RDKit: RDKit Namespace Reference

| RDKit Open-source cheminformatics and machine learning.

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Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
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 | EnumerateStereoisomers
namespace | EnumerationStrategyPickler
namespace | EnumerationTypes
namespace | FileParsers
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 | MolProcessing
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 | SynthonSpaceSearch
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...
struct | AtomCoordsMatchFunctor
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 | ControlCCaught
class | ControlCHandler
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
struct | ExtendedQueryMol
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 | HasPropWithValueQueryBase
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...
class | MaxFindBondOrdersItersExceeded
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 | PairHolder
class | PatternHolder
class | PDBWriter
class | PeriodicTable
| singleton class for retrieving information about atoms More...
struct | PNGMetadataParams
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 | RealValueVect
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 | RigorousEnhancedStereoException
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
struct | SubsetInfo
struct | SubsetOptions
| Subsetting Options for copyMolSubset. More...
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 class | FingerprintType { AtomPairFP = 1 , TopologicalTorsionFP , MorganFP , RDKitFP , PatternFP }
enum | ReactionMoleculeType { Reactant , Product , Agent }
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 | 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 class | StereoGroupAbsOptions { OnlyIncludeWhenOtherGroupsExist , NeverInclude , AlwaysInclude }
enum class | StereoGroupType { STEREO_ABSOLUTE = 0 , STEREO_OR = 1 , STEREO_AND = 2 }
enum class | SubsetMethod { BONDS_BETWEEN_ATOMS , BONDS = 1 }
| Subsetting Methods for copyMolSubset. More...
enum | EEndian { LITTLE_ENDIAN_ORDER , BIG_ENDIAN_ORDER }
enum | Mol2Type

## 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
RDKIT_GRAPHMOL_EXPORT unsigned int | numPiElectrons (const Atom &atom)
| returns the number of pi electrons on the atom
bool | isDative (const Bond::BondType bt)
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, const SmilesWriteParams &params)
| returns the reaction SMARTS for a reaction
std::string | ChemicalReactionToRxnSmarts (const ChemicalReaction &rxn)
| 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 std::string | ChemicalReactionToRxnSmiles (const ChemicalReaction &rxn, const SmilesWriteParams &params=SmilesWriteParams())
| returns the reaction SMILES for a reaction
std::string | ChemicalReactionToRxnSmiles (const ChemicalReaction &rxn, bool canonical)
| 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 std::string | ChemicalReactionToCXRxnSmarts (const ChemicalReaction &rxn, const SmilesWriteParams &params, std::uint32_t flags=SmilesWrite::CXSmilesFields::CX_ALL)
| returns the reaction SMARTS for a reaction with CX extension
std::string | ChemicalReactionToCXRxnSmarts (const ChemicalReaction &rxn)
| 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 std::string | ChemicalReactionToCXRxnSmiles (const ChemicalReaction &rxn, const SmilesWriteParams &params, std::uint32_t flags=SmilesWrite::CXSmilesFields::CX_ALL)
| returns the reaction SMILES for a reaction with CX extension
std::string | ChemicalReactionToCXRxnSmiles (const ChemicalReaction &rxn, bool canonical=true)
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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
| BETTER_ENUM_CLASS (MolzipLabel, unsigned int, AtomMapNumber, Isotope, FragmentOnBonds, AtomType, AtomProperty)
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.
RDKIT_CHEMTRANSFORMS_EXPORT void | parseMolzipParametersJSON (MolzipParams &params, const char *details_json)
| Parse MolzipParams from JSON.
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, size_t maxIterations=0)
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, size_t maxIterations=0)
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. Note: If the ChemDraw extensions are available, this auto detects between CDXML and CDX
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. Note: If the ChemDraw extensions are available, This function uses the file extension to determine the file type, .cdx or .cdxml If not, it defaults to CDXML
std::vector< std::unique_ptr< RWMol > > | CDXMLToMols (const std::string &cdxml, bool sanitize=true, bool removeHs=true)
| construct molecules from a CDXML block 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. Note: to parse CDX files see the CDXParserParams variant of this function
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 std::string | MolToV2KMolBlock (const ROMol &mol, const MolWriterParams &params=MolWriterParams(), int confId=-1)
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)
template<typename OutputType>
RDKIT_FINGERPRINTS_EXPORT std::string | generatorToJSON (const FingerprintGenerator< OutputType > &generator)
| generate JSON representation of a FingerprintGenerator
RDKIT_FINGERPRINTS_EXPORT std::unique_ptr< FingerprintGenerator< std::uint64_t > > | generatorFromJSON (const std::string &jsonStr)
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)
| BETTER_ENUM (DrawElement, uint32_t, NONE=0, PRESHAPES=1<< 0, BONDS=1<< 1, ATOMLABELS=1<< 2, HIGHLIGHTS=1<< 3, ANNOTATIONS=1<< 4, RADICALS=1<< 5, POSTSHAPES=1<< 6, ALL=0x7fffffff)
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, double tolerance=0.0)
template<class Target>
Queries::EqualityQuery< int, const Target *, true > * | makePropQuery (const std::string &propname, const ExplicitBitVect &val, double 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 void | updateRGroupDecompositionParametersFromJSON (RGroupDecompositionParameters &params, const std::string &details_json)
RDKIT_RGROUPDECOMPOSITION_EXPORT void | updateRGroupDecompositionParametersFromJSON (RGroupDecompositionParameters &params, const char *details_json)
| BETTER_ENUM (RGroupLabels, unsigned int, IsotopeLabels=0x01, AtomMapLabels=0x02, AtomIndexLabels=0x04, RelabelDuplicateLabels=0x08, MDLRGroupLabels=0x10, DummyAtomLabels=0x20, AutoDetect=0xFF)
| BETTER_ENUM (RGroupMatching, unsigned int, Greedy=0x01, GreedyChunks=0x02, Exhaustive=0x04, NoSymmetrization=0x08, GA=0x10)
| BETTER_ENUM (RGroupLabelling, unsigned int, AtomMap=0x01, Isotope=0x02, MDLRGroup=0x04)
| BETTER_ENUM (RGroupCoreAlignment, unsigned int, NoAlignment=0x0, MCS=0x01)
| BETTER_ENUM (RGroupScore, unsigned int, Match=0x1, FingerprintVariance=0x4)
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 std::string | toJSON (const RGroupColumns &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 void | canonicalizeStereoGroups (std::unique_ptr< ROMol > &mol, StereoGroupAbsOptions outputAbsoluteGroups=StereoGroupAbsOptions::OnlyIncludeWhenOtherGroupsExist, unsigned int maxStereoGroups=12)
RDKIT_SMILESPARSE_EXPORT std::string | MolToSmarts (const ROMol &mol, const SmilesWriteParams &params)
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 SmilesWriteParams &params, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr)
RDKIT_SMILESPARSE_EXPORT std::string | MolToCXSmarts (const ROMol &mol, const SmilesWriteParams &params)
| returns the CXSMARTS for a molecule
RDKIT_SMILESPARSE_EXPORT std::string | MolFragmentToCXSmarts (const ROMol &mol, const SmilesWriteParams &params, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr)
std::string | MolFragmentToSmarts (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, bool doIsomericSmarts=true)
std::string | MolToCXSmarts (const ROMol &mol, bool doIsomericSmarts=true)
| returns the CXSMARTS for a molecule
std::string | MolFragmentToCXSmarts (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, bool doIsomericSmarts=true)
RDKIT_SMILESPARSE_EXPORT void | updateSmilesWriteParamsFromJSON (SmilesWriteParams &params, const std::string &details_json)
RDKIT_SMILESPARSE_EXPORT void | updateSmilesWriteParamsFromJSON (SmilesWriteParams &params, const char *details_json)
RDKIT_SMILESPARSE_EXPORT void | updateCXSmilesFieldsFromJSON (std::uint32_t &cxSmilesFields, unsigned int &restoreBondDirs, const std::string &details_json)
RDKIT_SMILESPARSE_EXPORT void | updateCXSmilesFieldsFromJSON (std::uint32_t &cxSmilesFields, unsigned int &restoreBondDirs, const char *details_json)
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, bool ignoreAtomMapNumbers=false)
| returns SMILES for a molecule, canonical by default
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
| BETTER_ENUM (RestoreBondDirOption, unsigned int, RestoreBondDirOptionTrue=0, RestoreBondDirOptionClear=1)
RDKIT_SMILESPARSE_EXPORT std::string | MolToCXSmiles (const ROMol &mol, const SmilesWriteParams &ps, std::uint32_t flags=SmilesWrite::CXSmilesFields::CX_ALL, RestoreBondDirOption restoreBondDirs=RestoreBondDirOption::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 | removeBondFromGroups (const Bond *bond, 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_GRAPHMOL_EXPORT std::unique_ptr< RDKit::RWMol > | copyMolSubset (const RDKit::ROMol &mol, const std::vector< unsigned int > &atoms, const std::vector< unsigned int > &bonds, const SubsetOptions &options=SubsetOptions())
RDKIT_GRAPHMOL_EXPORT std::unique_ptr< RDKit::RWMol > | copyMolSubset (const RDKit::ROMol &mol, const std::vector< unsigned int > &atoms, const std::vector< unsigned int > &bonds, SubsetInfo &subsetInfo, const SubsetOptions &options=SubsetOptions())
RDKIT_GRAPHMOL_EXPORT std::unique_ptr< RDKit::RWMol > | copyMolSubset (const RDKit::ROMol &mol, const std::vector< unsigned int > &path, const SubsetOptions &options=SubsetOptions())
RDKIT_GRAPHMOL_EXPORT std::unique_ptr< RDKit::RWMol > | copyMolSubset (const RDKit::ROMol &mol, const std::vector< unsigned int > &path, SubsetInfo &subsetInfo, const SubsetOptions &options=SubsetOptions())
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)
RDKIT_DATASTRUCTS_EXPORT double | computeL1Norm (const RealValueVect &v1, const RealValueVect &v2)
| returns L1 Norm of vectors
RDKIT_DATASTRUCTS_EXPORT RealValueVect | operator+ (const RealValueVect &p1, const RealValueVect &p2)
| returns the sum of vectors
RDKIT_DATASTRUCTS_EXPORT RealValueVect | operator- (const RealValueVect &p1, const RealValueVect &p2)
| returns the difference of vectors
RDKIT_DATASTRUCTS_EXPORT RealValueVect | operator| (const RealValueVect &p1, const RealValueVect &p2)
| support rvv3 = rvv1|rvv2
RDKIT_DATASTRUCTS_EXPORT RealValueVect | operator& (const RealValueVect &p1, const RealValueVect &p2)
| support rvv3 = rvv1&rvv2
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, const PNGMetadataParams &params)
| adds metadata for an ROMol to the data from a PNG stream. The modified PNG data is returned.
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 | addMolToPNGString (const ROMol &mol, const std::string &pngString, const PNGMetadataParams &params)
| 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.
std::string | addMolToPNGFile (const ROMol &mol, const std::string &fname, const PNGMetadataParams &params)
| 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
static const unsigned int | ctdQUICKREMOVE_H_H_CONTACTS = 0x2
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
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 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 | NUM_PRIMES_AVAIL
| the number of primes available and stored
RDKIT_RDGENERAL_EXPORT int | firstThousandPrimes [NUM_PRIMES_AVAIL]
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 35 of file QueryOps.h.

## ◆ ATOM_BOOL_QUERY

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

Definition at line 32 of file QueryOps.h.

