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RDKit
Open-source cheminformatics and machine learning.
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Std stuff. More...
Namespaces | |
namespace | Abbreviations |
namespace | AtomPair |
namespace | AtomPairs |
namespace | Atropisomers |
namespace | Canon |
namespace | Chirality |
namespace | CIPLabeler |
namespace | CIPLabeler_detail |
namespace | common_properties |
namespace | constants |
namespace | Deprotect |
namespace | Descriptors |
namespace | detail |
namespace | details |
namespace | DGeomHelpers |
namespace | DTags |
namespace | EnumerationStrategyPickler |
namespace | EnumerationTypes |
namespace | 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... | |
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 | 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 |
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... | |
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... | |
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 |
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 ¶ms, 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:
| |
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 |
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 &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 ¶ms=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 ¶ms=DefaultStructuralFPParams) |
RDKIT_CHEMREACTIONS_EXPORT SparseIntVect< std::uint32_t > * | DifferenceFingerprintChemReaction (const ChemicalReaction &rxn, const ReactionFingerprintParams ¶ms=DefaultDifferenceFPParams) |
RDKIT_CHEMREACTIONS_EXPORT std::string | ChemicalReactionToRxnSmarts (const ChemicalReaction &rxn, const SmilesWriteParams ¶ms) |
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 ¶ms=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 ¶ms, 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 ¶ms, 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 | |
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > | molzip (const ROMol &a, const ROMol &b, const MolzipParams ¶ms=MolzipParams()) |
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > | molzip (const ROMol &a, const MolzipParams ¶ms=MolzipParams()) |
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > | molzip (std::vector< ROMOL_SPTR > &decomposition, const MolzipParams ¶ms=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 ¶ms=MolzipParams()) |
Molzip an RGroupRow back into the original molecule if possible. | |
bool | hasNonZeroZCoords (const Conformer &conf) |
Returns true if any of the z coords are non zero, false otherwise. | |
RDKIT_DETERMINEBONDS_EXPORT void | determineConnectivity (RWMol &mol, bool useHueckel=false, int charge=0, double covFactor=1.3, bool useVdw=false) |
RDKIT_DETERMINEBONDS_EXPORT void | determineBondOrders (RWMol &mol, int charge=0, bool allowChargedFragments=true, bool embedChiral=true, bool useAtomMap=false) |
RDKIT_DETERMINEBONDS_EXPORT void | determineBonds (RWMol &mol, bool useHueckel=false, int charge=0, double covFactor=1.3, bool allowChargedFragments=true, bool embedChiral=true, bool useAtomMap=false, bool useVdw=false) |
std::vector< std::unique_ptr< RWMol > > | CDXMLDataStreamToMols (std::istream &inStream, bool sanitize=true, bool removeHs=true) |
construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing. | |
std::vector< std::unique_ptr< RWMol > > | CDXMLFileToMols (const std::string &filename, bool sanitize=true, bool removeHs=true) |
construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing. | |
std::vector< std::unique_ptr< RWMol > > | CDXMLToMols (const std::string &cdxml, bool sanitize=true, bool removeHs=true) |
construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing. | |
RDKIT_FILEPARSERS_EXPORT std::string | strip (const std::string &orig) |
RWMol * | MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | MolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false) |
translate TPL data (BioCad format) into a multi-conf molecule | |
RWMol * | TPLFileToMol (const std::string &fName, bool sanitize=true, bool skipFirstConf=false) |
construct a multi-conf molecule from a TPL (BioCad format) file | |
RWMol * | Mol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true) |
RWMol * | Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true) |
RWMol * | Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true) |
RWMol * | Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true) |
RWMol * | XYZDataStreamToMol (std::istream &inStream) |
RWMol * | XYZBlockToMol (const std::string &xyzBlock) |
RWMol * | XYZFileToMol (const std::string &fName) |
RWMol * | PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
RWMol * | PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
RWMol * | PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
RWMol * | PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
RWMol * | PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | RDKitSVGToMol (const std::string &svg, bool sanitize=true, bool removeHs=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | RDKitSVGToMol (std::istream *instream, bool sanitize=true, bool removeHs=true) |
std::unique_ptr< RDKit::RWMol > | operator""_ctab (const char *text, size_t len) |
std::unique_ptr< RDKit::RWMol > | operator""_mol2 (const char *text, size_t len) |
std::unique_ptr< RDKit::RWMol > | operator""_pdb (const char *text, size_t len) |
RDKIT_FILEPARSERS_EXPORT std::string | MolToMolBlock (const ROMol &mol, const MolWriterParams ¶ms, 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 ¶ms, 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 ¶ms=MolWriterParams(), int confId=-1) |
RDKIT_FILEPARSERS_EXPORT void | MolToMolFile (const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, 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 ¶ms, int confId=-1) |
void | MolToV3KMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true) |
