, bool useChirality=false)
	Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule.
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *	replaceSidechains (const ROMol &mol, const ROMol &coreQuery, bool useChirality=false)
	Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed.
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *	replaceCore (const ROMol &mol, const ROMol &core, const MatchVectType &matchVect, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false)
	Returns a copy of an ROMol with the atoms and bonds that are referenced by the MatchVector removed. MatchVector must be defined between mol and the specified core.
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *	replaceCore (const ROMol &mol, const ROMol &coreQuery, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false, bool useChirality=false)
	Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed.
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *	MurckoDecompose (const ROMol &mol)
	Carries out a Murcko decomposition on the molecule provided.
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *	combineMols (const ROMol &mol1, const ROMol &mol2, RDGeom::Point3D offset=RDGeom::Point3D(0, 0, 0))
	Combined two molecules to create a new one.
RDKIT_CHEMTRANSFORMS_EXPORT void	addRecursiveQueries (ROMol &mol, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName, std::vector< std::pair< unsigned int, std::string > > *reactantLabels=nullptr)
	Adds named recursive queries to a molecule's atoms based on atom labels.
RDKIT_CHEMTRANSFORMS_EXPORT void	parseQueryDefFile (const std::string &filename, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\t", const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1)
	parses a query definition file and sets up a set of definitions suitable for use by addRecursiveQueries()
RDKIT_CHEMTRANSFORMS_EXPORT void	parseQueryDefFile (std::istream *inStream, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\t", const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_CHEMTRANSFORMS_EXPORT void	parseQueryDefText (const std::string &queryDefText, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\t", const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1)
	equivalent to parseQueryDefFile() but the query definitions are explicitly passed in
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol >	molzip (const ROMol &a, const ROMol &b, const MolzipParams &params=MolzipParams())
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol >	molzip (const ROMol &a, const MolzipParams &params=MolzipParams())
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol >	molzip (std::vector< ROMOL_SPTR > &decomposition, const MolzipParams &params=MolzipParams())
	Creates a molecule from an R group decomposition.
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol >	molzip (const std::map< std::string, ROMOL_SPTR > &row, const MolzipParams &params=MolzipParams())
	Molzip an RGroupRow back into the original molecule if possible.
bool	hasNonZeroZCoords (const Conformer &conf)
	Returns true if any of the z coords are non zero, false otherwise.
RDKIT_DETERMINEBONDS_EXPORT void	determineConnectivity (RWMol &mol, bool useHueckel=false, int charge=0, double covFactor=1.3, bool useVdw=false)
RDKIT_DETERMINEBONDS_EXPORT void	determineBondOrders (RWMol &mol, int charge=0, bool allowChargedFragments=true, bool embedChiral=true, bool useAtomMap=false)
RDKIT_DETERMINEBONDS_EXPORT void	determineBonds (RWMol &mol, bool useHueckel=false, int charge=0, double covFactor=1.3, bool allowChargedFragments=true, bool embedChiral=true, bool useAtomMap=false, bool useVdw=false)
std::vector< std::unique_ptr< RWMol > >	CDXMLDataStreamToMols (std::istream &inStream, bool sanitize=true, bool removeHs=true)
	construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.
std::vector< std::unique_ptr< RWMol > >	CDXMLFileToMols (const std::string &filename, bool sanitize=true, bool removeHs=true)
	construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.
std::vector< std::unique_ptr< RWMol > >	CDXMLToMols (const std::string &cdxml, bool sanitize=true, bool removeHs=true)
	construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.
RDKIT_FILEPARSERS_EXPORT std::string	strip (const std::string &orig)
RWMol *	MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol *	MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol *	MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol *	MolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol *	TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false)
	translate TPL data (BioCad format) into a multi-conf molecule
RWMol *	TPLFileToMol (const std::string &fName, bool sanitize=true, bool skipFirstConf=false)
	construct a multi-conf molecule from a TPL (BioCad format) file
RWMol *	Mol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol *	Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol *	Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol *	Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol *	XYZDataStreamToMol (std::istream &inStream)
RWMol *	XYZBlockToMol (const std::string &xyzBlock)
RWMol *	XYZFileToMol (const std::string &fName)
RWMol *	PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol *	PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol *	PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol *	PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol *	PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RDKIT_FILEPARSERS_EXPORT RWMol *	RDKitSVGToMol (const std::string &svg, bool sanitize=true, bool removeHs=true)
RDKIT_FILEPARSERS_EXPORT RWMol *	RDKitSVGToMol (std::istream *instream, bool sanitize=true, bool removeHs=true)
std::unique_ptr< RDKit::RWMol >	operator""_ctab (const char *text, size_t len)
std::unique_ptr< RDKit::RWMol >	operator""_mol2 (const char *text, size_t len)
std::unique_ptr< RDKit::RWMol >	operator""_pdb (const char *text, size_t len)
RDKIT_FILEPARSERS_EXPORT std::string	MolToMolBlock (const ROMol &mol, const MolWriterParams &params, int confId=-1)
std::string	MolToMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
std::string	MolToV3KMolBlock (const ROMol &mol, const MolWriterParams &params, int confId=-1)
std::string	MolToV3KMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true)
RDKIT_FILEPARSERS_EXPORT void	MolToMolFile (const ROMol &mol, const std::string &fName, const MolWriterParams &params, int confId=-1)
void	MolToMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
void	MolToV3KMolFile (const ROMol &mol, const std::string &fName, const MolWriterParams &params, int confId=-1)
void	MolToV3KMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true)
RDKIT_FILEPARSERS_EXPORT std::string	MolToCMLBlock (const ROMol &mol, int confId=-1, bool kekulize=true)
RDKIT_FILEPARSERS_EXPORT void	MolToCMLFile (const ROMol &mol, const std::string &fName, int confId=-1, bool kekulize=true)
RDKIT_FILEPARSERS_EXPORT std::string	MolToXYZBlock (const ROMol &mol, int confId=-1, unsigned int precision=6)
RDKIT_FILEPARSERS_EXPORT void	MolToXYZFile (const ROMol &mol, const std::string &fName, int confId=-1, unsigned int precision=6)
RDKIT_FILEPARSERS_EXPORT std::string	MolToTPLText (const ROMol &mol, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
RDKIT_FILEPARSERS_EXPORT void	MolToTPLFile (const ROMol &mol, const std::string &fName, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
RDKIT_FILEPARSERS_EXPORT std::string	MolToPDBBlock (const ROMol &mol, int confId=-1, unsigned int flavor=0)
RDKIT_FILEPARSERS_EXPORT void	MolToPDBFile (const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0)
RDKIT_FILEPARSERS_EXPORT void	DetectAtomStereoChemistry (RWMol &mol, const Conformer *conf)
	deprecated, please use MolOps::assignChiralTypesFromBondDirs instead
RDKIT_FILEPARSERS_EXPORT void	DetectBondStereoChemistry (ROMol &mol, const Conformer *conf)
	deprecated, please use MolOps::detectBondStereoChemistry instead
RDKIT_FILEPARSERS_EXPORT void	WedgeMolBonds (ROMol &mol, const Conformer *conf)
RDKIT_FILEPARSERS_EXPORT void	WedgeBond (Bond *bond, unsigned int fromAtomIdx, const Conformer *conf)
RDKIT_FILEPARSERS_EXPORT void	addWavyBondsForStereoAny (ROMol &mol, bool clearDoubleBondFlags=true, unsigned addWhenImpossible=StereoBondThresholds::DBL_BOND_NO_STEREO)
	set wavy bonds around double bonds with STEREOANY stereo
RDKIT_FILEPARSERS_EXPORT void	ClearSingleBondDirFlags (ROMol &mol)
RDKIT_FILEPARSERS_EXPORT Bond::BondDir	DetermineBondWedgeState (const Bond *bond, unsigned int fromAtomIdx, const Conformer *conf)
RDKIT_FILEPARSERS_EXPORT Bond::BondDir	DetermineBondWedgeState (const Bond *bond, const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > &wedgeBonds, const Conformer *conf)
RDKIT_FILEPARSERS_EXPORT void	reapplyMolBlockWedging (ROMol &mol)
RDKIT_FILEPARSERS_EXPORT void	clearMolBlockWedgingInfo (ROMol &mol)
RDKIT_FILEPARSERS_EXPORT void	invertMolBlockWedgingInfo (ROMol &mol)
RDKIT_FILEPARSERS_EXPORT void	markUnspecifiedStereoAsUnknown (ROMol &mol, int confId=-1)
RDKIT_FILEPARSERS_EXPORT void	translateChiralFlagToStereoGroups (ROMol &mol, StereoGroupType zeroFlagGroupType=StereoGroupType::STEREO_AND)
RDKIT_FILEPARSERS_EXPORT bool	IsBlacklistedPair (Atom *beg_atom, Atom *end_atom)
RDKIT_FILEPARSERS_EXPORT void	ConnectTheDots (RWMol *mol, unsigned int flags=0)
RDKIT_FILEPARSERS_EXPORT void	StandardPDBResidueBondOrders (RWMol *mol)
RDKIT_FILEPARSERS_EXPORT bool	SamePDBResidue (AtomPDBResidueInfo *p, AtomPDBResidueInfo *q)
RDKIT_FILEPARSERS_EXPORT RWMol *	SequenceToMol (const char *seq, bool sanitize, bool lowerD)
RDKIT_FILEPARSERS_EXPORT RWMol *	SequenceToMol (const std::string &seq, bool sanitize, bool lowerD)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FILEPARSERS_EXPORT RWMol *	SequenceToMol (const char *seq, bool sanitize=true, int flavor=0)
RDKIT_FILEPARSERS_EXPORT RWMol *	SequenceToMol (const std::string &seq, bool sanitize=true, int flavor=0)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FILEPARSERS_EXPORT RWMol *	FASTAToMol (const char *seq, bool sanitize, bool lowerD)
RDKIT_FILEPARSERS_EXPORT RWMol *	FASTAToMol (const std::string &seq, bool sanitize, bool lowerD)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FILEPARSERS_EXPORT RWMol *	FASTAToMol (const char *seq, bool sanitize=true, int flavor=0)
RDKIT_FILEPARSERS_EXPORT RWMol *	FASTAToMol (const std::string &seq, bool sanitize=true, int flavor=0)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FILEPARSERS_EXPORT RWMol *	HELMToMol (const char *helm, bool sanitize=true)
RDKIT_FILEPARSERS_EXPORT RWMol *	HELMToMol (const std::string &helm, bool sanitize=true)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FILEPARSERS_EXPORT std::string	MolToSequence (const ROMol &mol)
RDKIT_FILEPARSERS_EXPORT std::string	MolToFASTA (const ROMol &mol)
RDKIT_FILEPARSERS_EXPORT std::string	MolToHELM (const ROMol &mol)
RDKIT_FILTERCATALOG_EXPORT bool	FilterCatalogCanSerialize ()
RDKIT_FILTERCATALOG_EXPORT std::vector< std::vector< boost::shared_ptr< const FilterCatalogEntry > > >	RunFilterCatalog (const FilterCatalog &filterCatalog, const std::vector< std::string > &smiles, int numThreads=1)
	Run a filter catalog on a set of smiles strings.
unsigned int	GetNumEntries (FilterCatalogParams::FilterCatalogs catalog)
const FilterData_t *	GetFilterData (FilterCatalogParams::FilterCatalogs catalog)
unsigned int	GetNumPropertyEntries (FilterCatalogParams::FilterCatalogs catalog)
const FilterProperty_t *	GetFilterProperties (FilterCatalogParams::FilterCatalogs catalog)
FilterCatalogEntry *	MakeFilterCatalogEntry (const FilterData_t &, unsigned int num_props=0, const FilterProperty_t *props=nullptr)
RDKIT_FILTERCATALOG_EXPORT const FilterCatalog &	GetFunctionalGroupHierarchy ()
	Return the functional group hierarchy as a FilterCatalog.
RDKIT_FILTERCATALOG_EXPORT const std::map< std::string, ROMOL_SPTR > &	GetFlattenedFunctionalGroupHierarchy (bool normalized=false)
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint64_t > *	getSparseCountFP (const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT SparseBitVect *	getSparseFP (const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint32_t > *	getCountFP (const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *	getFP (const ROMol &mol, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint64_t > * > *	getSparseCountFPBulk (const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseBitVect * > *	getSparseFPBulk (const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint32_t > * > *	getCountFPBulk (const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT std::vector< ExplicitBitVect * > *	getFPBulk (const std::vector< const ROMol * > molVector, FPType fPType)
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *	RDKFingerprintMol (const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr)
	Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm.
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *	LayeredFingerprintMol (const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool branchedPaths=true, const std::vector< std::uint32_t > *fromAtoms=nullptr)
	Generates a topological (Daylight like) fingerprint for a molecule using a layer-based hashing algorithm.
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *	PatternFingerprintMol (const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false)
	Generates a topological fingerprint for a molecule using a series of pre-defined structural patterns.
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *	PatternFingerprintMol (const MolBundle &bundle, unsigned int fpSize=2048, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< boost::uint64_t > *	getUnfoldedRDKFingerprintMol (const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, bool useHs=true, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< boost::uint64_t > > *atomBits=nullptr, std::map< boost::uint64_t, std::vector< std::vector< int > > > *bitInfo=nullptr)
RDKIT_FMCS_EXPORT bool	checkAtomRingMatch (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2)
RDKIT_FMCS_EXPORT bool	checkAtomCharge (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2)
RDKIT_FMCS_EXPORT bool	checkAtomChirality (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2)
RDKIT_FMCS_EXPORT bool	checkAtomDistance (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2)
RDKIT_FMCS_EXPORT bool	MCSAtomCompareAny (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData)
RDKIT_FMCS_EXPORT bool	MCSAtomCompareAnyHeavyAtom (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData)
RDKIT_FMCS_EXPORT bool	MCSAtomCompareElements (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData)
RDKIT_FMCS_EXPORT bool	MCSAtomCompareIsotopes (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData)
RDKIT_FMCS_EXPORT bool	checkBondStereo (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2)
RDKIT_FMCS_EXPORT bool	havePairOfCompatibleRings (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2)
RDKIT_FMCS_EXPORT bool	checkBondRingMatch (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2)
RDKIT_FMCS_EXPORT bool	MCSBondCompareAny (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData)
RDKIT_FMCS_EXPORT bool	MCSBondCompareOrder (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData)
RDKIT_FMCS_EXPORT bool	MCSBondCompareOrderExact (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData)
RDKIT_FMCS_EXPORT bool	MCSProgressCallbackTimeout (const MCSProgressData &stat, const MCSParameters &params, void *userData)
RDKIT_FMCS_EXPORT void	parseMCSParametersJSON (const char *json, MCSParameters *params)
RDKIT_FMCS_EXPORT MCSResult	findMCS (const std::vector< ROMOL_SPTR > &mols, const MCSParameters *params=nullptr)
RDKIT_FMCS_EXPORT MCSResult	findMCS_P (const std::vector< ROMOL_SPTR > &mols, const char *params_json)
RDKIT_FMCS_EXPORT MCSResult	findMCS (const std::vector< ROMOL_SPTR > &mols, bool maximizeBonds, double threshold, unsigned int timeout, bool verbose, bool matchValences, bool ringMatchesRingOnly, bool completeRingsOnly, bool matchChiralTag, AtomComparator atomComp, BondComparator bondComp, RingComparator ringComp)
RDKIT_FMCS_EXPORT MCSResult	findMCS (const std::vector< ROMOL_SPTR > &mols, bool maximizeBonds, double threshold=1.0, unsigned int timeout=3600, bool verbose=false, bool matchValences=false, bool ringMatchesRingOnly=false, bool completeRingsOnly=false, bool matchChiralTag=false, AtomComparator atomComp=AtomCompareElements, BondComparator bondComp=BondCompareOrder)
bool	FinalChiralityCheckFunction (const std::uint32_t c1[], const std::uint32_t c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p)
bool	FinalMatchCheckFunction (const std::uint32_t c1[], const std::uint32_t c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p)
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT	readFuncGroups (std::string fileName)
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT	readFuncGroups (std::istream &inStream, int nToRead=-1)
RDKIT_FRAGCATALOG_EXPORT MatchVectType	findFuncGroupsOnMol (const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds)
RDKIT_FRAGCATALOG_EXPORT ROMol *	prepareMol (const ROMol &mol, const FragCatParams *fparams, MatchVectType &aToFmap)
template<typename T >
std::vector< std::unique_ptr< T > >::iterator	findUniquePtr (std::vector< std ::unique_ptr< T > > &vector, T *itemToFind)
template<typename T >
void	eraseUniquePtr (std::vector< std ::unique_ptr< T > > &vector, T *itemToErase)
template<typename T >
bool	getCleanNumber (std::string strToParse, T &outInt)
bool	MrvFileIsReaction (const std::string &fname)
bool	MrvDataStreamIsReaction (std::istream *inStream)
bool	MrvDataStreamIsReaction (std::istream &inStream)
bool	MrvBlockIsReaction (const std::string &molmrvText)
RWMol *	MrvDataStreamToMol (std::istream *inStream, bool sanitize=false, bool removeHs=false)
RWMol *	MrvDataStreamToMol (std::istream &inStream, bool sanitize=false, bool removeHs=false)
RWMol *	MrvBlockToMol (const std::string &molmrvText, bool sanitize=false, bool removeHs=false)
RWMol *	MrvFileToMol (const std::string &fName, bool sanitize=false, bool removeHs=false)
ChemicalReaction *	MrvDataStreamToChemicalReaction (std::istream *inStream, bool sanitize=false, bool removeHs=false)
ChemicalReaction *	MrvDataStreamToChemicalReaction (std::istream &inStream, bool sanitize=false, bool removeHs=false)
ChemicalReaction *	MrvBlockToChemicalReaction (const std::string &molmrvText, bool sanitize=false, bool removeHs=false)
ChemicalReaction *	MrvFileToChemicalReaction (const std::string &fName, bool sanitize=false, bool removeHs=false)
RDKIT_MARVINPARSER_EXPORT void	MolToMrvFile (const ROMol &mol, const std::string &fName, const MrvWriterParams &params, int confId=-1)
void	MolToMrvFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false)
RDKIT_MARVINPARSER_EXPORT std::string	MolToMrvBlock (const ROMol &mol, const MrvWriterParams &params, int confId=-1)
std::string	MolToMrvBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false)
RDKIT_MARVINPARSER_EXPORT std::string	ChemicalReactionToMrvBlock (const ChemicalReaction &rxn, bool prettyPrint=false)
RDKIT_MARVINPARSER_EXPORT void	ChemicalReactionToMrvFile (const ChemicalReaction &rxn, const std::string &fName, bool prettyPrint=false)
bool	MolBundleCanSerialize ()
RDKIT_MOLCHEMICALFEATURES_EXPORT int	parseFeatureData (const std::string &defnText, MolChemicalFeatureDef::CollectionType &featDefs)
RDKIT_MOLCHEMICALFEATURES_EXPORT int	parseFeatureData (std::istream &istream, MolChemicalFeatureDef::CollectionType &featDefs)
RDKIT_MOLCHEMICALFEATURES_EXPORT int	parseFeatureFile (const std::string &fileName, MolChemicalFeatureDef::CollectionType &featDefs)
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory *	buildFeatureFactory (std::istream &inStream)
	constructs a MolChemicalFeatureFactory from the data in a stream
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory *	buildFeatureFactory (const std::string &featureData)
	constructs a MolChemicalFeatureFactory from the data in a string
void	setDarkMode (MolDrawOptions &opts)
void	setDarkMode (MolDraw2D &d2d)
void	setMonochromeMode (MolDrawOptions &opts, const DrawColour &fgColour, const DrawColour &bgColour)
void	setMonochromeMode (MolDraw2D &drawer, const DrawColour &fgColour, const DrawColour &bgColour)
void	assignDefaultPalette (ColourPalette &palette)
	use the RDKit's default palette r
void	assignAvalonPalette (ColourPalette &palette)
	use the color palette from the Avalon renderer
void	assignCDKPalette (ColourPalette &palette)
	use (part of) the CDK color palette
void	assignDarkModePalette (ColourPalette &palette)
void	assignBWPalette (ColourPalette &palette)
RDKIT_PARTIALCHARGES_EXPORT void	computeGasteigerCharges (const ROMol *mol, int nIter=12, bool throwOnParamFailure=false)
RDKIT_PARTIALCHARGES_EXPORT void	computeGasteigerCharges (const ROMol &mol, int nIter=12, bool throwOnParamFailure=false)
RDKIT_PARTIALCHARGES_EXPORT void	computeGasteigerCharges (const ROMol &mol, std::vector< double > &charges, int nIter=12, bool throwOnParamFailure=false)
std::string	describeQuery (const Atom *atom)
std::string	describeQuery (const Bond *bond)
static int	queryAtomAromatic (Atom const *at)
static int	queryAtomAliphatic (Atom const *at)
static int	queryAtomExplicitDegree (Atom const *at)
static int	queryAtomTotalDegree (Atom const *at)
static int	queryAtomNonHydrogenDegree (Atom const *at)
	D and T are treated as "non-hydrogen" here.
static int	queryAtomHeavyAtomDegree (Atom const *at)
	D and T are not treated as heavy atoms here.
static int	queryAtomHCount (Atom const *at)
static int	queryAtomImplicitHCount (Atom const *at)
static int	queryAtomHasImplicitH (Atom const *at)
static int	queryAtomImplicitValence (Atom const *at)
static int	queryAtomExplicitValence (Atom const *at)
static int	queryAtomTotalValence (Atom const *at)
static int	queryAtomUnsaturated (Atom const *at)
static int	queryAtomNum (Atom const *at)
static int	makeAtomType (int atomic_num, bool aromatic)
static void	parseAtomType (int val, int &atomic_num, bool &aromatic)
static bool	getAtomTypeIsAromatic (int val)
static int	getAtomTypeAtomicNum (int val)
static int	queryAtomType (Atom const *at)
static int	queryAtomMass (Atom const *at)
static int	queryAtomIsotope (Atom const *at)
static int	queryAtomFormalCharge (Atom const *at)
static int	queryAtomNegativeFormalCharge (Atom const *at)
static int	queryAtomHybridization (Atom const *at)
static int	queryAtomNumRadicalElectrons (Atom const *at)
static int	queryAtomHasChiralTag (Atom const *at)
static int	queryAtomMissingChiralTag (Atom const *at)
static int	queryAtomHasHeteroatomNbrs (Atom const *at)
static int	queryAtomNumHeteroatomNbrs (Atom const *at)
static int	queryAtomHasAliphaticHeteroatomNbrs (Atom const *at)
static int	queryAtomNumAliphaticHeteroatomNbrs (Atom const *at)
RDKIT_GRAPHMOL_EXPORT unsigned int	queryAtomBondProduct (Atom const *at)
RDKIT_GRAPHMOL_EXPORT unsigned int	queryAtomAllBondProduct (Atom const *at)
static int	queryBondOrder (Bond const *bond)
static int	queryBondIsSingleOrAromatic (Bond const *bond)
static int	queryBondIsDoubleOrAromatic (Bond const *bond)
static int	queryBondIsSingleOrDouble (Bond const *bond)
static int	queryBondIsSingleOrDoubleOrAromatic (Bond const *bond)
static int	queryBondDir (Bond const *bond)
static int	queryIsBondInNRings (Bond const *at)
static int	queryBondHasStereo (Bond const *bnd)
static int	queryIsAtomInNRings (Atom const *at)
static int	queryIsAtomInRing (Atom const *at)
static int	queryAtomHasRingBond (Atom const *at)
RDKIT_GRAPHMOL_EXPORT int	queryIsAtomBridgehead (Atom const *at)
static int	queryIsBondInRing (Bond const *bond)
static int	queryAtomMinRingSize (Atom const *at)
static int	queryBondMinRingSize (Bond const *bond)
static int	queryAtomRingBondCount (Atom const *at)
template<int tgt>
int	queryAtomIsInRingOfSize (Atom const *at)
template<int tgt>
int	queryBondIsInRingOfSize (Bond const *bond)
template<class T >
T *	makeAtomSimpleQuery (int what, int func(Atom const *), const std::string &description="Atom Simple")
static ATOM_RANGE_QUERY *	makeAtomRangeQuery (int lower, int upper, bool lowerOpen, bool upperOpen, int func(Atom const *), const std::string &description="Atom Range")
template<class T >
T *	makeAtomNumQuery (int what, const std::string &descr)
	returns a Query for matching atomic number
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomNumQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomTypeQuery (int num, int aromatic, const std::string &descr)
	returns a Query for matching atomic number and aromaticity
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomTypeQuery (int num, int aromatic)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomImplicitValenceQuery (int what, const std::string &descr)
	returns a Query for matching implicit valence
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomImplicitValenceQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomExplicitValenceQuery (int what, const std::string &descr)
	returns a Query for matching explicit valence
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomExplicitValenceQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomTotalValenceQuery (int what, const std::string &descr)
	returns a Query for matching total valence
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomTotalValenceQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomExplicitDegreeQuery (int what, const std::string &descr)
	returns a Query for matching explicit degree
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomExplicitDegreeQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomTotalDegreeQuery (int what, const std::string &descr)
	returns a Query for matching atomic degree
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomTotalDegreeQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomHeavyAtomDegreeQuery (int what, const std::string &descr)
	returns a Query for matching heavy atom degree
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomHeavyAtomDegreeQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomHCountQuery (int what, const std::string &descr)
	returns a Query for matching hydrogen count
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomHCountQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomHasImplicitHQuery (const std::string &descr)
	returns a Query for matching ring atoms
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomHasImplicitHQuery ()
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomImplicitHCountQuery (int what, const std::string &descr)
	returns a Query for matching implicit hydrogen count
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomImplicitHCountQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomAromaticQuery (const std::string &descr)
	returns a Query for matching the isAromatic flag
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomAromaticQuery ()
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomAliphaticQuery (const std::string &descr)
	returns a Query for matching aliphatic atoms
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomAliphaticQuery ()
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomMassQuery (int what, const std::string &descr)
	returns a Query for matching atoms with a particular mass
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomMassQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomIsotopeQuery (int what, const std::string &descr)
	returns a Query for matching atoms with a particular isotope
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomIsotopeQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomFormalChargeQuery (int what, const std::string &descr)
	returns a Query for matching formal charge
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomFormalChargeQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomNegativeFormalChargeQuery (int what, const std::string &descr)
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomNegativeFormalChargeQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomHybridizationQuery (int what, const std::string &descr)
	returns a Query for matching hybridization
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomHybridizationQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomNumRadicalElectronsQuery (int what, const std::string &descr)
	returns a Query for matching the number of radical electrons
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomNumRadicalElectronsQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomHasChiralTagQuery (const std::string &descr)
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomHasChiralTagQuery ()
	\overloadquery
template<class T >
T *	makeAtomMissingChiralTagQuery (const std::string &descr)
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomMissingChiralTagQuery ()
	\overloadquery
template<class T >
T *	makeAtomUnsaturatedQuery (const std::string &descr)
	returns a Query for matching atoms with unsaturation:
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomUnsaturatedQuery ()
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomInRingQuery (const std::string &descr)
	returns a Query for matching ring atoms
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomInRingQuery ()
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomInNRingsQuery (int what, const std::string &descr)
	returns a Query for matching atoms in a particular number of rings
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomInNRingsQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomInRingOfSizeQuery (int tgt)
	returns a Query for matching atoms in rings of a particular size
template<class T >
T *	makeAtomMinRingSizeQuery (int tgt, const std::string &descr)
	returns a Query for matching an atom's minimum ring size
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomMinRingSizeQuery (int tgt)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomRingBondCountQuery (int what, const std::string &descr)
	returns a Query for matching atoms with a particular number of ring bonds
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomRingBondCountQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAAtomQuery ()
	returns a Query for matching generic A atoms (heavy atoms)
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY *	makeAHAtomQuery ()
	returns a Query for matching generic AH atoms (any atom)
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY *	makeQAtomQuery ()
	returns a Query for matching generic Q atoms (heteroatoms)
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeQHAtomQuery ()
	returns a Query for matching generic QH atoms (heteroatom or H)
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY *	makeXAtomQuery ()
	returns a Query for matching generic X atoms (halogens)
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY *	makeXHAtomQuery ()
	returns a Query for matching generic XH atoms (halogen or H)
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY *	makeMAtomQuery ()
	returns a Query for matching generic M atoms (metals)
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY *	makeMHAtomQuery ()
	returns a Query for matching generic MH atoms (metals or H)
RDKIT_GRAPHMOL_EXPORT void	convertComplexNameToQuery (Atom *query, std::string_view symb)
template<class T >
T *	makeAtomHasRingBondQuery (const std::string &descr)
	returns a Query for matching atoms that have ring bonds
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomHasRingBondQuery ()
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomNumHeteroatomNbrsQuery (int what, const std::string &descr)
	returns a Query for matching the number of heteroatom neighbors
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomNumHeteroatomNbrsQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomHasHeteroatomNbrsQuery (const std::string &descr)
	returns a Query for matching atoms that have heteroatom neighbors
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomHasHeteroatomNbrsQuery ()
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomNumAliphaticHeteroatomNbrsQuery (int what, const std::string &descr)
	returns a Query for matching the number of aliphatic heteroatom neighbors
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomNumAliphaticHeteroatomNbrsQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomHasAliphaticHeteroatomNbrsQuery (const std::string &descr)
	returns a Query for matching atoms that have heteroatom neighbors
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomHasAliphaticHeteroatomNbrsQuery ()
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomNonHydrogenDegreeQuery (int what, const std::string &descr)
	returns a Query for matching the number of non-hydrogen neighbors
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomNonHydrogenDegreeQuery (int what)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<class T >
T *	makeAtomIsBridgeheadQuery (const std::string &descr)
	returns a Query for matching bridgehead atoms
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY *	makeAtomIsBridgeheadQuery ()
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeBondOrderEqualsQuery (Bond::BondType what)
	returns a Query for matching bond orders
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeSingleOrAromaticBondQuery ()
	returns a Query for unspecified SMARTS bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeDoubleOrAromaticBondQuery ()
	returns a Query for double|aromatic bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeSingleOrDoubleBondQuery ()
	returns a Query for single|double bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeSingleOrDoubleOrAromaticBondQuery ()
	returns a Query for tautomeric bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeBondDirEqualsQuery (Bond::BondDir what)
	returns a Query for matching bond directions
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeBondHasStereoQuery ()
	returns a Query for matching bonds with stereo set
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeBondIsInRingQuery ()
	returns a Query for matching ring bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeBondInRingOfSizeQuery (int what)
	returns a Query for matching bonds in rings of a particular size
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeBondMinRingSizeQuery (int what)
	returns a Query for matching a bond's minimum ring size
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY *	makeBondInNRingsQuery (int tgt)
	returns a Query for matching bonds in a particular number of rings
RDKIT_GRAPHMOL_EXPORT BOND_NULL_QUERY *	makeBondNullQuery ()
	returns a Query for matching any bond
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY *	makeAtomNullQuery ()
	returns a Query for matching any atom
static int	queryAtomRingMembership (Atom const *at)
template<typename T >
int	nullDataFun (T)
template<typename T >
bool	nullQueryFun (T)
template<class Target >
Queries::EqualityQuery< int, const Target *, true > *	makeHasPropQuery (const std::string &property)
	returns a Query for matching atoms that have a particular property
template<class Target , class T >
Queries::EqualityQuery< int, const Target *, true > *	makePropQuery (const std::string &propname, const T &val, const T &tolerance=T())
template<class Target >
Queries::EqualityQuery< int, const Target *, true > *	makePropQuery (const std::string &propname, const ExplicitBitVect &val, float tolerance=0.0)
RDKIT_GRAPHMOL_EXPORT bool	isComplexQuery (const Bond *b)
RDKIT_GRAPHMOL_EXPORT bool	isComplexQuery (const Atom *a)
RDKIT_GRAPHMOL_EXPORT bool	isAtomAromatic (const Atom *a)
RDKIT_GRAPHMOL_EXPORT bool	isAtomListQuery (const Atom *a)
RDKIT_GRAPHMOL_EXPORT void	getAtomListQueryVals (const Atom::QUERYATOM_QUERY *q, std::vector< int > &vals)
bool	isAtomDummy (const Atom *a)
RDKIT_RGROUPDECOMPOSITION_EXPORT unsigned int	RGroupDecompose (const std::vector< ROMOL_SPTR > &cores, const std::vector< ROMOL_SPTR > &mols, RGroupRows &rows, std::vector< unsigned int > *unmatched=nullptr, const RGroupDecompositionParameters &options=RGroupDecompositionParameters())
RDKIT_RGROUPDECOMPOSITION_EXPORT unsigned int	RGroupDecompose (const std::vector< ROMOL_SPTR > &cores, const std::vector< ROMOL_SPTR > &mols, RGroupColumns &columns, std::vector< unsigned int > *unmatched=nullptr, const RGroupDecompositionParameters &options=RGroupDecompositionParameters())
bool	checkForTimeout (const std::chrono::steady_clock::time_point &t0, double timeout, bool throwOnTimeout=true)
RDKIT_RGROUPDECOMPOSITION_EXPORT double	fingerprintVarianceScore (const std::vector< size_t > &permutation, const std::vector< std::vector< RGroupMatch > > &matches, const std::set< int > &labels, FingerprintVarianceScoreData *fingerprintVarianceScoreData=nullptr)
void	copyVarianceData (const FingerprintVarianceScoreData &fromData, FingerprintVarianceScoreData &toData)
void	clearVarianceData (FingerprintVarianceScoreData &fingerprintVarianceScoreData)
std::string	labellingToString (Labelling type)
	return the user friendly name for the given labelling
std::map< int, Atom * >	getRlabels (const RWMol &mol)
	Get the RLabels,atom mapping for the current molecule.
void	clearInputLabels (Atom *atom)
	Remove the user labels from the atom.
bool	setLabel (Atom *atom, int label, std::set< int > &labels, int &maxLabel, bool relabel, Labelling type)
bool	hasDummy (const RWMol &core)
	Returns true if the core has a dummy atom.
bool	isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment (const Atom &atom)
bool	isUserRLabel (const Atom &atom)
	Return true if the atom has a user-defined R group label.
bool	isDummyRGroupAttachment (const Atom &atom)
bool	isAnyAtomWithMultipleNeighborsOrNotUserRLabel (const Atom &atom)
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string	toJSON (const RGroupRow &rgr, const std::string &prefix="")
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string	toJSON (const RGroupRows &rgr, const std::string &prefix="")
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string	toJSON (const RGroupColumn &rgr, const std::string &prefix="")
RDKIT_RGROUPDECOMPOSITION_EXPORT void	relabelMappedDummies (ROMol &mol, unsigned int inputLabels=AtomMap|Isotope|MDLRGroup, unsigned int outputLabels=MDLRGroup)
RDKIT_SLNPARSE_EXPORT RWMol *	SLNToMol (const std::string &smi, bool sanitize=true, int debugParse=0)
RDKIT_SLNPARSE_EXPORT RWMol *	SLNQueryToMol (const std::string &smi, bool mergeHs=true, int debugParse=0)
RDKIT_SMILESPARSE_EXPORT std::string	MolToSmarts (const ROMol &mol, bool doIsomericSmarts=true, int rootedAtAtom=-1)
	returns the SMARTS for a molecule
RDKIT_SMILESPARSE_EXPORT std::string	MolFragmentToSmarts (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, bool doIsomericSmarts=true)
RDKIT_SMILESPARSE_EXPORT std::string	MolToCXSmarts (const ROMol &mol, bool doIsomericSmarts=true)
	returns the CXSMARTS for a molecule
RDKIT_SMILESPARSE_EXPORT std::string	MolFragmentToCXSmarts (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, bool doIsomericSmarts=true)
RDKit::RWMol *	SmilesToMol (const std::string &smi, const SmilesParserParams &ps)
Atom *	SmilesToAtom (const std::string &smi)
Bond *	SmilesToBond (const std::string &smi)
RWMol *	SmilesToMol (const std::string &smi, int debugParse=0, bool sanitize=true, std::map< std::string, std::string > *replacements=nullptr)
	Construct a molecule from a SMILES string.
RWMol *	SmartsToMol (const std::string &sma, const SmartsParserParams &ps)
RWMol *	SmartsToMol (const std::string &sma, int debugParse=0, bool mergeHs=false, std::map< std::string, std::string > *replacements=nullptr)
	Construct a molecule from a SMARTS string.
Atom *	SmartsToAtom (const std::string &sma)
Bond *	SmartsToBond (const std::string &sma)
std::unique_ptr< RDKit::RWMol >	operator""_smiles (const char *text, size_t len)
std::unique_ptr< RDKit::RWMol >	operator""_smarts (const char *text, size_t len)
RDKIT_SMILESPARSE_EXPORT std::string	MolToSmiles (const ROMol &mol, const SmilesWriteParams &params)
	returns canonical SMILES for a molecule
std::string	MolToSmiles (const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false)
	returns canonical SMILES for a molecule
RDKIT_SMILESPARSE_EXPORT std::vector< std::string >	MolToRandomSmilesVect (const ROMol &mol, unsigned int numSmiles, unsigned int randomSeed=0, bool doIsomericSmiles=true, bool doKekule=false, bool allBondsExplicit=false, bool allHsExplicit=false)
	returns a vector of random SMILES for a molecule (may contain duplicates)
RDKIT_SMILESPARSE_EXPORT std::string	MolFragmentToSmiles (const ROMol &mol, const SmilesWriteParams &params, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr)
	returns canonical SMILES for part of a molecule
std::string	MolFragmentToSmiles (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false)
	returns canonical SMILES for part of a molecule
RDKIT_SMILESPARSE_EXPORT std::string	MolToCXSmiles (const ROMol &mol, const SmilesWriteParams &ps, std::uint32_t flags=SmilesWrite::CXSmilesFields::CX_ALL, RestoreBondDirOption restoreBondDirs=RestoreBondDirOptionClear)
	returns canonical CXSMILES for a molecule
std::string	MolToCXSmiles (const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false)
	returns canonical CXSMILES for a molecule
RDKIT_SMILESPARSE_EXPORT std::string	MolFragmentToCXSmiles (const ROMol &mol, const SmilesWriteParams &params, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr)
	returns canonical CXSMILES for part of a molecule
std::string	MolFragmentToCXSmiles (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false)
	returns canonical CXSMILES for part of a molecule
RDKIT_GRAPHMOL_EXPORT void	removeAtomFromGroups (const Atom *atom, std::vector< StereoGroup > &groups)
RDKIT_GRAPHMOL_EXPORT void	removeGroupsWithAtom (const Atom *atom, std::vector< StereoGroup > &groups)
RDKIT_GRAPHMOL_EXPORT void	removeGroupsWithAtoms (const std::vector< Atom * > &atoms, std::vector< StereoGroup > &groups)
RDKIT_GRAPHMOL_EXPORT void	assignStereoGroupIds (std::vector< StereoGroup > &groups)
RDKIT_GRAPHMOL_EXPORT void	forwardStereoGroupIds (ROMol &mol)
RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP	findAllSubgraphsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useHs=false, int rootedAtAtom=-1)
	find all bond subgraphs in a range of sizes
RDKIT_SUBGRAPHS_EXPORT PATH_LIST	findAllSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, int rootedAtAtom=-1)
	find all bond subgraphs of a particular size
RDKIT_SUBGRAPHS_EXPORT PATH_LIST	findUniqueSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, bool useBO=true, int rootedAtAtom=-1)
	find unique bond subgraphs of a particular size
RDKIT_SUBGRAPHS_EXPORT PATH_LIST	findAllPathsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1, bool onlyShortestPaths=false)
	find all paths of a particular size
RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP	findAllPathsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1, bool onlyShortestPaths=false)
RDKIT_SUBGRAPHS_EXPORT PATH_TYPE	findAtomEnvironmentOfRadiusN (const ROMol &mol, unsigned int radius, unsigned int rootedAtAtom, bool useHs=false, bool enforceSize=true, std::unordered_map< unsigned int, unsigned int > *atomMap=nullptr)
	Find bond subgraphs of a particular radius around an atom. Return empty result if there is no bond at the requested radius.
RDKIT_SUBSTRUCTMATCH_EXPORT void	updateSubstructMatchParamsFromJSON (SubstructMatchParameters &params, const std::string &json)
RDKIT_SUBSTRUCTMATCH_EXPORT std::string	substructMatchParamsToJSON (const SubstructMatchParameters &params)
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType >	SubstructMatch (const ROMol &mol, const ROMol &query, const SubstructMatchParameters &params=SubstructMatchParameters())
	Find a substructure match for a query in a molecule.
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType >	SubstructMatch (ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters &params=SubstructMatchParameters())
	Find all substructure matches for a query in a ResonanceMolSupplier object.
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType >	SubstructMatch (const MolBundle &bundle, const ROMol &query, const SubstructMatchParameters &params=SubstructMatchParameters())
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType >	SubstructMatch (const ROMol &mol, const MolBundle &query, const SubstructMatchParameters &params=SubstructMatchParameters())
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType >	SubstructMatch (const MolBundle &bundle, const MolBundle &query, const SubstructMatchParameters &params=SubstructMatchParameters())
template<typename T1 , typename T2 >
bool	SubstructMatch (T1 &mol, const T2 &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false)
	Find a substructure match for a query.
template<typename T1 , typename T2 >
unsigned int	SubstructMatch (T1 &mol, const T2 &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000, int numThreads=1)
	Find all substructure matches for a query.
template<>
bool	SubstructMatch (ResonanceMolSupplier &resMolSupplier, const ROMol &query, MatchVectType &matchVect, bool recursionPossible, bool useChirality, bool useQueryQueryMatches)
template<>
unsigned int	SubstructMatch (ResonanceMolSupplier &resMolSupplier, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify, bool recursionPossible, bool useChirality, bool useQueryQueryMatches, unsigned int maxMatches, int numThreads)
RDKIT_SUBSTRUCTMATCH_EXPORT double	toPrime (const MatchVectType &v)
RDKIT_SUBSTRUCTMATCH_EXPORT void	removeDuplicates (std::vector< MatchVectType > &v, unsigned int nAtoms)
RDKIT_SUBSTRUCTMATCH_EXPORT bool	propertyCompat (const RDProps *r1, const RDProps *r2, const std::vector< std::string > &properties)
RDKIT_SUBSTRUCTMATCH_EXPORT bool	atomCompat (const Atom *a1, const Atom *a2, const SubstructMatchParameters &ps)
RDKIT_SUBSTRUCTMATCH_EXPORT bool	chiralAtomCompat (const Atom *a1, const Atom *a2)
RDKIT_SUBSTRUCTMATCH_EXPORT bool	bondCompat (const Bond *b1, const Bond *b2, const SubstructMatchParameters &ps)
RDKIT_SUBSTRUCTMATCH_EXPORT const MatchVectType &	getMostSubstitutedCoreMatch (const ROMol &mol, const ROMol &core, const std::vector< MatchVectType > &matches)
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType >	sortMatchesByDegreeOfCoreSubstitution (const ROMol &mol, const ROMol &core, const std::vector< MatchVectType > &matches)
RDKIT_SUBSTRUCTMATCH_EXPORT bool	isAtomTerminalRGroupOrQueryHydrogen (const Atom *atom)
RDKIT_SUBSTRUCTLIBRARY_EXPORT void	addPatterns (SubstructLibrary &sslib, boost::shared_ptr< FPHolderBase > patterns, int numThreads=1)
RDKIT_SUBSTRUCTLIBRARY_EXPORT void	addPatterns (SubstructLibrary &sslib, int numThreads=1)
RDKIT_SUBSTRUCTLIBRARY_EXPORT bool	SubstructLibraryCanSerialize ()
RDKIT_TAUTOMERQUERY_EXPORT bool	TautomerQueryCanSerialize ()
RDKIT_TAUTOMERQUERY_EXPORT std::vector< MatchVectType >	SubstructMatch (const ROMol &mol, const TautomerQuery &query, const SubstructMatchParameters &params)
RDKIT_TRAJECTORY_EXPORT unsigned int	readAmberTrajectory (const std::string &fName, Trajectory &traj)
	Reads coordinates from an AMBER trajectory file into the traj Trajectory object.
RDKIT_TRAJECTORY_EXPORT unsigned int	readGromosTrajectory (const std::string &fName, Trajectory &traj)
	Reads coordinates from a GROMOS trajectory file into the traj Trajectory object.
DiscreteDistMat *	getDiscreteDistMat ()
RDKIT_DATASTRUCTS_EXPORT unsigned int	computeL1Norm (const DiscreteValueVect &v1, const DiscreteValueVect &v2)
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect	operator+ (const DiscreteValueVect &p1, const DiscreteValueVect &p2)
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect	operator- (const DiscreteValueVect &p1, const DiscreteValueVect &p2)
template<typename IndexType , typename SequenceType >
void	updateFromSequence (SparseIntVect< IndexType > &vect, const SequenceType &seq)
template<typename IndexType >
double	DiceSimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, bool returnDistance=false, double bounds=0.0)
template<typename IndexType >
double	TverskySimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, double a, double b, bool returnDistance=false, double bounds=0.0)
template<typename IndexType >
double	TanimotoSimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, bool returnDistance=false, double bounds=0.0)
template<class T >
void	mergeNullQueries (T *&returnQuery, bool isQueryNull, T *&otherQuery, bool isOtherQNull, Queries::CompositeQueryType how)
template<>
std::string	Dict::getVal< std::string > (const std::string &what) const
template<typename CompareFunc >
bool	hanoi (int *base, int nel, int *temp, int *count, int *changed, CompareFunc compar)
template<typename CompareFunc >
void	hanoisort (int *base, int nel, int *count, int *changed, CompareFunc compar)
template<class T >
const T	rdany_cast (const RDAny &d)
template<class T >
T	rdany_cast (RDAny &d)
template<class T >
boost::enable_if< boost::is_arithmetic< T >, T >::type	from_rdany (const RDAny &arg)
template<class T >
boost::disable_if< boost::is_arithmetic< T >, T >::type	from_rdany (const RDAny &arg)
unsigned int	getNumThreadsToUse (int target)
void	copy_rdvalue (RDValue &dest, const RDValue &src)
template<class T >
bool	rdvalue_is (const RDValue_cast_t)
template<>
bool	rdvalue_is< double > (const RDValue_cast_t)
template<>
bool	rdvalue_is< const double & > (const RDValue_cast_t)
template<class T >
T	rdvalue_cast (RDValue_cast_t v)
template<>
double	rdvalue_cast< double > (RDValue_cast_t v)
template<>
float	rdvalue_cast< float > (RDValue_cast_t v)
template<>
int	rdvalue_cast< int > (RDValue_cast_t v)
template<>
unsigned int	rdvalue_cast< unsigned int > (RDValue_cast_t v)
template<>
bool	rdvalue_cast< bool > (RDValue_cast_t v)
template<>
bool	rdvalue_is< std::any > (RDValue_cast_t v)
template<>
double	rdvalue_cast< double > (RDValue_cast_t v)
template<>
float	rdvalue_cast< float > (RDValue_cast_t v)
template<>
int	rdvalue_cast< int > (RDValue_cast_t v)
template<>
std::int8_t	rdvalue_cast< std::int8_t > (RDValue_cast_t v)
template<>
std::int16_t	rdvalue_cast< std::int16_t > (RDValue_cast_t v)
template<>
std::int64_t	rdvalue_cast< std::int64_t > (RDValue_cast_t v)
template<>
unsigned int	rdvalue_cast< unsigned int > (RDValue_cast_t v)
template<>
std::uint8_t	rdvalue_cast< std::uint8_t > (RDValue_cast_t v)
template<>
std::uint16_t	rdvalue_cast< std::uint16_t > (RDValue_cast_t v)
template<>
std::uint64_t	rdvalue_cast< std::uint64_t > (RDValue_cast_t v)
template<>
bool	rdvalue_cast< bool > (RDValue_cast_t v)
template<>
std::string	rdvalue_cast< std::string > (RDValue_cast_t v)
template<>
std::string &	rdvalue_cast< std::string & > (RDValue_cast_t v)
template<>
std::vector< double >	rdvalue_cast< std::vector< double > > (RDValue_cast_t v)
template<>
std::vector< double > &	rdvalue_cast< std::vector< double > & > (RDValue_cast_t v)
template<>
std::vector< float >	rdvalue_cast< std::vector< float > > (RDValue_cast_t v)
template<>
std::vector< float > &	rdvalue_cast< std::vector< float > & > (RDValue_cast_t v)
template<>
std::vector< std::string >	rdvalue_cast< std::vector< std::string > > (RDValue_cast_t v)
template<>
std::vector< std::string > &	rdvalue_cast< std::vector< std::string > & > (RDValue_cast_t v)
template<>
std::vector< int >	rdvalue_cast< std::vector< int > > (RDValue_cast_t v)
template<>
std::vector< int > &	rdvalue_cast< std::vector< int > & > (RDValue_cast_t v)
template<>
std::vector< unsigned int >	rdvalue_cast< std::vector< unsigned int > > (RDValue_cast_t v)
template<>
std::vector< unsigned int > &	rdvalue_cast< std::vector< unsigned int > & > (RDValue_cast_t v)
template<>
std::any	rdvalue_cast< std::any > (RDValue_cast_t v)
template<>
std::any &	rdvalue_cast< std::any & > (RDValue_cast_t v)
template<>
const std::any &	rdvalue_cast< const std::any & > (RDValue_cast_t v)
template<class T >
std::string	vectToString (RDValue val)
bool	rdvalue_tostring (RDValue_cast_t val, std::string &res)
template<class T >
boost::enable_if< boost::is_arithmetic< T >, T >::type	from_rdvalue (RDValue_cast_t arg)
template<class T >
boost::disable_if< boost::is_arithmetic< T >, T >::type	from_rdvalue (RDValue_cast_t arg)
template<class T , unsigned int size>
T	SwapBytes (T value)
template<EEndian from, EEndian to, class T >
T	EndianSwapBytes (T value)
template<EEndian from, EEndian to>
char	EndianSwapBytes (char value)
template<EEndian from, EEndian to>
unsigned char	EndianSwapBytes (unsigned char value)
template<EEndian from, EEndian to>
signed char	EndianSwapBytes (signed char value)
void	appendPackedIntToStream (std::stringstream &ss, boost::uint32_t num)
	Packs an integer and outputs it to a stream.
boost::uint32_t	readPackedIntFromStream (std::stringstream &ss)
	Reads an integer from a stream in packed format and returns the result.
boost::uint32_t	pullPackedIntFromString (const char *&text)
template<typename T >
void	streamWrite (std::ostream &ss, const T &val)
	does a binary write of an object to a stream
void	streamWrite (std::ostream &ss, const std::string &what)
	special case for string
template<typename T >
void	streamWriteVec (std::ostream &ss, const T &val)
template<typename T >
void	streamRead (std::istream &ss, T &loc)
	does a binary read of an object from a stream
template<class T >
void	streamRead (std::istream &ss, T &obj, int version)
	special case for string
void	streamRead (std::istream &ss, std::string &what, int version)
template<class T >
void	streamReadVec (std::istream &ss, T &val)
void	streamReadStringVec (std::istream &ss, std::vector< std::string > &val, int version)
std::string	getLine (std::istream *inStream)
	grabs the next line from an instream and returns it.
std::string	getLine (std::istream &inStream)
	grabs the next line from an instream and returns it.
bool	isSerializable (const Dict::Pair &pair, const CustomPropHandlerVec &handlers={})
bool	streamWriteProp (std::ostream &ss, const Dict::Pair &pair, const CustomPropHandlerVec &handlers={})
template<typename COUNT_TYPE = unsigned int>
bool	streamWriteProps (std::ostream &ss, const RDProps &props, bool savePrivate=false, bool saveComputed=false, const CustomPropHandlerVec &handlers={}, const std::unordered_set< std::string > &ignore={})
template<class T >
void	readRDValue (std::istream &ss, RDValue &value)
template<class T >
void	readRDVecValue (std::istream &ss, RDValue &value)
void	readRDValueString (std::istream &ss, RDValue &value)
void	readRDStringVecValue (std::istream &ss, RDValue &value)
bool	streamReadProp (std::istream &ss, Dict::Pair &pair, bool &dictHasNonPOD, const CustomPropHandlerVec &handlers={})
template<typename COUNT_TYPE = unsigned int>
unsigned int	streamReadProps (std::istream &ss, RDProps &props, const CustomPropHandlerVec &handlers={}, bool reset=true)
RDKIT_RDGENERAL_EXPORT void	Union (const INT_VECT &r1, const INT_VECT &r2, INT_VECT &res)
	calculate the union of two INT_VECTs and put the results in a third vector
RDKIT_RDGENERAL_EXPORT void	Intersect (const INT_VECT &r1, const INT_VECT &r2, INT_VECT &res)
	calculate the intersection of two INT_VECTs and put the results in a third vector
RDKIT_RDGENERAL_EXPORT void	Union (const VECT_INT_VECT &rings, INT_VECT &res, const INT_VECT *exclude=nullptr)
	calculating the union of the INT_VECT's in a VECT_INT_VECT
RDKIT_RDGENERAL_EXPORT int	nextCombination (INT_VECT &comb, int tot)
	given a current combination of numbers change it to the next possible
RDKIT_RDGENERAL_EXPORT double	computeIntVectPrimesProduct (const INT_VECT &ring)
	compute the product of the set of primes corresponding to the values in an INT_VECT
RDKIT_RDGENERAL_EXPORT bool	feq (double v1, double v2, double tol=1e-4)
	floating point comparison with a tolerance
RDKIT_RDGENERAL_EXPORT rng_type &	getRandomGenerator (int seed=-1)
RDKIT_RDGENERAL_EXPORT double	getRandomVal (int seed=-1)
RDKIT_RDGENERAL_EXPORT double_source_type &	getDoubleRandomSource ()
	return a reference to the global (Boost) random source
template<class T >
unsigned int	countSwapsToInterconvert (const T &ref, T probe)
RDKIT_RDGENERAL_EXPORT std::string	augmentTagName (const std::string &tag)
Reaction Mol Support
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *	RxnMolToChemicalReaction (const ROMol &mol)
	Parse a ROMol into a ChemicalReaction, RXN role must be set before.
RDKIT_CHEMREACTIONS_EXPORT ROMol *	ChemicalReactionToRxnMol (const ChemicalReaction &rxn)
	returns a ROMol with RXN roles used to describe the reaction
MDL rxn Support
RDKIT_CHEMREACTIONS_EXPORT std::string	ChemicalReactionToRxnBlock (const ChemicalReaction &rxn, bool separateAgents=false, bool forceV3000=false)
	returns an rxn block for a reaction
RDKIT_CHEMREACTIONS_EXPORT std::string	ChemicalReactionToV3KRxnBlock (const ChemicalReaction &rxn, bool separateAgents=false)
	returns an V3000 rxn block for a reaction
PNG Support
RDKIT_CHEMREACTIONS_EXPORT std::string	addChemicalReactionToPNGStream (const ChemicalReaction &rxn, std::istream &iStream, bool includePkl=true, bool includeSmiles=true, bool includeSmarts=false, bool includeRxn=false)
	adds metadata for a ChemicalReaction to the data from a PNG stream. The modified PNG data is returned.
std::string	addChemicalReactionToPNGString (const ChemicalReaction &rxn, const std::string &pngString, bool includePkl=true, bool includeSmiles=true, bool includeSmarts=false, bool includeRxn=false)
	adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.
std::string	addChemicalReactionToPNGFile (const ChemicalReaction &rxn, const std::string &fname, bool includePkl=true, bool includeSmiles=true, bool includeSmarts=false, bool includeRxn=false)
	adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.
CDXML rxn Support
RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > >	CDXMLToChemicalReactions (const std::string &rxnBlock, bool sanitize=false, bool removeHs=false)
	Parse text in CDXML rxn format into a vector of ChemicalReactions.
RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > >	CDXMLFileToChemicalReactions (const std::string &fileName, bool sanitize=false, bool removeHs=false)
	Parse a file in CDXML rxn format into a vector of ChemicalReactions.
RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > >	CDXMLDataStreamToChemicalReactions (std::istream &rxnStream, bool sanitize=false, bool removeHs=false)
	Parse a text stream in CDXML rxn format into a vector of ChemicalReactions.
metadata to/from PNG
RDKIT_FILEPARSERS_EXPORT std::vector< std::pair< std::string, std::string > >	PNGStreamToMetadata (std::istream &inStream)
	returns the metadata (tEXt and zTXt chunks) from PNG data
std::vector< std::pair< std::string, std::string > >	PNGFileToMetadata (const std::string &fname)
	returns the metadata (tEXt and zTXt chunks) from PNG data
std::vector< std::pair< std::string, std::string > >	PNGStringToMetadata (const std::string &data)
	returns the metadata (tEXt and zTXt chunks) from PNG data
RDKIT_FILEPARSERS_EXPORT std::string	addMetadataToPNGStream (std::istream &iStream, const std::vector< std::pair< std::string, std::string > > &metadata, bool compressed=true)
	adds metadata to a PNG stream. The modified PNG data is returned.
std::string	addMetadataToPNGString (const std::string &pngString, const std::vector< std::pair< std::string, std::string > > &metadata, bool compressed=true)
	adds metadata to a PNG string. The modified PNG data is returned.
std::string	addMetadataToPNGFile (const std::string &fname, const std::vector< std::pair< std::string, std::string > > &metadata, bool compressed=true)
	adds metadata to a PNG file. The modified PNG data is returned.
molecules to/from PNG
RDKIT_FILEPARSERS_EXPORT ROMol *	PNGStreamToMol (std::istream &inStream, const SmilesParserParams &params=SmilesParserParams())
	constructs an ROMol from the metadata in a PNG stream
ROMol *	PNGFileToMol (const std::string &fname, const SmilesParserParams &params=SmilesParserParams())
	constructs an ROMol from the metadata in a PNG file. See PNGStreamToMol() for more details.
ROMol *	PNGStringToMol (const std::string &data, const SmilesParserParams &params=SmilesParserParams())
	constructs an ROMol from the metadata in a PNG string. See PNGStreamToMol() for more details.
RDKIT_FILEPARSERS_EXPORT std::vector< std::unique_ptr< ROMol > >	PNGStreamToMols (std::istream &inStream, const std::string &tagToUse=PNGData::pklTag, const SmilesParserParams &params=SmilesParserParams())
	constructs a vector of ROMol from the metadata in a PNG stream
std::vector< std::unique_ptr< ROMol > >	PNGFileToMols (const std::string &fname, const std::string &tagToUse=PNGData::pklTag, const SmilesParserParams &params=SmilesParserParams())
	constructs a vector of ROMol from the metadata in a PNG file. See PNGStreamToMols() for more details.
std::vector< std::unique_ptr< ROMol > >	PNGStringToMols (const std::string &data, const std::string &tagToUse=PNGData::pklTag, const SmilesParserParams &params=SmilesParserParams())
	constructs a vector of ROMol from the metadata in a PNG string. See PNGStreamToMols() for more details.
RDKIT_FILEPARSERS_EXPORT std::string	addMolToPNGStream (const ROMol &mol, std::istream &iStream, bool includePkl=true, bool includeSmiles=true, bool includeMol=false)
	adds metadata for an ROMol to the data from a PNG stream. The modified PNG data is returned.
std::string	addMolToPNGString (const ROMol &mol, const std::string &pngString, bool includePkl=true, bool includeSmiles=true, bool includeMol=false)
	adds metadata for an ROMol to a PNG string. The modified PNG data is returned. See addMolToPNGStream() for more details.
std::string	addMolToPNGFile (const ROMol &mol, const std::string &fname, bool includePkl=true, bool includeSmiles=true, bool includeMol=false)
	adds metadata for an ROMol to the data from a PNG file. The modified PNG data is returned. See addMolToPNGStream() for more details.
SubstanceGroups and molecules
RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > &	getSubstanceGroups (ROMol &mol)
RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > &	getSubstanceGroups (const ROMol &mol)
RDKIT_GRAPHMOL_EXPORT unsigned int	addSubstanceGroup (ROMol &mol, SubstanceGroup sgroup)
RDKIT_GRAPHMOL_EXPORT void	removeSubstanceGroupsReferencingAtom (RWMol &mol, unsigned int idx)
	Removes SubstanceGroups which reference a particular atom index.
RDKIT_GRAPHMOL_EXPORT void	removeSubstanceGroupsReferencingBond (RWMol &mol, unsigned int idx)
	Removes SubstanceGroups which reference a particular bond index.