## ◆ ATOM_EQUALS_QUERY

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

Definition at line 44 of file QueryOps.h.

## ◆ ATOM_GREATER_QUERY

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

Definition at line 47 of file QueryOps.h.

## ◆ ATOM_GREATEREQUAL_QUERY

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

Definition at line 51 of file QueryOps.h.

## ◆ ATOM_LESS_QUERY

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

Definition at line 55 of file QueryOps.h.

## ◆ ATOM_LESSEQUAL_QUERY

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

Definition at line 58 of file QueryOps.h.

## ◆ ATOM_NULL_QUERY

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

Definition at line 68 of file QueryOps.h.

## ◆ ATOM_OR_QUERY

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

Definition at line 38 of file QueryOps.h.

## ◆ ATOM_PROP_QUERY

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

Definition at line 854 of file QueryOps.h.

## ◆ ATOM_RANGE_QUERY

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

Definition at line 61 of file QueryOps.h.

## ◆ ATOM_SET_QUERY

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

Definition at line 64 of file QueryOps.h.

## ◆ ATOM_XOR_QUERY

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

Definition at line 41 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 36 of file QueryOps.h.

## ◆ BOND_BOOL_QUERY

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

Definition at line 33 of file QueryOps.h.

## ◆ BOND_EQUALS_QUERY

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

Definition at line 45 of file QueryOps.h.

## ◆ BOND_GREATER_QUERY

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

Definition at line 48 of file QueryOps.h.

## ◆ BOND_GREATEREQUAL_QUERY

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

Definition at line 53 of file QueryOps.h.

## ◆ BOND_LESS_QUERY

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

Definition at line 56 of file QueryOps.h.

## ◆ BOND_LESSEQUAL_QUERY

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

Definition at line 59 of file QueryOps.h.

## ◆ BOND_NULL_QUERY

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

Definition at line 67 of file QueryOps.h.

## ◆ BOND_OR_QUERY

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

Definition at line 39 of file QueryOps.h.

## ◆ BOND_PROP_QUERY

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

Definition at line 855 of file QueryOps.h.

## ◆ BOND_RANGE_QUERY

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

Definition at line 62 of file QueryOps.h.

## ◆ BOND_SET_QUERY

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

Definition at line 65 of file QueryOps.h.

## ◆ BOND_XOR_QUERY

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

Definition at line 42 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 68 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 707 of file QueryOps.h.

## ◆ ConstBondPtr

typedef Bond const* RDKit::ConstBondPtr

Definition at line 817 of file QueryOps.h.

## ◆ CustomPropHandlerVec

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

Definition at line 387 of file StreamOps.h.

## ◆ DashPattern

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

Definition at line 69 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 373 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 328 of file types.h.

## ◆ DOUBLE_VECT_CI

typedef DOUBLE_VECT::const_iterator RDKit::DOUBLE_VECT_CI

Definition at line 330 of file types.h.

## ◆ DOUBLE_VECT_I

typedef DOUBLE_VECT::iterator RDKit::DOUBLE_VECT_I

Definition at line 329 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 19 of file MolChemicalFeatureFactory.h.

## ◆ FeatSPtrList

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

Definition at line 20 of file MolChemicalFeatureFactory.h.

## ◆ FeatSPtrList_I

typedef FeatSPtrList::iterator RDKit::FeatSPtrList_I

Definition at line 21 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 345 of file types.h.

## ◆ INT_DEQUE_CI

typedef INT_DEQUE::const_iterator RDKit::INT_DEQUE_CI

Definition at line 347 of file types.h.

## ◆ INT_DEQUE_I

typedef INT_DEQUE::iterator RDKit::INT_DEQUE_I

Definition at line 346 of file types.h.

## ◆ INT_INT_DEQ_MAP

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

Definition at line 349 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 350 of file types.h.

## ◆ INT_INT_VECT_MAP

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

Definition at line 338 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 339 of file types.h.

## ◆ INT_LIST

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

Definition at line 309 of file types.h.

## ◆ INT_LIST_CI

typedef INT_LIST::const_iterator RDKit::INT_LIST_CI

Definition at line 311 of file types.h.

## ◆ INT_LIST_I

typedef INT_LIST::iterator RDKit::INT_LIST_I

Definition at line 310 of file types.h.

## ◆ INT_MAP_INT

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

Definition at line 341 of file types.h.

## ◆ INT_MAP_INT_CI

typedef INT_MAP_INT::const_iterator RDKit::INT_MAP_INT_CI

Definition at line 343 of file types.h.

## ◆ INT_MAP_INT_I

typedef INT_MAP_INT::iterator RDKit::INT_MAP_INT_I

Definition at line 342 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 352 of file types.h.

## ◆ INT_SET_CI

typedef INT_SET::const_iterator RDKit::INT_SET_CI

Definition at line 354 of file types.h.

## ◆ INT_SET_I

typedef INT_SET::iterator RDKit::INT_SET_I

Definition at line 353 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 303 of file types.h.

## ◆ INT_VECT_CI

typedef INT_VECT::const_iterator RDKit::INT_VECT_CI

Definition at line 305 of file types.h.

## ◆ INT_VECT_CRI

typedef INT_VECT::const_reverse_iterator RDKit::INT_VECT_CRI

Definition at line 307 of file types.h.

## ◆ INT_VECT_I

typedef INT_VECT::iterator RDKit::INT_VECT_I

Definition at line 304 of file types.h.

## ◆ INT_VECT_RI

typedef INT_VECT::reverse_iterator RDKit::INT_VECT_RI

Definition at line 306 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 313 of file types.h.

## ◆ LIST_INT_VECT_CI

typedef LIST_INT_VECT::const_iterator RDKit::LIST_INT_VECT_CI

Definition at line 315 of file types.h.

## ◆ LIST_INT_VECT_I

typedef LIST_INT_VECT::iterator RDKit::LIST_INT_VECT_I

Definition at line 314 of file types.h.

## ◆ LONGINT

typedef long long int RDKit::LONGINT

Definition at line 282 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 878 of file ROMol.h.

## ◆ MOL_PTR_VECT_CI

typedef MOL_PTR_VECT::const_iterator RDKit::MOL_PTR_VECT_CI

Definition at line 881 of file ROMol.h.

## ◆ MOL_PTR_VECT_I

typedef MOL_PTR_VECT::iterator RDKit::MOL_PTR_VECT_I

Definition at line 882 of file ROMol.h.

## ◆ MOL_SPTR_VECT

typedef std::vector< boost::shared_ptr< ROMol > > RDKit::MOL_SPTR_VECT

Definition at line 21 of file FragCatParams.h.

## ◆ MOL_VECT

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

Definition at line 876 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 22 of file ChemTransforms.h.

## ◆ RWMOL_SPTR

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

Definition at line 222 of file RWMol.h.

## ◆ RWMOL_SPTR_VECT

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

Definition at line 223 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 335 of file types.h.

## ◆ STR_UINT_MAP_CI

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

Definition at line 336 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 324 of file types.h.

## ◆ STR_VECT_I

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

Definition at line 325 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 301 of file types.h.

## ◆ UINT

typedef unsigned int RDKit::UINT

Definition at line 299 of file types.h.

## ◆ UINT_VECT

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

Definition at line 322 of file types.h.

## ◆ UINT_VECT_CI

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

Definition at line 321 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 300 of file types.h.

## ◆ VECT_DOUBLE_VECT

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

Definition at line 331 of file types.h.

## ◆ VECT_DOUBLE_VECT_CI

typedef VECT_DOUBLE_VECT::const_iterator RDKit::VECT_DOUBLE_VECT_CI

Definition at line 333 of file types.h.

## ◆ VECT_DOUBLE_VECT_I

typedef VECT_DOUBLE_VECT::iterator RDKit::VECT_DOUBLE_VECT_I

Definition at line 332 of file types.h.

## ◆ VECT_INT_VECT

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

Definition at line 317 of file types.h.

## ◆ VECT_INT_VECT_CI

typedef VECT_INT_VECT::const_iterator RDKit::VECT_INT_VECT_CI

Definition at line 319 of file types.h.

## ◆ VECT_INT_VECT_I

typedef VECT_INT_VECT::iterator RDKit::VECT_INT_VECT_I

Definition at line 318 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 27 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 class RDKit::FingerprintType
| strong

Enumerator
AtomPairFP |
TopologicalTorsionFP |
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 485 of file FingerprintGenerator.h.

## ◆ IsSgroupInAtomSetResult

enum RDKit::IsSgroupInAtomSetResult

Enumerator
SgroupInAtomSet |
SgroupNotInAtomSet |
SgroupBothInAndNotInAtomSet |

Definition at line 49 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.

## ◆ MultiColourHighlightStyle

enum class RDKit::MultiColourHighlightStyle
| strong

Enumerator
CIRCLEANDLINE |
LASSO |

Definition at line 157 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.

## ◆ RingComparator

enum RDKit::RingComparator

Enumerator
IgnoreRingFusion |
PermissiveRingFusion |
StrictRingFusion |

Definition at line 35 of file FMCS.h.

## ◆ StereoGroupAbsOptions

enum class RDKit::StereoGroupAbsOptions
| strong

Enumerator
OnlyIncludeWhenOtherGroupsExist |
NeverInclude |
AlwaysInclude |

Definition at line 22 of file CanonicalizeStereoGroups.h.

## ◆ StereoGroupType

enum class RDKit::StereoGroupType
| strong

Enumerator
STEREO_ABSOLUTE |
STEREO_OR |
STEREO_AND |

Definition at line 30 of file StereoGroup.h.

## ◆ SubsetMethod

enum class RDKit::SubsetMethod
| strong

Subsetting Methods for copyMolSubset.

Enumerator
BONDS_BETWEEN_ATOMS |
BONDS |

Definition at line 29 of file Subset.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 381 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(), and RDKIT_CHEMREACTIONS_EXPORT.

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 369 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 103 of file PNGParser.h.

References addMetadataToPNGStream().

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

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 93 of file PNGParser.h.

References addMetadataToPNGStream().

## ◆ addMolToPNGFile() [1/2]

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 240 of file PNGParser.h.

References addMolToPNGStream().

## ◆ addMolToPNGFile() [2/2]

std::string RDKit::addMolToPNGFile | ( | const ROMol & | mol,
|  | const std::string & | fname,
|  | const PNGMetadataParams & | params )
| 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 252 of file PNGParser.h.

References addMolToPNGStream().

## ◆ addMolToPNGStream() [1/2]

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

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

Definition at line 203 of file PNGParser.h.

References addMolToPNGStream(), RDKit::PNGMetadataParams::includeMol, RDKit::PNGMetadataParams::includePkl, and RDKit::PNGMetadataParams::includeSmiles.

## ◆ addMolToPNGStream() [2/2]

RDKIT_FILEPARSERS_EXPORT std::string RDKit::addMolToPNGStream | ( | const ROMol & | mol,
|  | std::istream & | iStream,
|  | const PNGMetadataParams & | params )

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
  params | instance of PNGMetadataParams

References RDKIT_FILEPARSERS_EXPORT.

Referenced by addMolToPNGFile(), addMolToPNGFile(), addMolToPNGStream(), addMolToPNGString(), and addMolToPNGString().

## ◆ addMolToPNGString() [1/2]

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 217 of file PNGParser.h.

References addMolToPNGStream().

## ◆ addMolToPNGString() [2/2]

std::string RDKit::addMolToPNGString | ( | const ROMol & | mol,
|  | const std::string & | pngString,
|  | const PNGMetadataParams & | params )
| inline

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

Definition at line 230 of file PNGParser.h.