RDKIT_FILEPARSERS_EXPORT std::string | MolToCMLBlock (const ROMol &mol, int confId=-1, bool kekulize=true) |
RDKIT_FILEPARSERS_EXPORT void | MolToCMLFile (const ROMol &mol, const std::string &fName, int confId=-1, bool kekulize=true) |
RDKIT_FILEPARSERS_EXPORT std::string | MolToXYZBlock (const ROMol &mol, int confId=-1, unsigned int precision=6) |
RDKIT_FILEPARSERS_EXPORT void | MolToXYZFile (const ROMol &mol, const std::string &fName, int confId=-1, unsigned int precision=6) |
RDKIT_FILEPARSERS_EXPORT std::string | MolToTPLText (const ROMol &mol, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false) |
RDKIT_FILEPARSERS_EXPORT void | MolToTPLFile (const ROMol &mol, const std::string &fName, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false) |
RDKIT_FILEPARSERS_EXPORT std::string | MolToPDBBlock (const ROMol &mol, int confId=-1, unsigned int flavor=0) |
RDKIT_FILEPARSERS_EXPORT void | MolToPDBFile (const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) |
RDKIT_FILEPARSERS_EXPORT void | DetectAtomStereoChemistry (RWMol &mol, const Conformer *conf) |
deprecated, please use MolOps::assignChiralTypesFromBondDirs instead | |
RDKIT_FILEPARSERS_EXPORT void | DetectBondStereoChemistry (ROMol &mol, const Conformer *conf) |
deprecated, please use MolOps::detectBondStereoChemistry instead | |
RDKIT_FILEPARSERS_EXPORT void | WedgeMolBonds (ROMol &mol, const Conformer *conf) |
RDKIT_FILEPARSERS_EXPORT void | WedgeBond (Bond *bond, unsigned int fromAtomIdx, const Conformer *conf) |
RDKIT_FILEPARSERS_EXPORT void | addWavyBondsForStereoAny (ROMol &mol, bool clearDoubleBondFlags=true, unsigned addWhenImpossible=StereoBondThresholds::DBL_BOND_NO_STEREO) |
set wavy bonds around double bonds with STEREOANY stereo | |
RDKIT_FILEPARSERS_EXPORT void | ClearSingleBondDirFlags (ROMol &mol) |
RDKIT_FILEPARSERS_EXPORT Bond::BondDir | DetermineBondWedgeState (const Bond *bond, unsigned int fromAtomIdx, const Conformer *conf) |
RDKIT_FILEPARSERS_EXPORT Bond::BondDir | DetermineBondWedgeState (const Bond *bond, const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > &wedgeBonds, const Conformer *conf) |
RDKIT_FILEPARSERS_EXPORT void | reapplyMolBlockWedging (ROMol &mol) |
RDKIT_FILEPARSERS_EXPORT void | clearMolBlockWedgingInfo (ROMol &mol) |
RDKIT_FILEPARSERS_EXPORT void | invertMolBlockWedgingInfo (ROMol &mol) |
RDKIT_FILEPARSERS_EXPORT void | markUnspecifiedStereoAsUnknown (ROMol &mol, int confId=-1) |
RDKIT_FILEPARSERS_EXPORT void | translateChiralFlagToStereoGroups (ROMol &mol, StereoGroupType zeroFlagGroupType=StereoGroupType::STEREO_AND) |
RDKIT_FILEPARSERS_EXPORT bool | IsBlacklistedPair (Atom *beg_atom, Atom *end_atom) |
RDKIT_FILEPARSERS_EXPORT void | ConnectTheDots (RWMol *mol, unsigned int flags=0) |
RDKIT_FILEPARSERS_EXPORT void | StandardPDBResidueBondOrders (RWMol *mol) |
RDKIT_FILEPARSERS_EXPORT bool | SamePDBResidue (AtomPDBResidueInfo *p, AtomPDBResidueInfo *q) |
RDKIT_FILEPARSERS_EXPORT RWMol * | SequenceToMol (const char *seq, bool sanitize, bool lowerD) |
RDKIT_FILEPARSERS_EXPORT RWMol * | SequenceToMol (const std::string &seq, bool sanitize, bool lowerD) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_FILEPARSERS_EXPORT RWMol * | SequenceToMol (const char *seq, bool sanitize=true, int flavor=0) |
RDKIT_FILEPARSERS_EXPORT RWMol * | SequenceToMol (const std::string &seq, bool sanitize=true, int flavor=0) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_FILEPARSERS_EXPORT RWMol * | FASTAToMol (const char *seq, bool sanitize, bool lowerD) |
RDKIT_FILEPARSERS_EXPORT RWMol * | FASTAToMol (const std::string &seq, bool sanitize, bool lowerD) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_FILEPARSERS_EXPORT RWMol * | FASTAToMol (const char *seq, bool sanitize=true, int flavor=0) |
RDKIT_FILEPARSERS_EXPORT RWMol * | FASTAToMol (const std::string &seq, bool sanitize=true, int flavor=0) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_FILEPARSERS_EXPORT RWMol * | HELMToMol (const char *helm, bool sanitize=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | HELMToMol (const std::string &helm, bool sanitize=true) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_FILEPARSERS_EXPORT std::string | MolToSequence (const ROMol &mol) |
RDKIT_FILEPARSERS_EXPORT std::string | MolToFASTA (const ROMol &mol) |
RDKIT_FILEPARSERS_EXPORT std::string | MolToHELM (const ROMol &mol) |
RDKIT_FILTERCATALOG_EXPORT bool | FilterCatalogCanSerialize () |
RDKIT_FILTERCATALOG_EXPORT std::vector< std::vector< boost::shared_ptr< const FilterCatalogEntry > > > | RunFilterCatalog (const FilterCatalog &filterCatalog, const std::vector< std::string > &smiles, int numThreads=1) |
Run a filter catalog on a set of smiles strings. | |
unsigned int | GetNumEntries (FilterCatalogParams::FilterCatalogs catalog) |
const FilterData_t * | GetFilterData (FilterCatalogParams::FilterCatalogs catalog) |
unsigned int | GetNumPropertyEntries (FilterCatalogParams::FilterCatalogs catalog) |
const FilterProperty_t * | GetFilterProperties (FilterCatalogParams::FilterCatalogs catalog) |
FilterCatalogEntry * | MakeFilterCatalogEntry (const FilterData_t &, unsigned int num_props=0, const FilterProperty_t *props=nullptr) |
RDKIT_FILTERCATALOG_EXPORT const FilterCatalog & | GetFunctionalGroupHierarchy () |
Return the functional group hierarchy as a FilterCatalog. | |
RDKIT_FILTERCATALOG_EXPORT const std::map< std::string, ROMOL_SPTR > & | GetFlattenedFunctionalGroupHierarchy (bool normalized=false) |
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint64_t > * | getSparseCountFP (const ROMol &mol, FPType fPType) |
RDKIT_FINGERPRINTS_EXPORT SparseBitVect * | getSparseFP (const ROMol &mol, FPType fPType) |
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint32_t > * | getCountFP (const ROMol &mol, FPType fPType) |
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * | getFP (const ROMol &mol, FPType fPType) |