Variables
RDKIT_GRAPHMOL_EXPORT const std::string	periodicTableAtomData
RDKIT_GRAPHMOL_EXPORT const std::string	isotopesAtomData []
RDKIT_GRAPHMOL_EXPORT const std::vector< std::string >	elementNames
RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams	DefaultStructuralFPParams
RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams	DefaultDifferenceFPParams
static int	defaultConfId = -1
static const unsigned int	ctdIGNORE_H_H_CONTACTS = 0x1
RDKIT_FILTERCATALOG_EXPORT const char *	DEFAULT_FILTERMATCHERBASE_NAME
RDKIT_FILTERCATALOG_EXPORT const char *	SMARTS_MATCH_NAME_DEFAULT
const std::string	RDKFingerprintMolVersion = "2.0.0"
const unsigned int	maxFingerprintLayers = 10
const std::string	LayeredFingerprintMolVersion = "0.7.0"
const unsigned int	substructLayers = 0x07
const std::string	PatternFingerprintMolVersion = "1.0.0"
const std::vector< std::string >	sruSgroupConnectChoices {"hh", "ht", "eu"}
const std::vector< std::string >	marvinBondOrders {"1", "2", "3", "A"}
const std::vector< std::string >	marvinQueryBondsTypes {"SD", "SA", "DA", "Any"}
const std::vector< std::string >	marvinConventionTypes {"cxn:coord"}
const std::vector< std::string >	marvinStereoDictRefTypes {"cml:W", "cml:H"}
const std::vector< std::string >	marvinStereoConventionTypes {"1", "3", "4", "6"}
const std::vector< std::string >	marvinRadicalVals
const std::map< std::string, int >	marvinRadicalToRadicalElectrons
const std::map< int, std::string >	radicalElectronsToMarvinRadical
const DashPattern	noDash
const DashPattern	dots {2.0, 6.0}
const DashPattern	dashes {6.0, 4.0}
const DashPattern	shortDashes {2.0, 2.0}
static const double	lineWidthScaleFactor = 0.02
RDKIT_MOLDRAW2DQT_EXPORT const char *	rdkitQtVersion
std::string	paramData
std::string	additionalParamData
const double	IONXH = 20.02
const double	DAMP_SCALE = 0.5
const double	DAMP = 0.5
const int	massIntegerConversionFactor = 1000
const std::vector< std::string >	complexQueries
const std::string	_rgroupInputDummy
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string	RLABEL
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string	RLABEL_TYPE
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string	RLABEL_CORE_INDEX
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string	SIDECHAIN_RLABELS
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string	done
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string	UNLABELED_CORE_ATTACHMENT
const unsigned int	EMPTY_CORE_LABEL = -100000
RDKIT_GRAPHMOL_EXPORT const int	ci_RIGHTMOST_ATOM
RDKIT_GRAPHMOL_EXPORT const int	ci_LEADING_BOND
RDKIT_GRAPHMOL_EXPORT const int	ci_ATOM_HOLDER
const int	NUM_PRIMES_AVAIL = 1000
	the number of primes available and stored
int	firstThousandPrimes [NUM_PRIMES_AVAIL]
const unsigned int	BITS_PER_INT = 32
RDKIT_RDGENERAL_EXPORT const double	MAX_DOUBLE
RDKIT_RDGENERAL_EXPORT const double	EPS_DOUBLE
RDKIT_RDGENERAL_EXPORT const double	SMALL_DOUBLE
RDKIT_RDGENERAL_EXPORT const double	MAX_INT
RDKIT_RDGENERAL_EXPORT const double	MAX_LONGINT
const int	FILE_MAXLINE
	an assumed maximum length for lines read from files
RDKIT_RDGENERAL_EXPORT const char *	rdkitVersion
RDKIT_RDGENERAL_EXPORT const char *	boostVersion
RDKIT_RDGENERAL_EXPORT const char *	rdkitBuild

Detailed Description

Std stuff.

Includes a bunch of functionality for handling Atom and Bond queries.

Utilities to handle atomic numbers in Mancude (maximum number of noncumulative double bonds) rings

This guarantees that aromatic rings containing heteroatoms are always resolved in the same way

Typedef Documentation

ATOM_AND_QUERY

typedef Queries::AndQuery<int, Atom const *, true> RDKit::ATOM_AND_QUERY

Definition at line 34 of file QueryOps.h.

ATOM_BOOL_QUERY

typedef Queries::Query<bool, Atom const *, true> RDKit::ATOM_BOOL_QUERY

Definition at line 31 of file QueryOps.h.

ATOM_EQUALS_QUERY

typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_EQUALS_QUERY

Definition at line 43 of file QueryOps.h.

ATOM_GREATER_QUERY

typedef Queries::GreaterQuery<int, Atom const *, true> RDKit::ATOM_GREATER_QUERY

Definition at line 46 of file QueryOps.h.

ATOM_GREATEREQUAL_QUERY

typedef Queries::GreaterEqualQuery<int, Atom const *, true> RDKit::ATOM_GREATEREQUAL_QUERY

Definition at line 50 of file QueryOps.h.

ATOM_LESS_QUERY

typedef Queries::LessQuery<int, Atom const *, true> RDKit::ATOM_LESS_QUERY

Definition at line 54 of file QueryOps.h.

ATOM_LESSEQUAL_QUERY

typedef Queries::LessEqualQuery<int, Atom const *, true> RDKit::ATOM_LESSEQUAL_QUERY

Definition at line 57 of file QueryOps.h.

ATOM_NULL_QUERY

typedef Queries::Query<int, Atom const *, true> RDKit::ATOM_NULL_QUERY

Definition at line 67 of file QueryOps.h.

ATOM_OR_QUERY

typedef Queries::OrQuery<int, Atom const *, true> RDKit::ATOM_OR_QUERY

Definition at line 37 of file QueryOps.h.

ATOM_PROP_QUERY

typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_PROP_QUERY

Definition at line 852 of file QueryOps.h.

ATOM_RANGE_QUERY

typedef Queries::RangeQuery<int, Atom const *, true> RDKit::ATOM_RANGE_QUERY

Definition at line 60 of file QueryOps.h.

ATOM_SET_QUERY

typedef Queries::SetQuery<int, Atom const *, true> RDKit::ATOM_SET_QUERY

Definition at line 63 of file QueryOps.h.

ATOM_XOR_QUERY

typedef Queries::XOrQuery<int, Atom const *, true> RDKit::ATOM_XOR_QUERY

Definition at line 40 of file QueryOps.h.

atomindex_t

typedef std::uint32_t RDKit::atomindex_t

Definition at line 14 of file details.h.

BOND_AND_QUERY

typedef Queries::AndQuery<int, Bond const *, true> RDKit::BOND_AND_QUERY

Definition at line 35 of file QueryOps.h.

BOND_BOOL_QUERY

typedef Queries::Query<bool, Bond const *, true> RDKit::BOND_BOOL_QUERY

Definition at line 32 of file QueryOps.h.

BOND_EQUALS_QUERY

typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_EQUALS_QUERY

Definition at line 44 of file QueryOps.h.

BOND_GREATER_QUERY

typedef Queries::GreaterQuery<int, Bond const *, true> RDKit::BOND_GREATER_QUERY

Definition at line 47 of file QueryOps.h.