References addMolToPNGStream().

## ◆ 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

References RDKIT_SUBSTRUCTLIBRARY_EXPORT.

## ◆ 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

References RDKIT_SUBSTRUCTLIBRARY_EXPORT.

## ◆ 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`

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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(), and RDKIT_CHEMREACTIONS_EXPORT.

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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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

References RDKit::StereoBondThresholds::DBL_BOND_NO_STEREO, and RDKIT_FILEPARSERS_EXPORT.

## ◆ appendPackedIntToStream()

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

Packs an integer and outputs it to a stream.

Definition at line 109 of file StreamOps.h.

References CHECK_INVARIANT.

## ◆ assignAvalonPalette()

void RDKit::assignAvalonPalette | ( | ColourPalette & | palette | ) |
| inline

use the color palette from the Avalon renderer

Definition at line 96 of file MolDraw2DHelpers.h.

## ◆ assignBWPalette()

void RDKit::assignBWPalette | ( | ColourPalette & | palette | ) |
| inline

Definition at line 152 of file MolDraw2DHelpers.h.

## ◆ 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 118 of file MolDraw2DHelpers.h.

## ◆ assignDarkModePalette()

void RDKit::assignDarkModePalette | ( | ColourPalette & | palette | ) |
| inline

Definition at line 136 of file MolDraw2DHelpers.h.

Referenced by setDarkMode().

## ◆ assignDefaultPalette()

void RDKit::assignDefaultPalette | ( | ColourPalette & | palette | ) |
| inline

use the RDKit's default palette r

Definition at line 78 of file MolDraw2DHelpers.h.

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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ atomCompat()

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

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ augmentTagName()

RDKIT_RDGENERAL_EXPORT std::string RDKit::augmentTagName | ( | const std::string & | tag | ) |

References RDKIT_RDGENERAL_EXPORT.

## ◆ BETTER_ENUM() [1/7]

RDKit::BETTER_ENUM | ( | DrawElement | ,
|  | uint32_t | ,
|  | NONE | = 0,
|  | PRESHAPES | = 1<< 0,
|  | BONDS | = 1<< 1,
|  | ATOMLABELS | = 1<< 2,
|  | HIGHLIGHTS | = 1<< 3,
|  | ANNOTATIONS | = 1<< 4,
|  | RADICALS | = 1<< 5,
|  | POSTSHAPES | = 1<< 6,
|  | ALL | = 0x7fffffff )

References BONDS.

## ◆ BETTER_ENUM() [2/7]

RDKit::BETTER_ENUM | ( | RestoreBondDirOption | ,
|  | unsigned int | ,
|  | RestoreBondDirOptionTrue | = 0,
|  | RestoreBondDirOptionClear | = 1 )

## ◆ BETTER_ENUM() [3/7]

RDKit::BETTER_ENUM | ( | RGroupCoreAlignment | ,
|  | unsigned int | ,
|  | NoAlignment | = 0x0,
|  | MCS | = 0x01 )

## ◆ BETTER_ENUM() [4/7]

RDKit::BETTER_ENUM | ( | RGroupLabelling | ,
|  | unsigned int | ,
|  | AtomMap | = 0x01,
|  | Isotope | = 0x02,
|  | MDLRGroup | = 0x04 )

## ◆ BETTER_ENUM() [5/7]

RDKit::BETTER_ENUM | ( | RGroupLabels | ,
|  | unsigned int | ,
|  | IsotopeLabels | = 0x01,
|  | AtomMapLabels | = 0x02,
|  | AtomIndexLabels | = 0x04,
|  | RelabelDuplicateLabels | = 0x08,
|  | MDLRGroupLabels | = 0x10,
|  | DummyAtomLabels | = 0x20,
|  | AutoDetect | = 0xFF )

## ◆ BETTER_ENUM() [6/7]

RDKit::BETTER_ENUM | ( | RGroupMatching | ,
|  | unsigned int | ,
|  | Greedy | = 0x01,
|  | GreedyChunks | = 0x02,
|  | Exhaustive | = 0x04,
|  | NoSymmetrization | = 0x08,
|  | GA | = 0x10 )

## ◆ BETTER_ENUM() [7/7]

RDKit::BETTER_ENUM | ( | RGroupScore | ,
|  | unsigned int | ,
|  | Match | = 0x1,
|  | FingerprintVariance | = 0x4 )

## ◆ BETTER_ENUM_CLASS()

RDKit::BETTER_ENUM_CLASS | ( | MolzipLabel | ,
|  | unsigned int | ,
|  | AtomMapNumber | ,
|  | Isotope | ,
|  | FragmentOnBonds | ,
|  | AtomType | ,
|  | AtomProperty | )

## ◆ bondCompat()

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

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ buildFeatureFactory() [1/2]

RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * RDKit::buildFeatureFactory | ( | const std::string & | featureData | ) |

constructs a MolChemicalFeatureFactory from the data in a string

References RDKIT_MOLCHEMICALFEATURES_EXPORT.

## ◆ buildFeatureFactory() [2/2]

RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * RDKit::buildFeatureFactory | ( | std::istream & | inStream | ) |

constructs a MolChemicalFeatureFactory from the data in a stream

References RDKIT_MOLCHEMICALFEATURES_EXPORT.

## ◆ canHaveDirection()

bool RDKit::canHaveDirection | ( | const Bond & | bond | ) |
| inline

Definition at line 415 of file Bond.h.

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

## ◆ canonicalizeStereoGroups()

RDKIT_SMILESPARSE_EXPORT void RDKit::canonicalizeStereoGroups | ( | std::unique_ptr< ROMol > & | mol,
|  | StereoGroupAbsOptions | outputAbsoluteGroups = StereoGroupAbsOptions::OnlyIncludeWhenOtherGroupsExist,
|  | unsigned int | maxStereoGroups = 12 )

References OnlyIncludeWhenOtherGroupsExist, and RDKIT_SMILESPARSE_EXPORT.

## ◆ canSetDoubleBondStereo()

bool RDKit::canSetDoubleBondStereo | ( | const Bond & | bond | ) |
| inline

Definition at line 409 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(), and RDKIT_CHEMREACTIONS_EXPORT.

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(), and RDKIT_CHEMREACTIONS_EXPORT.

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 )

References RDKIT_FMCS_EXPORT.

## ◆ checkAtomChirality()

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

References RDKIT_FMCS_EXPORT.

## ◆ checkAtomDistance()

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

References RDKIT_FMCS_EXPORT.

## ◆ checkAtomRingMatch()

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

References RDKIT_FMCS_EXPORT.

## ◆ checkBondRingMatch()

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

References RDKIT_FMCS_EXPORT.

## ◆ checkBondStereo()

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

References RDKIT_FMCS_EXPORT.

## ◆ checkForTimeout()

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

Definition at line 125 of file RGroupDecomp.h.

## ◆ ChemicalReactionToCXRxnSmarts() [1/2]

std::string RDKit::ChemicalReactionToCXRxnSmarts | ( | const ChemicalReaction & | rxn | ) |
| inline

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

Definition at line 156 of file ReactionParser.h.

References RDKit::SmilesWriteParams::canonical, and ChemicalReactionToCXRxnSmarts().

## ◆ ChemicalReactionToCXRxnSmarts() [2/2]

RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToCXRxnSmarts | ( | const ChemicalReaction & | rxn,
|  | const SmilesWriteParams & | params,
|  | std::uint32_t | flags = SmilesWrite::CXSmilesFields::CX_ALL )

returns the reaction SMARTS for a reaction with CX extension

References ChemicalReactionToCXRxnSmarts(), and RDKIT_CHEMREACTIONS_EXPORT.

Referenced by ChemicalReactionToCXRxnSmarts(), and ChemicalReactionToCXRxnSmarts().

## ◆ ChemicalReactionToCXRxnSmiles() [1/2]

std::string RDKit::ChemicalReactionToCXRxnSmiles | ( | const ChemicalReaction & | rxn,
|  | bool | canonical = true )
| inline

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

Definition at line 167 of file ReactionParser.h.

References RDKit::SmilesWriteParams::canonical, and ChemicalReactionToCXRxnSmiles().

## ◆ ChemicalReactionToCXRxnSmiles() [2/2]

RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToCXRxnSmiles | ( | const ChemicalReaction & | rxn,
|  | const SmilesWriteParams & | params,
|  | std::uint32_t | flags = SmilesWrite::CXSmilesFields::CX_ALL )

returns the reaction SMILES for a reaction with CX extension

References ChemicalReactionToCXRxnSmiles(), and RDKIT_CHEMREACTIONS_EXPORT.

Referenced by ChemicalReactionToCXRxnSmiles(), and ChemicalReactionToCXRxnSmiles().

## ◆ ChemicalReactionToMrvBlock()

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

References RDKIT_MARVINPARSER_EXPORT.

## ◆ ChemicalReactionToMrvFile()

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

References RDKIT_MARVINPARSER_EXPORT.

## ◆ 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(), and RDKIT_CHEMREACTIONS_EXPORT.

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(), and RDKIT_CHEMREACTIONS_EXPORT.

Referenced by ChemicalReactionToRxnMol().

## ◆ ChemicalReactionToRxnSmarts() [1/2]

std::string RDKit::ChemicalReactionToRxnSmarts | ( | const ChemicalReaction & | rxn | ) |
| inline

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

Definition at line 133 of file ReactionParser.h.

References RDKit::SmilesWriteParams::canonical, and ChemicalReactionToRxnSmarts().

## ◆ ChemicalReactionToRxnSmarts() [2/2]

RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmarts | ( | const ChemicalReaction & | rxn,
|  | const SmilesWriteParams & | params )

returns the reaction SMARTS for a reaction

References ChemicalReactionToRxnSmarts(), and RDKIT_CHEMREACTIONS_EXPORT.

Referenced by ChemicalReactionToRxnSmarts(), and ChemicalReactionToRxnSmarts().

## ◆ ChemicalReactionToRxnSmiles() [1/2]

std::string RDKit::ChemicalReactionToRxnSmiles | ( | const ChemicalReaction & | rxn,
|  | bool | canonical )
| inline

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

Definition at line 144 of file ReactionParser.h.

References RDKit::SmilesWriteParams::canonical, and ChemicalReactionToRxnSmiles().

## ◆ ChemicalReactionToRxnSmiles() [2/2]

RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmiles | ( | const ChemicalReaction & | rxn,
|  | const SmilesWriteParams & | params = SmilesWriteParams() )

returns the reaction SMILES for a reaction

References ChemicalReactionToRxnSmiles(), and RDKIT_CHEMREACTIONS_EXPORT.

Referenced by ChemicalReactionToRxnSmiles(), and 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(), and RDKIT_CHEMREACTIONS_EXPORT.

Referenced by ChemicalReactionToV3KRxnBlock().

## ◆ chiralAtomCompat()

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

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ ClearSingleBondDirFlags()

RDKIT_FILEPARSERS_EXPORT void RDKit::ClearSingleBondDirFlags | ( | ROMol & | mol | ) |

Deprecated
  , please use MolOps::clearSingleBondDirFlags instead

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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.

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ computeGasteigerCharges() [1/3]

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

References RDKIT_PARTIALCHARGES_EXPORT.

## ◆ computeGasteigerCharges() [2/3]

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

References RDKIT_PARTIALCHARGES_EXPORT.