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint64_t > * > * | getSparseCountFPBulk (const std::vector< const ROMol * > molVector, FPType fPType) |
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseBitVect * > * | getSparseFPBulk (const std::vector< const ROMol * > molVector, FPType fPType) |
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint32_t > * > * | getCountFPBulk (const std::vector< const ROMol * > molVector, FPType fPType) |
RDKIT_FINGERPRINTS_EXPORT std::vector< ExplicitBitVect * > * | getFPBulk (const std::vector< const ROMol * > molVector, FPType fPType) |
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * | RDKFingerprintMol (const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) |
Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm. | |
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * | LayeredFingerprintMol (const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool branchedPaths=true, const std::vector< std::uint32_t > *fromAtoms=nullptr) |
Generates a topological (Daylight like) fingerprint for a molecule using a layer-based hashing algorithm. | |
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * | PatternFingerprintMol (const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false) |
Generates a topological fingerprint for a molecule using a series of pre-defined structural patterns. | |
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * | PatternFingerprintMol (const MolBundle &bundle, unsigned int fpSize=2048, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< boost::uint64_t > * | getUnfoldedRDKFingerprintMol (const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, bool useHs=true, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< boost::uint64_t > > *atomBits=nullptr, std::map< boost::uint64_t, std::vector< std::vector< int > > > *bitInfo=nullptr) |
RDKIT_FMCS_EXPORT bool | checkAtomRingMatch (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2) |
RDKIT_FMCS_EXPORT bool | checkAtomCharge (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2) |
RDKIT_FMCS_EXPORT bool | checkAtomChirality (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2) |
RDKIT_FMCS_EXPORT bool | checkAtomDistance (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2) |
RDKIT_FMCS_EXPORT bool | MCSAtomCompareAny (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
RDKIT_FMCS_EXPORT bool | MCSAtomCompareAnyHeavyAtom (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
RDKIT_FMCS_EXPORT bool | MCSAtomCompareElements (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
RDKIT_FMCS_EXPORT bool | MCSAtomCompareIsotopes (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
RDKIT_FMCS_EXPORT bool | checkBondStereo (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2) |
RDKIT_FMCS_EXPORT bool | havePairOfCompatibleRings (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2) |
RDKIT_FMCS_EXPORT bool | checkBondRingMatch (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2) |
RDKIT_FMCS_EXPORT bool | MCSBondCompareAny (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
RDKIT_FMCS_EXPORT bool | MCSBondCompareOrder (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
RDKIT_FMCS_EXPORT bool | MCSBondCompareOrderExact (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
RDKIT_FMCS_EXPORT bool | MCSProgressCallbackTimeout (const MCSProgressData &stat, const MCSParameters ¶ms, 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 ¶ms, 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 ¶ms, int confId=-1) |
std::string | MolToMrvBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false) |
RDKIT_MARVINPARSER_EXPORT std::string | ChemicalReactionToMrvBlock (const ChemicalReaction &rxn, bool prettyPrint=false) |
RDKIT_MARVINPARSER_EXPORT void | ChemicalReactionToMrvFile (const ChemicalReaction &rxn, const std::string &fName, bool prettyPrint=false) |
bool | MolBundleCanSerialize () |
RDKIT_MOLCHEMICALFEATURES_EXPORT int | parseFeatureData (const std::string &defnText, MolChemicalFeatureDef::CollectionType &featDefs) |
RDKIT_MOLCHEMICALFEATURES_EXPORT int | parseFeatureData (std::istream &istream, MolChemicalFeatureDef::CollectionType &featDefs) |
RDKIT_MOLCHEMICALFEATURES_EXPORT int | parseFeatureFile (const std::string &fileName, MolChemicalFeatureDef::CollectionType &featDefs) |
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * | buildFeatureFactory (std::istream &inStream) |
constructs a MolChemicalFeatureFactory from the data in a stream | |
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * | buildFeatureFactory (const std::string &featureData) |
constructs a MolChemicalFeatureFactory from the data in a string | |
void | setDarkMode (MolDrawOptions &opts) |
void | setDarkMode (MolDraw2D &d2d) |
void | setMonochromeMode (MolDrawOptions &opts, const DrawColour &fgColour, const DrawColour &bgColour) |
void | setMonochromeMode (MolDraw2D &drawer, const DrawColour &fgColour, const DrawColour &bgColour) |
void | assignDefaultPalette (ColourPalette &palette) |
use the RDKit's default palette r | |
void | assignAvalonPalette (ColourPalette &palette) |
use the color palette from the Avalon renderer | |
void | assignCDKPalette (ColourPalette &palette) |
use (part of) the CDK color palette | |
void | assignDarkModePalette (ColourPalette &palette) |
void | assignBWPalette (ColourPalette &palette) |
RDKIT_PARTIALCHARGES_EXPORT void | computeGasteigerCharges (const ROMol *mol, int nIter=12, bool throwOnParamFailure=false) |
RDKIT_PARTIALCHARGES_EXPORT void | computeGasteigerCharges (const ROMol &mol, int nIter=12, bool throwOnParamFailure=false) |
RDKIT_PARTIALCHARGES_EXPORT void | computeGasteigerCharges (const ROMol &mol, std::vector< double > &charges, int nIter=12, bool throwOnParamFailure=false) |
std::string | describeQuery (const Atom *atom) |
std::string | describeQuery (const Bond *bond) |
static int | queryAtomAromatic (Atom const *at) |
static int | queryAtomAliphatic (Atom const *at) |