BOND_GREATEREQUAL_QUERY

typedef Queries::GreaterEqualQuery<int, Bond const *, true> RDKit::BOND_GREATEREQUAL_QUERY

Definition at line 52 of file QueryOps.h.

BOND_LESS_QUERY

typedef Queries::LessQuery<int, Bond const *, true> RDKit::BOND_LESS_QUERY

Definition at line 55 of file QueryOps.h.

BOND_LESSEQUAL_QUERY

typedef Queries::LessEqualQuery<int, Bond const *, true> RDKit::BOND_LESSEQUAL_QUERY

Definition at line 58 of file QueryOps.h.

BOND_NULL_QUERY

typedef Queries::Query<int, Bond const *, true> RDKit::BOND_NULL_QUERY

Definition at line 66 of file QueryOps.h.

BOND_OR_QUERY

typedef Queries::OrQuery<int, Bond const *, true> RDKit::BOND_OR_QUERY

Definition at line 38 of file QueryOps.h.

BOND_PROP_QUERY

typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_PROP_QUERY

Definition at line 853 of file QueryOps.h.

BOND_RANGE_QUERY

typedef Queries::RangeQuery<int, Bond const *, true> RDKit::BOND_RANGE_QUERY

Definition at line 61 of file QueryOps.h.

BOND_SET_QUERY

typedef Queries::SetQuery<int, Bond const *, true> RDKit::BOND_SET_QUERY

Definition at line 64 of file QueryOps.h.

BOND_XOR_QUERY

typedef Queries::XOrQuery<int, Bond const *, true> RDKit::BOND_XOR_QUERY

Definition at line 41 of file QueryOps.h.

CEMap

typedef std::unordered_map<std::size_t, ConjElectrons *> RDKit::CEMap

Definition at line 32 of file Resonance.h.

CEVect

typedef std::vector<ConjElectrons *> RDKit::CEVect

Definition at line 29 of file Resonance.h.

CEVect3

typedef std::vector<CEVect2 *> RDKit::CEVect3

Definition at line 30 of file Resonance.h.

ColourPalette

typedef std::map<int, DrawColour> RDKit::ColourPalette

Definition at line 57 of file MolDraw2DHelpers.h.

CONFORMER_SPTR

typedef boost::shared_ptr<Conformer> RDKit::CONFORMER_SPTR

Definition at line 160 of file Conformer.h.

ConjAtomMap

typedef std::map<unsigned int, AtomElectrons *> RDKit::ConjAtomMap

Definition at line 28 of file Resonance.h.

ConjBondMap

typedef std::map<unsigned int, BondElectrons *> RDKit::ConjBondMap

Definition at line 27 of file Resonance.h.

ConjFP

typedef std::vector<std::uint8_t> RDKit::ConjFP

Definition at line 31 of file Resonance.h.

ConstAtomPtr

typedef Atom const* RDKit::ConstAtomPtr

Definition at line 705 of file QueryOps.h.

ConstBondPtr

typedef Bond const* RDKit::ConstBondPtr

Definition at line 815 of file QueryOps.h.

CustomPropHandlerVec

typedef std::vector<std::shared_ptr<const CustomPropHandler> > RDKit::CustomPropHandlerVec

Definition at line 382 of file StreamOps.h.

DashPattern

typedef std::vector<double> RDKit::DashPattern

Definition at line 58 of file MolDraw2DHelpers.h.

DOUBLE_INT_MAP

typedef std::map<double, int, ltDouble> RDKit::DOUBLE_INT_MAP

std::map from double to integer.

Definition at line 354 of file types.h.

double_source_type

typedef boost::variate_generator<rng_type &, uniform_double> RDKit::double_source_type

Definition at line 40 of file utils.h.

DOUBLE_VECT

typedef std::vector<double> RDKit::DOUBLE_VECT

Definition at line 309 of file types.h.

DOUBLE_VECT_CI

typedef DOUBLE_VECT::const_iterator RDKit::DOUBLE_VECT_CI

Definition at line 311 of file types.h.

DOUBLE_VECT_I

typedef DOUBLE_VECT::iterator RDKit::DOUBLE_VECT_I

Definition at line 310 of file types.h.

FCatalog

typedef RDCatalog::Catalog<FilterCatalogEntry, FilterCatalogParams> RDKit::FCatalog

Definition at line 121 of file FilterCatalog.h.

FeatSPtr

typedef boost::shared_ptr<MolChemicalFeature> RDKit::FeatSPtr

Definition at line 20 of file MolChemicalFeatureFactory.h.

FeatSPtrList

typedef std::list<FeatSPtr> RDKit::FeatSPtrList

Definition at line 21 of file MolChemicalFeatureFactory.h.

FeatSPtrList_I

typedef FeatSPtrList::iterator RDKit::FeatSPtrList_I

Definition at line 22 of file MolChemicalFeatureFactory.h.

FragCatalog

typedef RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int > RDKit::FragCatalog

Definition at line 23 of file FragCatGenerator.h.

INT_DEQUE

typedef std::deque<int> RDKit::INT_DEQUE

Definition at line 326 of file types.h.

INT_DEQUE_CI

typedef INT_DEQUE::const_iterator RDKit::INT_DEQUE_CI

Definition at line 328 of file types.h.

INT_DEQUE_I

typedef INT_DEQUE::iterator RDKit::INT_DEQUE_I

Definition at line 327 of file types.h.

INT_INT_DEQ_MAP

typedef std::map<int, INT_DEQUE> RDKit::INT_INT_DEQ_MAP

Definition at line 330 of file types.h.

INT_INT_DEQ_MAP_CI

typedef INT_INT_DEQ_MAP::const_iterator RDKit::INT_INT_DEQ_MAP_CI

Definition at line 331 of file types.h.

INT_INT_VECT_MAP

typedef std::map<int, INT_VECT> RDKit::INT_INT_VECT_MAP

Definition at line 319 of file types.h.

INT_INT_VECT_MAP_CI

typedef INT_INT_VECT_MAP::const_iterator RDKit::INT_INT_VECT_MAP_CI

Definition at line 320 of file types.h.

INT_LIST

typedef std::list<int> RDKit::INT_LIST

Definition at line 290 of file types.h.

INT_LIST_CI

typedef INT_LIST::const_iterator RDKit::INT_LIST_CI

Definition at line 292 of file types.h.

INT_LIST_I

typedef INT_LIST::iterator RDKit::INT_LIST_I

Definition at line 291 of file types.h.

INT_MAP_INT

typedef std::map<int, int> RDKit::INT_MAP_INT

Definition at line 322 of file types.h.

INT_MAP_INT_CI

typedef INT_MAP_INT::const_iterator RDKit::INT_MAP_INT_CI

Definition at line 324 of file types.h.

INT_MAP_INT_I

typedef INT_MAP_INT::iterator RDKit::INT_MAP_INT_I

Definition at line 323 of file types.h.

INT_PATH_LIST_MAP

typedef std::map<int, PATH_LIST> RDKit::INT_PATH_LIST_MAP

Definition at line 46 of file Subgraphs.h.

INT_PATH_LIST_MAP_CI

typedef INT_PATH_LIST_MAP::const_iterator RDKit::INT_PATH_LIST_MAP_CI

Definition at line 47 of file Subgraphs.h.

INT_PATH_LIST_MAP_I

typedef INT_PATH_LIST_MAP::iterator RDKit::INT_PATH_LIST_MAP_I

Definition at line 48 of file Subgraphs.h.

INT_SET

typedef std::set<int> RDKit::INT_SET

Definition at line 333 of file types.h.

INT_SET_CI

typedef INT_SET::const_iterator RDKit::INT_SET_CI

Definition at line 335 of file types.h.

INT_SET_I

typedef INT_SET::iterator RDKit::INT_SET_I

Definition at line 334 of file types.h.

int_source_type

typedef boost::variate_generator<rng_type &, uniform_int> RDKit::int_source_type

Definition at line 39 of file utils.h.

INT_VECT

typedef std::vector<int> RDKit::INT_VECT

Definition at line 284 of file types.h.

INT_VECT_CI

typedef INT_VECT::const_iterator RDKit::INT_VECT_CI

Definition at line 286 of file types.h.

INT_VECT_CRI

typedef INT_VECT::const_reverse_iterator RDKit::INT_VECT_CRI

Definition at line 288 of file types.h.

INT_VECT_I

typedef INT_VECT::iterator RDKit::INT_VECT_I

Definition at line 285 of file types.h.

INT_VECT_RI

typedef INT_VECT::reverse_iterator RDKit::INT_VECT_RI

Definition at line 287 of file types.h.

INVAR_VECT

typedef std::vector<double> RDKit::INVAR_VECT

Definition at line 33 of file MolOps.h.

INVAR_VECT_CI

typedef INVAR_VECT::const_iterator RDKit::INVAR_VECT_CI

Definition at line 35 of file MolOps.h.

INVAR_VECT_I

typedef INVAR_VECT::iterator RDKit::INVAR_VECT_I

Definition at line 34 of file MolOps.h.

LIST_INT_VECT

typedef std::list<INT_VECT> RDKit::LIST_INT_VECT

Definition at line 294 of file types.h.

LIST_INT_VECT_CI

typedef LIST_INT_VECT::const_iterator RDKit::LIST_INT_VECT_CI

Definition at line 296 of file types.h.

LIST_INT_VECT_I

typedef LIST_INT_VECT::iterator RDKit::LIST_INT_VECT_I

Definition at line 295 of file types.h.

LONGINT

typedef long long int RDKit::LONGINT

Definition at line 263 of file types.h.

MatchVectType

typedef std::vector< std::pair< int, int > > RDKit::MatchVectType

used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)

Definition at line 24 of file FragFPGenerator.h.

MCSAcceptanceFunction

typedef bool(* RDKit::MCSAcceptanceFunction) (const ROMol &, const ROMol &, const std::vector< std::pair< int, int > > &, const std::vector< std::pair< int, int > > &, const MCSParameters *)

Definition at line 65 of file FMCS.h.

MCSAtomCompareFunction

typedef bool(* RDKit::MCSAtomCompareFunction) (const MCSAtomCompareParameters &, const ROMol &, unsigned int, const ROMol &, unsigned int, void *)

Definition at line 59 of file FMCS.h.

MCSBondCompareFunction

typedef bool(* RDKit::MCSBondCompareFunction) (const MCSBondCompareParameters &, const ROMol &, unsigned int, const ROMol &, unsigned int, void *)

Definition at line 62 of file FMCS.h.

MCSFinalMatchCheckFunction

typedef bool(* RDKit::MCSFinalMatchCheckFunction) (const std::uint32_t[], const std::uint32_t[], const ROMol &, const FMCS::Graph &, const ROMol &, const FMCS::Graph &, const MCSParameters *)

Definition at line 69 of file FMCS.h.

MCSProgressCallback

typedef bool(* RDKit::MCSProgressCallback) (const MCSProgressData &stat, const MCSParameters &params, void *userData)

Definition at line 140 of file FMCS.h.

MOL_PTR_VECT

typedef std::vector<ROMol *> RDKit::MOL_PTR_VECT

Definition at line 877 of file ROMol.h.

MOL_PTR_VECT_CI

typedef MOL_PTR_VECT::const_iterator RDKit::MOL_PTR_VECT_CI

Definition at line 880 of file ROMol.h.

MOL_PTR_VECT_I

typedef MOL_PTR_VECT::iterator RDKit::MOL_PTR_VECT_I

Definition at line 881 of file ROMol.h.

MOL_SPTR_VECT

typedef std::vector< ROMOL_SPTR > RDKit::MOL_SPTR_VECT

Definition at line 21 of file FragCatParams.h.

MOL_VECT

typedef std::vector<ROMol> RDKit::MOL_VECT

Definition at line 875 of file ROMol.h.

MolCatalog

typedef RDCatalog::HierarchCatalog<MolCatalogEntry, MolCatalogParams, int> RDKit::MolCatalog

a hierarchical catalog for holding molecules

Definition at line 17 of file MolCatalog.h.

MolGraph

typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, Atom *, Bond *> RDKit::MolGraph

This is the BGL type used to store the topology:

Definition at line 55 of file ROMol.h.

PATH_LIST

typedef std::list<PATH_TYPE> RDKit::PATH_LIST

Definition at line 43 of file Subgraphs.h.

PATH_LIST_CI

typedef PATH_LIST::const_iterator RDKit::PATH_LIST_CI

Definition at line 44 of file Subgraphs.h.

PATH_TYPE

typedef std::vector<int> RDKit::PATH_TYPE

Definition at line 42 of file Subgraphs.h.

R_DECOMP

typedef std::map<int, RData> RDKit::R_DECOMP

Definition at line 16 of file RGroupMatch.h.

RData

typedef boost::shared_ptr<RGroupData> RDKit::RData

Definition at line 15 of file RGroupMatch.h.

RDValue_cast_t

typedef RDValue RDKit::RDValue_cast_t

Definition at line 417 of file RDValue-doublemagic.h.

RGroupColumn

typedef std::vector<ROMOL_SPTR> RDKit::RGroupColumn

Definition at line 32 of file RGroupDecomp.h.

RGroupColumns

typedef std::map<std::string, RGroupColumn> RDKit::RGroupColumns

Definition at line 35 of file RGroupDecomp.h.

RGroupGaPopulation

typedef LinkedPopLinearSel<RGroupDecompositionChromosome, RGroupGa> RDKit::RGroupGaPopulation

Definition at line 37 of file RGroupGa.h.

RGroupRow

typedef std::map<std::string, ROMOL_SPTR> RDKit::RGroupRow

Definition at line 31 of file RGroupDecomp.h.

RGroupRows

typedef std::vector<RGroupRow> RDKit::RGroupRows

Definition at line 34 of file RGroupDecomp.h.

rng_type

typedef boost::minstd_rand RDKit::rng_type

Definition at line 36 of file utils.h.

ROMOL_SPTR

typedef boost::shared_ptr< ROMol > RDKit::ROMOL_SPTR

Definition at line 23 of file ChemTransforms.h.

RWMOL_SPTR

typedef boost::shared_ptr<RWMol> RDKit::RWMOL_SPTR

Definition at line 221 of file RWMol.h.

RWMOL_SPTR_VECT

typedef std::vector<RWMOL_SPTR> RDKit::RWMOL_SPTR_VECT

Definition at line 222 of file RWMol.h.

SnapshotVect

typedef std::vector<Snapshot> RDKit::SnapshotVect

Definition at line 21 of file Snapshot.h.

STR_UINT_MAP

typedef std::map<std::string, UINT> RDKit::STR_UINT_MAP

Definition at line 316 of file types.h.

STR_UINT_MAP_CI

typedef std::map<std::string,UINT>::const_iterator RDKit::STR_UINT_MAP_CI

Definition at line 317 of file types.h.

STR_VECT

typedef std::vector< std::string > RDKit::STR_VECT

Definition at line 29 of file Dict.h.

STR_VECT_CI

typedef std::vector<std::string>::const_iterator RDKit::STR_VECT_CI

Definition at line 305 of file types.h.

STR_VECT_I

typedef std::vector<std::string>::iterator RDKit::STR_VECT_I

Definition at line 306 of file types.h.

STRING_PROPS

typedef std::map<std::string, std::string> RDKit::STRING_PROPS

Definition at line 54 of file FilterCatalogEntry.h.

UCHAR

typedef unsigned char RDKit::UCHAR

Definition at line 282 of file types.h.

UINT

typedef unsigned int RDKit::UINT

Definition at line 280 of file types.h.

UINT_VECT

typedef std::vector<UINT> RDKit::UINT_VECT

Definition at line 303 of file types.h.

UINT_VECT_CI

typedef std::vector<UINT>::const_iterator RDKit::UINT_VECT_CI

Definition at line 302 of file types.h.

uniform_double

typedef boost::uniform_real RDKit::uniform_double

Definition at line 38 of file utils.h.

uniform_int

typedef boost::uniform_int RDKit::uniform_int

Definition at line 37 of file utils.h.

USHORT

typedef unsigned short RDKit::USHORT

Definition at line 281 of file types.h.

VECT_DOUBLE_VECT

typedef std::vector<DOUBLE_VECT> RDKit::VECT_DOUBLE_VECT

Definition at line 312 of file types.h.

VECT_DOUBLE_VECT_CI

typedef VECT_DOUBLE_VECT::const_iterator RDKit::VECT_DOUBLE_VECT_CI

Definition at line 314 of file types.h.

VECT_DOUBLE_VECT_I

typedef VECT_DOUBLE_VECT::iterator RDKit::VECT_DOUBLE_VECT_I

Definition at line 313 of file types.h.

VECT_INT_VECT

typedef std::vector<INT_VECT> RDKit::VECT_INT_VECT

Definition at line 298 of file types.h.

VECT_INT_VECT_CI

typedef VECT_INT_VECT::const_iterator RDKit::VECT_INT_VECT_CI

Definition at line 300 of file types.h.

VECT_INT_VECT_I

typedef VECT_INT_VECT::iterator RDKit::VECT_INT_VECT_I

Definition at line 299 of file types.h.

Enumeration Type Documentation

AtomComparator

enum RDKit::AtomComparator

Enumerator
AtomCompareAny
AtomCompareElements
AtomCompareIsotopes
AtomCompareAnyHeavyAtom

Definition at line 22 of file FMCS.h.

BondComparator

enum RDKit::BondComparator

Enumerator
BondCompareAny
BondCompareOrder
BondCompareOrderExact

Definition at line 29 of file FMCS.h.

EEndian

enum RDKit::EEndian

Enumerator
LITTLE_ENDIAN_ORDER
BIG_ENDIAN_ORDER

Definition at line 28 of file StreamOps.h.

FIND_RING_TYPE

enum RDKit::FIND_RING_TYPE

A class to store information about a molecule's rings.

Enumerator
FIND_RING_TYPE_FAST
FIND_RING_TYPE_SSSR
FIND_RING_TYPE_SYMM_SSSR
FIND_RING_TYPE_OTHER_OR_UNKNOWN

Definition at line 31 of file RingInfo.h.

FingerprintType

enum RDKit::FingerprintType

Enumerator
AtomPairFP
TopologicalTorsion
MorganFP
RDKitFP
PatternFP

Definition at line 43 of file ReactionFingerprints.h.

FPType

enum class RDKit::FPType

strong

Enumerator
AtomPairFP
MorganFP
RDKitFP
TopologicalTorsionFP

Definition at line 454 of file FingerprintGenerator.h.

IsSgroupInAtomSetResult

enum RDKit::IsSgroupInAtomSetResult

Enumerator
SgroupInAtomSet
SgroupNotInAtomSet
SgroupBothInAndNotInAtomSet

Definition at line 56 of file MarvinDefs.h.

Labelling

enum class RDKit::Labelling

strong

Enumerator
RGROUP_LABELS
ISOTOPE_LABELS
ATOMMAP_LABELS
INDEX_LABELS
DUMMY_LABELS
INTERNAL_LABELS

Definition at line 32 of file RGroupUtils.h.

MolzipLabel

enum class RDKit::MolzipLabel

strong

Enumerator
AtomMapNumber
Isotope
FragmentOnBonds
AtomType
AtomProperty

Definition at line 106 of file MolFragmenter.h.

MultiColourHighlightStyle

enum class RDKit::MultiColourHighlightStyle

strong

Enumerator
CIRCLEANDLINE
LASSO

Definition at line 146 of file MolDraw2DHelpers.h.

OperationName

enum RDKit::OperationName

Enumerator
RgroupMutate
Crossover
Create

Definition at line 39 of file RGroupGa.h.

ReactionMoleculeType

enum RDKit::ReactionMoleculeType

Enumerator
Reactant
Product
Agent

Definition at line 41 of file ReactionUtils.h.

RestoreBondDirOption

enum RDKit::RestoreBondDirOption

Enumerator
RestoreBondDirOptionTrue
RestoreBondDirOptionClear

Definition at line 210 of file SmilesWrite.h.

RGroupCoreAlignment

enum RDKit::RGroupCoreAlignment

Enumerator
None
NoAlignment
MCS

Definition at line 44 of file RGroupDecompParams.h.

RGroupLabelling

enum RDKit::RGroupLabelling

Enumerator
AtomMap
Isotope
MDLRGroup

Definition at line 38 of file RGroupDecompParams.h.

RGroupLabels

enum RDKit::RGroupLabels

Enumerator
IsotopeLabels
AtomMapLabels
AtomIndexLabels
RelabelDuplicateLabels
MDLRGroupLabels
DummyAtomLabels
AutoDetect

Definition at line 20 of file RGroupDecompParams.h.

RGroupMatching

enum RDKit::RGroupMatching

Enumerator
Greedy
GreedyChunks
Exhaustive
NoSymmetrization
GA

Definition at line 30 of file RGroupDecompParams.h.

RGroupScore

enum RDKit::RGroupScore

Enumerator
Match
FingerprintVariance

Definition at line 51 of file RGroupDecompParams.h.

RingComparator

enum RDKit::RingComparator

Enumerator
IgnoreRingFusion
PermissiveRingFusion
StrictRingFusion

Definition at line 35 of file FMCS.h.

StereoGroupType

enum class RDKit::StereoGroupType

strong

Enumerator
STEREO_ABSOLUTE
STEREO_OR
STEREO_AND

Definition at line 31 of file StereoGroup.h.

Function Documentation

addChemicalReactionToPNGFile()

std::string RDKit::addChemicalReactionToPNGFile ( const ChemicalReaction & rxn, const std::string & fname, bool includePkl = true, bool includeSmiles = true, bool includeSmarts = false, bool includeRxn = false )

inline

adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.

Definition at line 344 of file ReactionParser.h.

References addChemicalReactionToPNGFile(), and addChemicalReactionToPNGStream().

Referenced by addChemicalReactionToPNGFile().

addChemicalReactionToPNGStream()

RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::addChemicalReactionToPNGStream	(	const ChemicalReaction &	rxn,
		std::istream &	iStream,
		bool	includePkl = true,
		bool	includeSmiles = true,
		bool	includeSmarts = false,
		bool	includeRxn = false )

adds metadata for a ChemicalReaction to the data from a PNG stream. The modified PNG data is returned.

Parameters

rxn	the reaction to add
iStream	the stream to read from
includePkl	include a reaction pickle
includeSmiles	include reaction SMILES for the reaction
includeSmarts	include reaction SMARTS for the reaction
includeRxn	include an RXN block for the reaction

References addChemicalReactionToPNGStream().

Referenced by addChemicalReactionToPNGFile(), addChemicalReactionToPNGStream(), and addChemicalReactionToPNGString().

addChemicalReactionToPNGString()

std::string RDKit::addChemicalReactionToPNGString ( const ChemicalReaction & rxn, const std::string & pngString, bool includePkl = true, bool includeSmiles = true, bool includeSmarts = false, bool includeRxn = false )

inline

adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.

Definition at line 332 of file ReactionParser.h.

References addChemicalReactionToPNGStream(), and addChemicalReactionToPNGString().

Referenced by addChemicalReactionToPNGString().

addMetadataToPNGFile()

std::string RDKit::addMetadataToPNGFile ( const std::string & fname, const std::vector< std::pair< std::string, std::string > > & metadata, bool compressed = true )

inline

adds metadata to a PNG file. The modified PNG data is returned.

Definition at line 84 of file PNGParser.h.

References addMetadataToPNGStream(), and rdvalue_is().

addMetadataToPNGStream()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::addMetadataToPNGStream	(	std::istream &	iStream,
		const std::vector< std::pair< std::string, std::string > > &	metadata,
		bool	compressed = true )

adds metadata to a PNG stream. The modified PNG data is returned.

The compressed flag is ignored if the RDKit is not built with boost::iostreams support

Referenced by addMetadataToPNGFile(), and addMetadataToPNGString().

addMetadataToPNGString()

std::string RDKit::addMetadataToPNGString ( const std::string & pngString, const std::vector< std::pair< std::string, std::string > > & metadata, bool compressed = true )

inline

adds metadata to a PNG string. The modified PNG data is returned.

Definition at line 74 of file PNGParser.h.

References addMetadataToPNGStream(), and rdvalue_is().

addMolToPNGFile()

std::string RDKit::addMolToPNGFile ( const ROMol & mol, const std::string & fname, bool includePkl = true, bool includeSmiles = true, bool includeMol = false )

inline

adds metadata for an ROMol to the data from a PNG file. The modified PNG data is returned. See addMolToPNGStream() for more details.

Definition at line 191 of file PNGParser.h.

References addMolToPNGStream(), and rdvalue_is().

addMolToPNGStream()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::addMolToPNGStream	(	const ROMol &	mol,
		std::istream &	iStream,
		bool	includePkl = true,
		bool	includeSmiles = true,
		bool	includeMol = false )

adds metadata for an ROMol to the data from a PNG stream. The modified PNG data is returned.

Parameters

mol	the molecule to add
iStream	the stream to read from
includePkl	include a molecule pickle
includeSmiles	include CXSMILES for the molecule
includeMol	include a mol block for the molecule

Referenced by addMolToPNGFile(), and addMolToPNGString().

addMolToPNGString()

std::string RDKit::addMolToPNGString ( const ROMol & mol, const std::string & pngString, bool includePkl = true, bool includeSmiles = true, bool includeMol = false )

inline

adds metadata for an ROMol to a PNG string. The modified PNG data is returned. See addMolToPNGStream() for more details.

Definition at line 179 of file PNGParser.h.

References addMolToPNGStream(), and rdvalue_is().

addPatterns() [1/2]

RDKIT_SUBSTRUCTLIBRARY_EXPORT void RDKit::addPatterns	(	SubstructLibrary &	sslib,
		boost::shared_ptr< FPHolderBase >	patterns,
		int	numThreads = 1 )

Create pattern fingerprints for the given substructure library The substructure library must not already have fingerprints

addPatterns() [2/2]

RDKIT_SUBSTRUCTLIBRARY_EXPORT void RDKit::addPatterns	(	SubstructLibrary &	sslib,
		int	numThreads = 1 )

Create default pattern fingerprints for the given substructure library The substructure library must not already have fingerprints

addRecursiveQueries()

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::addRecursiveQueries	(	ROMol &	mol,
		const std::map< std::string, ROMOL_SPTR > &	queries,
		const std::string &	propName,
		std::vector< std::pair< unsigned int, std::string > > *	reactantLabels = nullptr )

Adds named recursive queries to a molecule's atoms based on atom labels.

Parameters

mol	- the molecule to be modified
queries	- the dictionary of named queries to add
propName	- the atom property to use to get query names
reactantLabels	- to store pairs of (atom index, query string)

NOTES:

• existing query information, if present, will be supplemented (AND logic)
• non-query atoms will be replaced with query atoms using only the query logic
• query names can be present as comma separated lists, they will then be combined using OR logic.
• throws a KeyErrorException if a particular query name is not present in queries

addRecursiveQueriesToReaction()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::addRecursiveQueriesToReaction	(	ChemicalReaction &	rxn,
		const std::map< std::string, ROMOL_SPTR > &	queries,
		const std::string &	propName,
		std::vector< std::vector< std::pair< unsigned int, std::string > > > *	reactantLabels = nullptr )

add the recursive queries to the reactants of a reaction

This does its work using RDKit::addRecursiveQueries()

Parameters

rxn	the reaction we are interested in
queries	- the dictionary of named queries to add
propName	- the atom property to use to get query names optional:
reactantLabels	- to store pairs of (atom index, query string) per reactant

NOTES:

• existing query information, if present, will be supplemented (AND logic)
• non-query atoms will be replaced with query atoms using only the query logic
• query names can be present as comma separated lists, they will then be combined using OR logic.
• throws a KeyErrorException if a particular query name is not present in queries

References addRecursiveQueriesToReaction().

Referenced by addRecursiveQueriesToReaction().

addSubstanceGroup()

RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::addSubstanceGroup	(	ROMol &	mol,
		SubstanceGroup	sgroup )

Add a new SubstanceGroup. A copy is added, so we can be sure that no other references to the SubstanceGroup exist.

Parameters

sgroup

- SubstanceGroup to be added to the molecule.

addWavyBondsForStereoAny()

RDKIT_FILEPARSERS_EXPORT void RDKit::addWavyBondsForStereoAny	(	ROMol &	mol,
		bool	clearDoubleBondFlags = true,
		unsigned	addWhenImpossible = StereoBondThresholds::DBL_BOND_NO_STEREO )

set wavy bonds around double bonds with STEREOANY stereo

Parameters

mol	molecule to be modified
clearDoubleBondFlags	when this is true flags for unknown double bond stereo will also be removed.
addWhenImpossible	if nonzero a neighboring single bond will be made wavy even if it connects to a chiral center or double bond with specified stereo. one example of this would be the middle double bond in C/C=C/C=C/C=C/C (if that's set to STEREOANY after constructing the molecule) Otherwise, no wavy bond will be set

appendPackedIntToStream()

void RDKit::appendPackedIntToStream ( std::stringstream & ss, boost::uint32_t num )

inline

Packs an integer and outputs it to a stream.

Definition at line 106 of file StreamOps.h.

References CHECK_INVARIANT, and rdvalue_is().

assignAvalonPalette()

void RDKit::assignAvalonPalette ( ColourPalette & palette )

inline

use the color palette from the Avalon renderer

Definition at line 85 of file MolDraw2DHelpers.h.

References rdvalue_is().

assignBWPalette()

void RDKit::assignBWPalette ( ColourPalette & palette )

inline

Definition at line 141 of file MolDraw2DHelpers.h.

References rdvalue_is().

assignCDKPalette()

void RDKit::assignCDKPalette ( ColourPalette & palette )

inline

use (part of) the CDK color palette

data source: https://github.com/cdk/cdk/blob/master/display/render/src/main/java/org/openscience/cdk/renderer/color/CDK2DAtomColors.java

Definition at line 107 of file MolDraw2DHelpers.h.

References rdvalue_is().

assignDarkModePalette()

void RDKit::assignDarkModePalette ( ColourPalette & palette )

inline

Definition at line 125 of file MolDraw2DHelpers.h.

References rdvalue_is().

Referenced by setDarkMode().

assignDefaultPalette()

void RDKit::assignDefaultPalette ( ColourPalette & palette )

inline

use the RDKit's default palette r

Definition at line 67 of file MolDraw2DHelpers.h.

References rdvalue_is().

Referenced by RDKit::MolDrawOptions::MolDrawOptions().

assignStereoGroupIds()

RDKIT_GRAPHMOL_EXPORT void RDKit::assignStereoGroupIds

(

std::vector< StereoGroup > &

groups

)

Assign Group output IDs to all AND and OR StereoGroups in the vector that don't already have one. The IDs are assigned based on the order of the groups.

atomCompat()

RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::atomCompat	(	const Atom *	a1,
		const Atom *	a2,
		const SubstructMatchParameters &	ps )

augmentTagName()

RDKIT_RDGENERAL_EXPORT std::string RDKit::augmentTagName

(

const std::string &

tag

)

bondCompat()

RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::bondCompat	(	const Bond *	b1,
		const Bond *	b2,
		const SubstructMatchParameters &	ps )

buildFeatureFactory() [1/2]

RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * RDKit::buildFeatureFactory

(

const std::string &

featureData

)

constructs a MolChemicalFeatureFactory from the data in a string

buildFeatureFactory() [2/2]

RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * RDKit::buildFeatureFactory

(

std::istream &

inStream

)

constructs a MolChemicalFeatureFactory from the data in a stream

canHaveDirection()

bool RDKit::canHaveDirection ( const Bond & bond )

inline

Definition at line 401 of file Bond.h.

References RDKit::Bond::AROMATIC, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.

canSetDoubleBondStereo()

bool RDKit::canSetDoubleBondStereo ( const Bond & bond )

inline

Definition at line 395 of file Bond.h.

References RDKit::Bond::AROMATIC, RDKit::Bond::getBondType(), isDative(), and RDKit::Bond::SINGLE.

CDXMLDataStreamToChemicalReactions()

RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > > RDKit::CDXMLDataStreamToChemicalReactions	(	std::istream &	rxnStream,
		bool	sanitize = false,
		bool	removeHs = false )

Parse a text stream in CDXML rxn format into a vector of ChemicalReactions.

References CDXMLDataStreamToChemicalReactions().

Referenced by CDXMLDataStreamToChemicalReactions().

CDXMLFileToChemicalReactions()

RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > > RDKit::CDXMLFileToChemicalReactions	(	const std::string &	fileName,
		bool	sanitize = false,
		bool	removeHs = false )

Parse a file in CDXML rxn format into a vector of ChemicalReactions.

References CDXMLFileToChemicalReactions().

Referenced by CDXMLFileToChemicalReactions().

CDXMLToChemicalReactions()

RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > > RDKit::CDXMLToChemicalReactions	(	const std::string &	rxnBlock,
		bool	sanitize = false,
		bool	removeHs = false )

Parse text in CDXML rxn format into a vector of ChemicalReactions.

References CDXMLToChemicalReactions().

Referenced by CDXMLToChemicalReactions().

checkAtomCharge()

RDKIT_FMCS_EXPORT bool RDKit::checkAtomCharge	(	const MCSAtomCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	atom1,
		const ROMol &	mol2,
		unsigned int	atom2 )

checkAtomChirality()

RDKIT_FMCS_EXPORT bool RDKit::checkAtomChirality	(	const MCSAtomCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	atom1,
		const ROMol &	mol2,
		unsigned int	atom2 )

checkAtomDistance()

RDKIT_FMCS_EXPORT bool RDKit::checkAtomDistance	(	const MCSAtomCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	atom1,
		const ROMol &	mol2,
		unsigned int	atom2 )

checkAtomRingMatch()

RDKIT_FMCS_EXPORT bool RDKit::checkAtomRingMatch	(	const MCSAtomCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	atom1,
		const ROMol &	mol2,
		unsigned int	atom2 )

checkBondRingMatch()

RDKIT_FMCS_EXPORT bool RDKit::checkBondRingMatch	(	const MCSBondCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	bond1,
		const ROMol &	mol2,
		unsigned int	bond2 )

checkBondStereo()

RDKIT_FMCS_EXPORT bool RDKit::checkBondStereo	(	const MCSBondCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	bond1,
		const ROMol &	mol2,
		unsigned int	bond2 )

checkForTimeout()

bool RDKit::checkForTimeout ( const std::chrono::steady_clock::time_point & t0, double timeout, bool throwOnTimeout = true )

inline

Definition at line 123 of file RGroupDecomp.h.