## ◆ computeGasteigerCharges() [3/3]

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

References RDKIT_PARTIALCHARGES_EXPORT.

## ◆ 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

References RDKIT_RDGENERAL_EXPORT.

## ◆ computeL1Norm() [1/2]

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

References RDKIT_DATASTRUCTS_EXPORT.

## ◆ computeL1Norm() [2/2]

RDKIT_DATASTRUCTS_EXPORT double RDKit::computeL1Norm | ( | const RealValueVect & | v1,
|  | const RealValueVect & | v2 )

returns L1 Norm of vectors

References RDKIT_DATASTRUCTS_EXPORT.

## ◆ 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(), and RDKIT_CHEMREACTIONS_EXPORT.

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

## ◆ ConnectTheDots()

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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ convertComplexNameToQuery()

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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, RDKit::RDValue::destroy(), RDKit::RDValue::getTag(), RDKit::RDValue::ptrCast(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.

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

## ◆ copyMolSubset() [1/4]

RDKIT_GRAPHMOL_EXPORT std::unique_ptr< RDKit::RWMol > RDKit::copyMolSubset | ( | const RDKit::ROMol & | mol,
|  | const std::vector< unsigned int > & | atoms,
|  | const std::vector< unsigned int > & | bonds,
|  | const SubsetOptions & | options = SubsetOptions() )

References RDKIT_GRAPHMOL_EXPORT.

## ◆ copyMolSubset() [2/4]

RDKIT_GRAPHMOL_EXPORT std::unique_ptr< RDKit::RWMol > RDKit::copyMolSubset | ( | const RDKit::ROMol & | mol,
|  | const std::vector< unsigned int > & | atoms,
|  | const std::vector< unsigned int > & | bonds,
|  | SubsetInfo & | subsetInfo,
|  | const SubsetOptions & | options = SubsetOptions() )

## ◆ copyMolSubset() [3/4]

RDKIT_GRAPHMOL_EXPORT std::unique_ptr< RDKit::RWMol > RDKit::copyMolSubset | ( | const RDKit::ROMol & | mol,
|  | const std::vector< unsigned int > & | path,
|  | const SubsetOptions & | options = SubsetOptions() )

References RDKIT_GRAPHMOL_EXPORT.

## ◆ copyMolSubset() [4/4]

RDKIT_GRAPHMOL_EXPORT std::unique_ptr< RDKit::RWMol > RDKit::copyMolSubset | ( | const RDKit::ROMol & | mol,
|  | const std::vector< unsigned int > & | path,
|  | SubsetInfo & | subsetInfo,
|  | const SubsetOptions & | options = SubsetOptions() )

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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, and PRECONDITION.

## ◆ 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.

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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, and RDKit::detail::qhelper().

## ◆ 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, and RDKit::detail::qhelper().

## ◆ DetectAtomStereoChemistry()

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

deprecated, please use MolOps::assignChiralTypesFromBondDirs instead

References RDKIT_FILEPARSERS_EXPORT.

## ◆ DetectBondStereoChemistry()

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

deprecated, please use MolOps::detectBondStereoChemistry instead

References RDKIT_FILEPARSERS_EXPORT.

## ◆ determineBondOrders()

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

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
  maxIterations | (optional) maximum number of iterations to run in the bond order detection algorithm, after which a MaxFindBondOrdersItersExceeded exception will be thrown. Defaults to 0 (no limit)

Exceptions

  MaxFindBondOrdersItersExceeded |

References RDKIT_DETERMINEBONDS_EXPORT.

## ◆ 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,
|  | size_t | maxIterations = 0 )

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
  maxIterations | (optional) maximum number of iterations to run in the bond order detection algorithm, after which a MaxFindBondOrdersItersExceeded exception will be thrown. Defaults to 0 (no limit)

Exceptions

  MaxFindBondOrdersItersExceeded |

References RDKIT_DETERMINEBONDS_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_DETERMINEBONDS_EXPORT.

## ◆ 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 499 of file SparseIntVect.h.

## ◆ Dict::getVal< std::string >()

template<>

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

Definition at line 349 of file Dict.h.

References RDKit::Dict::getVal().

## ◆ 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 `delete`ing the result

References DefaultDifferenceFPParams.

## ◆ 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 102 of file StreamOps.h.

## ◆ EndianSwapBytes() [3/4]

template<EEndian from, EEndian to, class T>

T RDKit::EndianSwapBytes | ( | T | value | ) |
| inline

Definition at line 72 of file StreamOps.h.

References SwapBytes().

Referenced by streamRead(), and streamWrite().

## ◆ EndianSwapBytes() [4/4]

template<EEndian from, EEndian to>

unsigned char RDKit::EndianSwapBytes | ( | unsigned char | value | ) |
| inline

Definition at line 97 of file StreamOps.h.

## ◆ EnumerateLibraryCanSerialize()

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::EnumerateLibraryCanSerialize | ( |  | ) |

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ eraseUniquePtr()

template<typename T>

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

Definition at line 228 of file MarvinDefs.h.

References findUniquePtr().

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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.

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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.

References RDKIT_FILEPARSERS_EXPORT.

## ◆ feq()

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

floating point comparison with a tolerance

References RDKIT_RDGENERAL_EXPORT.

## ◆ FilterCatalogCanSerialize()

RDKIT_FILTERCATALOG_EXPORT bool RDKit::FilterCatalogCanSerialize | ( |  | ) |

References RDKIT_FILTERCATALOG_EXPORT.

## ◆ 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)

References RDKIT_SUBGRAPHS_EXPORT.

## ◆ 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 )

References RDKIT_SUBGRAPHS_EXPORT.

## ◆ 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)

References RDKIT_SUBGRAPHS_EXPORT.

## ◆ 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)

References RDKIT_SUBGRAPHS_EXPORT.

## ◆ findFuncGroupsOnMol()

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

References RDKIT_FRAGCATALOG_EXPORT.

## ◆ 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 )

References RDKIT_FMCS_EXPORT.

## ◆ 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 )

References AtomCompareElements, BondCompareOrder, and RDKIT_FMCS_EXPORT.

## ◆ findMCS() [3/3]

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

References RDKIT_FMCS_EXPORT.

## ◆ findMCS_P()

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

References RDKIT_FMCS_EXPORT.

## ◆ 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 213 of file MarvinDefs.h.

Referenced by eraseUniquePtr().

## ◆ 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)

References RDKIT_SUBGRAPHS_EXPORT.

## ◆ 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 )

References RDKIT_RGROUPDECOMPOSITION_EXPORT.

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 189 of file RDAny.h.

References RDKit::RDValue::getTag(), RDKit::RDAny::m_value, rdany_cast(), 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 210 of file RDAny.h.

References rdany_cast().

## ◆ 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 270 of file RDValue.h.

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

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

## ◆ 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 295 of file RDValue.h.

References rdvalue_cast().

## ◆ generatorFromJSON()

RDKIT_FINGERPRINTS_EXPORT std::unique_ptr< FingerprintGenerator< std::uint64_t > > RDKit::generatorFromJSON | ( | const std::string & | jsonStr | ) |

create a FingerprintGenerator from its JSON representation note that the returned generator always uses std::uint64_t as OutputType.

References RDKIT_FINGERPRINTS_EXPORT.

## ◆ generatorToJSON()

template<typename OutputType>

RDKIT_FINGERPRINTS_EXPORT std::string RDKit::generatorToJSON | ( | const FingerprintGenerator< OutputType > & | generator | ) |

generate JSON representation of a FingerprintGenerator

References RDKIT_FINGERPRINTS_EXPORT.

## ◆ getAtomAlias()

RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomAlias | ( | const Atom * | atom | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ getAtomListQueryVals()

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ getAtomRLabel()

RDKIT_GRAPHMOL_EXPORT int RDKit::getAtomRLabel | ( | const Atom * | atm | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ getAtomTypeAtomicNum()

static int RDKit::getAtomTypeAtomicNum | ( | int | val | ) |
| inlinestatic

Definition at line 146 of file QueryOps.h.

## ◆ getAtomTypeIsAromatic()

static bool RDKit::getAtomTypeIsAromatic | ( | int | val | ) |
| inlinestatic

Definition at line 145 of file QueryOps.h.

## ◆ getAtomValue()

RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomValue | ( | const Atom * | atom | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 )

References getCountFP(), and RDKIT_FINGERPRINTS_EXPORT.

Referenced by getCountFP().

## ◆ getCountFPBulk()

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

References getCountFPBulk().

Referenced by getCountFPBulk().

## ◆ getDiscreteDistMat()

DiscreteDistMat * RDKit::getDiscreteDistMat | ( |  | ) |
| extern

## ◆ getDoubleRandomSource()

RDKIT_RDGENERAL_EXPORT double_source_type & RDKit::getDoubleRandomSource | ( |  | ) |

return a reference to the global (Boost) random source

References RDKIT_RDGENERAL_EXPORT.

## ◆ getEndIterator()

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

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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 )

References getFP(), and RDKIT_FINGERPRINTS_EXPORT.

Referenced by getFP().

## ◆ getFPBulk()

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

References getFPBulk(), and RDKIT_FINGERPRINTS_EXPORT.

Referenced by getFPBulk().

## ◆ GetFunctionalGroupHierarchy()

RDKIT_FILTERCATALOG_EXPORT const FilterCatalog & RDKit::GetFunctionalGroupHierarchy | ( |  | ) |

Return the functional group hierarchy as a FilterCatalog.

References RDKIT_FILTERCATALOG_EXPORT.

## ◆ 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().

## ◆ getLine() [2/2]

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

grabs the next line from an instream and returns it.

Definition at line 337 of file StreamOps.h.

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

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ 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.

Referenced by RDKit::GeneralMolSupplier::getSupplier(), 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

References RDKIT_RDGENERAL_EXPORT.

## ◆ 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

References RDKIT_RDGENERAL_EXPORT.

## ◆ 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.

References getSizesFromBBs().

Referenced by getSizesFromBBs(), and 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(), and RDKIT_CHEMREACTIONS_EXPORT.

Referenced by getSizesFromReactants().

## ◆ getSparseCountFP()

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

References getSparseCountFP(), and RDKIT_FINGERPRINTS_EXPORT.

Referenced by getSparseCountFP().

## ◆ getSparseCountFPBulk()

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

References getSparseCountFPBulk().

Referenced by getSparseCountFPBulk().

## ◆ getSparseFP()

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

References getSparseFP(), and RDKIT_FINGERPRINTS_EXPORT.

Referenced by getSparseFP().

## ◆ getSparseFPBulk()

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

References getSparseFPBulk(), and RDKIT_FINGERPRINTS_EXPORT.

Referenced by getSparseFPBulk().

## ◆ getStartIterator()

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

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ getSubstanceGroups() [1/2]

RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & RDKit::getSubstanceGroups | ( | const ROMol & | mol | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ getSubstanceGroups() [2/2]

RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & RDKit::getSubstanceGroups | ( | ROMol & | mol | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ getSupplementalSmilesLabel()

RDKIT_GRAPHMOL_EXPORT std::string RDKit::getSupplementalSmilesLabel | ( | const Atom * | atom | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ getTwiceBondType()

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

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 26 of file hanoiSort.h.

References hanoi().

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 150 of file hanoiSort.h.

References hanoi().

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

## ◆ hasAgentTemplateSubstructMatch()

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

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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 )

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ hasReactantTemplateSubstructMatch()

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

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ hasReactionAtomMapping()

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactionAtomMapping | ( | const ChemicalReaction & | rxn | ) |

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ hasReactionSubstructMatch()

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

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ havePairOfCompatibleRings()

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

References RDKIT_FMCS_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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.