static int | queryAtomExplicitDegree (Atom const *at) |
static int | queryAtomTotalDegree (Atom const *at) |
static int | queryAtomNonHydrogenDegree (Atom const *at) |
D and T are treated as "non-hydrogen" here. | |
static int | queryAtomHeavyAtomDegree (Atom const *at) |
D and T are not treated as heavy atoms here. | |
static int | queryAtomHCount (Atom const *at) |
static int | queryAtomImplicitHCount (Atom const *at) |
static int | queryAtomHasImplicitH (Atom const *at) |
static int | queryAtomImplicitValence (Atom const *at) |
static int | queryAtomExplicitValence (Atom const *at) |
static int | queryAtomTotalValence (Atom const *at) |
static int | queryAtomUnsaturated (Atom const *at) |
static int | queryAtomNum (Atom const *at) |
static int | makeAtomType (int atomic_num, bool aromatic) |
static void | parseAtomType (int val, int &atomic_num, bool &aromatic) |
static bool | getAtomTypeIsAromatic (int val) |
static int | getAtomTypeAtomicNum (int val) |
static int | queryAtomType (Atom const *at) |
static int | queryAtomMass (Atom const *at) |
static int | queryAtomIsotope (Atom const *at) |
static int | queryAtomFormalCharge (Atom const *at) |
static int | queryAtomNegativeFormalCharge (Atom const *at) |
static int | queryAtomHybridization (Atom const *at) |
static int | queryAtomNumRadicalElectrons (Atom const *at) |
static int | queryAtomHasChiralTag (Atom const *at) |
static int | queryAtomMissingChiralTag (Atom const *at) |
static int | queryAtomHasHeteroatomNbrs (Atom const *at) |
static int | queryAtomNumHeteroatomNbrs (Atom const *at) |
static int | queryAtomHasAliphaticHeteroatomNbrs (Atom const *at) |
static int | queryAtomNumAliphaticHeteroatomNbrs (Atom const *at) |
RDKIT_GRAPHMOL_EXPORT unsigned int | queryAtomBondProduct (Atom const *at) |
RDKIT_GRAPHMOL_EXPORT unsigned int | queryAtomAllBondProduct (Atom const *at) |
static int | queryBondOrder (Bond const *bond) |
static int | queryBondIsSingleOrAromatic (Bond const *bond) |
static int | queryBondIsDoubleOrAromatic (Bond const *bond) |
static int | queryBondIsSingleOrDouble (Bond const *bond) |
static int | queryBondIsSingleOrDoubleOrAromatic (Bond const *bond) |
static int | queryBondDir (Bond const *bond) |
static int | queryIsBondInNRings (Bond const *at) |
static int | queryBondHasStereo (Bond const *bnd) |
static int | queryIsAtomInNRings (Atom const *at) |
static int | queryIsAtomInRing (Atom const *at) |
static int | queryAtomHasRingBond (Atom const *at) |
RDKIT_GRAPHMOL_EXPORT int | queryIsAtomBridgehead (Atom const *at) |
static int | queryIsBondInRing (Bond const *bond) |
static int | queryAtomMinRingSize (Atom const *at) |
static int | queryBondMinRingSize (Bond const *bond) |
static int | queryAtomRingBondCount (Atom const *at) |
template<int tgt> | |
int | queryAtomIsInRingOfSize (Atom const *at) |
template<int tgt> | |
int | queryBondIsInRingOfSize (Bond const *bond) |
template<class T > | |
T * | makeAtomSimpleQuery (int what, int func(Atom const *), const std::string &description="Atom Simple") |
static ATOM_RANGE_QUERY * | makeAtomRangeQuery (int lower, int upper, bool lowerOpen, bool upperOpen, int func(Atom const *), const std::string &description="Atom Range") |
template<class T > | |
T * | makeAtomNumQuery (int what, const std::string &descr) |
returns a Query for matching atomic number | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomNumQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomTypeQuery (int num, int aromatic, const std::string &descr) |
returns a Query for matching atomic number and aromaticity | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomTypeQuery (int num, int aromatic) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomImplicitValenceQuery (int what, const std::string &descr) |
returns a Query for matching implicit valence | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomImplicitValenceQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomExplicitValenceQuery (int what, const std::string &descr) |
returns a Query for matching explicit valence | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomExplicitValenceQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomTotalValenceQuery (int what, const std::string &descr) |
returns a Query for matching total valence | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomTotalValenceQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomExplicitDegreeQuery (int what, const std::string &descr) |
returns a Query for matching explicit degree | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomExplicitDegreeQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomTotalDegreeQuery (int what, const std::string &descr) |
returns a Query for matching atomic degree | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomTotalDegreeQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomHeavyAtomDegreeQuery (int what, const std::string &descr) |
returns a Query for matching heavy atom degree | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHeavyAtomDegreeQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomHCountQuery (int what, const std::string &descr) |
returns a Query for matching hydrogen count | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHCountQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomHasImplicitHQuery (const std::string &descr) |
returns a Query for matching ring atoms | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHasImplicitHQuery () |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomImplicitHCountQuery (int what, const std::string &descr) |
returns a Query for matching implicit hydrogen count | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomImplicitHCountQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomAromaticQuery (const std::string &descr) |
returns a Query for matching the isAromatic flag | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomAromaticQuery () |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomAliphaticQuery (const std::string &descr) |