References rdvalue_is().

ChemicalReactionToMrvBlock()

RDKIT_MARVINPARSER_EXPORT std::string RDKit::ChemicalReactionToMrvBlock	(	const ChemicalReaction &	rxn,
		bool	prettyPrint = false )

ChemicalReactionToMrvFile()

RDKIT_MARVINPARSER_EXPORT void RDKit::ChemicalReactionToMrvFile	(	const ChemicalReaction &	rxn,
		const std::string &	fName,
		bool	prettyPrint = false )

ChemicalReactionToRxnBlock()

RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnBlock	(	const ChemicalReaction &	rxn,
		bool	separateAgents = false,
		bool	forceV3000 = false )

returns an rxn block for a reaction

Parameters

rxn	chemical reaction
separateAgents	flag to decide if agents are put in a separate block, otherwise they are included in the reactants block (default)
forceV3000	flag to cause the V3000 format to be used instead of V2000

References ChemicalReactionToRxnBlock().

Referenced by ChemicalReactionToRxnBlock().

ChemicalReactionToRxnMol()

RDKIT_CHEMREACTIONS_EXPORT ROMol * RDKit::ChemicalReactionToRxnMol

(

const ChemicalReaction &

rxn

)

returns a ROMol with RXN roles used to describe the reaction

References ChemicalReactionToRxnMol().

Referenced by ChemicalReactionToRxnMol().

ChemicalReactionToRxnSmarts()

RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmarts

(

const ChemicalReaction &

rxn

)

returns the reaction SMARTS for a reaction

References ChemicalReactionToRxnSmarts().

Referenced by ChemicalReactionToRxnSmarts().

ChemicalReactionToRxnSmiles()

RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmiles	(	const ChemicalReaction &	rxn,
		bool	canonical = true )

returns the reaction SMILES for a reaction

References ChemicalReactionToRxnSmiles().

Referenced by ChemicalReactionToRxnSmiles().

ChemicalReactionToV3KRxnBlock()

RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToV3KRxnBlock	(	const ChemicalReaction &	rxn,
		bool	separateAgents = false )

returns an V3000 rxn block for a reaction

Parameters

rxn	chemical reaction
separateAgents	flag to decide if agents are put in a separate block, otherwise they are included in the reactants block (default)

References ChemicalReactionToV3KRxnBlock().

Referenced by ChemicalReactionToV3KRxnBlock().

chiralAtomCompat()

RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::chiralAtomCompat	(	const Atom *	a1,
		const Atom *	a2 )

clearInputLabels()

void RDKit::clearInputLabels

(

Atom *

atom

)

Remove the user labels from the atom.

clearMolBlockWedgingInfo()

RDKIT_FILEPARSERS_EXPORT void RDKit::clearMolBlockWedgingInfo

(

ROMol &

mol

)

Deprecated

use Chirality::clearMolBlockWedgingInfo instead

ClearSingleBondDirFlags()

RDKIT_FILEPARSERS_EXPORT void RDKit::ClearSingleBondDirFlags

(

ROMol &

mol

)

Deprecated

, please use MolOps::clearSingleBondDirFlags instead

clearVarianceData()

void RDKit::clearVarianceData

(

FingerprintVarianceScoreData &

fingerprintVarianceScoreData

)

combineMols()

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::combineMols	(	const ROMol &	mol1,
		const ROMol &	mol2,
		RDGeom::Point3D	offset = RDGeom::Point3D(0, 0, 0) )

Combined two molecules to create a new one.

Parameters

mol1	- the first ROMol to be combined
mol2	- the second ROMol to be combined
offset	- a constant offset to be added to every atom position in mol2

Returns

a new ROMol with the two molecules combined. The new molecule has not been sanitized. The client is responsible for deleting this molecule.

computeGasteigerCharges() [1/3]

RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges	(	const ROMol &	mol,
		int	nIter = 12,
		bool	throwOnParamFailure = false )

computeGasteigerCharges() [2/3]

RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges	(	const ROMol &	mol,
		std::vector< double > &	charges,
		int	nIter = 12,
		bool	throwOnParamFailure = false )

computeGasteigerCharges() [3/3]

RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges	(	const ROMol *	mol,
		int	nIter = 12,
		bool	throwOnParamFailure = false )

computeIntVectPrimesProduct()

RDKIT_RDGENERAL_EXPORT double RDKit::computeIntVectPrimesProduct

(

const INT_VECT &

ring

)

compute the product of the set of primes corresponding to the values in an INT_VECT

computeL1Norm()

RDKIT_DATASTRUCTS_EXPORT unsigned int RDKit::computeL1Norm	(	const DiscreteValueVect &	v1,
		const DiscreteValueVect &	v2 )

computeNumProducts()

RDKIT_CHEMREACTIONS_EXPORT boost::uint64_t RDKit::computeNumProducts

(

const EnumerationTypes::RGROUPS &

sizes

)

computeNumProducts Returns the number of possible product combination from The given numbers of building blocks for each rgroup or EnumerationStrategyBase::EnumerationOverflow if the number will not fit into the machines integer type. n.b. An overflow simply means there are a lot of products not that they cannot be enumerated

References computeNumProducts().

Referenced by computeNumProducts(), RDKit::EnumerationStrategyBase::initialize(), and RDKit::EnumerationStrategyBase::internalInitialize().

ConnectTheDots()

RDKIT_FILEPARSERS_EXPORT void RDKit::ConnectTheDots	(	RWMol *	mol,
		unsigned int	flags = 0 )

convertComplexNameToQuery()

RDKIT_GRAPHMOL_EXPORT void RDKit::convertComplexNameToQuery	(	Atom *	query,
		std::string_view	symb )

copy_rdvalue()

void RDKit::copy_rdvalue ( RDValue & dest, const RDValue & src )

inline

Definition at line 339 of file RDValue-doublemagic.h.

References RDKit::RDTypeTag::AnyTag, rdvalue_is(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.

Referenced by RDKit::Dict::Dict(), RDKit::Dict::operator=(), RDKit::RDAny::operator=(), RDKit::RDAny::RDAny(), and RDKit::Dict::update().

copyVarianceData()

void RDKit::copyVarianceData	(	const FingerprintVarianceScoreData &	fromData,
		FingerprintVarianceScoreData &	toData )

countSwapsToInterconvert()

template<class T >

unsigned int RDKit::countSwapsToInterconvert	(	const T &	ref,
		T	probe )

Definition at line 54 of file utils.h.

References CHECK_INVARIANT, PRECONDITION, and rdvalue_is().

deleteSubstructs()

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::deleteSubstructs	(	const ROMol &	mol,
		const ROMol &	query,
		bool	onlyFrags = false,
		bool	useChirality = false )

Returns a copy of an ROMol with the atoms and bonds that match a pattern removed.

Parameters

mol	the ROMol of interest
query	the query ROMol
onlyFrags	if this is set, atoms will only be removed if the entire fragment in which they are found is matched by the query.
useChirality	- if set, match the coreQuery using chirality

Returns

a copy of mol with the matching atoms and bonds (if any) removed.

describeQuery() [1/2]

std::string RDKit::describeQuery ( const Atom * atom )

inline

Definition at line 150 of file QueryAtom.h.

References RDKit::Atom::getQuery(), RDKit::Atom::hasQuery(), PRECONDITION, RDKit::detail::qhelper(), and rdvalue_is().

describeQuery() [2/2]

std::string RDKit::describeQuery ( const Bond * bond )

inline

Definition at line 136 of file QueryBond.h.

References RDKit::Bond::getQuery(), RDKit::Bond::hasQuery(), PRECONDITION, RDKit::detail::qhelper(), and rdvalue_is().

DetectAtomStereoChemistry()

RDKIT_FILEPARSERS_EXPORT void RDKit::DetectAtomStereoChemistry	(	RWMol &	mol,
		const Conformer *	conf )

deprecated, please use MolOps::assignChiralTypesFromBondDirs instead

DetectBondStereoChemistry()

RDKIT_FILEPARSERS_EXPORT void RDKit::DetectBondStereoChemistry	(	ROMol &	mol,
		const Conformer *	conf )

deprecated, please use MolOps::detectBondStereoChemistry instead

determineBondOrders()

RDKIT_DETERMINEBONDS_EXPORT void RDKit::determineBondOrders	(	RWMol &	mol,
		int	charge = 0,
		bool	allowChargedFragments = true,
		bool	embedChiral = true,
		bool	useAtomMap = false )

This is based on xyz2mol: https://github.com/jensengroup/xyz2mol

Parameters

mol	is the molecule of interest; it must have single bonds corresponding to the atomic connectivity
charge	(optional) the charge of the molecule; it must be provided if charge is non-zero
allowChargedFragments	(optional) if this is true, formal charges will be placed on atoms according to their valency; otherwise, radical electrons will be placed on the atoms
embedChiral	(optional) if this is true, chirality information will be embedded into the molecule; the function calls sanitizeMol() when this is true
useAtomMap	(optional) if this is true, an atom map will be created for the molecule

determineBonds()

RDKIT_DETERMINEBONDS_EXPORT void RDKit::determineBonds	(	RWMol &	mol,
		bool	useHueckel = false,
		int	charge = 0,
		double	covFactor = 1.3,
		bool	allowChargedFragments = true,
		bool	embedChiral = true,
		bool	useAtomMap = false,
		bool	useVdw = false )

This is based on xyz2mol: https://github.com/jensengroup/xyz2mol

Parameters

mol	is the molecule of interest; it must have a 3D conformer
useHueckel	(optional) if this is true, extended Hueckel theory will be used to determine connectivity rather than the van der Waals or connect-the-dots method
charge	(optional) the charge of the molecule; it must be provided if charge is non-zero
covFactor	(optional) the factor with which to multiply each covalent radius if the van der Waals method is used
allowChargedFragments	(optional) if this is true, formal charges will be placed on atoms according to their valency; otherwise, radical electrons will be placed on the atoms
embedChiral	(optional) if this is true, chirality information will be embedded into the molecule; the function calls sanitizeMol() when this is true
useAtomMap	(optional) if this is true, an atom map will be created for the molecule
useVdw	(optional) if this is false, the connect-the-dots method will be used instead of the van der Waals method

DetermineBondWedgeState() [1/2]

RDKIT_FILEPARSERS_EXPORT Bond::BondDir RDKit::DetermineBondWedgeState	(	const Bond *	bond,
		const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > &	wedgeBonds,
		const Conformer *	conf )

Deprecated

use Chirality::detail::determineBondWedgeState instead

DetermineBondWedgeState() [2/2]

RDKIT_FILEPARSERS_EXPORT Bond::BondDir RDKit::DetermineBondWedgeState	(	const Bond *	bond,
		unsigned int	fromAtomIdx,
		const Conformer *	conf )

Deprecated

use Chirality::detail::determineBondWedgeState instead

determineConnectivity()

RDKIT_DETERMINEBONDS_EXPORT void RDKit::determineConnectivity	(	RWMol &	mol,
		bool	useHueckel = false,
		int	charge = 0,
		double	covFactor = 1.3,
		bool	useVdw = false )

This is based on xyz2mol: https://github.com/jensengroup/xyz2mol

Parameters

mol	is the molecule of interest; it must have a 3D conformer
useHueckel	(optional) if this is true, extended Hueckel theory will be used to determine connectivity rather than the van der Waals or connect-the-dots method
charge	(optional) the charge of the molecule; it must be provided if the Hueckel method is used and charge is non-zero
covFactor	(optional) the factor with which to multiply each covalent radius if the van der Waals method is used
useVdw	(optional) if this is false, the connect-the-dots method will be used instead of the van der Waals method

DiceSimilarity()

template<typename IndexType >

double RDKit::DiceSimilarity	(	const SparseIntVect< IndexType > &	v1,
		const SparseIntVect< IndexType > &	v2,
		bool	returnDistance = false,
		double	bounds = 0.0 )

Definition at line 492 of file SparseIntVect.h.

References RDKit::SparseIntVect< IndexType >::getLength(), RDKit::SparseIntVect< IndexType >::getTotalVal(), and rdvalue_is().

Dict::getVal< std::string >()

template<>

std::string RDKit::Dict::getVal< std::string > ( const std::string & what ) const

inline

Definition at line 346 of file Dict.h.

References rdvalue_is().

DifferenceFingerprintChemReaction()

RDKIT_CHEMREACTIONS_EXPORT SparseIntVect< std::uint32_t > * RDKit::DifferenceFingerprintChemReaction	(	const ChemicalReaction &	rxn,
		const ReactionFingerprintParams &	params = DefaultDifferenceFPParams )

Generates a difference fingerprint for a reaction to use in similarity search of reactions

A difference fingerprint is generated as a SparseIntVect to use for similarity search of reactions. By default the fingerprint is generated as 2048 bit hashed fingerprint subtracting AtompairFP of the reactants from the products' AtompairFP and tentatively the agent AtompairFP is added

Parameters

rxn	the reaction to be fingerprinted
params	specific settings to manipulate fingerprint generation

Returns

the reaction fingerprint, as an SparseIntVec

Notes:

• the caller is responsible for deleteing the result

EndianSwapBytes() [1/4]

template<EEndian from, EEndian to>

char RDKit::EndianSwapBytes ( char value )

inline

Definition at line 92 of file StreamOps.h.

EndianSwapBytes() [2/4]

template<EEndian from, EEndian to>

signed char RDKit::EndianSwapBytes ( signed char value )

inline

Definition at line 100 of file StreamOps.h.

EndianSwapBytes() [3/4]

template<EEndian from, EEndian to, class T >

T RDKit::EndianSwapBytes ( T value )

inline

Definition at line 73 of file StreamOps.h.

References rdvalue_is().

EndianSwapBytes() [4/4]

template<EEndian from, EEndian to>

unsigned char RDKit::EndianSwapBytes ( unsigned char value )

inline

Definition at line 96 of file StreamOps.h.

EnumerateLibraryCanSerialize()

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::EnumerateLibraryCanSerialize

(

)

eraseUniquePtr()

template<typename T >

void RDKit::eraseUniquePtr	(	std::vector< std ::unique_ptr< T > > &	vector,
		T *	itemToErase )

Definition at line 235 of file MarvinDefs.h.

References rdvalue_is().

FASTAToMol() [1/4]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::FASTAToMol	(	const char *	seq,
		bool	sanitize,
		bool	lowerD )

Parameters

seq	- the string to be processed
sanitize	- toggles sanitization and stereochemistry perception of the molecule
lowerD	- if set, lower case letters will be parsed as the d form of the corresponding amino acid

FASTAToMol() [2/4]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::FASTAToMol	(	const char *	seq,
		bool	sanitize = true,
		int	flavor = 0 )

Parameters

seq	- the string to be processed
sanitize	- toggles sanitization and stereochemistry perception of the molecule
flavor	- 0 Protein, L amino acids (default) 1 Protein, D amino acids 2 RNA, no cap 3 RNA, 5' cap 4 RNA, 3' cap 5 RNA, both caps 6 DNA, no cap 7 DNA, 5' cap 8 DNA, 3' cap 9 DNA, both caps

FASTAToMol() [3/4]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::FASTAToMol	(	const std::string &	seq,
		bool	sanitize,
		bool	lowerD )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

FASTAToMol() [4/4]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::FASTAToMol	(	const std::string &	seq,
		bool	sanitize = true,
		int	flavor = 0 )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

feq()

RDKIT_RDGENERAL_EXPORT bool RDKit::feq	(	double	v1,
		double	v2,
		double	tol = 1e-4 )

floating point comparison with a tolerance

FilterCatalogCanSerialize()

RDKIT_FILTERCATALOG_EXPORT bool RDKit::FilterCatalogCanSerialize

(

)

FinalChiralityCheckFunction()

bool RDKit::FinalChiralityCheckFunction ( const std::uint32_t c1[], const std::uint32_t c2[], const ROMol & mol1, const FMCS::Graph & query, const ROMol & mol2, const FMCS::Graph & target, const MCSParameters * p )

inline

FinalMatchCheckFunction()

bool RDKit::FinalMatchCheckFunction	(	const std::uint32_t	c1[],
		const std::uint32_t	c2[],
		const ROMol &	mol1,
		const FMCS::Graph &	query,
		const ROMol &	mol2,
		const FMCS::Graph &	target,
		const MCSParameters *	p )

findAllPathsOfLengthN()

RDKIT_SUBGRAPHS_EXPORT PATH_LIST RDKit::findAllPathsOfLengthN	(	const ROMol &	mol,
		unsigned int	targetLen,
		bool	useBonds = true,
		bool	useHs = false,
		int	rootedAtAtom = -1,
		bool	onlyShortestPaths = false )

find all paths of a particular size

Parameters

mol	- the molecule to be considered
targetLen	- the length of the paths to be returned
useBonds	- if set, the path indices will be bond indices, not atom indices
useHs	- if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph.
rootedAtAtom	- if non-negative, only subgraphs that start at this atom will be returned.
onlyShortestPaths	- if set then only paths which are <= the shortest path between the begin and end atoms will be included in the results

The result is a list of paths (i.e. list of list of bond indices)

findAllPathsOfLengthsMtoN()

RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP RDKit::findAllPathsOfLengthsMtoN	(	const ROMol &	mol,
		unsigned int	lowerLen,
		unsigned int	upperLen,
		bool	useBonds = true,
		bool	useHs = false,
		int	rootedAtAtom = -1,
		bool	onlyShortestPaths = false )

findAllSubgraphsOfLengthN()

RDKIT_SUBGRAPHS_EXPORT PATH_LIST RDKit::findAllSubgraphsOfLengthN	(	const ROMol &	mol,
		unsigned int	targetLen,
		bool	useHs = false,
		int	rootedAtAtom = -1 )

find all bond subgraphs of a particular size

Parameters

mol	- the molecule to be considered
targetLen	- the length of the subgraphs to be returned
useHs	- if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph.
rootedAtAtom	- if non-negative, only subgraphs that start at this atom will be returned.

The result is a list of paths (i.e. list of list of bond indices)

findAllSubgraphsOfLengthsMtoN()

RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP RDKit::findAllSubgraphsOfLengthsMtoN	(	const ROMol &	mol,
		unsigned int	lowerLen,
		unsigned int	upperLen,
		bool	useHs = false,
		int	rootedAtAtom = -1 )

find all bond subgraphs in a range of sizes

Parameters

mol	- the molecule to be considered
lowerLen	- the minimum subgraph size to find
upperLen	- the maximum subgraph size to find
useHs	- if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph.
rootedAtAtom	- if non-negative, only subgraphs that start at this atom will be returned.

The result is a map from subgraph size -> list of paths (i.e. list of list of bond indices)

findAtomEnvironmentOfRadiusN()

RDKIT_SUBGRAPHS_EXPORT PATH_TYPE RDKit::findAtomEnvironmentOfRadiusN	(	const ROMol &	mol,
		unsigned int	radius,
		unsigned int	rootedAtAtom,
		bool	useHs = false,
		bool	enforceSize = true,
		std::unordered_map< unsigned int, unsigned int > *	atomMap = nullptr )

Find bond subgraphs of a particular radius around an atom. Return empty result if there is no bond at the requested radius.

Parameters

mol	- the molecule to be considered
radius	- the radius of the subgraphs to be considered
rootedAtAtom	- the atom to consider
useHs	- if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph.
enforceSize	- If false, all the bonds within the requested radius (<= radius) is collected. Otherwise, at least one bond located at the requested radius must be found and added.
atomMap	- Optional: If provided, it will measure the minimum distance of the atom from the rooted atom (start with 0 from the rooted atom). The result is a pair of the atom ID and the distance. The result is a path (a vector of bond indices)

findFuncGroupsOnMol()

RDKIT_FRAGCATALOG_EXPORT MatchVectType RDKit::findFuncGroupsOnMol	(	const ROMol &	mol,
		const FragCatParams *	params,
		INT_VECT &	fgBonds )

findMCS() [1/3]

RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS	(	const std::vector< ROMOL_SPTR > &	mols,
		bool	maximizeBonds,
		double	threshold,
		unsigned int	timeout,
		bool	verbose,
		bool	matchValences,
		bool	ringMatchesRingOnly,
		bool	completeRingsOnly,
		bool	matchChiralTag,
		AtomComparator	atomComp,
		BondComparator	bondComp,
		RingComparator	ringComp )

findMCS() [2/3]

RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS	(	const std::vector< ROMOL_SPTR > &	mols,
		bool	maximizeBonds,
		double	threshold = 1.0,
		unsigned int	timeout = 3600,
		bool	verbose = false,
		bool	matchValences = false,
		bool	ringMatchesRingOnly = false,
		bool	completeRingsOnly = false,
		bool	matchChiralTag = false,
		AtomComparator	atomComp = AtomCompareElements,
		BondComparator	bondComp = BondCompareOrder )

findMCS() [3/3]

RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS	(	const std::vector< ROMOL_SPTR > &	mols,
		const MCSParameters *	params = nullptr )

findMCS_P()

RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS_P	(	const std::vector< ROMOL_SPTR > &	mols,
		const char *	params_json )

findUniquePtr()

template<typename T >

std::vector< std::unique_ptr< T > >::iterator RDKit::findUniquePtr	(	std::vector< std ::unique_ptr< T > > &	vector,
		T *	itemToFind )

Definition at line 220 of file MarvinDefs.h.

References rdvalue_is().

findUniqueSubgraphsOfLengthN()

RDKIT_SUBGRAPHS_EXPORT PATH_LIST RDKit::findUniqueSubgraphsOfLengthN	(	const ROMol &	mol,
		unsigned int	targetLen,
		bool	useHs = false,
		bool	useBO = true,
		int	rootedAtAtom = -1 )

find unique bond subgraphs of a particular size

Parameters

mol	- the molecule to be considered
targetLen	- the length of the subgraphs to be returned
useHs	- if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph.
useBO	- if set, bond orders will be considered when uniquifying the paths
rootedAtAtom	- if non-negative, only subgraphs that start at this atom will be returned.

The result is a list of paths (i.e. list of list of bond indices)

fingerprintVarianceScore()

RDKIT_RGROUPDECOMPOSITION_EXPORT double RDKit::fingerprintVarianceScore	(	const std::vector< size_t > &	permutation,
		const std::vector< std::vector< RGroupMatch > > &	matches,
		const std::set< int > &	labels,
		FingerprintVarianceScoreData *	fingerprintVarianceScoreData = nullptr )

forwardStereoGroupIds()

RDKIT_GRAPHMOL_EXPORT void RDKit::forwardStereoGroupIds

(

ROMol &

mol

)

Copy StereoGroup "read" IDs to "write" IDs so that they will be preserved when the mol is exported.

from_rdany() [1/2]

template<class T >

boost::enable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdany

(

const RDAny &

arg

)

Definition at line 190 of file RDAny.h.

References rdvalue_is(), and RDKit::RDTypeTag::StringTag.

from_rdany() [2/2]

template<class T >

boost::disable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdany

(

const RDAny &

arg

)

Definition at line 211 of file RDAny.h.

References rdvalue_is().

from_rdvalue() [1/2]

template<class T >

boost::enable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdvalue

(

RDValue_cast_t

arg

)

Definition at line 265 of file RDValue.h.

References rdvalue_cast< std::string >(), rdvalue_is(), and RDKit::RDTypeTag::StringTag.

from_rdvalue() [2/2]

template<class T >

boost::disable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdvalue

(

RDValue_cast_t

arg

)

Definition at line 286 of file RDValue.h.

References rdvalue_is().

getAtomAlias()

RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomAlias

(

const Atom *

atom

)

getAtomListQueryVals()

RDKIT_GRAPHMOL_EXPORT void RDKit::getAtomListQueryVals	(	const Atom::QUERYATOM_QUERY *	q,
		std::vector< int > &	vals )

getAtomRLabel()

RDKIT_GRAPHMOL_EXPORT int RDKit::getAtomRLabel

(

const Atom *

atm

)

getAtomTypeAtomicNum()

static int RDKit::getAtomTypeAtomicNum ( int val )

inlinestatic

Definition at line 145 of file QueryOps.h.

getAtomTypeIsAromatic()

static bool RDKit::getAtomTypeIsAromatic ( int val )

inlinestatic

Definition at line 144 of file QueryOps.h.

getAtomValue()

RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomValue

(

const Atom *

atom

)

getCleanNumber()

template<typename T >

bool RDKit::getCleanNumber	(	std::string	strToParse,
		T &	outInt )

getCountFP()

RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint32_t > * RDKit::getCountFP	(	const ROMol &	mol,
		FPType	fPType )

getCountFPBulk()

RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint32_t > * > * RDKit::getCountFPBulk	(	const std::vector< const ROMol * >	molVector,
		FPType	fPType )

getDiscreteDistMat()

DiscreteDistMat * RDKit::getDiscreteDistMat ( )

extern

getDoubleRandomSource()

RDKIT_RDGENERAL_EXPORT double_source_type & RDKit::getDoubleRandomSource

(

)

return a reference to the global (Boost) random source

getEndIterator()

RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT::const_iterator RDKit::getEndIterator	(	const ChemicalReaction &	rxn,
		ReactionMoleculeType	t )

GetFilterData()

const FilterData_t * RDKit::GetFilterData

(

FilterCatalogParams::FilterCatalogs

catalog

)

GetFilterProperties()

const FilterProperty_t * RDKit::GetFilterProperties

(

FilterCatalogParams::FilterCatalogs

catalog

)

GetFlattenedFunctionalGroupHierarchy()

RDKIT_FILTERCATALOG_EXPORT const std::map< std::string, ROMOL_SPTR > & RDKit::GetFlattenedFunctionalGroupHierarchy

(

bool

normalized = false

)

Return the flattened functional group hierarchy as a string->ROMOL_SPTR map The label is the name of the functional group in the hiearchy e.g. Halogen.Bromine.Aliphatic

getFP()

RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::getFP	(	const ROMol &	mol,
		FPType	fPType )

Referenced by RDKit::FPBReader::operator[]().

getFPBulk()

RDKIT_FINGERPRINTS_EXPORT std::vector< ExplicitBitVect * > * RDKit::getFPBulk	(	const std::vector< const ROMol * >	molVector,
		FPType	fPType )

GetFunctionalGroupHierarchy()

RDKIT_FILTERCATALOG_EXPORT const FilterCatalog & RDKit::GetFunctionalGroupHierarchy

(

)

Return the functional group hierarchy as a FilterCatalog.

getLine() [1/2]

std::string RDKit::getLine ( std::istream & inStream )

inline

grabs the next line from an instream and returns it.

Definition at line 347 of file StreamOps.h.

References getLine(), and rdvalue_is().

getLine() [2/2]

std::string RDKit::getLine ( std::istream * inStream )

inline

grabs the next line from an instream and returns it.

Definition at line 338 of file StreamOps.h.

References rdvalue_is().

Referenced by getLine().

getMostSubstitutedCoreMatch()

RDKIT_SUBSTRUCTMATCH_EXPORT const MatchVectType & RDKit::getMostSubstitutedCoreMatch	(	const ROMol &	mol,
		const ROMol &	core,
		const std::vector< MatchVectType > &	matches )

This postprocesses the passed substruct matches and returns the match that has the largest number of non-hydrogen atoms in correspondence of terminal dummy atoms

GetNumEntries()

unsigned int RDKit::GetNumEntries

(

FilterCatalogParams::FilterCatalogs

catalog

)

GetNumPropertyEntries()

unsigned int RDKit::GetNumPropertyEntries

(

FilterCatalogParams::FilterCatalogs

catalog

)

getNumThreadsToUse()

unsigned int RDKit::getNumThreadsToUse ( int target )

inline

Definition at line 37 of file RDThreads.h.

References RDUNUSED_PARAM, and rdvalue_is().

Referenced by RDPickers::LeaderPicker::lazyPick(), and RDKit::ForceFieldsHelper::OptimizeMoleculeConfs().

getRandomGenerator()

RDKIT_RDGENERAL_EXPORT rng_type & RDKit::getRandomGenerator

(

int

seed = -1

)

Optionally seed and return a reference to the global (Boost) random generator

getRandomVal()

RDKIT_RDGENERAL_EXPORT double RDKit::getRandomVal

(

int

seed = -1

)

Return a random double value between 0.0 and 1.0 Optionally seed the random number generator

getReactantsFromRGroups()

RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT RDKit::getReactantsFromRGroups	(	const std::vector< MOL_SPTR_VECT > &	bbs,
		const EnumerationTypes::RGROUPS &	rgroups )

getReactantsFromRGroups Helper function for enumeration, bbs are stored in a std::vector< std::vector<boost:shared_ptr<ROMol> >

References getReactantsFromRGroups().

Referenced by getReactantsFromRGroups().

getReactingAtoms()

RDKIT_CHEMREACTIONS_EXPORT VECT_INT_VECT RDKit::getReactingAtoms	(	const ChemicalReaction &	rxn,
		bool	mappedAtomsOnly = false )

returns indices of the atoms in each reactant that are changed in the reaction

Parameters

rxn	the reaction we are interested in
mappedAtomsOnly	if set, atoms that are not mapped will not be included in the list of changed atoms (otherwise they are automatically included)

How are changed atoms recognized? 1) Atoms whose degree changes 2) Atoms whose bonding pattern changes 3) unmapped atoms (unless the mappedAtomsOnly flag is set) 4) Atoms connected to unmapped atoms 5) Atoms whose atomic number changes (unless the corresponding product atom is a dummy) 6) Atoms with more than one atomic number query (unless the corresponding product atom is a dummy)

Note that the atomic number of a query atom depends on how it's constructed. When coming from SMARTS: if the first query is an atomic label/number that sets the atomic number, otherwise it's zero. For example [O;] is atomic number 8 while [;O] is atomic number 0. When coming from RXN: the atomic number of the atom in the rxn file sets the value.

References getReactingAtoms().

Referenced by getReactingAtoms().

getRlabels()

std::map< int, Atom * > RDKit::getRlabels

(

const RWMol &

mol

)

Get the RLabels,atom mapping for the current molecule.

getSizesFromBBs()

template<class T >

EnumerationTypes::RGROUPS RDKit::getSizesFromBBs

(

const std::vector< std::vector< T > > &

bbs

)

Return the number of elements per input vector.

Parameters

bbs	vector<vector<T> >

Returns

vector<unint64_t> number of elements in each vector

Definition at line 75 of file EnumerationStrategyBase.h.

Referenced by RDKit::EnumerationStrategyBase::initialize().

getSizesFromReactants()

RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::RGROUPS RDKit::getSizesFromReactants

(

const std::vector< MOL_SPTR_VECT > &

bbs

)

getSizesFromReactants Helper function for enumeration, bbs are stored in a std::vector< std::vector<boost:shared_ptr<ROMol> >

References getSizesFromReactants().

Referenced by getSizesFromReactants().

getSparseCountFP()

RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint64_t > * RDKit::getSparseCountFP	(	const ROMol &	mol,
		FPType	fPType )

getSparseCountFPBulk()

RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint64_t > * > * RDKit::getSparseCountFPBulk	(	const std::vector< const ROMol * >	molVector,
		FPType	fPType )

getSparseFP()

RDKIT_FINGERPRINTS_EXPORT SparseBitVect * RDKit::getSparseFP	(	const ROMol &	mol,
		FPType	fPType )

getSparseFPBulk()

RDKIT_FINGERPRINTS_EXPORT std::vector< SparseBitVect * > * RDKit::getSparseFPBulk	(	const std::vector< const ROMol * >	molVector,
		FPType	fPType )

getStartIterator()

RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT::const_iterator RDKit::getStartIterator	(	const ChemicalReaction &	rxn,
		ReactionMoleculeType	t )

getSubstanceGroups() [1/2]

RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & RDKit::getSubstanceGroups

(

const ROMol &

mol

)

getSubstanceGroups() [2/2]

RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & RDKit::getSubstanceGroups

(

ROMol &

mol

)

getSupplementalSmilesLabel()

RDKIT_GRAPHMOL_EXPORT std::string RDKit::getSupplementalSmilesLabel

(

const Atom *

atom

)

getTwiceBondType()

RDKIT_GRAPHMOL_EXPORT uint8_t RDKit::getTwiceBondType ( const RDKit::Bond & b )

extern

returns twice the bondType (e.g. SINGLE->2, AROMATIC->3, etc.)

getUnfoldedRDKFingerprintMol()

RDKIT_FINGERPRINTS_EXPORT SparseIntVect< boost::uint64_t > * RDKit::getUnfoldedRDKFingerprintMol	(	const ROMol &	mol,
		unsigned int	minPath = 1,
		unsigned int	maxPath = 7,
		bool	useHs = true,
		bool	branchedPaths = true,
		bool	useBondOrder = true,
		std::vector< std::uint32_t > *	atomInvariants = nullptr,
		const std::vector< std::uint32_t > *	fromAtoms = nullptr,
		std::vector< std::vector< boost::uint64_t > > *	atomBits = nullptr,
		std::map< boost::uint64_t, std::vector< std::vector< int > > > *	bitInfo = nullptr )

hanoi()

template<typename CompareFunc >

bool RDKit::hanoi	(	int *	base,
		int	nel,
		int *	temp,
		int *	count,
		int *	changed,
		CompareFunc	compar )

changed ||

changed ||

Definition at line 27 of file hanoiSort.h.

References hanoi(), and rdvalue_is().

Referenced by hanoi(), and hanoisort().

hanoisort()

template<typename CompareFunc >

void RDKit::hanoisort	(	int *	base,
		int	nel,
		int *	count,
		int *	changed,
		CompareFunc	compar )

Definition at line 151 of file hanoiSort.h.