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_RDGENERAL_EXPORT.

## ◆ invertMolBlockWedgingInfo()

RDKIT_FILEPARSERS_EXPORT void RDKit::invertMolBlockWedgingInfo | ( | ROMol & | mol | ) |

Deprecated
  use Chirality::invertMolBlockWedgingInfo instead

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ isAtomAromatic()

RDKIT_GRAPHMOL_EXPORT bool RDKit::isAtomAromatic | ( | const Atom * | a | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ isAtomDummy()

bool RDKit::isAtomDummy | ( | const Atom * | a | ) |
| inline

Definition at line 1125 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 | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ isAtomTerminalRGroupOrQueryHydrogen()

RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::isAtomTerminalRGroupOrQueryHydrogen | ( | const Atom * | atom | ) |

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ 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 )

References RDKIT_FILEPARSERS_EXPORT.

## ◆ isComplexQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery | ( | const Atom * | a | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ isComplexQuery() [2/2]

RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery | ( | const Bond * | b | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ isDative() [1/2]

bool RDKit::isDative | ( | const Bond & | bond | ) |
| inline

Definition at line 404 of file Bond.h.

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

## ◆ isDative() [2/2]

bool RDKit::isDative | ( | const Bond::BondType | bt | ) |
| inline

Definition at line 399 of file Bond.h.

References RDKit::Bond::DATIVE, RDKit::Bond::DATIVEL, RDKit::Bond::DATIVEONE, and RDKit::Bond::DATIVER.

Referenced by canSetDoubleBondStereo(), and isDative().

## ◆ 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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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(), and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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(), and RDKIT_CHEMREACTIONS_EXPORT.

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(), and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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(), and RDKIT_CHEMREACTIONS_EXPORT.

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(), and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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(), and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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(), and RDKIT_CHEMREACTIONS_EXPORT.

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(), and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ isReactionTemplateMoleculeAgent()

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

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ isSerializable()

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

Definition at line 389 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 `delete`ing the result

Layer definitions:

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

References RDKIT_FINGERPRINTS_EXPORT.

## ◆ makeAAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAAtomQuery | ( |  | ) |

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeAHAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * RDKit::makeAHAtomQuery | ( |  | ) |

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeAtomAliphaticQuery() [2/2]

template<class T>

T * RDKit::makeAtomAliphaticQuery | ( | const std::string & | descr | ) |

returns a Query for matching aliphatic atoms

Definition at line 462 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomAliphatic().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeAtomAromaticQuery() [2/2]

template<class T>

T * RDKit::makeAtomAromaticQuery | ( | const std::string & | descr | ) |

returns a Query for matching the `isAromatic` flag

Definition at line 454 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomAromatic().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 406 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomExplicitDegree().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 390 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomExplicitValence().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 487 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomFormalCharge().

## ◆ 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 642 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomHasAliphaticHeteroatomNbrs().

## ◆ makeAtomHasChiralTagQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHasChiralTagQuery | ( |  | ) |

\overloadquery

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 523 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomHasChiralTag().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 624 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomHasHeteroatomNbrs().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeAtomHasImplicitHQuery() [2/2]

template<class T>

T * RDKit::makeAtomHasImplicitHQuery | ( | const std::string & | descr | ) |

returns a Query for matching ring atoms

Definition at line 438 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomHasImplicitH().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 607 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomHasRingBond().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 430 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomHCount().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 422 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomHeavyAtomDegree().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeAtomHybridizationQuery() [2/2]

template<class T>

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

returns a Query for matching hybridization

Definition at line 505 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomHybridization().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 446 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomImplicitHCount().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 382 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomImplicitValence().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 556 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryIsAtomInNRings().

## ◆ makeAtomInRingOfSizeQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomInRingOfSizeQuery | ( | int | tgt | ) |

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeAtomInRingQuery() [2/2]

template<class T>

T * RDKit::makeAtomInRingQuery | ( | const std::string & | descr | ) |

returns a Query for matching ring atoms

Definition at line 548 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryIsAtomInRing().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeAtomIsBridgeheadQuery() [2/2]

template<class T>

T * RDKit::makeAtomIsBridgeheadQuery | ( | const std::string & | descr | ) |

returns a Query for matching bridgehead atoms

Definition at line 660 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryIsAtomBridgehead().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 479 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomIsotope().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 470 of file QueryOps.h.

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

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 567 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomMinRingSize().

## ◆ makeAtomMissingChiralTagQuery() [1/2]

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomMissingChiralTagQuery | ( |  | ) |

\overloadquery

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 532 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomMissingChiralTag().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 496 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomNegativeFormalCharge().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 651 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomNonHydrogenDegree().

## ◆ makeAtomNullQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * RDKit::makeAtomNullQuery | ( |  | ) |

returns a Query for matching any atom

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 632 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomNumAliphaticHeteroatomNbrs().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 615 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomNumHeteroatomNbrs().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 364 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomNum().

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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 513 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomNumRadicalElectrons().

## ◆ 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 352 of file QueryOps.h.

References Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::setDataFunc(), Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::setDescription(), and Queries::RangeQuery< MatchFuncArgType, DataFuncArgType, needsConversion >::setEndsOpen().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 575 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomRingBondCount().

## ◆ makeAtomSimpleQuery()

template<class T>

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

Definition at line 343 of file QueryOps.h.

Referenced by 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(), makeAtomRingBondCountQuery(), makeAtomTotalDegreeQuery(), makeAtomTotalValenceQuery(), makeAtomTypeQuery(), and makeAtomUnsaturatedQuery().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 414 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomTotalDegree().

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 398 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomTotalValence().

## ◆ makeAtomType()

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

Definition at line 133 of file QueryOps.h.

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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 372 of file QueryOps.h.

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

## ◆ 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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeAtomUnsaturatedQuery() [2/2]

template<class T>

T * RDKit::makeAtomUnsaturatedQuery | ( | const std::string & | descr | ) |

returns a Query for matching atoms with unsaturation:

Definition at line 540 of file QueryOps.h.

References makeAtomSimpleQuery(), and queryAtomUnsaturated().

## ◆ makeBondDirEqualsQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondDirEqualsQuery | ( | Bond::BondDir | what | ) |

returns a Query for matching bond directions

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeBondHasStereoQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondHasStereoQuery | ( |  | ) |

returns a Query for matching bonds with stereo set

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeBondInNRingsQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondInNRingsQuery | ( | int | tgt | ) |

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeBondInRingOfSizeQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondInRingOfSizeQuery | ( | int | what | ) |

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeBondIsInRingQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondIsInRingQuery | ( |  | ) |

returns a Query for matching ring bonds

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeBondMinRingSizeQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondMinRingSizeQuery | ( | int | what | ) |

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeBondNullQuery()

RDKIT_GRAPHMOL_EXPORT BOND_NULL_QUERY * RDKit::makeBondNullQuery | ( |  | ) |

returns a Query for matching any bond

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeBondOrderEqualsQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondOrderEqualsQuery | ( | Bond::BondType | what | ) |

returns a Query for matching bond orders

References RDKIT_GRAPHMOL_EXPORT.

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

## ◆ makeDoubleOrAromaticBondQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeDoubleOrAromaticBondQuery | ( |  | ) |

returns a Query for double|aromatic bonds

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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 859 of file QueryOps.h.

## ◆ makeMAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeMAtomQuery | ( |  | ) |

returns a Query for matching generic M atoms (metals)

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeMHAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeMHAtomQuery | ( |  | ) |

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makePropQuery() [1/2]

template<class Target>

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

Definition at line 1105 of file QueryOps.h.

## ◆ makePropQuery() [2/2]

template<class Target, class T>

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

Definition at line 1099 of file QueryOps.h.

## ◆ makeQAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeQAtomQuery | ( |  | ) |

returns a Query for matching generic Q atoms (heteroatoms)

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeQHAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeQHAtomQuery | ( |  | ) |

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeSingleOrAromaticBondQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrAromaticBondQuery | ( |  | ) |

returns a Query for unspecified SMARTS bonds

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeSingleOrDoubleBondQuery()

RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrDoubleBondQuery | ( |  | ) |

returns a Query for single|double bonds

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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)

References RDKIT_GRAPHMOL_EXPORT.

## ◆ makeXHAtomQuery()

RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeXHAtomQuery | ( |  | ) |

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ MCSAtomCompareAny()

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

References RDKIT_FMCS_EXPORT.

## ◆ MCSAtomCompareAnyHeavyAtom()

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

References RDKIT_FMCS_EXPORT.

## ◆ MCSAtomCompareElements()

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

References RDKIT_FMCS_EXPORT.

## ◆ MCSAtomCompareIsotopes()

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

References RDKIT_FMCS_EXPORT.

## ◆ MCSBondCompareAny()

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

References RDKIT_FMCS_EXPORT.

## ◆ MCSBondCompareOrder()

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

References RDKIT_FMCS_EXPORT.

## ◆ MCSBondCompareOrderExact()

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

References RDKIT_FMCS_EXPORT.

## ◆ MCSProgressCallbackTimeout()

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

References RDKIT_FMCS_EXPORT.

## ◆ 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, and PRECONDITION.

## ◆ MolBundleCanSerialize()

bool RDKit::MolBundleCanSerialize | ( |  | ) |
| inline

Definition at line 46 of file MolBundle.h.

## ◆ MolFragmentToCXSmarts() [1/2]

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

References RDKIT_SMILESPARSE_EXPORT.

Referenced by MolFragmentToCXSmarts().

## ◆ MolFragmentToCXSmarts() [2/2]

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

Definition at line 87 of file SmartsWrite.h.

References RDKit::SmilesWriteParams::doIsomericSmiles, and MolFragmentToCXSmarts().

## ◆ 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

References RDKIT_SMILESPARSE_EXPORT.

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 344 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::allBondsExplicit, RDKit::SmilesWriteParams::allHsExplicit, RDKit::SmilesWriteParams::canonical, RDKit::SmilesWriteParams::doIsomericSmiles, RDKit::SmilesWriteParams::doKekule, MolFragmentToCXSmiles(), and RDKit::SmilesWriteParams::rootedAtAtom.

## ◆ MolFragmentToSmarts() [1/2]

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

References RDKIT_SMILESPARSE_EXPORT.

Referenced by MolFragmentToSmarts().

## ◆ MolFragmentToSmarts() [2/2]

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

Definition at line 70 of file SmartsWrite.h.

References RDKit::SmilesWriteParams::doIsomericSmiles, and MolFragmentToSmarts().

## ◆ 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

References RDKIT_SMILESPARSE_EXPORT.

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 249 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::allBondsExplicit, RDKit::SmilesWriteParams::allHsExplicit, RDKit::SmilesWriteParams::canonical, RDKit::SmilesWriteParams::doIsomericSmiles, RDKit::SmilesWriteParams::doKekule, MolFragmentToSmiles(), and RDKit::SmilesWriteParams::rootedAtAtom.

## ◆ MolToCMLBlock()

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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ MolToCMLFile()

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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ MolToCXSmarts() [1/2]

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

returns the CXSMARTS for a molecule

Definition at line 80 of file SmartsWrite.h.

References RDKit::SmilesWriteParams::doIsomericSmiles, and MolToCXSmarts().

## ◆ MolToCXSmarts() [2/2]

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

returns the CXSMARTS for a molecule

References RDKIT_SMILESPARSE_EXPORT.