returns a Query for matching aliphatic atoms | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomAliphaticQuery () |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomMassQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular mass | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomMassQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomIsotopeQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular isotope | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomIsotopeQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomFormalChargeQuery (int what, const std::string &descr) |
returns a Query for matching formal charge | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomFormalChargeQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomNegativeFormalChargeQuery (int what, const std::string &descr) |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomNegativeFormalChargeQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomHybridizationQuery (int what, const std::string &descr) |
returns a Query for matching hybridization | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHybridizationQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomNumRadicalElectronsQuery (int what, const std::string &descr) |
returns a Query for matching the number of radical electrons | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomNumRadicalElectronsQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomHasChiralTagQuery (const std::string &descr) |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHasChiralTagQuery () |
\overloadquery | |
template<class T > | |
T * | makeAtomMissingChiralTagQuery (const std::string &descr) |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomMissingChiralTagQuery () |
\overloadquery | |
template<class T > | |
T * | makeAtomUnsaturatedQuery (const std::string &descr) |
returns a Query for matching atoms with unsaturation: | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomUnsaturatedQuery () |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomInRingQuery (const std::string &descr) |
returns a Query for matching ring atoms | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomInRingQuery () |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomInNRingsQuery (int what, const std::string &descr) |
returns a Query for matching atoms in a particular number of rings | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomInNRingsQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomInRingOfSizeQuery (int tgt) |
returns a Query for matching atoms in rings of a particular size | |
template<class T > | |
T * | makeAtomMinRingSizeQuery (int tgt, const std::string &descr) |
returns a Query for matching an atom's minimum ring size | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomMinRingSizeQuery (int tgt) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomRingBondCountQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular number of ring bonds | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomRingBondCountQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAAtomQuery () |
returns a Query for matching generic A atoms (heavy atoms) | |
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * | makeAHAtomQuery () |
returns a Query for matching generic AH atoms (any atom) | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeQAtomQuery () |
returns a Query for matching generic Q atoms (heteroatoms) | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeQHAtomQuery () |
returns a Query for matching generic QH atoms (heteroatom or H) | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeXAtomQuery () |
returns a Query for matching generic X atoms (halogens) | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeXHAtomQuery () |
returns a Query for matching generic XH atoms (halogen or H) | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeMAtomQuery () |
returns a Query for matching generic M atoms (metals) | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeMHAtomQuery () |
returns a Query for matching generic MH atoms (metals or H) | |
RDKIT_GRAPHMOL_EXPORT void | convertComplexNameToQuery (Atom *query, std::string_view symb) |
template<class T > | |
T * | makeAtomHasRingBondQuery (const std::string &descr) |
returns a Query for matching atoms that have ring bonds | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHasRingBondQuery () |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomNumHeteroatomNbrsQuery (int what, const std::string &descr) |
returns a Query for matching the number of heteroatom neighbors | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomNumHeteroatomNbrsQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomHasHeteroatomNbrsQuery (const std::string &descr) |
returns a Query for matching atoms that have heteroatom neighbors | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHasHeteroatomNbrsQuery () |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomNumAliphaticHeteroatomNbrsQuery (int what, const std::string &descr) |
returns a Query for matching the number of aliphatic heteroatom neighbors | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomNumAliphaticHeteroatomNbrsQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomHasAliphaticHeteroatomNbrsQuery (const std::string &descr) |
returns a Query for matching atoms that have heteroatom neighbors | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHasAliphaticHeteroatomNbrsQuery () |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomNonHydrogenDegreeQuery (int what, const std::string &descr) |
returns a Query for matching the number of non-hydrogen neighbors | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomNonHydrogenDegreeQuery (int what) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<class T > | |
T * | makeAtomIsBridgeheadQuery (const std::string &descr) |