References hanoi(), and rdvalue_is().

Referenced by RDKit::Canon::RefinePartitions().

hasAgentTemplateSubstructMatch()

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasAgentTemplateSubstructMatch	(	const ChemicalReaction &	rxn,
		const ChemicalReaction &	query_rxn )

hasDummy()

bool RDKit::hasDummy

(

const RWMol &

core

)

Returns true if the core has a dummy atom.

hasNonZeroZCoords()

bool RDKit::hasNonZeroZCoords ( const Conformer & conf )

inline

Returns true if any of the z coords are non zero, false otherwise.

Parameters

conf	Conformer object to analyze

Definition at line 166 of file Conformer.h.

References RDKit::Conformer::getPositions(), and hasNonZeroZCoords().

Referenced by hasNonZeroZCoords().

hasProductTemplateSubstructMatch()

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasProductTemplateSubstructMatch	(	const ChemicalReaction &	rxn,
		const ChemicalReaction &	query_rxn )

hasReactantTemplateSubstructMatch()

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactantTemplateSubstructMatch	(	const ChemicalReaction &	rxn,
		const ChemicalReaction &	query_rxn )

hasReactionAtomMapping()

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactionAtomMapping

(

const ChemicalReaction &

rxn

)

hasReactionSubstructMatch()

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactionSubstructMatch	(	const ChemicalReaction &	rxn,
		const ChemicalReaction &	query_rxn,
		bool	includeAgents = false )

havePairOfCompatibleRings()

RDKIT_FMCS_EXPORT bool RDKit::havePairOfCompatibleRings	(	const MCSBondCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	bond1,
		const ROMol &	mol2,
		unsigned int	bond2 )

HELMToMol() [1/2]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::HELMToMol	(	const char *	helm,
		bool	sanitize = true )

Parameters

seq	- the string to be processed
sanitize	- toggles sanitization and stereochemistry perception of the molecule

HELMToMol() [2/2]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::HELMToMol	(	const std::string &	helm,
		bool	sanitize = true )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Intersect()

RDKIT_RDGENERAL_EXPORT void RDKit::Intersect	(	const INT_VECT &	r1,
		const INT_VECT &	r2,
		INT_VECT &	res )

calculate the intersection of two INT_VECTs and put the results in a third vector

invertMolBlockWedgingInfo()

RDKIT_FILEPARSERS_EXPORT void RDKit::invertMolBlockWedgingInfo

(

ROMol &

mol

)

Deprecated

use Chirality::invertMolBlockWedgingInfo instead

isAnyAtomWithMultipleNeighborsOrNotUserRLabel()

bool RDKit::isAnyAtomWithMultipleNeighborsOrNotUserRLabel ( const Atom & atom )

inline

Returns true if the core atom is either a dummy atom with multiple connections or a dummy atom with a single connection that has no user defined rgroup label

Definition at line 73 of file RGroupUtils.h.

References RDKit::Atom::getAtomicNum(), and isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment().

isAromaticAtom()

RDKIT_GRAPHMOL_EXPORT bool RDKit::isAromaticAtom

(

const Atom &

atom

)

returns true if the atom is aromatic or has an aromatic bond

isAtomAromatic()

RDKIT_GRAPHMOL_EXPORT bool RDKit::isAtomAromatic

(

const Atom *

a

)

isAtomDummy()

bool RDKit::isAtomDummy ( const Atom * a )

inline

Definition at line 1093 of file QueryOps.h.

References RDKit::Atom::getAtomicNum(), Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::getDescription(), Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::getNegation(), RDKit::Atom::getQuery(), and RDKit::Atom::hasQuery().

isAtomListQuery()

RDKIT_GRAPHMOL_EXPORT bool RDKit::isAtomListQuery

(

const Atom *

a

)

isAtomTerminalRGroupOrQueryHydrogen()

RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::isAtomTerminalRGroupOrQueryHydrogen

(

const Atom *

atom

)

isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment()

bool RDKit::isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment

(

const Atom &

atom

)

Returns true if the core atom is either an atom with multiple connections or an atom with a single connection that has no user defined rgroup label

Referenced by isAnyAtomWithMultipleNeighborsOrNotUserRLabel().

IsBlacklistedPair()

RDKIT_FILEPARSERS_EXPORT bool RDKit::IsBlacklistedPair	(	Atom *	beg_atom,
		Atom *	end_atom )

isComplexQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery

(

const Atom *

a

)

isComplexQuery() [2/2]

RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery

(

const Bond *

b

)

isDative()

bool RDKit::isDative ( const Bond & bond )

inline

Definition at line 389 of file Bond.h.

References RDKit::Bond::DATIVE, RDKit::Bond::DATIVEL, RDKit::Bond::DATIVEONE, RDKit::Bond::DATIVER, RDKit::Bond::getBondType(), and rdvalue_is().

Referenced by canSetDoubleBondStereo().

isDummyRGroupAttachment()

bool RDKit::isDummyRGroupAttachment

(

const Atom &

atom

)

isEarlyAtom()

RDKIT_GRAPHMOL_EXPORT bool RDKit::isEarlyAtom

(

int

atomicNum

)

returns true if the atom is to the left of C

isMoleculeAgentOfReaction() [1/2]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeAgentOfReaction	(	const ChemicalReaction &	rxn,
		const ROMol &	mol )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

References isMoleculeAgentOfReaction().

isMoleculeAgentOfReaction() [2/2]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeAgentOfReaction	(	const ChemicalReaction &	rxn,
		const ROMol &	mol,
		unsigned int &	which )

tests whether or not the molecule has a substructure match to any of the reaction's agents the which argument is used to return which of the agents the molecule matches. If there's no match, it is equal to the number of agents on return

References isMoleculeAgentOfReaction().

Referenced by isMoleculeAgentOfReaction(), and isMoleculeAgentOfReaction().

isMoleculeProductOfReaction() [1/3]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeProductOfReaction	(	const ChemicalReaction &	rxn,
		const ROMol &	mol )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

References isMoleculeProductOfReaction().

isMoleculeProductOfReaction() [2/3]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeProductOfReaction	(	const ChemicalReaction &	rxn,
		const ROMol &	mol,
		std::vector< unsigned int > &	which,
		bool	stopAtFirstMatch = false )

tests whether or not the molecule has a substructure match to the reaction's products the which argument is used to return which of the products the molecule matches.

References isMoleculeProductOfReaction().

Referenced by isMoleculeProductOfReaction(), isMoleculeProductOfReaction(), and isMoleculeProductOfReaction().

isMoleculeProductOfReaction() [3/3]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeProductOfReaction	(	const ChemicalReaction &	rxn,
		const ROMol &	mol,
		unsigned int &	which )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

References isMoleculeProductOfReaction().

isMoleculeReactantOfReaction() [1/3]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeReactantOfReaction	(	const ChemicalReaction &	rxn,
		const ROMol &	mol )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

References isMoleculeReactantOfReaction().

isMoleculeReactantOfReaction() [2/3]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeReactantOfReaction	(	const ChemicalReaction &	rxn,
		const ROMol &	mol,
		std::vector< unsigned int > &	which,
		bool	stopAtFirstMatch = false )

tests whether or not the molecule has a substructure match to the reaction's reactants the which argument is used to return which of the reactants the molecule matches.

References isMoleculeReactantOfReaction().

Referenced by isMoleculeReactantOfReaction(), isMoleculeReactantOfReaction(), and isMoleculeReactantOfReaction().

isMoleculeReactantOfReaction() [3/3]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeReactantOfReaction	(	const ChemicalReaction &	rxn,
		const ROMol &	mol,
		unsigned int &	which )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

References isMoleculeReactantOfReaction().

isReactionTemplateMoleculeAgent()

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isReactionTemplateMoleculeAgent	(	const ROMol &	mol,
		double	agentThreshold )

isSerializable()

bool RDKit::isSerializable ( const Dict::Pair & pair, const CustomPropHandlerVec & handlers = {} )

inline

Definition at line 384 of file StreamOps.h.

isUserRLabel()

bool RDKit::isUserRLabel

(

const Atom &

atom

)

Return true if the atom has a user-defined R group label.

labellingToString()

std::string RDKit::labellingToString

(

Labelling

type

)

return the user friendly name for the given labelling

LayeredFingerprintMol()

RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::LayeredFingerprintMol	(	const ROMol &	mol,
		unsigned int	layerFlags = 0xFFFFFFFF,
		unsigned int	minPath = 1,
		unsigned int	maxPath = 7,
		unsigned int	fpSize = 2048,
		std::vector< unsigned int > *	atomCounts = nullptr,
		ExplicitBitVect *	setOnlyBits = nullptr,
		bool	branchedPaths = true,
		const std::vector< std::uint32_t > *	fromAtoms = nullptr )

Generates a topological (Daylight like) fingerprint for a molecule using a layer-based hashing algorithm.

Experimental: This function is experimental. The API or results may change from release to release.

Parameters

mol	the molecule to be fingerprinted
layerFlags	the layers to be included (see below)
minPath	the minimum path length (in bonds) to be included
maxPath	the minimum path length (in bonds) to be included
fpSize	the size of the fingerprint
atomCounts	if provided, this will be used to provide the count of the number of paths that set bits each atom is involved in. The vector should have at least as many entries as the molecule has atoms and is not zeroed out here.
setOnlyBits	if provided, only bits that are set in this bit vector will be set in the result. This is essentially the same as doing: (*res) &= (*setOnlyBits); but also has an impact on the atomCounts (if being used)
branchedPaths	toggles generation of branched subgraphs, not just linear paths

Returns

the molecular fingerprint, as an ExplicitBitVect

Notes:

• the caller is responsible for deleteing the result

Layer definitions:

• 0x01: pure topology
• 0x02: bond order
• 0x04: atom types
• 0x08: presence of rings
• 0x10: ring sizes
• 0x20: aromaticity

makeAAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAAtomQuery

(

)

returns a Query for matching generic A atoms (heavy atoms)

makeAHAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * RDKit::makeAHAtomQuery

(

)

returns a Query for matching generic AH atoms (any atom)

makeAtomAliphaticQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomAliphaticQuery

(

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomAliphaticQuery() [2/2]

template<class T >

T * RDKit::makeAtomAliphaticQuery

(

const std::string &

descr

)

returns a Query for matching aliphatic atoms

Definition at line 461 of file QueryOps.h.

References queryAtomAliphatic(), and rdvalue_is().

makeAtomAromaticQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomAromaticQuery

(

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomAromaticQuery() [2/2]

template<class T >

T * RDKit::makeAtomAromaticQuery

(

const std::string &

descr

)

returns a Query for matching the isAromatic flag

Definition at line 453 of file QueryOps.h.

References queryAtomAromatic(), and rdvalue_is().

makeAtomExplicitDegreeQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomExplicitDegreeQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomExplicitDegreeQuery() [2/2]

template<class T >

T * RDKit::makeAtomExplicitDegreeQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching explicit degree

Definition at line 405 of file QueryOps.h.

References queryAtomExplicitDegree(), and rdvalue_is().

makeAtomExplicitValenceQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomExplicitValenceQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomExplicitValenceQuery() [2/2]

template<class T >

T * RDKit::makeAtomExplicitValenceQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching explicit valence

Definition at line 389 of file QueryOps.h.

References queryAtomExplicitValence(), and rdvalue_is().

makeAtomFormalChargeQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomFormalChargeQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomFormalChargeQuery() [2/2]

template<class T >

T * RDKit::makeAtomFormalChargeQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching formal charge

Definition at line 486 of file QueryOps.h.

References queryAtomFormalCharge(), and rdvalue_is().

Referenced by RDKit::QueryAtom::QueryAtom().

makeAtomHasAliphaticHeteroatomNbrsQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHasAliphaticHeteroatomNbrsQuery

(

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomHasAliphaticHeteroatomNbrsQuery() [2/2]

template<class T >

T * RDKit::makeAtomHasAliphaticHeteroatomNbrsQuery

(

const std::string &

descr

)

returns a Query for matching atoms that have heteroatom neighbors

Definition at line 640 of file QueryOps.h.

References queryAtomHasAliphaticHeteroatomNbrs(), and rdvalue_is().

makeAtomHasChiralTagQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHasChiralTagQuery

(

)

\overloadquery

makeAtomHasChiralTagQuery() [2/2]

template<class T >

T * RDKit::makeAtomHasChiralTagQuery

(

const std::string &

descr

)

returns a Query for matching whether or not chirality has been set on the atom

Definition at line 522 of file QueryOps.h.

References queryAtomHasChiralTag(), and rdvalue_is().

makeAtomHasHeteroatomNbrsQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHasHeteroatomNbrsQuery

(

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomHasHeteroatomNbrsQuery() [2/2]

template<class T >

T * RDKit::makeAtomHasHeteroatomNbrsQuery

(

const std::string &

descr

)

returns a Query for matching atoms that have heteroatom neighbors

Definition at line 622 of file QueryOps.h.

References queryAtomHasHeteroatomNbrs(), and rdvalue_is().

makeAtomHasImplicitHQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHasImplicitHQuery

(

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomHasImplicitHQuery() [2/2]

template<class T >

T * RDKit::makeAtomHasImplicitHQuery

(

const std::string &

descr

)

returns a Query for matching ring atoms

Definition at line 437 of file QueryOps.h.

References queryAtomHasImplicitH(), and rdvalue_is().

makeAtomHasRingBondQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHasRingBondQuery

(

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomHasRingBondQuery() [2/2]

template<class T >

T * RDKit::makeAtomHasRingBondQuery

(

const std::string &

descr

)

returns a Query for matching atoms that have ring bonds

Definition at line 605 of file QueryOps.h.

References queryAtomHasRingBond(), and rdvalue_is().

makeAtomHCountQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHCountQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomHCountQuery() [2/2]

template<class T >

T * RDKit::makeAtomHCountQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching hydrogen count

Definition at line 429 of file QueryOps.h.

References queryAtomHCount(), and rdvalue_is().

makeAtomHeavyAtomDegreeQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHeavyAtomDegreeQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomHeavyAtomDegreeQuery() [2/2]

template<class T >

T * RDKit::makeAtomHeavyAtomDegreeQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching heavy atom degree

Definition at line 421 of file QueryOps.h.

References queryAtomHeavyAtomDegree(), and rdvalue_is().

makeAtomHybridizationQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHybridizationQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomHybridizationQuery() [2/2]

template<class T >

T * RDKit::makeAtomHybridizationQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching hybridization

Definition at line 504 of file QueryOps.h.

References queryAtomHybridization(), and rdvalue_is().

makeAtomImplicitHCountQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomImplicitHCountQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomImplicitHCountQuery() [2/2]

template<class T >

T * RDKit::makeAtomImplicitHCountQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching implicit hydrogen count

Definition at line 445 of file QueryOps.h.

References queryAtomImplicitHCount(), and rdvalue_is().

makeAtomImplicitValenceQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomImplicitValenceQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomImplicitValenceQuery() [2/2]

template<class T >

T * RDKit::makeAtomImplicitValenceQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching implicit valence

Definition at line 381 of file QueryOps.h.

References queryAtomImplicitValence(), and rdvalue_is().

makeAtomInNRingsQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomInNRingsQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomInNRingsQuery() [2/2]

template<class T >

T * RDKit::makeAtomInNRingsQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching atoms in a particular number of rings

Definition at line 555 of file QueryOps.h.

References queryIsAtomInNRings(), and rdvalue_is().

makeAtomInRingOfSizeQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomInRingOfSizeQuery

(

int

tgt

)

returns a Query for matching atoms in rings of a particular size

makeAtomInRingQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomInRingQuery

(

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomInRingQuery() [2/2]

template<class T >

T * RDKit::makeAtomInRingQuery

(

const std::string &

descr

)

returns a Query for matching ring atoms

Definition at line 547 of file QueryOps.h.

References queryIsAtomInRing(), and rdvalue_is().

makeAtomIsBridgeheadQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomIsBridgeheadQuery

(

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomIsBridgeheadQuery() [2/2]

template<class T >

T * RDKit::makeAtomIsBridgeheadQuery

(

const std::string &

descr

)

returns a Query for matching bridgehead atoms

Definition at line 658 of file QueryOps.h.

References queryIsAtomBridgehead(), and rdvalue_is().

makeAtomIsotopeQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomIsotopeQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomIsotopeQuery() [2/2]

template<class T >

T * RDKit::makeAtomIsotopeQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching atoms with a particular isotope

Definition at line 478 of file QueryOps.h.

References queryAtomIsotope(), and rdvalue_is().

Referenced by RDKit::QueryAtom::QueryAtom().

makeAtomMassQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomMassQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomMassQuery() [2/2]

template<class T >

T * RDKit::makeAtomMassQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching atoms with a particular mass

Definition at line 469 of file QueryOps.h.

References massIntegerConversionFactor, queryAtomMass(), and rdvalue_is().

makeAtomMinRingSizeQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomMinRingSizeQuery

(

int

tgt

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomMinRingSizeQuery() [2/2]

template<class T >

T * RDKit::makeAtomMinRingSizeQuery	(	int	tgt,
		const std::string &	descr )

returns a Query for matching an atom's minimum ring size

Definition at line 566 of file QueryOps.h.

References queryAtomMinRingSize(), and rdvalue_is().

makeAtomMissingChiralTagQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomMissingChiralTagQuery

(

)

\overloadquery

makeAtomMissingChiralTagQuery() [2/2]

template<class T >

T * RDKit::makeAtomMissingChiralTagQuery

(

const std::string &

descr

)

returns a Query for matching whether or not a potentially chiral atom is missing a chiral tag

Definition at line 531 of file QueryOps.h.

References queryAtomMissingChiralTag(), and rdvalue_is().

makeAtomNegativeFormalChargeQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNegativeFormalChargeQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomNegativeFormalChargeQuery() [2/2]

template<class T >

T * RDKit::makeAtomNegativeFormalChargeQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching negative formal charges (i.e. a query val of 1 matches a formal charge of -1)

Definition at line 495 of file QueryOps.h.

References queryAtomNegativeFormalCharge(), and rdvalue_is().

makeAtomNonHydrogenDegreeQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNonHydrogenDegreeQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomNonHydrogenDegreeQuery() [2/2]

template<class T >

T * RDKit::makeAtomNonHydrogenDegreeQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching the number of non-hydrogen neighbors

Definition at line 649 of file QueryOps.h.

References queryAtomNonHydrogenDegree(), and rdvalue_is().

makeAtomNullQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * RDKit::makeAtomNullQuery

(

)

returns a Query for matching any atom

makeAtomNumAliphaticHeteroatomNbrsQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNumAliphaticHeteroatomNbrsQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomNumAliphaticHeteroatomNbrsQuery() [2/2]

template<class T >

T * RDKit::makeAtomNumAliphaticHeteroatomNbrsQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching the number of aliphatic heteroatom neighbors

Definition at line 630 of file QueryOps.h.

References queryAtomNumAliphaticHeteroatomNbrs(), and rdvalue_is().

makeAtomNumHeteroatomNbrsQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNumHeteroatomNbrsQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomNumHeteroatomNbrsQuery() [2/2]

template<class T >

T * RDKit::makeAtomNumHeteroatomNbrsQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching the number of heteroatom neighbors

Definition at line 613 of file QueryOps.h.

References queryAtomNumHeteroatomNbrs(), and rdvalue_is().

makeAtomNumQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNumQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomNumQuery() [2/2]

template<class T >

T * RDKit::makeAtomNumQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching atomic number

Definition at line 363 of file QueryOps.h.

References queryAtomNum(), and rdvalue_is().

Referenced by RDKit::QueryAtom::QueryAtom(), and RDKit::QueryAtom::QueryAtom().

makeAtomNumRadicalElectronsQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNumRadicalElectronsQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomNumRadicalElectronsQuery() [2/2]

template<class T >

T * RDKit::makeAtomNumRadicalElectronsQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching the number of radical electrons

Definition at line 512 of file QueryOps.h.

References queryAtomNumRadicalElectrons(), and rdvalue_is().

Referenced by RDKit::QueryAtom::QueryAtom().

makeAtomRangeQuery()

static ATOM_RANGE_QUERY * RDKit::makeAtomRangeQuery ( int lower, int upper, bool lowerOpen, bool upperOpen, int funcAtom const *, const std::string & description = "Atom Range" )

inlinestatic

Definition at line 351 of file QueryOps.h.

References rdvalue_is().

makeAtomRingBondCountQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomRingBondCountQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomRingBondCountQuery() [2/2]

template<class T >

T * RDKit::makeAtomRingBondCountQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching atoms with a particular number of ring bonds

Definition at line 574 of file QueryOps.h.

References queryAtomRingBondCount(), and rdvalue_is().

makeAtomSimpleQuery()

template<class T >

T * RDKit::makeAtomSimpleQuery	(	int	what,
		int	funcAtom const *,
		const std::string &	description = "Atom Simple" )

Definition at line 342 of file QueryOps.h.

References rdvalue_is().

makeAtomTotalDegreeQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomTotalDegreeQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomTotalDegreeQuery() [2/2]

template<class T >

T * RDKit::makeAtomTotalDegreeQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching atomic degree

Definition at line 413 of file QueryOps.h.

References queryAtomTotalDegree(), and rdvalue_is().

makeAtomTotalValenceQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomTotalValenceQuery

(

int

what

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomTotalValenceQuery() [2/2]

template<class T >

T * RDKit::makeAtomTotalValenceQuery	(	int	what,
		const std::string &	descr )

returns a Query for matching total valence

Definition at line 397 of file QueryOps.h.

References queryAtomTotalValence(), and rdvalue_is().

makeAtomType()

static int RDKit::makeAtomType ( int atomic_num, bool aromatic )

inlinestatic

Definition at line 132 of file QueryOps.h.

References rdvalue_is().

Referenced by makeAtomTypeQuery(), and queryAtomType().

makeAtomTypeQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomTypeQuery	(	int	num,
		int	aromatic )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomTypeQuery() [2/2]

template<class T >

T * RDKit::makeAtomTypeQuery	(	int	num,
		int	aromatic,
		const std::string &	descr )

returns a Query for matching atomic number and aromaticity

Definition at line 371 of file QueryOps.h.

References makeAtomType(), queryAtomType(), and rdvalue_is().

makeAtomUnsaturatedQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomUnsaturatedQuery

(

)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

makeAtomUnsaturatedQuery() [2/2]

template<class T >

T * RDKit::makeAtomUnsaturatedQuery

(

const std::string &

descr

)

returns a Query for matching atoms with unsaturation:

Definition at line 539 of file QueryOps.h.

References queryAtomUnsaturated(), and rdvalue_is().

makeBondDirEqualsQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondDirEqualsQuery

(

Bond::BondDir

what

)

returns a Query for matching bond directions

makeBondHasStereoQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondHasStereoQuery

(

)

returns a Query for matching bonds with stereo set

makeBondInNRingsQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondInNRingsQuery

(

int

tgt

)

returns a Query for matching bonds in a particular number of rings

makeBondInRingOfSizeQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondInRingOfSizeQuery

(

int

what

)

returns a Query for matching bonds in rings of a particular size

makeBondIsInRingQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondIsInRingQuery

(

)

returns a Query for matching ring bonds

makeBondMinRingSizeQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondMinRingSizeQuery

(

int

what

)

returns a Query for matching a bond's minimum ring size

makeBondNullQuery()

RDKIT_GRAPHMOL_EXPORT BOND_NULL_QUERY * RDKit::makeBondNullQuery

(

)

returns a Query for matching any bond

makeBondOrderEqualsQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondOrderEqualsQuery

(

Bond::BondType

what

)

returns a Query for matching bond orders

Referenced by RDKit::QueryBond::QueryBond().

makeDoubleOrAromaticBondQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeDoubleOrAromaticBondQuery

(

)

returns a Query for double|aromatic bonds

MakeFilterCatalogEntry()

FilterCatalogEntry * RDKit::MakeFilterCatalogEntry	(	const FilterData_t &	,
		unsigned int	num_props = 0,
		const FilterProperty_t *	props = nullptr )

makeHasPropQuery()

template<class Target >

Queries::EqualityQuery< int, const Target *, true > * RDKit::makeHasPropQuery

(

const std::string &

property

)

returns a Query for matching atoms that have a particular property

Definition at line 857 of file QueryOps.h.

References rdvalue_is().

makeMAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeMAtomQuery

(

)

returns a Query for matching generic M atoms (metals)

makeMHAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeMHAtomQuery

(

)

returns a Query for matching generic MH atoms (metals or H)

makePropQuery() [1/2]

template<class Target >

Queries::EqualityQuery< int, const Target *, true > * RDKit::makePropQuery	(	const std::string &	propname,
		const ExplicitBitVect &	val,
		float	tolerance = 0.0 )

Definition at line 1073 of file QueryOps.h.

References rdvalue_is().

makePropQuery() [2/2]

template<class Target , class T >

Queries::EqualityQuery< int, const Target *, true > * RDKit::makePropQuery	(	const std::string &	propname,
		const T &	val,
		const T &	tolerance = T() )

Definition at line 1067 of file QueryOps.h.

References rdvalue_is().

makeQAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeQAtomQuery

(

)

returns a Query for matching generic Q atoms (heteroatoms)

makeQHAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeQHAtomQuery

(

)

returns a Query for matching generic QH atoms (heteroatom or H)

makeSingleOrAromaticBondQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrAromaticBondQuery

(

)

returns a Query for unspecified SMARTS bonds

makeSingleOrDoubleBondQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrDoubleBondQuery

(

)

returns a Query for single|double bonds

makeSingleOrDoubleOrAromaticBondQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrDoubleOrAromaticBondQuery

(

)

returns a Query for tautomeric bonds

makeXAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeXAtomQuery

(

)

returns a Query for matching generic X atoms (halogens)

makeXHAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeXHAtomQuery

(

)

returns a Query for matching generic XH atoms (halogen or H)

markUnspecifiedStereoAsUnknown()

RDKIT_FILEPARSERS_EXPORT void RDKit::markUnspecifiedStereoAsUnknown	(	ROMol &	mol,
		int	confId = -1 )

Set double bonds with unspecified stereo to STEREOANY and add wavy bonds to potential stereocenters with unspecified chirality

MCSAtomCompareAny()

RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareAny	(	const MCSAtomCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	atom1,
		const ROMol &	mol2,
		unsigned int	atom2,
		void *	userData )

MCSAtomCompareAnyHeavyAtom()

RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareAnyHeavyAtom	(	const MCSAtomCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	atom1,
		const ROMol &	mol2,
		unsigned int	atom2,
		void *	userData )

MCSAtomCompareElements()

RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareElements	(	const MCSAtomCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	atom1,
		const ROMol &	mol2,
		unsigned int	atom2,
		void *	userData )

MCSAtomCompareIsotopes()

RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareIsotopes	(	const MCSAtomCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	atom1,
		const ROMol &	mol2,
		unsigned int	atom2,
		void *	userData )

MCSBondCompareAny()

RDKIT_FMCS_EXPORT bool RDKit::MCSBondCompareAny	(	const MCSBondCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	bond1,
		const ROMol &	mol2,
		unsigned int	bond2,
		void *	userData )

MCSBondCompareOrder()

RDKIT_FMCS_EXPORT bool RDKit::MCSBondCompareOrder	(	const MCSBondCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	bond1,
		const ROMol &	mol2,
		unsigned int	bond2,
		void *	userData )

MCSBondCompareOrderExact()

RDKIT_FMCS_EXPORT bool RDKit::MCSBondCompareOrderExact	(	const MCSBondCompareParameters &	p,
		const ROMol &	mol1,
		unsigned int	bond1,
		const ROMol &	mol2,
		unsigned int	bond2,
		void *	userData )

MCSProgressCallbackTimeout()

RDKIT_FMCS_EXPORT bool RDKit::MCSProgressCallbackTimeout	(	const MCSProgressData &	stat,
		const MCSParameters &	params,
		void *	userData )

mergeNullQueries()

template<class T >

void RDKit::mergeNullQueries	(	T *&	returnQuery,
		bool	isQueryNull,
		T *&	otherQuery,
		bool	isOtherQNull,
		Queries::CompositeQueryType	how )

Definition at line 67 of file NullQueryAlgebra.h.

References Queries::COMPOSITE_AND, Queries::COMPOSITE_OR, Queries::COMPOSITE_XOR, PRECONDITION, and rdvalue_is().

MolBundleCanSerialize()

bool RDKit::MolBundleCanSerialize ( )

inline

Definition at line 46 of file MolBundle.h.

MolFragmentToCXSmarts()

RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToCXSmarts	(	const ROMol &	mol,
		const std::vector< int > &	atomsToUse,
		const std::vector< int > *	bondsToUse = nullptr,
		bool	doIsomericSmarts = true )

MolFragmentToCXSmiles() [1/2]

RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToCXSmiles	(	const ROMol &	mol,
		const SmilesWriteParams &	params,
		const std::vector< int > &	atomsToUse,
		const std::vector< int > *	bondsToUse = nullptr,
		const std::vector< std::string > *	atomSymbols = nullptr,
		const std::vector< std::string > *	bondSymbols = nullptr )

returns canonical CXSMILES for part of a molecule

Referenced by MolFragmentToCXSmiles().

MolFragmentToCXSmiles() [2/2]

std::string RDKit::MolFragmentToCXSmiles ( const ROMol & mol, const std::vector< int > & atomsToUse, const std::vector< int > * bondsToUse = nullptr, const std::vector< std::string > * atomSymbols = nullptr, const std::vector< std::string > * bondSymbols = nullptr, bool doIsomericSmiles = true, bool doKekule = false, int rootedAtAtom = -1, bool canonical = true, bool allBondsExplicit = false, bool allHsExplicit = false )

inline

returns canonical CXSMILES for part of a molecule

Parameters

mol	: the molecule in question.
atomsToUse	: indices of the atoms in the fragment
bondsToUse	: indices of the bonds in the fragment. If this is not provided, all bonds between the atoms in atomsToUse will be included
atomSymbols	: symbols to use for the atoms in the output SMILES
bondSymbols	: symbols to use for the bonds in the output SMILES
doIsomericSmiles	: include stereochemistry and isotope information in the SMILES
doKekule	: do Kekule smiles (i.e. don't use aromatic bonds)
rootedAtAtom	: make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical.
canonical	: if false, no attempt will be made to canonicalize the SMILES
allBondsExplicit	: if true, symbols will be included for all bonds.
allHsExplicit	: if true, hydrogen counts will be provided for every atom.

NOTE: the bondSymbols are not currently used in the canonicalization.

Definition at line 285 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::doIsomericSmiles, MolFragmentToCXSmiles(), and rdvalue_is().

MolFragmentToSmarts()

RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToSmarts	(	const ROMol &	mol,
		const std::vector< int > &	atomsToUse,
		const std::vector< int > *	bondsToUse = nullptr,
		bool	doIsomericSmarts = true )

MolFragmentToSmiles() [1/2]

RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToSmiles	(	const ROMol &	mol,
		const SmilesWriteParams &	params,
		const std::vector< int > &	atomsToUse,
		const std::vector< int > *	bondsToUse = nullptr,
		const std::vector< std::string > *	atomSymbols = nullptr,
		const std::vector< std::string > *	bondSymbols = nullptr )

returns canonical SMILES for part of a molecule

Referenced by MolFragmentToSmiles().

MolFragmentToSmiles() [2/2]

std::string RDKit::MolFragmentToSmiles ( const ROMol & mol, const std::vector< int > & atomsToUse, const std::vector< int > * bondsToUse = nullptr, const std::vector< std::string > * atomSymbols = nullptr, const std::vector< std::string > * bondSymbols = nullptr, bool doIsomericSmiles = true, bool doKekule = false, int rootedAtAtom = -1, bool canonical = true, bool allBondsExplicit = false, bool allHsExplicit = false )

inline

returns canonical SMILES for part of a molecule

Parameters

mol	: the molecule in question.
atomsToUse	: indices of the atoms in the fragment
bondsToUse	: indices of the bonds in the fragment. If this is not provided, all bonds between the atoms in atomsToUse will be included
atomSymbols	: symbols to use for the atoms in the output SMILES
bondSymbols	: symbols to use for the bonds in the output SMILES
doIsomericSmiles	: include stereochemistry and isotope information in the SMILES
doKekule	: do Kekule smiles (i.e. don't use aromatic bonds)
rootedAtAtom	: make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical.
canonical	: if false, no attempt will be made to canonicalize the SMILES
allBondsExplicit	: if true, symbols will be included for all bonds.
allHsExplicit	: if true, hydrogen counts will be provided for every atom.
doRandom	: generate a randomized smiles string by randomly choosing the priority to follow in the DFS traversal. [default false]

NOTE: the bondSymbols are not currently used in the canonicalization.

Definition at line 191 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::doIsomericSmiles, MolFragmentToSmiles(), and rdvalue_is().

MolToCMLBlock()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToCMLBlock	(	const ROMol &	mol,
		int	confId = -1,
		bool	kekulize = true )

MolToCMLFile()

RDKIT_FILEPARSERS_EXPORT void RDKit::MolToCMLFile	(	const ROMol &	mol,
		const std::string &	fName,
		int	confId = -1,
		bool	kekulize = true )

MolToCXSmarts()

RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToCXSmarts	(	const ROMol &	mol,
		bool	doIsomericSmarts = true )

returns the CXSMARTS for a molecule

MolToCXSmiles() [1/2]

std::string RDKit::MolToCXSmiles ( const ROMol & mol, bool doIsomericSmiles = true, bool doKekule = false, int rootedAtAtom = -1, bool canonical = true, bool allBondsExplicit = false, bool allHsExplicit = false, bool doRandom = false )

inline

returns canonical CXSMILES for a molecule

Parameters

mol	: the molecule in question.
doIsomericSmiles	: include stereochemistry and isotope information in the SMILES
doKekule	: do Kekule smiles (i.e. don't use aromatic bonds)
rootedAtAtom	: make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical.
canonical	: if false, no attempt will be made to canonicalize the SMILES
allBondsExplicit	: if true, symbols will be included for all bonds.
allHsExplicit	: if true, hydrogen counts will be provided for every
doRandom	: generate a randomized smiles string by randomly choosing the priority to follow in the DFS traversal. [default false] atom.