Referenced by MolToCXSmarts().

## ◆ 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 296 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::allBondsExplicit, RDKit::SmilesWriteParams::allHsExplicit, RDKit::SmilesWriteParams::canonical, RDKit::SmilesWriteParams::doIsomericSmiles, RDKit::SmilesWriteParams::doKekule, RDKit::SmilesWriteParams::doRandom, MolToCXSmiles(), and RDKit::SmilesWriteParams::rootedAtAtom.

## ◆ 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 = RestoreBondDirOption::RestoreBondDirOptionClear )

returns canonical CXSMILES for a molecule

References RDKIT_SMILESPARSE_EXPORT.

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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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 56 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)

References RDKIT_FILEPARSERS_EXPORT.

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 132 of file FileWriters.h.

References MolToMolFile().

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

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

    \param mol           - the molecule
    \param includeStereo - toggles inclusion of stereochemical information in

the output

Parameters

  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 186 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

References RDKIT_MARVINPARSER_EXPORT.

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

    \param mol           - the molecule
    \param fName         - the file to write to
    \param includeStereo - toggles inclusion of stereochemical information in

the output

Parameters

  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 162 of file MarvinParser.h.

References MolToMrvFile().

## ◆ 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

References RDKIT_MARVINPARSER_EXPORT.

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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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.

References RDKIT_SMILESPARSE_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ MolToSmarts() [1/2]

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

returns the SMARTS for a molecule

Definition at line 48 of file SmartsWrite.h.

References RDKit::SmilesWriteParams::doIsomericSmiles, MolToSmarts(), and RDKit::SmilesWriteParams::rootedAtAtom.

## ◆ MolToSmarts() [2/2]

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

References RDKIT_SMILESPARSE_EXPORT.

Referenced by MolToSmarts().

## ◆ 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,
|  | bool | ignoreAtomMapNumbers = false )
| inline

returns SMILES for a molecule, canonical by default

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.
  doRandom | : if true, the first atom in the SMILES string will be selected at random and the SMILES string will not be canonical
  ignoreAtomMapNumbers | : if true, ignores any atom map numbers when canonicalizing the molecule

Definition at line 179 of file SmilesWrite.h.

References RDKit::SmilesWriteParams::allBondsExplicit, RDKit::SmilesWriteParams::allHsExplicit, RDKit::SmilesWriteParams::canonical, RDKit::SmilesWriteParams::doIsomericSmiles, RDKit::SmilesWriteParams::doKekule, RDKit::SmilesWriteParams::doRandom, RDKit::SmilesWriteParams::ignoreAtomMapNumbers, MolToSmiles(), and RDKit::SmilesWriteParams::rootedAtAtom.

## ◆ MolToSmiles() [2/2]

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

returns canonical SMILES for a molecule

References RDKIT_SMILESPARSE_EXPORT.

Referenced by RDKit::CachedSmilesMolHolder::addMol(), RDKit::CachedTrustedSmilesMolHolder::addMol(), MolToSmiles(), and RDKit::MolStandardize::TautomerEnumerator::pickCanonical().

## ◆ MolToTPLFile()

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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ MolToTPLText()

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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ MolToV2KMolBlock()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToV2KMolBlock | ( | const ROMol & | mol,
|  | const MolWriterParams & | params = MolWriterParams(),
|  | int | confId = -1 )

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)

Note
  This function will throw a ValueError exception if the molecule has more than 999 atoms, bonds, or SGroups.

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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 88 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 70 of file FileWriters.h.

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

## ◆ 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 163 of file FileWriters.h.

References MolToMolFile().

## ◆ 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 146 of file FileWriters.h.

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

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ molzip() [1/4]

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

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ molzip() [2/4]

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

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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.

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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.

References RDKIT_RDGENERAL_EXPORT.

## ◆ nullDataFun()

template<typename T>

int RDKit::nullDataFun | ( | T |  | ) |

Definition at line 809 of file QueryOps.h.

## ◆ nullQueryFun()

template<typename T>

bool RDKit::nullQueryFun | ( | T |  | ) |

Definition at line 813 of file QueryOps.h.

## ◆ numPiElectrons()

RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::numPiElectrons | ( | const Atom & | atom | ) |

returns the number of pi electrons on the atom

References RDKIT_GRAPHMOL_EXPORT.

## ◆ operator""_ctab()

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

Definition at line 491 of file FileParsers.h.

References RDKit::v2::FileParsers::MolFromMolBlock().

## ◆ operator""_mol2()

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

Definition at line 500 of file FileParsers.h.

References RDKit::v2::FileParsers::MolFromMol2Block().

## ◆ operator""_pdb()

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

Definition at line 510 of file FileParsers.h.

References RDKit::v2::FileParsers::MolFromPDBBlock().

## ◆ operator""_rxnsmarts()

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

Definition at line 393 of file ReactionParser.h.

References RDKit::v2::ReactionParser::ReactionFromSmarts().

## ◆ operator""_rxnsmiles()

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

Definition at line 404 of file ReactionParser.h.

References RDKit::v2::ReactionParser::ReactionFromSmiles().

## ◆ 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.

References RDKit::v2::SmilesParse::MolFromSmarts().

## ◆ 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.

References RDKit::v2::SmilesParse::MolFromSmiles().

## ◆ operator&()

RDKIT_DATASTRUCTS_EXPORT RealValueVect RDKit::operator& | ( | const RealValueVect & | p1,
|  | const RealValueVect & | p2 )

support rvv3 = rvv1&rvv2

operator& returns the minimum value for each element. e.g.: [0,1,2,0] & [0,1,1,1] -> [0,1,1,0]

References RDKIT_DATASTRUCTS_EXPORT.

## ◆ operator+() [1/2]

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

References RDKIT_DATASTRUCTS_EXPORT.

## ◆ operator+() [2/2]

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

returns the sum of vectors

References RDKIT_DATASTRUCTS_EXPORT.

## ◆ operator-() [1/2]

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

## ◆ operator-() [2/2]

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

returns the difference of vectors

References RDKIT_DATASTRUCTS_EXPORT.

## ◆ operator|()

RDKIT_DATASTRUCTS_EXPORT RealValueVect RDKit::operator| | ( | const RealValueVect & | p1,
|  | const RealValueVect & | p2 )

support rvv3 = rvv1|rvv2

operator| returns the maximum value for each element. e.g.: [0,1,2,0] | [0,1,1,1] -> [0,1,2,1]

References RDKIT_DATASTRUCTS_EXPORT.

## ◆ parseAtomType()

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

Definition at line 136 of file QueryOps.h.

## ◆ parseFeatureData() [1/2]

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

References parseFeatureData(), and RDKIT_MOLCHEMICALFEATURES_EXPORT.

Referenced by parseFeatureData(), and parseFeatureData().

## ◆ parseFeatureData() [2/2]

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

References parseFeatureData(), and RDKIT_MOLCHEMICALFEATURES_EXPORT.

## ◆ parseFeatureFile()

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

References parseFeatureFile(), and RDKIT_MOLCHEMICALFEATURES_EXPORT.

Referenced by parseFeatureFile().

## ◆ parseMCSParametersJSON()

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

References RDKIT_FMCS_EXPORT.

## ◆ parseMolzipParametersJSON()

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::parseMolzipParametersJSON | ( | MolzipParams & | params,
|  | const char * | details_json )

Parse MolzipParams from JSON.

The passed MolzipParams instance is updated from the JSON-parsed content.

Parameters

  params | - molzip parameters
  details_json | - JSON string

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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.

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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.

References RDKIT_FINGERPRINTS_EXPORT.

## ◆ 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 `delete`ing the result

References RDKIT_FINGERPRINTS_EXPORT.

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 62 of file PNGParser.h.

References PNGStreamToMetadata().

## ◆ 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 131 of file PNGParser.h.

References PNGStreamToMol().

## ◆ 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 162 of file PNGParser.h.

References RDKit::PNGData::pklTag, and PNGStreamToMols().

## ◆ 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.

References RDKIT_FILEPARSERS_EXPORT.

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.

References RDKit::PNGData::pklTag, and RDKIT_FILEPARSERS_EXPORT.

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 72 of file PNGParser.h.

References PNGStreamToMetadata().

## ◆ 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 142 of file PNGParser.h.

References PNGStreamToMol().

## ◆ 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 173 of file PNGParser.h.

References RDKit::PNGData::pklTag, and PNGStreamToMols().

## ◆ prepareMol()

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

References RDKIT_FRAGCATALOG_EXPORT.

## ◆ 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 )

References RDKit::common_properties::molFileValue, and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ preprocessReaction() [2/4]

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

References RDKit::common_properties::molFileValue, and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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 )

References RDKit::common_properties::molFileValue, and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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 )

References RDKit::common_properties::molFileValue, and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ propertyCompat()

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

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ 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 219 of file StreamOps.h.

## ◆ queryAtomAliphatic()

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

Definition at line 76 of file QueryOps.h.

References RDKit::Atom::getIsAromatic().

Referenced by makeAtomAliphaticQuery().

## ◆ queryAtomAllBondProduct()

RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomAllBondProduct | ( | Atom const * | at | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ queryAtomAromatic()

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

Definition at line 73 of file QueryOps.h.

References RDKit::Atom::getIsAromatic().

Referenced by makeAtomAromaticQuery().

## ◆ queryAtomBondProduct()

RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomBondProduct | ( | Atom const * | at | ) |

References RDKIT_GRAPHMOL_EXPORT.

## ◆ queryAtomExplicitDegree()

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

Definition at line 79 of file QueryOps.h.

References RDKit::Atom::getDegree().

Referenced by makeAtomExplicitDegreeQuery().

## ◆ queryAtomExplicitValence()

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

Definition at line 123 of file QueryOps.h.

References RDKit::Atom::EXPLICIT, RDKit::Atom::getNumExplicitHs(), and RDKit::Atom::getValence().

Referenced by makeAtomExplicitValenceQuery().

## ◆ queryAtomFormalCharge()

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

Definition at line 164 of file QueryOps.h.

References RDKit::Atom::getFormalCharge().

Referenced by makeAtomFormalChargeQuery().

## ◆ queryAtomHasAliphaticHeteroatomNbrs()

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

Definition at line 211 of file QueryOps.h.

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

Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().

## ◆ queryAtomHasChiralTag()

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

Definition at line 176 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 184 of file QueryOps.h.

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

Referenced by makeAtomHasHeteroatomNbrsQuery().

## ◆ queryAtomHasImplicitH()

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

Definition at line 117 of file QueryOps.h.

References RDKit::Atom::getTotalNumHs().

Referenced by makeAtomHasImplicitHQuery().

## ◆ queryAtomHasRingBond()

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

Definition at line 285 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 111 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 99 of file QueryOps.h.

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

Referenced by makeAtomHeavyAtomDegreeQuery().

## ◆ queryAtomHybridization()

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

Definition at line 170 of file QueryOps.h.

References RDKit::Atom::getHybridization().

Referenced by makeAtomHybridizationQuery().

## ◆ queryAtomImplicitHCount()

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

Definition at line 114 of file QueryOps.h.

References RDKit::Atom::getTotalNumHs().

Referenced by makeAtomImplicitHCountQuery().

## ◆ queryAtomImplicitValence()

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

Definition at line 120 of file QueryOps.h.

References RDKit::Atom::getValence(), and RDKit::Atom::IMPLICIT.

Referenced by makeAtomImplicitValenceQuery().