returns a Query for matching bridgehead atoms | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomIsBridgeheadQuery () |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondOrderEqualsQuery (Bond::BondType what) |
returns a Query for matching bond orders | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeSingleOrAromaticBondQuery () |
returns a Query for unspecified SMARTS bonds | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeDoubleOrAromaticBondQuery () |
returns a Query for double|aromatic bonds | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeSingleOrDoubleBondQuery () |
returns a Query for single|double bonds | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeSingleOrDoubleOrAromaticBondQuery () |
returns a Query for tautomeric bonds | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondDirEqualsQuery (Bond::BondDir what) |
returns a Query for matching bond directions | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondHasStereoQuery () |
returns a Query for matching bonds with stereo set | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondIsInRingQuery () |
returns a Query for matching ring bonds | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondInRingOfSizeQuery (int what) |
returns a Query for matching bonds in rings of a particular size | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondMinRingSizeQuery (int what) |
returns a Query for matching a bond's minimum ring size | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondInNRingsQuery (int tgt) |
returns a Query for matching bonds in a particular number of rings | |
RDKIT_GRAPHMOL_EXPORT BOND_NULL_QUERY * | makeBondNullQuery () |
returns a Query for matching any bond | |
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * | makeAtomNullQuery () |
returns a Query for matching any atom | |
static int | queryAtomRingMembership (Atom const *at) |
template<typename T > | |
int | nullDataFun (T) |
template<typename T > | |
bool | nullQueryFun (T) |
template<class Target > | |
Queries::EqualityQuery< int, const Target *, true > * | makeHasPropQuery (const std::string &property) |
returns a Query for matching atoms that have a particular property | |
template<class Target , class T > | |
Queries::EqualityQuery< int, const Target *, true > * | makePropQuery (const std::string &propname, const T &val, 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) |
void | updateRGroupDecompositionParametersFromJSON (RGroupDecompositionParameters ¶ms, const std::string &details_json) |
void | updateRGroupDecompositionParametersFromJSON (RGroupDecompositionParameters ¶ms, const char *details_json) |
RDKIT_RGROUPDECOMPOSITION_EXPORT double | fingerprintVarianceScore (const std::vector< size_t > &permutation, const std::vector< std::vector< RGroupMatch > > &matches, const std::set< int > &labels, FingerprintVarianceScoreData *fingerprintVarianceScoreData=nullptr) |
void | copyVarianceData (const FingerprintVarianceScoreData &fromData, FingerprintVarianceScoreData &toData) |
void | clearVarianceData (FingerprintVarianceScoreData &fingerprintVarianceScoreData) |
std::string | labellingToString (Labelling type) |
return the user friendly name for the given labelling | |
std::map< int, Atom * > | getRlabels (const RWMol &mol) |
Get the RLabels,atom mapping for the current molecule. | |
void | clearInputLabels (Atom *atom) |
Remove the user labels from the atom. | |
bool | setLabel (Atom *atom, int label, std::set< int > &labels, int &maxLabel, bool relabel, Labelling type) |
bool | hasDummy (const RWMol &core) |
Returns true if the core has a dummy atom. | |
bool | isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment (const Atom &atom) |
bool | isUserRLabel (const Atom &atom) |
Return true if the atom has a user-defined R group label. | |
bool | isDummyRGroupAttachment (const Atom &atom) |
bool | isAnyAtomWithMultipleNeighborsOrNotUserRLabel (const Atom &atom) |
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string | toJSON (const RGroupRow &rgr, const std::string &prefix="") |
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string | toJSON (const RGroupRows &rgr, const std::string &prefix="") |
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string | toJSON (const RGroupColumn &rgr, const std::string &prefix="") |
RDKIT_RGROUPDECOMPOSITION_EXPORT void | relabelMappedDummies (ROMol &mol, unsigned int inputLabels=AtomMap|Isotope|MDLRGroup, unsigned int outputLabels=MDLRGroup) |
RDKIT_SLNPARSE_EXPORT RWMol * | SLNToMol (const std::string &smi, bool sanitize=true, int debugParse=0) |
RDKIT_SLNPARSE_EXPORT RWMol * | SLNQueryToMol (const std::string &smi, bool mergeHs=true, int debugParse=0) |
RDKIT_SMILESPARSE_EXPORT void | canonicalizeStereoGroups (std::unique_ptr< ROMol > &mol, StereoGroupAbsOptions outputAbsoluteGroups=StereoGroupAbsOptions::OnlyIncludeWhenOtherGroupsExist) |
RDKIT_SMILESPARSE_EXPORT std::string | MolToSmarts (const ROMol &mol, const SmilesWriteParams ¶ms) |
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 ¶ms, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr) |
RDKIT_SMILESPARSE_EXPORT std::string | MolToCXSmarts (const ROMol &mol, const SmilesWriteParams ¶ms) |
returns the CXSMARTS for a molecule | |
RDKIT_SMILESPARSE_EXPORT std::string | MolFragmentToCXSmarts (const ROMol &mol, const SmilesWriteParams ¶ms, 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::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 ¶ms) |
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 ¶ms, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr) |
returns canonical SMILES for part of a molecule | |
std::string | MolFragmentToSmiles (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) |
returns canonical SMILES for part of a molecule | |
RDKIT_SMILESPARSE_EXPORT std::string | MolToCXSmiles (const ROMol &mol, const SmilesWriteParams &ps, std::uint32_t flags=SmilesWrite::CXSmilesFields::CX_ALL, RestoreBondDirOption restoreBondDirs=RestoreBondDirOptionClear) |