Definition at line 237 of file SmilesWrite.h.

References RDKit::SmilesWrite::CX_ALL, RDKit::SmilesWriteParams::doIsomericSmiles, MolToCXSmiles(), and rdvalue_is().

MolToCXSmiles() [2/2]

RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToCXSmiles	(	const ROMol &	mol,
		const SmilesWriteParams &	ps,
		std::uint32_t	flags = SmilesWrite::CXSmilesFields::CX_ALL,
		RestoreBondDirOption	restoreBondDirs = RestoreBondDirOptionClear )

returns canonical CXSMILES for a molecule

Referenced by MolToCXSmiles().

MolToFASTA()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToFASTA

(

const ROMol &

mol

)

Parameters

mol	- the molecule to work with

Note

mol should contain monomer information in AtomMonomerInfo structures

MolToHELM()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToHELM

(

const ROMol &

mol

)

Parameters

mol	- the molecule to work with

Note

mol should contain monomer information in AtomMonomerInfo structures

MolToMolBlock() [1/2]

std::string RDKit::MolToMolBlock ( const ROMol & mol, bool includeStereo = true, int confId = -1, bool kekulize = true, bool forceV3000 = false )

inline

Parameters

mol	- the molecule in question
includeStereo	- toggles inclusion of stereochemistry information (default=true)
confId	- selects the conformer to be used (default=-1 - find first in mol)
kekulize	- triggers kekulization of the molecule before it is written (default=true)
forceV3000	- force generation a V3000 mol block (happens automatically with more than 999 atoms or bonds)(default=false)

Definition at line 57 of file FileWriters.h.

References MolToMolBlock().

MolToMolBlock() [2/2]

RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToMolBlock	(	const ROMol &	mol,
		const MolWriterParams &	params,
		int	confId = -1 )

Parameters

mol	- the molecule in question
MolWriterParams	- parmeter struct with write options
confId	- selects the conformer to be used (default=-1 - find first in mol)

Referenced by MolToMolBlock(), MolToV3KMolBlock(), and MolToV3KMolBlock().

MolToMolFile() [1/2]

void RDKit::MolToMolFile ( const ROMol & mol, const std::string & fName, bool includeStereo = true, int confId = -1, bool kekulize = true, bool forceV3000 = false )

inline

Parameters

mol	- the molecule in question
fName	- the name of the file to use
includeStereo	- toggles inclusion of stereochemistry information
confId	- selects the conformer to be used
kekulize	- triggers kekulization of the molecule before it is written
forceV3000	- force generation a V3000 mol block (happens automatically with more than 999 atoms or bonds)

Definition at line 121 of file FileWriters.h.

References MolToMolFile(), and rdvalue_is().

MolToMolFile() [2/2]

RDKIT_FILEPARSERS_EXPORT void RDKit::MolToMolFile	(	const ROMol &	mol,
		const std::string &	fName,
		const MolWriterParams &	params,
		int	confId = -1 )

Parameters

mol	- the molecule in question
fName	- the name of the file to use
MolWriterParams	- parameter struct with write options
confId	- selects the conformer to be used

Referenced by MolToMolFile(), MolToV3KMolFile(), and MolToV3KMolFile().

MolToMrvBlock() [1/2]

std::string RDKit::MolToMrvBlock ( const ROMol & mol, bool includeStereo = true, int confId = -1, bool kekulize = true, bool prettyPrint = false )

inline

Parameters

mol	- the molecule
includeStereo	- toggles inclusion of stereochemical information in the output
confId	- selects which conformation to output
kekulize	- triggers kekulization of the molecule before it's written
prettyPrint	- makes the output more human readable

Definition at line 185 of file MarvinParser.h.

References MolToMrvBlock().

MolToMrvBlock() [2/2]

RDKIT_MARVINPARSER_EXPORT std::string RDKit::MolToMrvBlock	(	const ROMol &	mol,
		const MrvWriterParams &	params,
		int	confId = -1 )

Parameters

mol	- the molecule
params	- marvin write params
confId	- selects which conformation to output

Referenced by MolToMrvBlock().

MolToMrvFile() [1/2]

void RDKit::MolToMrvFile ( const ROMol & mol, const std::string & fName, bool includeStereo = true, int confId = -1, bool kekulize = true, bool prettyPrint = false )

inline

Parameters

mol	- the molecule
fName	- the file to write to
includeStereo	- toggles inclusion of stereochemical information in the output
confId	- selects which conformation to output
kekulize	- triggers kekulization of the molecule before it's written
prettyPrint	- makes the output more human readable

Definition at line 160 of file MarvinParser.h.

References MolToMrvFile(), and rdvalue_is().

MolToMrvFile() [2/2]

RDKIT_MARVINPARSER_EXPORT void RDKit::MolToMrvFile	(	const ROMol &	mol,
		const std::string &	fName,
		const MrvWriterParams &	params,
		int	confId = -1 )

Parameters

mol	- the molecule
fName	- the file to write to
params	- marvin write params
confId	- selects which conformation to output

Referenced by MolToMrvFile().

MolToPDBBlock()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToPDBBlock	(	const ROMol &	mol,
		int	confId = -1,
		unsigned int	flavor = 0 )

Parameters

mol	- the molecule in question
confId	- selects the conformer to be used
flavor	- controls what gets written: flavor & 1 : Write MODEL/ENDMDL lines around each record flavor & 2 : Don't write single CONECT records flavor & 4 : Write CONECT records in both directions flavor & 8 : Don't use multiple CONECTs to encode bond order flavor & 16 : Write MASTER record flavor & 32 : Write TER record

MolToPDBFile()

RDKIT_FILEPARSERS_EXPORT void RDKit::MolToPDBFile	(	const ROMol &	mol,
		const std::string &	fname,
		int	confId = -1,
		unsigned int	flavor = 0 )

Parameters

mol	- the molecule in question
fName	- the name of the file to use
confId	- selects the conformer to be used
flavor	- controls what gets written: flavor & 1 : Write MODEL/ENDMDL lines around each record flavor & 2 : Don't write single CONECT records flavor & 4 : Write CONECT records in both directions flavor & 8 : Don't use multiple CONECTs to encode bond order flavor & 16 : Write MASTER record flavor & 32 : Write TER record

MolToRandomSmilesVect()

RDKIT_SMILESPARSE_EXPORT std::vector< std::string > RDKit::MolToRandomSmilesVect	(	const ROMol &	mol,
		unsigned int	numSmiles,
		unsigned int	randomSeed = 0,
		bool	doIsomericSmiles = true,
		bool	doKekule = false,
		bool	allBondsExplicit = false,
		bool	allHsExplicit = false )

returns a vector of random SMILES for a molecule (may contain duplicates)

Parameters

mol	: the molecule in question.
numSmiles	: the number of SMILES to return
randomSeed	: if >0, will be used to seed the random number generator
doIsomericSmiles	: include stereochemistry and isotope information in the SMILES
doKekule	: do Kekule smiles (i.e. don't use aromatic bonds)
allBondsExplicit	: if true, symbols will be included for all bonds.
allHsExplicit	: if true, hydrogen counts will be provided for every atom.

MolToSequence()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToSequence

(

const ROMol &

mol

)

Parameters

mol	- the molecule to work with

Note

mol should contain monomer information in AtomMonomerInfo structures

MolToSmarts()

RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToSmarts	(	const ROMol &	mol,
		bool	doIsomericSmarts = true,
		int	rootedAtAtom = -1 )

returns the SMARTS for a molecule

MolToSmiles() [1/2]

std::string RDKit::MolToSmiles ( const ROMol & mol, bool doIsomericSmiles = true, bool doKekule = false, int rootedAtAtom = -1, bool canonical = true, bool allBondsExplicit = false, bool allHsExplicit = false, bool doRandom = false )

inline

returns canonical SMILES for a molecule

Parameters

mol	: the molecule in question.
doIsomericSmiles	: include stereochemistry and isotope information in the SMILES
doKekule	: do Kekule smiles (i.e. don't use aromatic bonds) NOTE that this will throw an exception if the molecule cannot be kekulized.
rootedAtAtom	: make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical.
canonical	: if false, no attempt will be made to canonicalize the SMILES
allBondsExplicit	: if true, symbols will be included for all bonds.
allHsExplicit	: if true, hydrogen counts will be provided for every atom.

Definition at line 123 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::doIsomericSmiles, MolToSmiles(), and rdvalue_is().

MolToSmiles() [2/2]

RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToSmiles	(	const ROMol &	mol,
		const SmilesWriteParams &	params )

returns canonical SMILES for a molecule

Referenced by MolToSmiles().

MolToTPLFile()

RDKIT_FILEPARSERS_EXPORT void RDKit::MolToTPLFile	(	const ROMol &	mol,
		const std::string &	fName,
		const std::string &	partialChargeProp = "_GasteigerCharge",
		bool	writeFirstConfTwice = false )

MolToTPLText()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToTPLText	(	const ROMol &	mol,
		const std::string &	partialChargeProp = "_GasteigerCharge",
		bool	writeFirstConfTwice = false )

MolToV3KMolBlock() [1/2]

std::string RDKit::MolToV3KMolBlock ( const ROMol & mol, bool includeStereo = true, int confId = -1, bool kekulize = true )

inline

Parameters

mol	- the molecule in question
includeStereo	- toggles inclusion of stereochemistry information
confId	- selects the conformer to be used (default=-1 - find first in mol)
kekulize	- triggers kekulization of the molecule before it is written

Definition at line 91 of file FileWriters.h.

References MolToMolBlock().

MolToV3KMolBlock() [2/2]

std::string RDKit::MolToV3KMolBlock ( const ROMol & mol, const MolWriterParams & params, int confId = -1 )

inline

Parameters

mol	- the molecule in question
MolWriterParams	- parameter struct with write options
confId	- selects the conformer to be used (default=-1 - find first in mol)

Definition at line 73 of file FileWriters.h.

References RDKit::MolWriterParams::forceV3000, MolToMolBlock(), and rdvalue_is().

MolToV3KMolFile() [1/2]

void RDKit::MolToV3KMolFile ( const ROMol & mol, const std::string & fName, bool includeStereo = true, int confId = -1, bool kekulize = true )

inline

Parameters

mol	- the molecule in question
fName	- the name of the file to use
includeStereo	- toggles inclusion of stereochemistry information
confId	- selects the conformer to be used
kekulize	- triggers kekulization of the molecule before it is written

Definition at line 154 of file FileWriters.h.

References MolToMolFile(), and rdvalue_is().

MolToV3KMolFile() [2/2]

void RDKit::MolToV3KMolFile ( const ROMol & mol, const std::string & fName, const MolWriterParams & params, int confId = -1 )

inline

Parameters

mol	- the molecule in question
fName	- the name of the file to use
MolWriterParams	- parameter struct with write options
confId	- selects the conformer to be used

Definition at line 135 of file FileWriters.h.

References RDKit::MolWriterParams::forceV3000, MolToMolFile(), and rdvalue_is().

MolToXYZBlock()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToXYZBlock	(	const ROMol &	mol,
		int	confId = -1,
		unsigned int	precision = 6 )

Parameters

mol	- the molecule in question
confId	- selects which conformation to output
precision	- precision of the coordinates

MolToXYZFile()

RDKIT_FILEPARSERS_EXPORT void RDKit::MolToXYZFile	(	const ROMol &	mol,
		const std::string &	fName,
		int	confId = -1,
		unsigned int	precision = 6 )

Parameters

mol	- the molecule in question
fName	- the file to write to
confId	- selects which conformation to output
precision	- precision of the coordinates

molzip() [1/4]

RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > RDKit::molzip	(	const ROMol &	a,
		const MolzipParams &	params = MolzipParams() )

molzip() [2/4]

RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > RDKit::molzip	(	const ROMol &	a,
		const ROMol &	b,
		const MolzipParams &	params = MolzipParams() )

molzip() [3/4]

RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > RDKit::molzip	(	const std::map< std::string, ROMOL_SPTR > &	row,
		const MolzipParams &	params = MolzipParams() )

Molzip an RGroupRow back into the original molecule if possible.

This correctly handles broken cycles that can happend during arbitrary RGroup Decomposition.

Parameters

row	- rgroup row as returned by the rgroup decompisition

optional:

Parameters

params

- molzip parameters

Returns

- the zipped molecule

molzip() [4/4]

RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > RDKit::molzip	(	std::vector< ROMOL_SPTR > &	decomposition,
		const MolzipParams &	params = MolzipParams() )

Creates a molecule from an R group decomposition.

Parameters

decomposition

- A list of molecules that comprises an R group decomposition. The core must be the first molecule in the list. If generateCoordinates is set in the parameters then aligned depiction coordinates will be set on the returned molecule and the input decomposition

optional:

Parameters

params

- molzip parameters

Returns

the zipped molecule

MurckoDecompose()

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::MurckoDecompose

(

const ROMol &

mol

)

Carries out a Murcko decomposition on the molecule provided.

Parameters

mol	- the ROMol of interest

Returns

a new ROMol with the Murcko scaffold The client is responsible for deleting this molecule.

nextCombination()

RDKIT_RDGENERAL_EXPORT int RDKit::nextCombination	(	INT_VECT &	comb,
		int	tot )

given a current combination of numbers change it to the next possible

Parameters

comb	the sorted vector to consider
tot	the maximum number possible in the vector

Returns

-1 on failure, the index of the last number changed on success. Example: for all combinations 3 of numbers between 0 and tot=5 given (0,1,2) the function wil return (0,1,3) etc.

nullDataFun()

template<typename T >

int RDKit::nullDataFun

(

T

)

Definition at line 807 of file QueryOps.h.

nullQueryFun()

template<typename T >

bool RDKit::nullQueryFun

(

T

)

Definition at line 811 of file QueryOps.h.

operator""_ctab()

std::unique_ptr< RDKit::RWMol > RDKit::operator""_ctab ( const char * text, size_t len )

inline

Definition at line 447 of file FileParsers.h.

References RDKit::v2::FileParsers::MolFromMolBlock(), and rdvalue_is().

operator""_mol2()

std::unique_ptr< RDKit::RWMol > RDKit::operator""_mol2 ( const char * text, size_t len )

inline

Definition at line 456 of file FileParsers.h.

References RDKit::v2::FileParsers::MolFromMol2Block(), and rdvalue_is().

operator""_pdb()

std::unique_ptr< RDKit::RWMol > RDKit::operator""_pdb ( const char * text, size_t len )

inline

Definition at line 466 of file FileParsers.h.

References RDKit::v2::FileParsers::MolFromPDBBlock(), and rdvalue_is().

operator""_rxnsmarts()

std::unique_ptr< ChemicalReaction > RDKit::operator""_rxnsmarts ( const char * text, size_t len )

inline

Definition at line 356 of file ReactionParser.h.

operator""_rxnsmiles()

std::unique_ptr< ChemicalReaction > RDKit::operator""_rxnsmiles ( const char * text, size_t len )

inline

Definition at line 367 of file ReactionParser.h.

operator""_smarts()

std::unique_ptr< RDKit::RWMol > RDKit::operator""_smarts ( const char * text, size_t len )

inline

Definition at line 246 of file SmilesParse.h.

operator""_smiles()

std::unique_ptr< RDKit::RWMol > RDKit::operator""_smiles ( const char * text, size_t len )

inline

Definition at line 237 of file SmilesParse.h.

operator+()

RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect RDKit::operator+	(	const DiscreteValueVect &	p1,
		const DiscreteValueVect &	p2 )

operator-()

RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect RDKit::operator-	(	const DiscreteValueVect &	p1,
		const DiscreteValueVect &	p2 )

parseAtomType()

static void RDKit::parseAtomType ( int val, int & atomic_num, bool & aromatic )

inlinestatic

Definition at line 135 of file QueryOps.h.

References rdvalue_is().

parseFeatureData() [1/2]

RDKIT_MOLCHEMICALFEATURES_EXPORT int RDKit::parseFeatureData	(	const std::string &	defnText,
		MolChemicalFeatureDef::CollectionType &	featDefs )

parseFeatureData() [2/2]

RDKIT_MOLCHEMICALFEATURES_EXPORT int RDKit::parseFeatureData	(	std::istream &	istream,
		MolChemicalFeatureDef::CollectionType &	featDefs )

parseFeatureFile()

RDKIT_MOLCHEMICALFEATURES_EXPORT int RDKit::parseFeatureFile	(	const std::string &	fileName,
		MolChemicalFeatureDef::CollectionType &	featDefs )

parseMCSParametersJSON()

RDKIT_FMCS_EXPORT void RDKit::parseMCSParametersJSON	(	const char *	json,
		MCSParameters *	params )

parseQueryDefFile() [1/2]

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::parseQueryDefFile	(	const std::string &	filename,
		std::map< std::string, ROMOL_SPTR > &	queryDefs,
		bool	standardize = true,
		const std::string &	delimiter = "\t",
		const std::string &	comment = "//",
		unsigned int	nameColumn = 0,
		unsigned int	smartsColumn = 1 )

parses a query definition file and sets up a set of definitions suitable for use by addRecursiveQueries()

Parameters

filename	- the name of the file to be read
queryDefs	- the dictionary of named queries (return value)
standardize	- if true, query names will be converted to lower case
delimiter	- the line delimiter in the file
comment	- text used to recognize comment lines
nameColumn	- column with the names of queries
smartsColumn	- column with the SMARTS definitions of the queries

parseQueryDefFile() [2/2]

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::parseQueryDefFile	(	std::istream *	inStream,
		std::map< std::string, ROMOL_SPTR > &	queryDefs,
		bool	standardize = true,
		const std::string &	delimiter = "\t",
		const std::string &	comment = "//",
		unsigned int	nameColumn = 0,
		unsigned int	smartsColumn = 1 )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

parseQueryDefText()

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::parseQueryDefText	(	const std::string &	queryDefText,
		std::map< std::string, ROMOL_SPTR > &	queryDefs,
		bool	standardize = true,
		const std::string &	delimiter = "\t",
		const std::string &	comment = "//",
		unsigned int	nameColumn = 0,
		unsigned int	smartsColumn = 1 )

equivalent to parseQueryDefFile() but the query definitions are explicitly passed in

PatternFingerprintMol() [1/2]

RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::PatternFingerprintMol	(	const MolBundle &	bundle,
		unsigned int	fpSize = 2048,
		ExplicitBitVect *	setOnlyBits = nullptr,
		bool	tautomericFingerprint = false )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

PatternFingerprintMol() [2/2]

RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::PatternFingerprintMol	(	const ROMol &	mol,
		unsigned int	fpSize = 2048,
		std::vector< unsigned int > *	atomCounts = nullptr,
		ExplicitBitVect *	setOnlyBits = nullptr,
		bool	tautomericFingerprint = false )

Generates a topological fingerprint for a molecule using a series of pre-defined structural patterns.

Experimental: This function is experimental. The API or results may change from release to release.

Parameters

mol	the molecule to be fingerprinted
fpSize	the size of the fingerprint
atomCounts	if provided, this will be used to provide the count of the number of paths that set bits each atom is involved in. The vector should have at least as many entries as the molecule has atoms and is not zeroed out here.
setOnlyBits	if provided, only bits that are set in this bit vector will be set in the result. This is essentially the same as doing: (*res) &= (*setOnlyBits); but also has an impact on the atomCounts (if being used)

Returns

the molecular fingerprint, as an ExplicitBitVect

Notes:

• the caller is responsible for deleteing the result

Referenced by RDKit::PatternHolder::makeFingerprint(), and RDKit::TautomerPatternHolder::makeFingerprint().

PNGFileToMetadata()

std::vector< std::pair< std::string, std::string > > RDKit::PNGFileToMetadata ( const std::string & fname )

inline

returns the metadata (tEXt and zTXt chunks) from PNG data

Definition at line 43 of file PNGParser.h.

References PNGStreamToMetadata(), and rdvalue_is().

PNGFileToMol()

ROMol * RDKit::PNGFileToMol ( const std::string & fname, const SmilesParserParams & params = SmilesParserParams() )

inline

constructs an ROMol from the metadata in a PNG file. See PNGStreamToMol() for more details.

Definition at line 112 of file PNGParser.h.

References PNGStreamToMol(), and rdvalue_is().

PNGFileToMols()

std::vector< std::unique_ptr< ROMol > > RDKit::PNGFileToMols ( const std::string & fname, const std::string & tagToUse = PNGData::pklTag, const SmilesParserParams & params = SmilesParserParams() )

inline

constructs a vector of ROMol from the metadata in a PNG file. See PNGStreamToMols() for more details.

Definition at line 143 of file PNGParser.h.

References PNGStreamToMols(), and rdvalue_is().

PNGStreamToMetadata()

RDKIT_FILEPARSERS_EXPORT std::vector< std::pair< std::string, std::string > > RDKit::PNGStreamToMetadata

(

std::istream &

inStream

)

returns the metadata (tEXt and zTXt chunks) from PNG data

Referenced by PNGFileToMetadata(), and PNGStringToMetadata().

PNGStreamToMol()

RDKIT_FILEPARSERS_EXPORT ROMol * RDKit::PNGStreamToMol	(	std::istream &	inStream,
		const SmilesParserParams &	params = SmilesParserParams() )

constructs an ROMol from the metadata in a PNG stream

Looks through the metadata in the PNG to find the first tag that matches one of the tags in RDKit::PNGData. A molecule is constructed from this chunk.

Throws a FileParseException if no suitable tag is found.

The caller is responsible for the returned pointer.

Referenced by PNGFileToMol(), and PNGStringToMol().

PNGStreamToMols()

RDKIT_FILEPARSERS_EXPORT std::vector< std::unique_ptr< ROMol > > RDKit::PNGStreamToMols	(	std::istream &	inStream,
		const std::string &	tagToUse = PNGData::pklTag,
		const SmilesParserParams &	params = SmilesParserParams() )

constructs a vector of ROMol from the metadata in a PNG stream

Looks through the metadata in the PNG to find tags that start with tagToUse (must be one of the tags in RDKit::PNGData). The molecules constructed from these data are returned.

Referenced by PNGFileToMols(), and PNGStringToMols().

PNGStringToMetadata()

std::vector< std::pair< std::string, std::string > > RDKit::PNGStringToMetadata ( const std::string & data )

inline

returns the metadata (tEXt and zTXt chunks) from PNG data

Definition at line 53 of file PNGParser.h.

References PNGStreamToMetadata(), and rdvalue_is().

PNGStringToMol()

ROMol * RDKit::PNGStringToMol ( const std::string & data, const SmilesParserParams & params = SmilesParserParams() )

inline

constructs an ROMol from the metadata in a PNG string. See PNGStreamToMol() for more details.

Definition at line 123 of file PNGParser.h.

References PNGStreamToMol(), and rdvalue_is().

PNGStringToMols()

std::vector< std::unique_ptr< ROMol > > RDKit::PNGStringToMols ( const std::string & data, const std::string & tagToUse = PNGData::pklTag, const SmilesParserParams & params = SmilesParserParams() )

inline

constructs a vector of ROMol from the metadata in a PNG string. See PNGStreamToMols() for more details.

Definition at line 154 of file PNGParser.h.

References PNGStreamToMols(), and rdvalue_is().

prepareMol()

RDKIT_FRAGCATALOG_EXPORT ROMol * RDKit::prepareMol	(	const ROMol &	mol,
		const FragCatParams *	fparams,
		MatchVectType &	aToFmap )

preprocessReaction() [1/4]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction	(	ChemicalReaction &	rxn,
		const std::map< std::string, ROMOL_SPTR > &	queries,
		const std::string &	propName = common_properties::molFileValue )

preprocessReaction() [2/4]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction	(	ChemicalReaction &	rxn,
		const std::string &	propName = common_properties::molFileValue )

preprocessReaction() [3/4]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction	(	ChemicalReaction &	rxn,
		unsigned int &	numWarnings,
		unsigned int &	numErrors,
		std::vector< std::vector< std::pair< unsigned int, std::string > > > &	reactantLabels,
		const std::map< std::string, ROMOL_SPTR > &	queries,
		const std::string &	propName = common_properties::molFileValue )

preprocessReaction() [4/4]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction	(	ChemicalReaction &	rxn,
		unsigned int &	numWarnings,
		unsigned int &	numErrors,
		std::vector< std::vector< std::pair< unsigned int, std::string > > > &	reactantLabels,
		const std::string &	propName = common_properties::molFileValue )

propertyCompat()

RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::propertyCompat	(	const RDProps *	r1,
		const RDProps *	r2,
		const std::vector< std::string > &	properties )

pullPackedIntFromString()

boost::uint32_t RDKit::pullPackedIntFromString ( const char *& text )

inline

Reads an integer from a char * in packed format and returns the result. The argument is advanced

Definition at line 216 of file StreamOps.h.

References rdvalue_is().

queryAtomAliphatic()

static int RDKit::queryAtomAliphatic ( Atom const * at )

inlinestatic

Definition at line 75 of file QueryOps.h.

References RDKit::Atom::getIsAromatic().

Referenced by makeAtomAliphaticQuery().

queryAtomAllBondProduct()

RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomAllBondProduct

(

Atom const *

at

)

queryAtomAromatic()

static int RDKit::queryAtomAromatic ( Atom const * at )

inlinestatic

Definition at line 72 of file QueryOps.h.

References RDKit::Atom::getIsAromatic().

Referenced by makeAtomAromaticQuery().

queryAtomBondProduct()

RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomBondProduct

(

Atom const *

at

)

queryAtomExplicitDegree()

static int RDKit::queryAtomExplicitDegree ( Atom const * at )

inlinestatic

Definition at line 78 of file QueryOps.h.

References RDKit::Atom::getDegree().

Referenced by makeAtomExplicitDegreeQuery().

queryAtomExplicitValence()

static int RDKit::queryAtomExplicitValence ( Atom const * at )

inlinestatic

Definition at line 122 of file QueryOps.h.

References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getNumExplicitHs().

Referenced by makeAtomExplicitValenceQuery().

queryAtomFormalCharge()

static int RDKit::queryAtomFormalCharge ( Atom const * at )

inlinestatic

Definition at line 163 of file QueryOps.h.

References RDKit::Atom::getFormalCharge().

Referenced by makeAtomFormalChargeQuery().

queryAtomHasAliphaticHeteroatomNbrs()

static int RDKit::queryAtomHasAliphaticHeteroatomNbrs ( Atom const * at )

inlinestatic

Definition at line 210 of file QueryOps.h.

References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().

Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().

queryAtomHasChiralTag()

static int RDKit::queryAtomHasChiralTag ( Atom const * at )

inlinestatic

Definition at line 175 of file QueryOps.h.

References RDKit::Atom::CHI_UNSPECIFIED, and RDKit::Atom::getChiralTag().

Referenced by makeAtomHasChiralTagQuery().

queryAtomHasHeteroatomNbrs()

static int RDKit::queryAtomHasHeteroatomNbrs ( Atom const * at )

inlinestatic

Definition at line 183 of file QueryOps.h.

References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().

Referenced by makeAtomHasHeteroatomNbrsQuery().

queryAtomHasImplicitH()

static int RDKit::queryAtomHasImplicitH ( Atom const * at )

inlinestatic

Definition at line 116 of file QueryOps.h.

References RDKit::Atom::getTotalNumHs(), and rdvalue_is().

Referenced by makeAtomHasImplicitHQuery().

queryAtomHasRingBond()

static int RDKit::queryAtomHasRingBond ( Atom const * at )

inlinestatic

Definition at line 284 of file QueryOps.h.

References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), and RDKit::RingInfo::numBondRings().

Referenced by makeAtomHasRingBondQuery().

queryAtomHCount()

static int RDKit::queryAtomHCount ( Atom const * at )

inlinestatic

Definition at line 110 of file QueryOps.h.

References RDKit::Atom::getTotalNumHs().

Referenced by makeAtomHCountQuery().

queryAtomHeavyAtomDegree()

static int RDKit::queryAtomHeavyAtomDegree ( Atom const * at )

inlinestatic

D and T are not treated as heavy atoms here.

Definition at line 98 of file QueryOps.h.

References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().

Referenced by makeAtomHeavyAtomDegreeQuery().

queryAtomHybridization()

static int RDKit::queryAtomHybridization ( Atom const * at )

inlinestatic

Definition at line 169 of file QueryOps.h.

References RDKit::Atom::getHybridization().

Referenced by makeAtomHybridizationQuery().

queryAtomImplicitHCount()

static int RDKit::queryAtomImplicitHCount ( Atom const * at )

inlinestatic

Definition at line 113 of file QueryOps.h.

References RDKit::Atom::getTotalNumHs().

Referenced by makeAtomImplicitHCountQuery().

queryAtomImplicitValence()

static int RDKit::queryAtomImplicitValence ( Atom const * at )

inlinestatic

Definition at line 119 of file QueryOps.h.

References RDKit::Atom::getImplicitValence().

Referenced by makeAtomImplicitValenceQuery().

queryAtomIsInRingOfSize()

template<int tgt>

int RDKit::queryAtomIsInRingOfSize

(

Atom const *

at

)

Definition at line 324 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::RingInfo::isAtomInRingOfSize(), and rdvalue_is().

queryAtomIsotope()

static int RDKit::queryAtomIsotope ( Atom const * at )

inlinestatic

Definition at line 160 of file QueryOps.h.

References RDKit::Atom::getIsotope().

Referenced by makeAtomIsotopeQuery().

queryAtomMass()

static int RDKit::queryAtomMass ( Atom const * at )

inlinestatic

Definition at line 156 of file QueryOps.h.

References RDKit::Atom::getMass(), and massIntegerConversionFactor.

Referenced by makeAtomMassQuery().

queryAtomMinRingSize()

static int RDKit::queryAtomMinRingSize ( Atom const * at )

inlinestatic

Definition at line 301 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minAtomRingSize().

Referenced by makeAtomMinRingSizeQuery().

queryAtomMissingChiralTag()

static int RDKit::queryAtomMissingChiralTag ( Atom const * at )

inlinestatic

Definition at line 178 of file QueryOps.h.

References RDKit::common_properties::_ChiralityPossible, RDKit::Atom::CHI_UNSPECIFIED, RDKit::Atom::getChiralTag(), and RDKit::RDProps::hasProp().

Referenced by makeAtomMissingChiralTagQuery().

queryAtomNegativeFormalCharge()

static int RDKit::queryAtomNegativeFormalCharge ( Atom const * at )

inlinestatic

Definition at line 166 of file QueryOps.h.

References RDKit::Atom::getFormalCharge().

Referenced by makeAtomNegativeFormalChargeQuery().

queryAtomNonHydrogenDegree()

static int RDKit::queryAtomNonHydrogenDegree ( Atom const * at )

inlinestatic

D and T are treated as "non-hydrogen" here.

Definition at line 85 of file QueryOps.h.

References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().

Referenced by makeAtomNonHydrogenDegreeQuery().

queryAtomNum()

static int RDKit::queryAtomNum ( Atom const * at )

inlinestatic

Definition at line 131 of file QueryOps.h.

References RDKit::Atom::getAtomicNum().

Referenced by makeAtomNumQuery().

queryAtomNumAliphaticHeteroatomNbrs()

static int RDKit::queryAtomNumAliphaticHeteroatomNbrs ( Atom const * at )

inlinestatic

Definition at line 224 of file QueryOps.h.

References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().

Referenced by makeAtomNumAliphaticHeteroatomNbrsQuery().

queryAtomNumHeteroatomNbrs()

static int RDKit::queryAtomNumHeteroatomNbrs ( Atom const * at )

inlinestatic

Definition at line 196 of file QueryOps.h.

References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().

Referenced by makeAtomNumHeteroatomNbrsQuery().

queryAtomNumRadicalElectrons()

static int RDKit::queryAtomNumRadicalElectrons ( Atom const * at )

inlinestatic

Definition at line 172 of file QueryOps.h.

References RDKit::Atom::getNumRadicalElectrons().

Referenced by makeAtomNumRadicalElectronsQuery().

queryAtomRingBondCount()

static int RDKit::queryAtomRingBondCount ( Atom const * at )

inlinestatic

Definition at line 308 of file QueryOps.h.

References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), RDKit::RingInfo::numBondRings(), and rdvalue_is().

Referenced by makeAtomRingBondCountQuery().

queryAtomRingMembership()

static int RDKit::queryAtomRingMembership ( Atom const * at )

inlinestatic

Definition at line 696 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().

Referenced by RDKit::AtomRingQuery::AtomRingQuery(), and RDKit::AtomRingQuery::AtomRingQuery().

queryAtomTotalDegree()

static int RDKit::queryAtomTotalDegree ( Atom const * at )

inlinestatic

Definition at line 81 of file QueryOps.h.

References RDKit::Atom::getTotalDegree().

Referenced by makeAtomTotalDegreeQuery().

queryAtomTotalValence()

static int RDKit::queryAtomTotalValence ( Atom const * at )

inlinestatic

Definition at line 125 of file QueryOps.h.

References RDKit::Atom::getTotalValence().

Referenced by makeAtomTotalValenceQuery().

queryAtomType()

static int RDKit::queryAtomType ( Atom const * at )

inlinestatic

Definition at line 152 of file QueryOps.h.

References RDKit::Atom::getAtomicNum(), RDKit::Atom::getIsAromatic(), and makeAtomType().

Referenced by makeAtomTypeQuery().

queryAtomUnsaturated()

static int RDKit::queryAtomUnsaturated ( Atom const * at )

inlinestatic

Definition at line 128 of file QueryOps.h.