## ◆ queryAtomIsInRingOfSize()

template<int tgt>

int RDKit::queryAtomIsInRingOfSize | ( | Atom const * | at | ) |

Definition at line 325 of file QueryOps.h.

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

## ◆ queryAtomIsotope()

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

Definition at line 161 of file QueryOps.h.

References RDKit::Atom::getIsotope().

Referenced by makeAtomIsotopeQuery().

## ◆ queryAtomMass()

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

Definition at line 157 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 302 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 179 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 167 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 86 of file QueryOps.h.

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

Referenced by makeAtomNonHydrogenDegreeQuery().

## ◆ queryAtomNum()

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

Definition at line 132 of file QueryOps.h.

References RDKit::Atom::getAtomicNum().

Referenced by makeAtomNumQuery().

## ◆ queryAtomNumAliphaticHeteroatomNbrs()

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

Definition at line 225 of file QueryOps.h.

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

Referenced by makeAtomNumAliphaticHeteroatomNbrsQuery().

## ◆ queryAtomNumHeteroatomNbrs()

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

Definition at line 197 of file QueryOps.h.

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

Referenced by makeAtomNumHeteroatomNbrsQuery().

## ◆ queryAtomNumRadicalElectrons()

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

Definition at line 173 of file QueryOps.h.

References RDKit::Atom::getNumRadicalElectrons().

Referenced by makeAtomNumRadicalElectronsQuery().

## ◆ queryAtomRingBondCount()

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

Definition at line 309 of file QueryOps.h.

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

Referenced by makeAtomRingBondCountQuery().

## ◆ queryAtomRingMembership()

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

Definition at line 698 of file QueryOps.h.

References RDKit::Atom::getIdx(), and RDKit::Atom::getOwningMol().

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

## ◆ queryAtomTotalDegree()

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

Definition at line 82 of file QueryOps.h.

References RDKit::Atom::getTotalDegree().

Referenced by makeAtomTotalDegreeQuery().

## ◆ queryAtomTotalValence()

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

Definition at line 126 of file QueryOps.h.

References RDKit::Atom::getTotalValence().

Referenced by makeAtomTotalValenceQuery().

## ◆ queryAtomType()

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

Definition at line 153 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 129 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 266 of file QueryOps.h.

References RDKit::Bond::getBondDir().

## ◆ queryBondHasStereo()

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

Definition at line 272 of file QueryOps.h.

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

## ◆ queryBondIsDoubleOrAromatic()

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

Definition at line 253 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 333 of file QueryOps.h.

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

## ◆ queryBondIsSingleOrAromatic()

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

Definition at line 249 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 257 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 261 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 305 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 246 of file QueryOps.h.

References RDKit::Bond::getBondType().

## ◆ queryIsAtomBridgehead()

RDKIT_GRAPHMOL_EXPORT int RDKit::queryIsAtomBridgehead | ( | Atom const * | at | ) |

References RDKIT_GRAPHMOL_EXPORT.

Referenced by makeAtomIsBridgeheadQuery().

## ◆ queryIsAtomInNRings()

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

Definition at line 279 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 282 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 269 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 299 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 178 of file RDAny.h.

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

Referenced by from_rdany().

## ◆ rdany_cast() [2/2]

template<class T>

T RDKit::rdany_cast | ( | RDAny & | d | ) |

Definition at line 184 of file RDAny.h.

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

## ◆ 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 `delete`ing the result

References RDKIT_FINGERPRINTS_EXPORT.

## ◆ 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.

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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.

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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(), and rdvalue_is().

Referenced by from_rdvalue(), rdany_cast(), rdany_cast(), rdvalue_tostring(), vectToString(), and RDKit::DataStructsExplicitBitVecPropHandler::write().

## ◆ rdvalue_cast< bool >() [1/2]

template<>

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

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

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

## ◆ 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 168 of file RDValue.h.

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

## ◆ 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().

## ◆ 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(), 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().

## ◆ 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(), 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().

## ◆ 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 160 of file RDValue.h.

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

Referenced by rdvalue_tostring().

## ◆ rdvalue_cast< std::any >()

template<>

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

Definition at line 152 of file RDValue.h.

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

## ◆ 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(), 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 56 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 48 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(), 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 56 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 56 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 56 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 56 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 56 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 56 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 56 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 56 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 56 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 56 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 465 of file RDValue-doublemagic.h.

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

## ◆ 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 RDKit::RDTypeTag::GetTag().

Referenced by RDKit::DataStructsExplicitBitVecPropHandler::canSerialize(), rdvalue_cast(), rdvalue_cast< bool >(), rdvalue_cast< const std::any & >(), rdvalue_cast< double >(), rdvalue_cast< float >(), rdvalue_cast< int >(), rdvalue_cast< std::any & >(), rdvalue_cast< std::any >(), 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 >(), and rdvalue_cast< unsigned int >().

## ◆ 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_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(), and RDKit::RDTypeTag::GetTag< std::any >().

## ◆ rdvalue_tostring()

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

Definition at line 192 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(), rdvalue_cast< std::any & >(), rdvalue_cast< std::string >(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, vectToString(), 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

References RDKIT_TRAJECTORY_EXPORT.

## ◆ readFuncGroups() [1/2]

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

References RDKIT_FRAGCATALOG_EXPORT.

## ◆ readFuncGroups() [2/2]

RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::string | fileName | ) |

References RDKIT_FRAGCATALOG_EXPORT.

## ◆ 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

References RDKIT_TRAJECTORY_EXPORT.

## ◆ 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 153 of file StreamOps.h.

## ◆ readRDStringVecValue()

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

Definition at line 554 of file StreamOps.h.

References streamReadStringVec().

## ◆ readRDValue()

template<class T>

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

Definition at line 534 of file StreamOps.h.

References streamRead().

## ◆ readRDValueString()

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

Definition at line 547 of file StreamOps.h.

References streamRead().

## ◆ readRDVecValue()

template<class T>

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

Definition at line 541 of file StreamOps.h.

References streamReadVec().

## ◆ reapplyMolBlockWedging()

RDKIT_FILEPARSERS_EXPORT void RDKit::reapplyMolBlockWedging | ( | ROMol & | mol | ) |

Deprecated
  use Chirality::reapplyMolBlockWedging instead

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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.

References RDKIT_RGROUPDECOMPOSITION_EXPORT.

## ◆ removeAtomFromGroups()

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ removeBondFromGroups()

RDKIT_GRAPHMOL_EXPORT void RDKit::removeBondFromGroups | ( | const Bond * | bond,
|  | std::vector< StereoGroup > & | groups )

References RDKIT_GRAPHMOL_EXPORT.

## ◆ removeDuplicates()

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

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ removeGroupsWithAtom()

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ removeGroupsWithAtoms()

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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ removeMappingNumbersFromReactions()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::removeMappingNumbersFromReactions | ( | const ChemicalReaction & | rxn | ) |

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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.

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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.

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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.

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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

References RDKIT_CHEMTRANSFORMS_EXPORT.

## ◆ 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() )

References RDKIT_RGROUPDECOMPOSITION_EXPORT.

## ◆ 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() )

References RDKIT_RGROUPDECOMPOSITION_EXPORT.

## ◆ 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.

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ run_Reactant() [2/2]

RDKIT_CHEMREACTIONS_EXPORT bool RDKit::run_Reactant | ( | const ChemicalReaction & | rxn,
|  | RWMol & | reactant,
|  | bool | removeUnmatchedAtoms = true )

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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.

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ 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 RDKIT_CHEMREACTIONS_EXPORT, and RxnMolToChemicalReaction().

Referenced by RxnMolToChemicalReaction().

## ◆ SamePDBResidue()

RDKIT_FILEPARSERS_EXPORT bool RDKit::SamePDBResidue | ( | AtomPDBResidueInfo * | p,
|  | AtomPDBResidueInfo * | q )

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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.

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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.

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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]

References RDKIT_GRAPHMOL_EXPORT.

## ◆ 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

References RDKIT_GRAPHMOL_EXPORT.

## ◆ setDarkMode() [1/2]

void RDKit::setDarkMode | ( | MolDraw2D & | d2d | ) |
| inline

Definition at line 557 of file MolDraw2D.h.

References RDKit::MolDraw2D::drawOptions(), and setDarkMode().

## ◆ setDarkMode() [2/2]

void RDKit::setDarkMode | ( | MolDrawOptions & | opts | ) |
| inline

Definition at line 549 of file MolDraw2D.h.

References RDKit::MolDrawOptions::annotationColour, assignDarkModePalette(), RDKit::MolDrawOptions::atomColourPalette, RDKit::MolDrawOptions::atomNoteColour, RDKit::MolDrawOptions::backgroundColour, RDKit::MolDrawOptions::legendColour, RDKit::MolDrawOptions::symbolColour, and RDKit::MolDrawOptions::variableAttachmentColour.

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 568 of file MolDraw2D.h.

References RDKit::MolDraw2D::drawOptions(), and setMonochromeMode().

## ◆ setMonochromeMode() [2/2]

void RDKit::setMonochromeMode | ( | MolDrawOptions & | opts,
|  | const DrawColour & | fgColour,
|  | const DrawColour & | bgColour )
| inline

Definition at line 558 of file MolDraw2D.h.

References RDKit::MolDrawOptions::annotationColour, RDKit::MolDrawOptions::atomColourPalette, RDKit::MolDrawOptions::atomNoteColour, RDKit::MolDrawOptions::backgroundColour, RDKit::MolDrawOptions::bondNoteColour, RDKit::MolDrawOptions::legendColour, RDKit::MolDrawOptions::symbolColour, and RDKit::MolDrawOptions::variableAttachmentColour.

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.

References RDKIT_GRAPHMOL_EXPORT.

## ◆ SLNQueryToMol()

RDKIT_SLNPARSE_EXPORT RWMol * RDKit::SLNQueryToMol | ( | const std::string & | smi,
|  | bool | mergeHs = true,
|  | int | debugParse = 0 )

References RDKIT_SLNPARSE_EXPORT.

## ◆ SLNToMol()

RDKIT_SLNPARSE_EXPORT RWMol * RDKit::SLNToMol | ( | const std::string & | smi,
|  | bool | sanitize = true,
|  | int | debugParse = 0 )

References RDKIT_SLNPARSE_EXPORT.

## ◆ 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 | ) |

References RDKIT_FILEPARSERS_EXPORT.

## ◆ streamRead() [1/3]

void RDKit::streamRead | ( | std::istream & | ss,
|  | std::string & | what,
|  | int | version )
| inline

Definition at line 302 of file StreamOps.h.

References RDUNUSED_PARAM, and streamRead().

## ◆ 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 286 of file StreamOps.h.

References EndianSwapBytes().

Referenced by RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::initFromStream(), RDKit::DataStructsExplicitBitVecPropHandler::read(), readRDValue(), readRDValueString(), streamRead(), 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 297 of file StreamOps.h.

References RDUNUSED_PARAM, and streamRead().

## ◆ streamReadProp()

bool RDKit::streamReadProp | ( | std::istream & | ss,
|  | Dict::Pair & | pair,
|  | bool & | dictHasNonPOD,
|  | const CustomPropHandlerVec & | handlers = {} )
| inline

Definition at line 561 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 631 of file StreamOps.h.

## ◆ streamReadStringVec()

void RDKit::streamReadStringVec | ( | std::istream & | ss,
|  | std::vector< std::string > & | val,
|  | int | version )
| inline

Definition at line 325 of file StreamOps.h.