returns canonical CXSMILES for a molecule | |
std::string | MolToCXSmiles (const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false) |
returns canonical CXSMILES for a molecule | |
RDKIT_SMILESPARSE_EXPORT std::string | MolFragmentToCXSmiles (const ROMol &mol, const SmilesWriteParams ¶ms, 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 | |
void | updateSmilesWriteParamsFromJSON (SmilesWriteParams ¶ms, const std::string &details_json) |
void | updateSmilesWriteParamsFromJSON (SmilesWriteParams ¶ms, const char *details_json) |
void | updateCXSmilesFieldsFromJSON (SmilesWrite::CXSmilesFields &cxSmilesFields, RestoreBondDirOption &restoreBondDirs, const std::string &details_json) |
void | updateCXSmilesFieldsFromJSON (SmilesWrite::CXSmilesFields &cxSmilesFields, RestoreBondDirOption &restoreBondDirs, const char *details_json) |
RDKIT_GRAPHMOL_EXPORT void | removeAtomFromGroups (const Atom *atom, std::vector< StereoGroup > &groups) |
RDKIT_GRAPHMOL_EXPORT void | removeGroupsWithAtom (const Atom *atom, std::vector< StereoGroup > &groups) |
RDKIT_GRAPHMOL_EXPORT void | removeGroupsWithAtoms (const std::vector< Atom * > &atoms, std::vector< StereoGroup > &groups) |
RDKIT_GRAPHMOL_EXPORT void | assignStereoGroupIds (std::vector< StereoGroup > &groups) |
RDKIT_GRAPHMOL_EXPORT void | forwardStereoGroupIds (ROMol &mol) |
RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP | findAllSubgraphsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useHs=false, int rootedAtAtom=-1) |
find all bond subgraphs in a range of sizes | |
RDKIT_SUBGRAPHS_EXPORT PATH_LIST | findAllSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, int rootedAtAtom=-1) |
find all bond subgraphs of a particular size | |
RDKIT_SUBGRAPHS_EXPORT PATH_LIST | findUniqueSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, bool useBO=true, int rootedAtAtom=-1) |
find unique bond subgraphs of a particular size | |
RDKIT_SUBGRAPHS_EXPORT PATH_LIST | findAllPathsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1, bool onlyShortestPaths=false) |
find all paths of a particular size | |
RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP | findAllPathsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1, bool onlyShortestPaths=false) |
RDKIT_SUBGRAPHS_EXPORT PATH_TYPE | findAtomEnvironmentOfRadiusN (const ROMol &mol, unsigned int radius, unsigned int rootedAtAtom, bool useHs=false, bool enforceSize=true, std::unordered_map< unsigned int, unsigned int > *atomMap=nullptr) |
Find bond subgraphs of a particular radius around an atom. Return empty result if there is no bond at the requested radius. | |
RDKIT_SUBSTRUCTMATCH_EXPORT void | updateSubstructMatchParamsFromJSON (SubstructMatchParameters ¶ms, const std::string &json) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::string | substructMatchParamsToJSON (const SubstructMatchParameters ¶ms) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > | SubstructMatch (const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=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 ¶ms=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 ¶ms=SubstructMatchParameters()) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > | SubstructMatch (const ROMol &mol, const MolBundle &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > | SubstructMatch (const MolBundle &bundle, const MolBundle &query, const SubstructMatchParameters ¶ms=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 ¶ms) |
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 ¶ms=SmilesParserParams()) |
constructs an ROMol from the metadata in a PNG stream | |
ROMol * | PNGFileToMol (const std::string &fname, const SmilesParserParams ¶ms=SmilesParserParams()) |
constructs an ROMol from the metadata in a PNG file. See PNGStreamToMol() for more details. | |
ROMol * | PNGStringToMol (const std::string &data, const SmilesParserParams ¶ms=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 ¶ms=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 ¶ms=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 ¶ms=SmilesParserParams()) |
constructs a vector of ROMol from the metadata in a PNG string. See PNGStreamToMols() for more details. | |
RDKIT_FILEPARSERS_EXPORT std::string | addMolToPNGStream (const ROMol &mol, std::istream &iStream, bool includePkl=true, bool includeSmiles=true, bool includeMol=false) |
adds metadata for an ROMol to the data from a PNG stream. The modified PNG data is returned. | |
std::string | addMolToPNGString (const ROMol &mol, const std::string &pngString, bool includePkl=true, bool includeSmiles=true, bool includeMol=false) |
adds metadata for an ROMol to a PNG string. The modified PNG data is returned. See addMolToPNGStream() for more details. | |
std::string | addMolToPNGFile (const ROMol &mol, const std::string &fname, bool includePkl=true, bool includeSmiles=true, bool includeMol=false) |
adds metadata for an ROMol to the data from a PNG file. The modified PNG data is returned. See addMolToPNGStream() for more details. | |
SubstanceGroups and molecules | |
RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & | getSubstanceGroups (ROMol &mol) |
RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & | getSubstanceGroups (const ROMol &mol) |
RDKIT_GRAPHMOL_EXPORT unsigned int | addSubstanceGroup (ROMol &mol, SubstanceGroup sgroup) |
RDKIT_GRAPHMOL_EXPORT void | removeSubstanceGroupsReferencingAtom (RWMol &mol, unsigned int idx) |
Removes SubstanceGroups which reference a particular atom index. | |
RDKIT_GRAPHMOL_EXPORT void | removeSubstanceGroupsReferencingBond (RWMol &mol, unsigned int idx) |
Removes SubstanceGroups which reference a particular bond index. | |
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 Queries::AndQuery<int, Atom const *, true> RDKit::ATOM_AND_QUERY |
Definition at line 35 of file QueryOps.h.