References RDKit::Atom::getTotalDegree(), and RDKit::Atom::getTotalValence().

Referenced by makeAtomUnsaturatedQuery().

queryBondDir()

static int RDKit::queryBondDir ( Bond const * bond )

inlinestatic

Definition at line 265 of file QueryOps.h.

References RDKit::Bond::getBondDir().

queryBondHasStereo()

static int RDKit::queryBondHasStereo ( Bond const * bnd )

inlinestatic

Definition at line 271 of file QueryOps.h.

References rdvalue_is(), and RDKit::Bond::STEREONONE.

queryBondIsDoubleOrAromatic()

static int RDKit::queryBondIsDoubleOrAromatic ( Bond const * bond )

inlinestatic

Definition at line 252 of file QueryOps.h.

References RDKit::Bond::AROMATIC, RDKit::Bond::DOUBLE, and RDKit::Bond::getBondType().

queryBondIsInRingOfSize()

template<int tgt>

int RDKit::queryBondIsInRingOfSize

(

Bond const *

bond

)

Definition at line 332 of file QueryOps.h.

References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::RingInfo::isBondInRingOfSize(), and rdvalue_is().

queryBondIsSingleOrAromatic()

static int RDKit::queryBondIsSingleOrAromatic ( Bond const * bond )

inlinestatic

Definition at line 248 of file QueryOps.h.

References RDKit::Bond::AROMATIC, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.

queryBondIsSingleOrDouble()

static int RDKit::queryBondIsSingleOrDouble ( Bond const * bond )

inlinestatic

Definition at line 256 of file QueryOps.h.

References RDKit::Bond::DOUBLE, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.

queryBondIsSingleOrDoubleOrAromatic()

static int RDKit::queryBondIsSingleOrDoubleOrAromatic ( Bond const * bond )

inlinestatic

Definition at line 260 of file QueryOps.h.

References RDKit::Bond::AROMATIC, RDKit::Bond::DOUBLE, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.

queryBondMinRingSize()

static int RDKit::queryBondMinRingSize ( Bond const * bond )

inlinestatic

Definition at line 304 of file QueryOps.h.

References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minBondRingSize().

queryBondOrder()

static int RDKit::queryBondOrder ( Bond const * bond )

inlinestatic

Definition at line 245 of file QueryOps.h.

References RDKit::Bond::getBondType().

queryIsAtomBridgehead()

RDKIT_GRAPHMOL_EXPORT int RDKit::queryIsAtomBridgehead

(

Atom const *

at

)

Referenced by makeAtomIsBridgeheadQuery().

queryIsAtomInNRings()

static int RDKit::queryIsAtomInNRings ( Atom const * at )

inlinestatic

Definition at line 278 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().

Referenced by makeAtomInNRingsQuery().

queryIsAtomInRing()

static int RDKit::queryIsAtomInRing ( Atom const * at )

inlinestatic

Definition at line 281 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().

Referenced by makeAtomInRingQuery().

queryIsBondInNRings()

static int RDKit::queryIsBondInNRings ( Bond const * at )

inlinestatic

Definition at line 268 of file QueryOps.h.

References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().

queryIsBondInRing()

static int RDKit::queryIsBondInRing ( Bond const * bond )

inlinestatic

Definition at line 298 of file QueryOps.h.

References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().

rdany_cast() [1/2]

template<class T >

const T RDKit::rdany_cast

(

const RDAny &

d

)

Definition at line 179 of file RDAny.h.

References RDKit::RDAny::m_value, and rdvalue_is().

rdany_cast() [2/2]

template<class T >

T RDKit::rdany_cast

(

RDAny &

d

)

Definition at line 185 of file RDAny.h.

References RDKit::RDAny::m_value, and rdvalue_is().

RDKFingerprintMol()

RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::RDKFingerprintMol	(	const ROMol &	mol,
		unsigned int	minPath = 1,
		unsigned int	maxPath = 7,
		unsigned int	fpSize = 2048,
		unsigned int	nBitsPerHash = 2,
		bool	useHs = true,
		double	tgtDensity = 0.0,
		unsigned int	minSize = 128,
		bool	branchedPaths = true,
		bool	useBondOrder = true,
		std::vector< std::uint32_t > *	atomInvariants = nullptr,
		const std::vector< std::uint32_t > *	fromAtoms = nullptr,
		std::vector< std::vector< std::uint32_t > > *	atomBits = nullptr,
		std::map< std::uint32_t, std::vector< std::vector< int > > > *	bitInfo = nullptr )

Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm.

Parameters

mol	the molecule to be fingerprinted
minPath	the minimum path length (in bonds) to be included
maxPath	the minimum path length (in bonds) to be included
fpSize	the size of the fingerprint
nBitsPerHash	the number of bits to be set by each path
useHs	toggles inclusion of Hs in paths (if the molecule has explicit Hs)
tgtDensity	if the generated fingerprint is below this density, it will be folded until the density is reached.
minSize	the minimum size to which the fingerprint will be folded
branchedPaths	toggles generation of branched subgraphs, not just linear paths
useBondOrders	toggles inclusion of bond orders in the path hashes
atomInvariants	a vector of atom invariants to use while hashing the paths
fromAtoms	only paths starting at these atoms will be included
atomBits	used to return the bits that each atom is involved in (should be at least mol.numAtoms long)

Returns

the molecular fingerprint, as an ExplicitBitVect

Notes:

• the caller is responsible for deleteing the result

RDKitSVGToMol() [1/2]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::RDKitSVGToMol	(	const std::string &	svg,
		bool	sanitize = true,
		bool	removeHs = true )

Parameters

svg	- string containing the SVG
sanitize	- toggles sanitization of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized

NOTE This functionality should be considered beta.

RDKitSVGToMol() [2/2]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::RDKitSVGToMol	(	std::istream *	instream,
		bool	sanitize = true,
		bool	removeHs = true )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

rdvalue_cast()

template<class T >

T RDKit::rdvalue_cast ( RDValue_cast_t v )

inline

Definition at line 420 of file RDValue-doublemagic.h.

References RDKit::RDValue::ptrCast(), rdvalue_is(), and rdvalue_is< std::any >().

rdvalue_cast< bool >() [1/2]

template<>

bool RDKit::rdvalue_cast< bool > ( RDValue_cast_t v )

inline

Definition at line 471 of file RDValue-doublemagic.h.

References RDKit::RDValue::otherBits, and rdvalue_is().

Referenced by rdvalue_tostring().

rdvalue_cast< bool >() [2/2]

template<>

bool RDKit::rdvalue_cast< bool > ( RDValue_cast_t v )

inline

Definition at line 520 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::b, rdvalue_is(), and RDKit::RDValue::value.

rdvalue_cast< const std::any & >()

template<>

const std::any & RDKit::rdvalue_cast< const std::any & > ( RDValue_cast_t v )

inline

Definition at line 166 of file RDValue.h.

References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().

rdvalue_cast< double >() [1/2]

template<>

double RDKit::rdvalue_cast< double > ( RDValue_cast_t v )

inline

Definition at line 440 of file RDValue-doublemagic.h.

References RDKit::RDValue::doubleBits, and rdvalue_is< double >().

Referenced by rdvalue_tostring().

rdvalue_cast< double >() [2/2]

template<>

double RDKit::rdvalue_cast< double > ( RDValue_cast_t v )

inline

Definition at line 404 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::d, RDKit::RDTypeTag::detail::Value::f, rdvalue_is(), rdvalue_is< double >(), and RDKit::RDValue::value.

rdvalue_cast< float >() [1/2]

template<>

float RDKit::rdvalue_cast< float > ( RDValue_cast_t v )

inline

Definition at line 446 of file RDValue-doublemagic.h.

References RDKit::RDValue::otherBits, and rdvalue_is().

Referenced by rdvalue_tostring().

rdvalue_cast< float >() [2/2]

template<>

float RDKit::rdvalue_cast< float > ( RDValue_cast_t v )

inline

Definition at line 415 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::d, RDKit::RDTypeTag::detail::Value::f, rdvalue_is(), rdvalue_is< double >(), and RDKit::RDValue::value.

rdvalue_cast< int >() [1/2]

template<>

int RDKit::rdvalue_cast< int > ( RDValue_cast_t v )

inline

Definition at line 458 of file RDValue-doublemagic.h.

References RDKit::RDValue::otherBits, and rdvalue_is().

Referenced by rdvalue_tostring().

rdvalue_cast< int >() [2/2]

template<>

int RDKit::rdvalue_cast< int > ( RDValue_cast_t v )

inline

Definition at line 426 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.

rdvalue_cast< std::any & >()

template<>

std::any & RDKit::rdvalue_cast< std::any & > ( RDValue_cast_t v )

inline

Definition at line 158 of file RDValue.h.

References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().

Referenced by rdvalue_tostring().

rdvalue_cast< std::any >()

template<>

std::any RDKit::rdvalue_cast< std::any > ( RDValue_cast_t v )

inline

Definition at line 150 of file RDValue.h.

References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().

rdvalue_cast< std::int16_t >()

template<>

std::int16_t RDKit::rdvalue_cast< std::int16_t > ( RDValue_cast_t v )

inline

Definition at line 448 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.

rdvalue_cast< std::int64_t >()

template<>

std::int64_t RDKit::rdvalue_cast< std::int64_t > ( RDValue_cast_t v )

inline

Definition at line 459 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::i, RDKit::RDValue::ptrCast(), rdvalue_is(), rdvalue_is< std::any >(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.

rdvalue_cast< std::int8_t >()

template<>

std::int8_t RDKit::rdvalue_cast< std::int8_t > ( RDValue_cast_t v )

inline

Definition at line 437 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.

rdvalue_cast< std::string & >()

template<>

std::string & RDKit::rdvalue_cast< std::string & > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

References RDKit::RDValue::ptrCast(), and rdvalue_is().

rdvalue_cast< std::string >()

template<>

std::string RDKit::rdvalue_cast< std::string > ( RDValue_cast_t v )

inline

Definition at line 46 of file RDValue.h.

References RDKit::RDValue::ptrCast(), and rdvalue_is().

Referenced by from_rdvalue(), and rdvalue_tostring().

rdvalue_cast< std::uint16_t >()

template<>

std::uint16_t RDKit::rdvalue_cast< std::uint16_t > ( RDValue_cast_t v )

inline

Definition at line 495 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.

rdvalue_cast< std::uint64_t >()

template<>

std::uint64_t RDKit::rdvalue_cast< std::uint64_t > ( RDValue_cast_t v )

inline

Definition at line 506 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::i, RDKit::RDValue::ptrCast(), rdvalue_is(), rdvalue_is< std::any >(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.

rdvalue_cast< std::uint8_t >()

template<>

std::uint8_t RDKit::rdvalue_cast< std::uint8_t > ( RDValue_cast_t v )

inline

Definition at line 484 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.

rdvalue_cast< std::vector< double > & >()

template<>

std::vector< double > & RDKit::rdvalue_cast< std::vector< double > & > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< std::vector< double > >()

template<>

std::vector< double > RDKit::rdvalue_cast< std::vector< double > > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< std::vector< float > & >()

template<>

std::vector< float > & RDKit::rdvalue_cast< std::vector< float > & > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< std::vector< float > >()

template<>

std::vector< float > RDKit::rdvalue_cast< std::vector< float > > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< std::vector< int > & >()

template<>

std::vector< int > & RDKit::rdvalue_cast< std::vector< int > & > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< std::vector< int > >()

template<>

std::vector< int > RDKit::rdvalue_cast< std::vector< int > > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< std::vector< std::string > & >()

template<>

std::vector< std::string > & RDKit::rdvalue_cast< std::vector< std::string > & > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< std::vector< std::string > >()

template<>

std::vector< std::string > RDKit::rdvalue_cast< std::vector< std::string > > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< std::vector< unsigned int > & >()

template<>

std::vector< unsigned int > & RDKit::rdvalue_cast< std::vector< unsigned int > & > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< std::vector< unsigned int > >()

template<>

std::vector< unsigned int > RDKit::rdvalue_cast< std::vector< unsigned int > > ( RDValue_cast_t v )

inline

Definition at line 54 of file RDValue.h.

rdvalue_cast< unsigned int >() [1/2]

template<>

unsigned int RDKit::rdvalue_cast< unsigned int > ( RDValue_cast_t v )

inline

Definition at line 464 of file RDValue-doublemagic.h.

References RDKit::RDValue::otherBits, and rdvalue_is().

Referenced by rdvalue_tostring().

rdvalue_cast< unsigned int >() [2/2]

template<>

unsigned int RDKit::rdvalue_cast< unsigned int > ( RDValue_cast_t v )

inline

Definition at line 473 of file RDValue-taggedunion.h.

References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.

rdvalue_is()

template<class T >

bool RDKit::rdvalue_is ( const RDValue_cast_t v )

inline

Definition at line 372 of file RDValue-doublemagic.h.

References RDKit::RDTypeTag::AnyTag, and rdvalue_is().

Referenced by RDKit::FMCS::DuplicatedSeedCache::add(), RDKit::CIPLabeler::Rules::add(), RDKit::CIPLabeler::PairList::addAll(), RDKit::FMCS::DuplicatedSeedCache::TKey::addAtom(), RDKit::MolDraw2D_detail::addAtomIndices(), RDKit::SLNParse::addAtomToMol(), RDKit::SLNParse::addAtomToMol(), RDKit::FMCS::DuplicatedSeedCache::TKey::addBond(), RDKit::MolDraw2D_detail::addBondIndices(), RDKit::SLNParse::addBranchToMol(), RDKit::SLNParse::addBranchToMol(), RDKit::SLNParse::addFragToMol(), addMetadataToPNGFile(), addMetadataToPNGString(), RDKit::MolBundle::addMol(), RDKit::FixedMolSizeMolBundle::addMol(), addMolToPNGFile(), addMolToPNGString(), appendPackedIntToStream(), RDKit::FileParserUtils::applyMolListPropsToAtoms(), RDKit::FileParserUtils::applyMolListPropToAtoms(), assignAvalonPalette(), assignBWPalette(), assignCDKPalette(), assignDarkModePalette(), assignDefaultPalette(), RDKit::Canon::BreakTies(), RDKit::MolDraw2D_detail::StringRect::calcCentre(), RDKit::MolDraw2D_detail::StringRect::calcCorners(), RDKit::DataStructsExplicitBitVecPropHandler::canSerialize(), checkForTimeout(), RDKit::RDValue::cleanup_rdvalue(), RDKit::RDProps::clearComputedProps(), RDKit::RDProps::clearProp(), RDKit::SLNParse::closeRingBond(), RDKit::SLNParse::closeRingBond(), RDKit::CIPLabeler::Rules::compare(), RDKit::CIPLabeler::PairList::compareTo(), RDKit::MolDraw2DUtils::contourAndDrawGaussians(), RDKit::MolDraw2DUtils::contourAndDrawGrid(), RDKit::SLNParse::convertToString(), RDKit::HasPropQuery< TargetPtr >::copy(), RDKit::HasPropWithValueQuery< TargetPtr, T >::copy(), RDKit::HasPropWithValueQuery< TargetPtr, std::string >::copy(), RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >::copy(), copy_rdvalue(), countSwapsToInterconvert(), RDKit::FileParserUtils::createAtomBoolPropertyList(), RDKit::FileParserUtils::createAtomDoublePropertyList(), RDKit::FileParserUtils::createAtomIntPropertyList(), RDKit::FileParserUtils::createAtomStringPropertyList(), RDKit::ScaffoldNetwork::createScaffoldNetwork(), describeQuery(), describeQuery(), RDKit::RDValue::destroy(), RDKit::GeneralMolSupplier::determineFormat(), DiceSimilarity(), Dict::getVal< std::string >(), RDKit::MolDraw2D_detail::StringRect::doesItIntersect(), RDKit::DGeomHelpers::EmbedMolecule(), RDKit::DGeomHelpers::EmbedMultipleConfs(), RDKit::DGeomHelpers::EmbedMultipleConfs(), RDKit::DGeomHelpers::EmbedMultipleConfs(), EndianSwapBytes(), eraseUniquePtr(), RDKit::DrawColour::feq(), RDKit::FMCS::DuplicatedSeedCache::find(), findUniquePtr(), RDKit::FileParserUtils::finishMolProcessing(), RDKit::SGroupWriting::FormatV2000DoubleField(), RDKit::SGroupWriting::FormatV2000IntField(), RDKit::SGroupWriting::FormatV2000NumEntriesField(), RDKit::SGroupWriting::FormatV2000StringField(), RDKit::MolStandardize::fragmentRemoverFromParams(), from_rdany(), from_rdvalue(), RDKit::SparseIntVect< IndexType >::fromString(), RDKit::FMCS::Composition2N::generateNext(), RDKit::FileParserUtils::getAtomPropertyList(), RDKit::CIPLabeler::Rules::getComparision(), getLine(), getLine(), RDKit::MolEnumerator::utils::getMolLinkNodes(), getNumThreadsToUse(), RDKit::RDProps::getProp(), RDKit::RDProps::getPropIfPresent(), RDKit::RDProps::getPropList(), RDKit::GeneralMolSupplier::getSupplier(), RDKit::RDValue::getTag(), RDKit::SparseIntVect< IndexType >::getTotalVal(), RDKit::MolStandardize::getV1TautomerEnumerator(), RDKit::SparseIntVect< IndexType >::getVal(), hanoi(), hanoisort(), RDKit::MHFPFingerprints::FNV::hash(), RDKit::GeneralizedSubstruct::hasSubstructMatch(), RDKit::CartesianProduct::increment(), RDKit::FMCS::TargetMatch::init(), RDKit::MolBundle::initFromStream(), RDKit::MolBundle::initFromString(), RDKit::FMCS::Composition2N::is2Power(), isDative(), RDKit::MolDraw2D_detail::StringRect::isPointInside(), RDKit::FMCS::Composition2N::isSet(), makeAtomAliphaticQuery(), makeAtomAromaticQuery(), makeAtomExplicitDegreeQuery(), makeAtomExplicitValenceQuery(), makeAtomFormalChargeQuery(), makeAtomHasAliphaticHeteroatomNbrsQuery(), makeAtomHasChiralTagQuery(), makeAtomHasHeteroatomNbrsQuery(), makeAtomHasImplicitHQuery(), makeAtomHasRingBondQuery(), makeAtomHCountQuery(), makeAtomHeavyAtomDegreeQuery(), makeAtomHybridizationQuery(), makeAtomImplicitHCountQuery(), makeAtomImplicitValenceQuery(), makeAtomInNRingsQuery(), makeAtomInRingQuery(), makeAtomIsBridgeheadQuery(), makeAtomIsotopeQuery(), makeAtomMassQuery(), makeAtomMinRingSizeQuery(), makeAtomMissingChiralTagQuery(), makeAtomNegativeFormalChargeQuery(), makeAtomNonHydrogenDegreeQuery(), makeAtomNumAliphaticHeteroatomNbrsQuery(), makeAtomNumHeteroatomNbrsQuery(), makeAtomNumQuery(), makeAtomNumRadicalElectronsQuery(), makeAtomRangeQuery(), makeAtomRingBondCountQuery(), makeAtomSimpleQuery(), makeAtomTotalDegreeQuery(), makeAtomTotalValenceQuery(), makeAtomType(), makeAtomTypeQuery(), makeAtomUnsaturatedQuery(), makeHasPropQuery(), RDKit::Descriptors::makePropertyQuery(), makePropQuery(), makePropQuery(), RDKit::HasPropQuery< TargetPtr >::Match(), RDKit::HasPropWithValueQuery< TargetPtr, T >::Match(), RDKit::HasPropWithValueQuery< TargetPtr, std::string >::Match(), RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >::Match(), mergeNullQueries(), RDKit::MMFF::MMFFOptimizeMolecule(), RDKit::MMFF::MMFFOptimizeMoleculeConfs(), RDKit::MolBundle::MolBundle(), RDKit::MolBundle::MolBundle(), MolFragmentToCXSmiles(), MolFragmentToSmiles(), MolToCXSmiles(), RDKit::MolInterchange::MolToJSONData(), MolToMolFile(), MolToMrvFile(), MolToSmiles(), MolToV3KMolBlock(), MolToV3KMolFile(), MolToV3KMolFile(), RDKit::CIPLabeler::CIPMolSpan< T, U >::CIPMolIter::operator!=(), RDKit::CXXAtomIterator< Graph, Vertex, Iterator >::CXXAtomIter::operator!=(), RDKit::CXXBondIterator< Graph, Edge, Iterator >::CXXBondIter::operator!=(), RDKit::DrawColour::operator!=(), operator""_ctab(), operator""_mol2(), operator""_pdb(), RDKit::SparseIntVect< IndexType >::operator&(), RDKit::SparseIntVect< IndexType >::operator&=(), RDKit::SparseIntVect< IndexType >::operator*(), RDKit::SparseIntVect< IndexType >::operator*=(), RDKit::DrawColour::operator+(), RDKit::SparseIntVect< IndexType >::operator+(), RDKit::SparseIntVect< IndexType >::operator+(), RDKit::SparseIntVect< IndexType >::operator+=(), RDKit::SparseIntVect< IndexType >::operator+=(), RDKit::DrawColour::operator-(), RDKit::SparseIntVect< IndexType >::operator-(), RDKit::SparseIntVect< IndexType >::operator-(), RDKit::SparseIntVect< IndexType >::operator-=(), RDKit::SparseIntVect< IndexType >::operator-=(), RDKit::SparseIntVect< IndexType >::operator/(), RDKit::SparseIntVect< IndexType >::operator/=(), RDKit::CIPLabeler::PairList::operator<(), RDKit::FMCS::DuplicatedSeedCache::TKey::operator<(), RDKit::ScaffoldNetwork::operator<<(), RDKit::ScaffoldNetwork::operator<<(), RDKit::RDAny::operator=(), RDKit::RDProps::operator=(), RDKit::SparseIntVect< IndexType >::operator=(), RDKit::FMCS::TargetMatch::operator=(), RDKit::CXXAtomIterator< Graph, Vertex, Iterator >::CXXAtomIter::operator==(), RDKit::CXXBondIterator< Graph, Edge, Iterator >::CXXBondIter::operator==(), RDKit::DrawColour::operator==(), RDKit::FMCS::DuplicatedSeedCache::TKey::operator==(), RDKit::SparseIntVect< IndexType >::operator|(), RDKit::SparseIntVect< IndexType >::operator|=(), RDKit::ForceFieldsHelper::OptimizeMolecule(), RDKit::ForceFieldsHelper::OptimizeMoleculeConfs(), RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST(), RDKit::CIPLabeler::PairList::PairList(), RDKit::CIPLabeler::Configuration::parity4(), parseAtomType(), RDKit::SGroupParsing::ParseV3000Array(), PNGFileToMetadata(), PNGFileToMol(), PNGFileToMols(), PNGStringToMetadata(), PNGStringToMol(), PNGStringToMols(), RDKit::FileParserUtils::processMolPropertyList(), RDKit::FileParserUtils::processMolPropertyLists(), RDKit::RDValue::ptrCast(), pullPackedIntFromString(), RDKit::detail::qhelper(), RDKit::detail::qhelper(), queryAtomHasAliphaticHeteroatomNbrs(), queryAtomHasHeteroatomNbrs(), queryAtomHasImplicitH(), queryAtomHeavyAtomDegree(), queryAtomIsInRingOfSize(), queryAtomNonHydrogenDegree(), queryAtomNumAliphaticHeteroatomNbrs(), queryAtomNumHeteroatomNbrs(), queryAtomRingBondCount(), queryBondHasStereo(), queryBondIsInRingOfSize(), RDKit::Canon::rankFragmentAtoms(), RDKit::RDAny::RDAny(), rdany_cast(), rdany_cast(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), rdvalue_cast(), rdvalue_cast< bool >(), rdvalue_cast< double >(), rdvalue_cast< float >(), rdvalue_cast< int >(), rdvalue_cast< std::int16_t >(), rdvalue_cast< std::int64_t >(), rdvalue_cast< std::int8_t >(), rdvalue_cast< std::string & >(), rdvalue_cast< std::string >(), rdvalue_cast< std::uint16_t >(), rdvalue_cast< std::uint64_t >(), rdvalue_cast< std::uint8_t >(), rdvalue_cast< unsigned int >(), rdvalue_is(), rdvalue_is< std::any >(), rdvalue_tostring(), RDKit::DataStructsExplicitBitVecPropHandler::read(), readPackedIntFromStream(), readRDStringVecValue(), readRDValue(), readRDValueString(), readRDVecValue(), RDKit::Canon::RefinePartitions(), RDKit::CIPLabeler::Rules::Rules(), RDKit::MolBundle::serialize(), setDarkMode(), setDarkMode(), setMonochromeMode(), setMonochromeMode(), RDKit::RDProps::setProp(), RDKit::SparseIntVect< IndexType >::setVal(), RDKit::SGroupParsing::SGroupWarnOrThrow(), RDKit::SparseIntVect< IndexType >::SparseIntVect(), RDKit::SparseIntVect< IndexType >::SparseIntVect(), RDKit::SparseIntVect< IndexType >::SparseIntVect(), RDKit::SLNParse::startMol(), streamRead(), streamRead(), streamRead(), streamReadStringVec(), streamReadVec(), streamWrite(), streamWrite(), streamWriteVec(), RDKit::FileParserUtils::strip(), RDKit::FileParserUtils::stripSpacesAndCast(), RDKit::FileParserUtils::stripSpacesAndCast(), SubstructMatch(), SubstructMatch(), SubstructMatch(), SubstructMatch(), SwapBytes(), TanimotoSimilarity(), RDKit::FMCS::TargetMatch::TargetMatch(), RDKit::CIPLabeler::to_string(), RDKit::MolBundle::toStream(), RDKit::SparseIntVect< IndexType >::toString(), RDKit::CIPLabeler::PairList::toString(), RDKit::RGroupMatch::toString(), TverskySimilarity(), RDKit::UFF::UFFOptimizeMolecule(), RDKit::UFF::UFFOptimizeMoleculeConfs(), updateFromSequence(), RDKit::RDProps::updateProps(), RDKit::UsedLabelMap::UsedLabelMap(), vectToString(), RDKit::Chirality::WedgeInfoAtropisomer::WedgeInfoAtropisomer(), RDKit::DataStructsExplicitBitVecPropHandler::write(), and RDKit::CIPLabeler::Rules::~Rules().

rdvalue_is< const double & >()

template<>

bool RDKit::rdvalue_is< const double & > ( const RDValue_cast_t )

inline

Definition at line 392 of file RDValue-doublemagic.h.

References rdvalue_is< double >().

rdvalue_is< double >()

template<>

bool RDKit::rdvalue_is< double > ( const RDValue_cast_t )

inline

Definition at line 386 of file RDValue-doublemagic.h.

References RDKit::RDTypeTag::MaxDouble, and RDKit::RDTypeTag::NaN.

Referenced by rdvalue_cast< double >(), rdvalue_cast< float >(), and rdvalue_is< const double & >().

rdvalue_is< std::any >()

template<>

bool RDKit::rdvalue_is< std::any > ( RDValue_cast_t v )

inline

Definition at line 369 of file RDValue-taggedunion.h.

References RDKit::RDValue::getTag(), RDKit::RDTypeTag::GetTag< std::any >(), and rdvalue_is().

Referenced by rdvalue_cast(), rdvalue_cast< const std::any & >(), rdvalue_cast< std::any & >(), rdvalue_cast< std::any >(), rdvalue_cast< std::int64_t >(), and rdvalue_cast< std::uint64_t >().

rdvalue_tostring()

bool RDKit::rdvalue_tostring ( RDValue_cast_t val, std::string & res )

inline

Definition at line 187 of file RDValue.h.

References RDKit::RDTypeTag::AnyTag, RDKit::RDTypeTag::BoolTag, RDKit::RDTypeTag::DoubleTag, RDKit::RDTypeTag::FloatTag, RDKit::RDValue::getTag(), RDKit::RDTypeTag::IntTag, rdvalue_cast< bool >(), rdvalue_cast< double >(), rdvalue_cast< float >(), rdvalue_cast< int >(), rdvalue_cast< std::any & >(), rdvalue_cast< std::string >(), rdvalue_cast< unsigned int >(), rdvalue_is(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.

Referenced by RDKit::Dict::getVal(), and RDKit::Dict::getValIfPresent().

readAmberTrajectory()

RDKIT_TRAJECTORY_EXPORT unsigned int RDKit::readAmberTrajectory	(	const std::string &	fName,
		Trajectory &	traj )

Reads coordinates from an AMBER trajectory file into the traj Trajectory object.

Returns

the number of Snapshot objects read in

readFuncGroups() [1/2]

RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT RDKit::readFuncGroups	(	std::istream &	inStream,
		int	nToRead = -1 )

readFuncGroups() [2/2]

RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT RDKit::readFuncGroups

(

std::string

fileName

)

readGromosTrajectory()

RDKIT_TRAJECTORY_EXPORT unsigned int RDKit::readGromosTrajectory	(	const std::string &	fName,
		Trajectory &	traj )

Reads coordinates from a GROMOS trajectory file into the traj Trajectory object.

Returns

the number of Snapshot objects read in

readPackedIntFromStream()

boost::uint32_t RDKit::readPackedIntFromStream ( std::stringstream & ss )

inline

Reads an integer from a stream in packed format and returns the result.

Definition at line 150 of file StreamOps.h.

References rdvalue_is().

readRDStringVecValue()

void RDKit::readRDStringVecValue ( std::istream & ss, RDValue & value )

inline

Definition at line 549 of file StreamOps.h.

References rdvalue_is(), and streamReadStringVec().

readRDValue()

template<class T >

void RDKit::readRDValue	(	std::istream &	ss,
		RDValue &	value )

Definition at line 529 of file StreamOps.h.

References rdvalue_is(), and streamRead().

readRDValueString()

void RDKit::readRDValueString ( std::istream & ss, RDValue & value )

inline

Definition at line 542 of file StreamOps.h.

References rdvalue_is(), and streamRead().

readRDVecValue()

template<class T >

void RDKit::readRDVecValue	(	std::istream &	ss,
		RDValue &	value )

Definition at line 536 of file StreamOps.h.

References rdvalue_is(), and streamReadVec().

reapplyMolBlockWedging()

RDKIT_FILEPARSERS_EXPORT void RDKit::reapplyMolBlockWedging

(

ROMol &

mol

)

Deprecated

use Chirality::reapplyMolBlockWedging instead

reduceProductToSideChains()

RDKIT_CHEMREACTIONS_EXPORT ROMol * RDKit::reduceProductToSideChains	(	const ROMOL_SPTR &	product,
		bool	addDummyAtoms = true )

Reduce the product generated by run_Reactants or run_Reactant to the sidechains that come from the reagents

Parameters

addDummyAtoms

If true, add dummy atoms to the sidechains for the non-reagent parts of the sidechain. Dummy atoms are annotated with the atom maps from the reaction. If False, then any sidechain atom where a bond was cleaved is annotated with: _rgroupAtomMaps property which indicates the scaffold atommaps that where bonded _rgroupBonds property which indicates the bondtype for each atommap bonded

relabelMappedDummies()

RDKIT_RGROUPDECOMPOSITION_EXPORT void RDKit::relabelMappedDummies	(	ROMol &	mol,
		unsigned int	inputLabels = AtomMap|Isotope|MDLRGroup,
		unsigned int	outputLabels = MDLRGroup )

Relabel dummy atoms bearing an R-group mapping (as atom map number, isotope or MDLRGroup label) such that they will be displayed by the rendering code as R# rather than #*, *:#, #*:#, etc. By default, only the MDLRGroup label is retained on output; this may be configured through the outputLabels parameter. In case there are multiple potential R-group mappings, the priority on input is Atom map number > Isotope > MDLRGroup. The inputLabels parameter allows to configure which mappings are taken into consideration.

removeAtomFromGroups()

RDKIT_GRAPHMOL_EXPORT void RDKit::removeAtomFromGroups	(	const Atom *	atom,
		std::vector< StereoGroup > &	groups )

removeDuplicates()

RDKIT_SUBSTRUCTMATCH_EXPORT void RDKit::removeDuplicates	(	std::vector< MatchVectType > &	v,
		unsigned int	nAtoms )

removeGroupsWithAtom()

RDKIT_GRAPHMOL_EXPORT void RDKit::removeGroupsWithAtom	(	const Atom *	atom,
		std::vector< StereoGroup > &	groups )

removeGroupsWithAtoms()

RDKIT_GRAPHMOL_EXPORT void RDKit::removeGroupsWithAtoms	(	const std::vector< Atom * > &	atoms,
		std::vector< StereoGroup > &	groups )

removeMappingNumbersFromReactions()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::removeMappingNumbersFromReactions

(

const ChemicalReaction &

rxn

)

removeNonmatchingReagents()

RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::BBS RDKit::removeNonmatchingReagents	(	const ChemicalReaction &	rxn,
		EnumerationTypes::BBS	bbs,
		const EnumerationParams &	params = EnumerationParams() )

Helper function, remove reagents that are incompatible with the reaction. rxn must be sanitized, initialized and preprocessed. this happens automatically in EnumerateLibrary

removeSubstanceGroupsReferencingAtom()

RDKIT_GRAPHMOL_EXPORT void RDKit::removeSubstanceGroupsReferencingAtom	(	RWMol &	mol,
		unsigned int	idx )

Removes SubstanceGroups which reference a particular atom index.

Parameters

mol	- molecule to be edited.
idx	- atom index

removeSubstanceGroupsReferencingBond()

RDKIT_GRAPHMOL_EXPORT void RDKit::removeSubstanceGroupsReferencingBond	(	RWMol &	mol,
		unsigned int	idx )

Removes SubstanceGroups which reference a particular bond index.