References streamRead().

Referenced by readRDStringVecValue().

## ◆ streamReadVec()

template<class T>

void RDKit::streamReadVec | ( | std::istream & | ss,
|  | T & | val )

Definition at line 315 of file StreamOps.h.

References 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 270 of file StreamOps.h.

References streamWrite().

## ◆ 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 264 of file StreamOps.h.

References EndianSwapBytes().

Referenced by streamWrite(), streamWriteVec(), RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::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 417 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 490 of file StreamOps.h.

## ◆ streamWriteVec()

template<typename T>

void RDKit::streamWriteVec | ( | std::ostream & | ss,
|  | const T & | val )

Definition at line 277 of file StreamOps.h.

References streamWrite().

## ◆ strip()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::strip | ( | const std::string & | orig | ) |

References RDKIT_FILEPARSERS_EXPORT.

## ◆ 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 `delete`ing the result

References DefaultStructuralFPParams, and RDKIT_CHEMREACTIONS_EXPORT.

## ◆ SubstructLibraryCanSerialize()

RDKIT_SUBSTRUCTLIBRARY_EXPORT bool RDKit::SubstructLibraryCanSerialize | ( |  | ) |

References RDKIT_SUBSTRUCTLIBRARY_EXPORT.

## ◆ SubstructMatch() [1/10]

RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const MolBundle & | bundle,
|  | const MolBundle & | query,
|  | const SubstructMatchParameters & | params = SubstructMatchParameters() )

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ SubstructMatch() [2/10]

RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const MolBundle & | bundle,
|  | const ROMol & | query,
|  | const SubstructMatchParameters & | params = SubstructMatchParameters() )

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ SubstructMatch() [3/10]

RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const ROMol & | mol,
|  | const MolBundle & | query,
|  | const SubstructMatchParameters & | params = SubstructMatchParameters() )

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ 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

References RDKIT_SUBSTRUCTMATCH_EXPORT.

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 )

References RDKIT_TAUTOMERQUERY_EXPORT.

## ◆ 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

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ SubstructMatch() [7/10]

template<>

bool RDKit::SubstructMatch | ( | ResonanceMolSupplier & | resMolSupplier,
|  | const ROMol & | query,
|  | MatchVectType & | matchVect,
|  | bool | recursionPossible,
|  | bool | useChirality,
|  | bool | useQueryQueryMatches )
| inline

Definition at line 211 of file SubstructMatch.h.

References RDKit::SubstructMatchParameters::maxMatches, 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 231 of file SubstructMatch.h.

References RDKit::SubstructMatchParameters::maxMatches, RDKit::SubstructMatchParameters::numThreads, 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 148 of file SubstructMatch.h.

References RDKit::SubstructMatchParameters::maxMatches, 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 188 of file SubstructMatch.h.

References RDKit::SubstructMatchParameters::maxMatches, RDKit::SubstructMatchParameters::numThreads, 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 | ) |

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ SwapBytes()

template<class T, unsigned int size>

T RDKit::SwapBytes | ( | T | value | ) |
| inline

Definition at line 44 of file StreamOps.h.

Referenced by EndianSwapBytes().

## ◆ 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 571 of file SparseIntVect.h.

References TverskySimilarity().

Referenced by RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >::Match().

## ◆ TautomerQueryCanSerialize()

RDKIT_TAUTOMERQUERY_EXPORT bool RDKit::TautomerQueryCanSerialize | ( |  | ) |

References RDKIT_TAUTOMERQUERY_EXPORT.

## ◆ toJSON() [1/4]

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

References RDKIT_RGROUPDECOMPOSITION_EXPORT.

## ◆ toJSON() [2/4]

RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON | ( | const RGroupColumns & | rgr,
|  | const std::string & | prefix = "" )

Returns a JSON form The prefix argument is added to each line in the output

References RDKIT_RGROUPDECOMPOSITION_EXPORT.

## ◆ toJSON() [3/4]

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

References RDKIT_RGROUPDECOMPOSITION_EXPORT.

## ◆ toJSON() [4/4]

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

References RDKIT_RGROUPDECOMPOSITION_EXPORT.

## ◆ toPrime()

RDKIT_SUBSTRUCTMATCH_EXPORT double RDKit::toPrime | ( | const MatchVectType & | v | ) |

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ 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

References RDKIT_FILEPARSERS_EXPORT, and STEREO_AND.

## ◆ 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 542 of file SparseIntVect.h.

References RDUNUSED_PARAM.

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

References RDKIT_RDGENERAL_EXPORT.

## ◆ 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.

References RDKIT_RDGENERAL_EXPORT.

## ◆ updateCXSmilesFieldsFromJSON() [1/2]

RDKIT_SMILESPARSE_EXPORT void RDKit::updateCXSmilesFieldsFromJSON | ( | std::uint32_t & | cxSmilesFields,
|  | unsigned int & | restoreBondDirs,
|  | const char * | details_json )

References RDKIT_SMILESPARSE_EXPORT.

## ◆ updateCXSmilesFieldsFromJSON() [2/2]

RDKIT_SMILESPARSE_EXPORT void RDKit::updateCXSmilesFieldsFromJSON | ( | std::uint32_t & | cxSmilesFields,
|  | unsigned int & | restoreBondDirs,
|  | const std::string & | details_json )

References RDKIT_SMILESPARSE_EXPORT.

## ◆ updateFromSequence()

template<typename IndexType, typename SequenceType>

void RDKit::updateFromSequence | ( | SparseIntVect< IndexType > & | vect,
|  | const SequenceType & | seq )

Definition at line 423 of file SparseIntVect.h.

References RDKit::SparseIntVect< IndexType >::getVal(), and RDKit::SparseIntVect< IndexType >::setVal().

## ◆ updateProductsStereochem()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::updateProductsStereochem | ( | ChemicalReaction * | rxn | ) |

References RDKIT_CHEMREACTIONS_EXPORT.

## ◆ updateRGroupDecompositionParametersFromJSON() [1/2]

RDKIT_RGROUPDECOMPOSITION_EXPORT void RDKit::updateRGroupDecompositionParametersFromJSON | ( | RGroupDecompositionParameters & | params,
|  | const char * | details_json )

## ◆ updateRGroupDecompositionParametersFromJSON() [2/2]

RDKIT_RGROUPDECOMPOSITION_EXPORT void RDKit::updateRGroupDecompositionParametersFromJSON | ( | RGroupDecompositionParameters & | params,
|  | const std::string & | details_json )

References RDKIT_RGROUPDECOMPOSITION_EXPORT.

## ◆ updateSmilesWriteParamsFromJSON() [1/2]

RDKIT_SMILESPARSE_EXPORT void RDKit::updateSmilesWriteParamsFromJSON | ( | SmilesWriteParams & | params,
|  | const char * | details_json )

References RDKIT_SMILESPARSE_EXPORT.

## ◆ updateSmilesWriteParamsFromJSON() [2/2]

RDKIT_SMILESPARSE_EXPORT void RDKit::updateSmilesWriteParamsFromJSON | ( | SmilesWriteParams & | params,
|  | const std::string & | details_json )

References RDKIT_SMILESPARSE_EXPORT.

## ◆ updateSubstructMatchParamsFromJSON()

RDKIT_SUBSTRUCTMATCH_EXPORT void RDKit::updateSubstructMatchParamsFromJSON | ( | SubstructMatchParameters & | params,
|  | const std::string & | json )

References RDKIT_SUBSTRUCTMATCH_EXPORT.

## ◆ vectToString()

template<class T>

std::string RDKit::vectToString | ( | RDValue | val | ) |

Definition at line 178 of file RDValue.h.

References rdvalue_cast().

Referenced by rdvalue_tostring().

## ◆ WedgeBond()

RDKIT_FILEPARSERS_EXPORT void RDKit::WedgeBond | ( | Bond * | bond,
|  | unsigned int | fromAtomIdx,
|  | const Conformer * | conf )

Deprecated
  use Chirality::wedgeBond instead

References RDKIT_FILEPARSERS_EXPORT.

## ◆ WedgeMolBonds()

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

Deprecated
  use Chirality::wedgeMolBonds instead

References RDKIT_FILEPARSERS_EXPORT.

## 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 600 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.

## ◆ ctdQUICKREMOVE_H_H_CONTACTS

const unsigned int RDKit::ctdQUICKREMOVE_H_H_CONTACTS = 0x2
| static

Definition at line 17 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

Referenced by RDKit::FilterMatcherBase::FilterMatcherBase().

## ◆ defaultConfId

int RDKit::defaultConfId = -1
| static

Definition at line 34 of file MolWriters.h.

Referenced by RDKit::SDWriter::getText(), RDKit::MolWriter::write(), RDKit::PDBWriter::write(), RDKit::SDWriter::write(), RDKit::SmilesWriter::write(), and RDKit::TDTWriter::write().

## ◆ DefaultDifferenceFPParams

RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams RDKit::DefaultDifferenceFPParams
| extern

Referenced by DifferenceFingerprintChemReaction().

## ◆ DefaultStructuralFPParams

RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams RDKit::DefaultStructuralFPParams
| extern

Referenced by StructuralFingerprintChemReaction().

## ◆ 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[NUM_PRIMES_AVAIL]
| extern

## ◆ 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 74 of file MolDraw2DHelpers.h.

## ◆ marvinBondOrders

const std::vector<std::string> RDKit::marvinBondOrders {"1", "2", "3", "A"}

Definition at line 32 of file MarvinDefs.h.

## ◆ marvinConventionTypes

const std::vector<std::string> RDKit::marvinConventionTypes

Initial value:
{"cxn:coord",
"cxn:hydrogen"}

Definition at line 34 of file MarvinDefs.h.

## ◆ marvinQueryBondsTypes

const std::vector<std::string> RDKit::marvinQueryBondsTypes {"SD", "SA", "DA", "Any"}

Definition at line 33 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 42 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 39 of file MarvinDefs.h.

## ◆ marvinStereoConventionTypes

const std::vector<std::string> RDKit::marvinStereoConventionTypes {"1", "3", "4", "6"}

Definition at line 37 of file MarvinDefs.h.

## ◆ marvinStereoDictRefTypes

const std::vector<std::string> RDKit::marvinStereoDictRefTypes {"cml:W", "cml:H"}

Definition at line 36 of file MarvinDefs.h.

## ◆ massIntegerConversionFactor

const int RDKit::massIntegerConversionFactor = 1000

Definition at line 156 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.

Referenced by RDKit::MolDraw2D_detail::DrawShapePolyLine::DrawShapePolyLine(), and RDKit::MolDraw2D_detail::DrawShapeSimpleLine::DrawShapeSimpleLine().

## ◆ NUM_PRIMES_AVAIL

const int RDKit::NUM_PRIMES_AVAIL

Initial value:
=
1000

the number of primes available and stored

Definition at line 22 of file utils.h.

## ◆ paramData

std::string RDKit::paramData
| extern

Referenced by RDKit::Descriptors::CrippenParamCollection::CrippenParamCollection(), RDKit::GasteigerParams::GasteigerParams(), RDKit::UFF::getAtomTypes(), RDKit::Descriptors::CrippenParamCollection::getParams(), and RDKit::GasteigerParams::getParams().

## ◆ 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 46 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

Referenced by RDKit::SmartsMatcher::SmartsMatcher().

## ◆ sruSgroupConnectChoices

const std::vector<std::string> RDKit::sruSgroupConnectChoices {"hh", "ht", "eu"}

Definition at line 31 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