Parameters

mol	- molecule to be edited.
idx	- bond index

replaceCore() [1/2]

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::replaceCore	(	const ROMol &	mol,
		const ROMol &	core,
		const MatchVectType &	matchVect,
		bool	replaceDummies = true,
		bool	labelByIndex = false,
		bool	requireDummyMatch = false )

Returns a copy of an ROMol with the atoms and bonds that are referenced by the MatchVector removed. MatchVector must be defined between mol and the specified core.

dummy atoms are left to indicate attachment points. These dummy atoms can be labeled either by the matching index in the query or by an arbitrary "first match" found. Additional matching options are given below.

Note that this is essentially identical to the replaceSidechains function, except we invert the query and replace the atoms that do match the query.

Parameters

mol	- the ROMol of interest
core	- the core being matched against
matchVect	- a matchVect of the type returned by Substructure Matching
replaceDummies	- if set, atoms matching dummies in the core will also be replaced
labelByIndex	- if set, the dummy atoms at attachment points are labelled with the index+1 of the corresponding atom in the core
requireDummyMatch	- if set, only side chains that are connected to atoms in the core that have attached dummies will be considered. Molecules that have sidechains that are attached at other points will be rejected (NULL returned).
useChirality	- if set, match the coreQuery using chirality

Returns

a copy of mol with the non-matching atoms and bonds (if any) removed and dummies at the connection points. The client is responsible for deleting this molecule. If the core query is not matched, NULL is returned.

replaceCore() [2/2]

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::replaceCore	(	const ROMol &	mol,
		const ROMol &	coreQuery,
		bool	replaceDummies = true,
		bool	labelByIndex = false,
		bool	requireDummyMatch = false,
		bool	useChirality = false )

Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed.

dummy atoms are left to indicate attachment points.

Note that this is essentially identical to the replaceSidechains function, except we invert the query and replace the atoms that do match the query.

Parameters

mol	- the ROMol of interest
coreQuery	- a query ROMol to be used to match the core
replaceDummies	- if set, atoms matching dummies in the core will also be replaced
labelByIndex	- if set, the dummy atoms at attachment points are labelled with the index+1 of the corresponding atom in the core
requireDummyMatch	- if set, only side chains that are connected to atoms in the core that have attached dummies will be considered. Molecules that have sidechains that are attached at other points will be rejected (NULL returned).
useChirality	- if set, match the coreQuery using chirality

Returns

a copy of mol with the non-matching atoms and bonds (if any) removed and dummies at the connection points. The client is responsible for deleting this molecule. If the core query is not matched, NULL is returned.

replaceSidechains()

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::replaceSidechains	(	const ROMol &	mol,
		const ROMol &	coreQuery,
		bool	useChirality = false )

Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed.

dummy atoms are left to indicate attachment points.

Parameters

mol	the ROMol of interest
coreQuery	a query ROMol to be used to match the core
useChirality	- if set, match the coreQuery using chirality

Returns

a copy of mol with the non-matching atoms and bonds (if any) removed and dummies at the connection points.

replaceSubstructs()

RDKIT_CHEMTRANSFORMS_EXPORT std::vector< ROMOL_SPTR > RDKit::replaceSubstructs	(	const ROMol &	mol,
		const ROMol &	query,
		const ROMol &	replacement,
		bool	replaceAll = false,
		unsigned int	replacementConnectionPoint = 0,
		bool	useChirality = false )

Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule.

Bonds are created between the joining atom in the existing molecule and the atoms in the new molecule. So, using SMILES instead of molecules: replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]') -> ['[X]NCCNC(=O)O','OC(=O)NCCN[X]'] replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]',true) -> ['[X]NCCN[X]'] Chains should be handled "correctly": replaceSubstructs('CC(=O)C','C(=O)','[X]') -> ['C[X]C'] As should rings: replaceSubstructs('C1C(=O)C1','C(=O)','[X]') -> ['C1[X]C1'] And higher order branches: replaceSubstructs('CC(=O)(C)C','C(=O)','[X]') -> ['C[X](C)C'] Note that the client is responsible for making sure that the resulting molecule actually makes sense - this function does not perform sanitization.

Parameters

mol	the ROMol of interest
query	the query ROMol
replacement	the ROMol to be inserted
replaceAll	if this is true, only a single result, with all
useChirality	- if set, match the coreQuery using chirality

occurrences of the substructure replaced, will be returned.

Parameters

replacementConnectionPoint

index of the atom in the replacement that the bond should made to

Returns

a vector of pointers to copies of mol with the matching atoms and bonds (if any) replaced

RGroupDecompose() [1/2]

RDKIT_RGROUPDECOMPOSITION_EXPORT unsigned int RDKit::RGroupDecompose	(	const std::vector< ROMOL_SPTR > &	cores,
		const std::vector< ROMOL_SPTR > &	mols,
		RGroupColumns &	columns,
		std::vector< unsigned int > *	unmatched = nullptr,
		const RGroupDecompositionParameters &	options = RGroupDecompositionParameters() )

RGroupDecompose() [2/2]

RDKIT_RGROUPDECOMPOSITION_EXPORT unsigned int RDKit::RGroupDecompose	(	const std::vector< ROMOL_SPTR > &	cores,
		const std::vector< ROMOL_SPTR > &	mols,
		RGroupRows &	rows,
		std::vector< unsigned int > *	unmatched = nullptr,
		const RGroupDecompositionParameters &	options = RGroupDecompositionParameters() )

run_Reactant() [1/2]

RDKIT_CHEMREACTIONS_EXPORT std::vector< MOL_SPTR_VECT > RDKit::run_Reactant	(	const ChemicalReaction &	rxn,
		const ROMOL_SPTR &	reactant,
		unsigned int	reactantIdx )

Runs a single reactant against a single reactant template.

Parameters

reactant	The single reactant to use
reactantTemplateIdx	the reactant template to target in the reaction

Returns

a vector of vectors of products. Each subvector will be rxn->getNumProductTemplates() long.

We return a vector of vectors of products because each individual template may map multiple times onto its reactant. This leads to multiple possible result sets.

run_Reactant() [2/2]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::run_Reactant	(	const ChemicalReaction &	rxn,
		RWMol &	reactant,
		bool	removeUnmatchedAtoms = true )

run_Reactants()

RDKIT_CHEMREACTIONS_EXPORT std::vector< MOL_SPTR_VECT > RDKit::run_Reactants	(	const ChemicalReaction &	rxn,
		const MOL_SPTR_VECT &	reactants,
		unsigned int	maxProducts = 1000 )

Runs the reaction on a set of reactants.

Parameters

rxn	the template reaction we are interested
reactants	the reactants to be used. The length of this must be equal to rxn->getNumReactantTemplates() Caution: The order of the reactant templates determines the order of the reactants!
maxProducts	if non zero, the maximum number of products to generate before stopping. If hit a warning will be generated.

Returns

a vector of vectors of products. Each subvector will be rxn->getNumProductTemplates() long.

We return a vector of vectors of products because each individual template may map multiple times onto its reactant. This leads to multiple possible result sets.

RunFilterCatalog()

RDKIT_FILTERCATALOG_EXPORT std::vector< std::vector< boost::shared_ptr< const FilterCatalogEntry > > > RDKit::RunFilterCatalog	(	const FilterCatalog &	filterCatalog,
		const std::vector< std::string > &	smiles,
		int	numThreads = 1 )

Run a filter catalog on a set of smiles strings.

RxnMolToChemicalReaction()

RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RDKit::RxnMolToChemicalReaction

(

const ROMol &

mol

)

Parse a ROMol into a ChemicalReaction, RXN role must be set before.

Alternative to build a reaction from a molecule (fragments) which have RXN roles set as atom properties: common_properties::molRxnRole (1=reactant, 2=product, 3=agent)

Parameters

mol	ROMol with RXN roles set

References RxnMolToChemicalReaction().

Referenced by RxnMolToChemicalReaction().

SamePDBResidue()

RDKIT_FILEPARSERS_EXPORT bool RDKit::SamePDBResidue	(	AtomPDBResidueInfo *	p,
		AtomPDBResidueInfo *	q )

SequenceToMol() [1/4]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol	(	const char *	seq,
		bool	sanitize,
		bool	lowerD )

Parameters

seq	- the string to be processed
sanitize	- toggles sanitization and stereochemistry perception of the molecule
lowerD	- if set, lower case letters will be parsed as the d form of the corresponding amino acid

SequenceToMol() [2/4]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol	(	const char *	seq,
		bool	sanitize = true,
		int	flavor = 0 )

Parameters

seq	- the string to be processed
sanitize	- toggles sanitization and stereochemistry perception of the molecule
flavor	- 0 Protein, L amino acids (default) 1 Protein, D amino acids 2 RNA, no cap 3 RNA, 5' cap 4 RNA, 3' cap 5 RNA, both caps 6 DNA, no cap 7 DNA, 5' cap 8 DNA, 3' cap 9 DNA, both caps

SequenceToMol() [3/4]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol	(	const std::string &	seq,
		bool	sanitize,
		bool	lowerD )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

SequenceToMol() [4/4]

RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol	(	const std::string &	seq,
		bool	sanitize = true,
		int	flavor = 0 )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

setAtomAlias()

RDKIT_GRAPHMOL_EXPORT void RDKit::setAtomAlias	(	Atom *	atom,
		const std::string &	alias )

Set the atom's MDL atom alias Setting to an empty string clears the alias

setAtomRLabel()

RDKIT_GRAPHMOL_EXPORT void RDKit::setAtomRLabel	(	Atom *	atm,
		int	rlabel )

Set the atom's MDL integer RLabel Setting to 0 clears the rlabel. Rlabel must be in the range [0..99]

setAtomValue()

RDKIT_GRAPHMOL_EXPORT void RDKit::setAtomValue	(	Atom *	atom,
		const std::string &	value )

Set the atom's MDL atom value Setting to an empty string clears the value This is where recursive smarts get stored in MolBlock Queries

setDarkMode() [1/2]

void RDKit::setDarkMode ( MolDraw2D & d2d )

inline

Definition at line 555 of file MolDraw2D.h.

References rdvalue_is(), and setDarkMode().

setDarkMode() [2/2]

void RDKit::setDarkMode ( MolDrawOptions & opts )

inline

Definition at line 547 of file MolDraw2D.h.

References assignDarkModePalette(), and rdvalue_is().

Referenced by setDarkMode().

setLabel()

bool RDKit::setLabel	(	Atom *	atom,
		int	label,
		std::set< int > &	labels,
		int &	maxLabel,
		bool	relabel,
		Labelling	type )

Set the rgroup label for the current atom, this also sets the appropriate MDL or other label

setMonochromeMode() [1/2]

void RDKit::setMonochromeMode ( MolDraw2D & drawer, const DrawColour & fgColour, const DrawColour & bgColour )

inline

Definition at line 566 of file MolDraw2D.h.

References rdvalue_is(), and setMonochromeMode().

setMonochromeMode() [2/2]

void RDKit::setMonochromeMode ( MolDrawOptions & opts, const DrawColour & fgColour, const DrawColour & bgColour )

inline

Definition at line 556 of file MolDraw2D.h.

References rdvalue_is().

Referenced by setMonochromeMode().

setSupplementalSmilesLabel()

RDKIT_GRAPHMOL_EXPORT void RDKit::setSupplementalSmilesLabel	(	Atom *	atom,
		const std::string &	label )

Sets the supplemental label that will follow the atom when writing smiles strings.

SLNQueryToMol()

RDKIT_SLNPARSE_EXPORT RWMol * RDKit::SLNQueryToMol	(	const std::string &	smi,
		bool	mergeHs = true,
		int	debugParse = 0 )

SLNToMol()

RDKIT_SLNPARSE_EXPORT RWMol * RDKit::SLNToMol	(	const std::string &	smi,
		bool	sanitize = true,
		int	debugParse = 0 )

sortMatchesByDegreeOfCoreSubstitution()

RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::sortMatchesByDegreeOfCoreSubstitution	(	const ROMol &	mol,
		const ROMol &	core,
		const std::vector< MatchVectType > &	matches )

This returns a copy of the passed substruct matches sorted by decreasing number of non-hydrogen atoms in correspondence of terminal dummy atoms

StandardPDBResidueBondOrders()

RDKIT_FILEPARSERS_EXPORT void RDKit::StandardPDBResidueBondOrders

(

RWMol *

mol

)

streamRead() [1/3]

void RDKit::streamRead ( std::istream & ss, std::string & what, int version )

inline

Definition at line 299 of file StreamOps.h.

References RDUNUSED_PARAM, and rdvalue_is().

streamRead() [2/3]

template<typename T >

void RDKit::streamRead	(	std::istream &	ss,
		T &	loc )

does a binary read of an object from a stream

Definition at line 283 of file StreamOps.h.

References rdvalue_is().

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream(), RDKit::DataStructsExplicitBitVecPropHandler::read(), readRDValue(), readRDValueString(), streamRead(), streamReadStringVec(), and streamReadVec().

streamRead() [3/3]

template<class T >

void RDKit::streamRead	(	std::istream &	ss,
		T &	obj,
		int	version )

special case for string

Definition at line 294 of file StreamOps.h.

References RDUNUSED_PARAM, rdvalue_is(), and streamRead().

streamReadProp()

bool RDKit::streamReadProp ( std::istream & ss, Dict::Pair & pair, bool & dictHasNonPOD, const CustomPropHandlerVec & handlers = {} )

inline

Definition at line 556 of file StreamOps.h.

streamReadProps()

template<typename COUNT_TYPE = unsigned int>

unsigned int RDKit::streamReadProps ( std::istream & ss, RDProps & props, const CustomPropHandlerVec & handlers = {}, bool reset = true )

inline

Definition at line 626 of file StreamOps.h.

streamReadStringVec()

void RDKit::streamReadStringVec ( std::istream & ss, std::vector< std::string > & val, int version )

inline

Definition at line 326 of file StreamOps.h.

References rdvalue_is(), and streamRead().

Referenced by readRDStringVecValue().

streamReadVec()

template<class T >

void RDKit::streamReadVec	(	std::istream &	ss,
		T &	val )

Definition at line 316 of file StreamOps.h.

References rdvalue_is(), and streamRead().

Referenced by readRDVecValue().

streamWrite() [1/2]

void RDKit::streamWrite ( std::ostream & ss, const std::string & what )

inline

special case for string

Definition at line 267 of file StreamOps.h.

References rdvalue_is().

streamWrite() [2/2]

template<typename T >

void RDKit::streamWrite	(	std::ostream &	ss,
		const T &	val )

does a binary write of an object to a stream

Definition at line 261 of file StreamOps.h.

References rdvalue_is().

Referenced by streamWriteVec(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream(), RDKit::SparseIntVect< IndexType >::toString(), and RDKit::DataStructsExplicitBitVecPropHandler::write().

streamWriteProp()

bool RDKit::streamWriteProp ( std::ostream & ss, const Dict::Pair & pair, const CustomPropHandlerVec & handlers = {} )

inline

Definition at line 412 of file StreamOps.h.

streamWriteProps()

template<typename COUNT_TYPE = unsigned int>

bool RDKit::streamWriteProps ( std::ostream & ss, const RDProps & props, bool savePrivate = false, bool saveComputed = false, const CustomPropHandlerVec & handlers = {}, const std::unordered_set< std::string > & ignore = {} )

inline

Definition at line 485 of file StreamOps.h.

streamWriteVec()

template<typename T >

void RDKit::streamWriteVec	(	std::ostream &	ss,
		const T &	val )

Definition at line 274 of file StreamOps.h.

References rdvalue_is(), and streamWrite().

strip()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::strip

(

const std::string &

orig

)

StructuralFingerprintChemReaction()

RDKIT_CHEMREACTIONS_EXPORT ExplicitBitVect * RDKit::StructuralFingerprintChemReaction	(	const ChemicalReaction &	rxn,
		const ReactionFingerprintParams &	params = DefaultStructuralFPParams )

Generates a structural fingerprint for a reaction to use in screening

A structural fingerprint is generated as an ExplicitBitVect to use for searching e.g. substructure in reactions. By default the fingerprint is generated as 4096 BitVect using a PatternFP for reactants and products and tentatively agents which were finally concatenated

Parameters

rxn	the reaction to be fingerprinted
params	specific settings to manipulate fingerprint generation

Returns

the reaction fingerprint, as an ExplicitBitVect

Notes:

• the caller is responsible for deleteing the result

SubstructLibraryCanSerialize()

RDKIT_SUBSTRUCTLIBRARY_EXPORT bool RDKit::SubstructLibraryCanSerialize

(

)

SubstructMatch() [1/10]

RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch	(	const MolBundle &	bundle,
		const MolBundle &	query,
		const SubstructMatchParameters &	params = SubstructMatchParameters() )

SubstructMatch() [2/10]

RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch	(	const MolBundle &	bundle,
		const ROMol &	query,
		const SubstructMatchParameters &	params = SubstructMatchParameters() )

SubstructMatch() [3/10]

RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch	(	const ROMol &	mol,
		const MolBundle &	query,
		const SubstructMatchParameters &	params = SubstructMatchParameters() )

SubstructMatch() [4/10]

RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch	(	const ROMol &	mol,
		const ROMol &	query,
		const SubstructMatchParameters &	params = SubstructMatchParameters() )

Find a substructure match for a query in a molecule.

Parameters

mol	The ROMol to be searched
query	The query ROMol
matchParams	Parameters controlling the matching

Returns

The matches, if any

Referenced by SubstructMatch(), SubstructMatch(), SubstructMatch(), and SubstructMatch().

SubstructMatch() [5/10]

RDKIT_TAUTOMERQUERY_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch	(	const ROMol &	mol,
		const TautomerQuery &	query,
		const SubstructMatchParameters &	params )

SubstructMatch() [6/10]

RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch	(	ResonanceMolSupplier &	resMolSuppl,
		const ROMol &	query,
		const SubstructMatchParameters &	params = SubstructMatchParameters() )

Find all substructure matches for a query in a ResonanceMolSupplier object.

Parameters

resMolSuppl	The ResonanceMolSupplier object to be searched
query	The query ROMol
matchParams	Parameters controlling the matching

Returns

The matches, if any

SubstructMatch() [7/10]

template<>

bool RDKit::SubstructMatch ( ResonanceMolSupplier & resMolSupplier, const ROMol & query, MatchVectType & matchVect, bool recursionPossible, bool useChirality, bool useQueryQueryMatches )

inline

Definition at line 193 of file SubstructMatch.h.

References RDKit::SubstructMatchParameters::maxMatches, rdvalue_is(), RDKit::SubstructMatchParameters::recursionPossible, SubstructMatch(), RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

SubstructMatch() [8/10]

template<>

unsigned int RDKit::SubstructMatch ( ResonanceMolSupplier & resMolSupplier, const ROMol & query, std::vector< MatchVectType > & matchVect, bool uniquify, bool recursionPossible, bool useChirality, bool useQueryQueryMatches, unsigned int maxMatches, int numThreads )

inline

Definition at line 213 of file SubstructMatch.h.

References RDKit::SubstructMatchParameters::maxMatches, RDKit::SubstructMatchParameters::numThreads, rdvalue_is(), RDKit::SubstructMatchParameters::recursionPossible, SubstructMatch(), RDKit::SubstructMatchParameters::uniquify, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

SubstructMatch() [9/10]

template<typename T1 , typename T2 >

bool RDKit::SubstructMatch	(	T1 &	mol,
		const T2 &	query,
		MatchVectType &	matchVect,
		bool	recursionPossible = true,
		bool	useChirality = false,
		bool	useQueryQueryMatches = false )

Find a substructure match for a query.

Parameters

mol	The object to be searched
query	The query
matchVect	Used to return the match (pre-existing contents will be deleted)
recursionPossible	flags whether or not recursive matches are allowed
useChirality	use atomic CIP codes as part of the comparison
useQueryQueryMatches	if set, the contents of atom and bond queries will be used as part of the matching

Returns

whether or not a match was found

Definition at line 130 of file SubstructMatch.h.

References RDKit::SubstructMatchParameters::maxMatches, rdvalue_is(), RDKit::SubstructMatchParameters::recursionPossible, SubstructMatch(), RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

SubstructMatch() [10/10]

template<typename T1 , typename T2 >

unsigned int RDKit::SubstructMatch	(	T1 &	mol,
		const T2 &	query,
		std::vector< MatchVectType > &	matchVect,
		bool	uniquify = true,
		bool	recursionPossible = true,
		bool	useChirality = false,
		bool	useQueryQueryMatches = false,
		unsigned int	maxMatches = 1000,
		int	numThreads = 1 )

Find all substructure matches for a query.

Parameters

mol	The object to be searched
query	The query
matchVect	Used to return the matches (pre-existing contents will be deleted)
uniquify	Toggles uniquification (by atom index) of the results
recursionPossible	flags whether or not recursive matches are allowed
useChirality	use atomic CIP codes as part of the comparison
useQueryQueryMatches	if set, the contents of atom and bond queries will be used as part of the matching
maxMatches	The maximum number of matches that will be returned. In high-symmetry cases with medium-sized molecules, it is very easy to end up with a combinatorial explosion in the number of possible matches. This argument prevents that from having unintended consequences

Returns

the number of matches found

Definition at line 170 of file SubstructMatch.h.

References RDKit::SubstructMatchParameters::maxMatches, RDKit::SubstructMatchParameters::numThreads, rdvalue_is(), RDKit::SubstructMatchParameters::recursionPossible, SubstructMatch(), RDKit::SubstructMatchParameters::uniquify, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

substructMatchParamsToJSON()

RDKIT_SUBSTRUCTMATCH_EXPORT std::string RDKit::substructMatchParamsToJSON

(

const SubstructMatchParameters &

params

)

SwapBytes()

template<class T , unsigned int size>

T RDKit::SwapBytes ( T value )

inline

Definition at line 45 of file StreamOps.h.

References rdvalue_is().

TanimotoSimilarity()

template<typename IndexType >

double RDKit::TanimotoSimilarity	(	const SparseIntVect< IndexType > &	v1,
		const SparseIntVect< IndexType > &	v2,
		bool	returnDistance = false,
		double	bounds = 0.0 )

Definition at line 564 of file SparseIntVect.h.

References rdvalue_is(), and TverskySimilarity().

Referenced by RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >::Match().

TautomerQueryCanSerialize()

RDKIT_TAUTOMERQUERY_EXPORT bool RDKit::TautomerQueryCanSerialize

(

)

toJSON() [1/3]

RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON	(	const RGroupColumn &	rgr,
		const std::string &	prefix = "" )

Returns a JSON form The prefix argument is added to each line in the output

toJSON() [2/3]

RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON	(	const RGroupRow &	rgr,
		const std::string &	prefix = "" )

Returns a JSON form The prefix argument is added to each line in the output

toJSON() [3/3]

RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON	(	const RGroupRows &	rgr,
		const std::string &	prefix = "" )

Returns a JSON form The prefix argument is added to each line in the output

toPrime()

RDKIT_SUBSTRUCTMATCH_EXPORT double RDKit::toPrime

(

const MatchVectType &

v

)

translateChiralFlagToStereoGroups()

RDKIT_FILEPARSERS_EXPORT void RDKit::translateChiralFlagToStereoGroups	(	ROMol &	mol,
		StereoGroupType	zeroFlagGroupType = StereoGroupType::STEREO_AND )

generate enhanced stereo groups based on the status of the chiral flag property

TverskySimilarity()

template<typename IndexType >

double RDKit::TverskySimilarity	(	const SparseIntVect< IndexType > &	v1,
		const SparseIntVect< IndexType > &	v2,
		double	a,
		double	b,
		bool	returnDistance = false,
		double	bounds = 0.0 )

Definition at line 535 of file SparseIntVect.h.

References RDKit::SparseIntVect< IndexType >::getLength(), RDUNUSED_PARAM, and rdvalue_is().

Referenced by TanimotoSimilarity().

Union() [1/2]

RDKIT_RDGENERAL_EXPORT void RDKit::Union	(	const INT_VECT &	r1,
		const INT_VECT &	r2,
		INT_VECT &	res )

calculate the union of two INT_VECTs and put the results in a third vector

Union() [2/2]

RDKIT_RDGENERAL_EXPORT void RDKit::Union	(	const VECT_INT_VECT &	rings,
		INT_VECT &	res,
		const INT_VECT *	exclude = nullptr )

calculating the union of the INT_VECT's in a VECT_INT_VECT

Parameters

rings	the INT_VECT's to consider
res	used to return results
exclude	any values in this optional INT_VECT will be excluded from the union.

updateFromSequence()

template<typename IndexType , typename SequenceType >

void RDKit::updateFromSequence	(	SparseIntVect< IndexType > &	vect,
		const SequenceType &	seq )

Definition at line 416 of file SparseIntVect.h.

References rdvalue_is().

updateProductsStereochem()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::updateProductsStereochem

(

ChemicalReaction *

rxn

)

updateSubstructMatchParamsFromJSON()

RDKIT_SUBSTRUCTMATCH_EXPORT void RDKit::updateSubstructMatchParamsFromJSON	(	SubstructMatchParameters &	params,
		const std::string &	json )

vectToString()

template<class T >

std::string RDKit::vectToString

(

RDValue

val

)

Definition at line 176 of file RDValue.h.

References rdvalue_is().

WedgeBond()

RDKIT_FILEPARSERS_EXPORT void RDKit::WedgeBond	(	Bond *	bond,
		unsigned int	fromAtomIdx,
		const Conformer *	conf )

Deprecated

use Chirality::wedgeBond instead

WedgeMolBonds()

RDKIT_FILEPARSERS_EXPORT void RDKit::WedgeMolBonds	(	ROMol &	mol,
		const Conformer *	conf )

Deprecated

use Chirality::wedgeMolBonds instead

Variable Documentation

_rgroupInputDummy

const std::string RDKit::_rgroupInputDummy

extern

additionalParamData

std::string RDKit::additionalParamData

extern

BITS_PER_INT

const unsigned int RDKit::BITS_PER_INT = 32

Definition at line 21 of file DiscreteValueVect.h.

Referenced by RDKit::DiscreteValueVect::DiscreteValueVect().

boostVersion

RDKIT_RDGENERAL_EXPORT const char* RDKit::boostVersion

extern

ci_ATOM_HOLDER

RDKIT_GRAPHMOL_EXPORT const int RDKit::ci_ATOM_HOLDER

extern

ci_LEADING_BOND

RDKIT_GRAPHMOL_EXPORT const int RDKit::ci_LEADING_BOND

extern

ci_RIGHTMOST_ATOM

RDKIT_GRAPHMOL_EXPORT const int RDKit::ci_RIGHTMOST_ATOM

extern

complexQueries

const std::vector<std::string> RDKit::complexQueries

Initial value:

= {"A", "AH", "Q", "QH",
                                                 "X", "XH", "M", "MH"}

Definition at line 599 of file QueryOps.h.

ctdIGNORE_H_H_CONTACTS

const unsigned int RDKit::ctdIGNORE_H_H_CONTACTS = 0x1

static

Definition at line 16 of file ProximityBonds.h.

DAMP

const double RDKit::DAMP = 0.5

Definition at line 28 of file GasteigerParams.h.

DAMP_SCALE

const double RDKit::DAMP_SCALE = 0.5

Definition at line 27 of file GasteigerParams.h.

dashes

const DashPattern RDKit::dashes {6.0, 4.0}

Definition at line 28 of file DrawShape.h.

DEFAULT_FILTERMATCHERBASE_NAME

RDKIT_FILTERCATALOG_EXPORT const char* RDKit::DEFAULT_FILTERMATCHERBASE_NAME

extern

defaultConfId

int RDKit::defaultConfId = -1

static

Definition at line 35 of file MolWriters.h.

DefaultDifferenceFPParams

RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams RDKit::DefaultDifferenceFPParams

extern

DefaultStructuralFPParams

RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams RDKit::DefaultStructuralFPParams

extern

done

RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RDKit::done

extern

dots

const DashPattern RDKit::dots {2.0, 6.0}

Definition at line 27 of file DrawShape.h.

elementNames

RDKIT_GRAPHMOL_EXPORT const std::vector<std::string> RDKit::elementNames

extern

EMPTY_CORE_LABEL

const unsigned int RDKit::EMPTY_CORE_LABEL = -100000

Definition at line 28 of file RGroupUtils.h.

EPS_DOUBLE

RDKIT_RDGENERAL_EXPORT const double RDKit::EPS_DOUBLE

extern

FILE_MAXLINE

const int RDKit::FILE_MAXLINE

Initial value:

=
    256

an assumed maximum length for lines read from files

Definition at line 26 of file utils.h.

firstThousandPrimes

RDKIT_RDGENERAL_EXPORT int RDKit::firstThousandPrimes

extern

Definition at line 24 of file utils.h.

IONXH

const double RDKit::IONXH = 20.02

Definition at line 25 of file GasteigerParams.h.

isotopesAtomData

RDKIT_GRAPHMOL_EXPORT const std::string RDKit::isotopesAtomData[]

extern

LayeredFingerprintMolVersion

const std::string RDKit::LayeredFingerprintMolVersion = "0.7.0"

Definition at line 113 of file Fingerprints.h.

lineWidthScaleFactor

const double RDKit::lineWidthScaleFactor = 0.02

static

Definition at line 63 of file MolDraw2DHelpers.h.

marvinBondOrders

const std::vector<std::string> RDKit::marvinBondOrders {"1", "2", "3", "A"}

Definition at line 40 of file MarvinDefs.h.

marvinConventionTypes

const std::vector<std::string> RDKit::marvinConventionTypes {"cxn:coord"}

Definition at line 42 of file MarvinDefs.h.

marvinQueryBondsTypes

const std::vector<std::string> RDKit::marvinQueryBondsTypes {"SD", "SA", "DA", "Any"}

Definition at line 41 of file MarvinDefs.h.

marvinRadicalToRadicalElectrons

const std::map<std::string, int> RDKit::marvinRadicalToRadicalElectrons

Initial value:

{
    {"monovalent", 1}, {"divalent", 2},   {"divalent1", 2},  {"divalent3", 2},
    {"trivalent", 3},  {"trivalent2", 3}, {"trivalent4", 3}, {"4", 4}}

Definition at line 49 of file MarvinDefs.h.

marvinRadicalVals

const std::vector<std::string> RDKit::marvinRadicalVals

Initial value:

{
    "monovalent", "divalent",   "divalent1",  "divalent3",
    "trivalent",  "trivalent2", "trivalent4", "4"}

Definition at line 46 of file MarvinDefs.h.

marvinStereoConventionTypes

const std::vector<std::string> RDKit::marvinStereoConventionTypes {"1", "3", "4", "6"}

Definition at line 44 of file MarvinDefs.h.

marvinStereoDictRefTypes

const std::vector<std::string> RDKit::marvinStereoDictRefTypes {"cml:W", "cml:H"}

Definition at line 43 of file MarvinDefs.h.

massIntegerConversionFactor

const int RDKit::massIntegerConversionFactor = 1000

Definition at line 155 of file QueryOps.h.

Referenced by makeAtomMassQuery(), and queryAtomMass().

MAX_DOUBLE

RDKIT_RDGENERAL_EXPORT const double RDKit::MAX_DOUBLE

extern

MAX_INT

RDKIT_RDGENERAL_EXPORT const double RDKit::MAX_INT

extern

MAX_LONGINT

RDKIT_RDGENERAL_EXPORT const double RDKit::MAX_LONGINT

extern

maxFingerprintLayers

const unsigned int RDKit::maxFingerprintLayers = 10

Definition at line 112 of file Fingerprints.h.

noDash

const DashPattern RDKit::noDash

Definition at line 26 of file DrawShape.h.

NUM_PRIMES_AVAIL

const int RDKit::NUM_PRIMES_AVAIL = 1000

the number of primes available and stored

Definition at line 15 of file primes.h.

paramData

std::string RDKit::paramData

extern

PatternFingerprintMolVersion

const std::string RDKit::PatternFingerprintMolVersion = "1.0.0"

Definition at line 149 of file Fingerprints.h.

periodicTableAtomData

RDKIT_GRAPHMOL_EXPORT const std::string RDKit::periodicTableAtomData

extern

radicalElectronsToMarvinRadical

const std::map<int, std::string> RDKit::radicalElectronsToMarvinRadical

Initial value:

{
    {1, "monovalent"}, {2, "divalent"}, {3, "trivalent4"}, {4, "4"}}

Definition at line 53 of file MarvinDefs.h.

RDKFingerprintMolVersion

const std::string RDKit::RDKFingerprintMolVersion = "2.0.0"

Definition at line 63 of file Fingerprints.h.

rdkitBuild

RDKIT_RDGENERAL_EXPORT const char* RDKit::rdkitBuild

extern

rdkitQtVersion

RDKIT_MOLDRAW2DQT_EXPORT const char* RDKit::rdkitQtVersion

extern

rdkitVersion

RDKIT_RDGENERAL_EXPORT const char* RDKit::rdkitVersion

extern

RLABEL

RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RDKit::RLABEL

extern

RLABEL_CORE_INDEX

RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RDKit::RLABEL_CORE_INDEX

extern

RLABEL_TYPE

RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RDKit::RLABEL_TYPE

extern

shortDashes

const DashPattern RDKit::shortDashes {2.0, 2.0}

Definition at line 29 of file DrawShape.h.

SIDECHAIN_RLABELS

RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RDKit::SIDECHAIN_RLABELS

extern

SMALL_DOUBLE

RDKIT_RDGENERAL_EXPORT const double RDKit::SMALL_DOUBLE

extern

SMARTS_MATCH_NAME_DEFAULT

RDKIT_FILTERCATALOG_EXPORT const char* RDKit::SMARTS_MATCH_NAME_DEFAULT

extern

sruSgroupConnectChoices

const std::vector<std::string> RDKit::sruSgroupConnectChoices {"hh", "ht", "eu"}

Definition at line 39 of file MarvinDefs.h.

substructLayers

const unsigned int RDKit::substructLayers = 0x07

Definition at line 114 of file Fingerprints.h.

UNLABELED_CORE_ATTACHMENT

RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RDKit::UNLABELED_CORE_ATTACHMENT

extern