typedef Queries::Query<bool, Atom const *, true> RDKit::ATOM_BOOL_QUERY |
Definition at line 32 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_EQUALS_QUERY |
Definition at line 44 of file QueryOps.h.
typedef Queries::GreaterQuery<int, Atom const *, true> RDKit::ATOM_GREATER_QUERY |
Definition at line 47 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int, Atom const *, true> RDKit::ATOM_GREATEREQUAL_QUERY |
Definition at line 51 of file QueryOps.h.
typedef Queries::LessQuery<int, Atom const *, true> RDKit::ATOM_LESS_QUERY |
Definition at line 55 of file QueryOps.h.
typedef Queries::LessEqualQuery<int, Atom const *, true> RDKit::ATOM_LESSEQUAL_QUERY |
Definition at line 58 of file QueryOps.h.
typedef Queries::Query<int, Atom const *, true> RDKit::ATOM_NULL_QUERY |
Definition at line 68 of file QueryOps.h.
typedef Queries::OrQuery<int, Atom const *, true> RDKit::ATOM_OR_QUERY |
Definition at line 38 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_PROP_QUERY |
Definition at line 854 of file QueryOps.h.
typedef Queries::RangeQuery<int, Atom const *, true> RDKit::ATOM_RANGE_QUERY |
Definition at line 61 of file QueryOps.h.
typedef Queries::SetQuery<int, Atom const *, true> RDKit::ATOM_SET_QUERY |
Definition at line 64 of file QueryOps.h.
typedef Queries::XOrQuery<int, Atom const *, true> RDKit::ATOM_XOR_QUERY |
Definition at line 41 of file QueryOps.h.
typedef std::uint32_t RDKit::atomindex_t |
typedef Queries::AndQuery<int, Bond const *, true> RDKit::BOND_AND_QUERY |
Definition at line 36 of file QueryOps.h.
typedef Queries::Query<bool, Bond const *, true> RDKit::BOND_BOOL_QUERY |
Definition at line 33 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_EQUALS_QUERY |
Definition at line 45 of file QueryOps.h.
typedef Queries::GreaterQuery<int, Bond const *, true> RDKit::BOND_GREATER_QUERY |
Definition at line 48 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int, Bond const *, true> RDKit::BOND_GREATEREQUAL_QUERY |
Definition at line 53 of file QueryOps.h.
typedef Queries::LessQuery<int, Bond const *, true> RDKit::BOND_LESS_QUERY |
Definition at line 56 of file QueryOps.h.
typedef Queries::LessEqualQuery<int, Bond const *, true> RDKit::BOND_LESSEQUAL_QUERY |
Definition at line 59 of file QueryOps.h.
typedef Queries::Query<int, Bond const *, true> RDKit::BOND_NULL_QUERY |
Definition at line 67 of file QueryOps.h.
typedef Queries::OrQuery<int, Bond const *, true> RDKit::BOND_OR_QUERY |
Definition at line 39 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_PROP_QUERY |
Definition at line 855 of file QueryOps.h.
typedef Queries::RangeQuery<int, Bond const *, true> RDKit::BOND_RANGE_QUERY |
Definition at line 62 of file QueryOps.h.
typedef Queries::SetQuery<int, Bond const *, true> RDKit::BOND_SET_QUERY |
Definition at line 65 of file QueryOps.h.
typedef Queries::XOrQuery<int, Bond const *, true> RDKit::BOND_XOR_QUERY |
Definition at line 42 of file QueryOps.h.
typedef std::unordered_map<std::size_t, ConjElectrons *> RDKit::CEMap |
Definition at line 32 of file Resonance.h.
typedef std::vector<ConjElectrons *> RDKit::CEVect |
Definition at line 29 of file Resonance.h.
typedef std::vector<CEVect2 *> RDKit::CEVect3 |
Definition at line 30 of file Resonance.h.
typedef std::map<int, DrawColour> RDKit::ColourPalette |
Definition at line 67 of file MolDraw2DHelpers.h.
typedef boost::shared_ptr<Conformer> RDKit::CONFORMER_SPTR |
Definition at line 160 of file Conformer.h.
typedef std::map<unsigned int, AtomElectrons *> RDKit::ConjAtomMap |
Definition at line 28 of file Resonance.h.
typedef std::map<unsigned int, BondElectrons *> RDKit::ConjBondMap |
Definition at line 27 of file Resonance.h.
typedef std::vector<std::uint8_t> RDKit::ConjFP |
Definition at line 31 of file Resonance.h.
typedef Atom const* RDKit::ConstAtomPtr |
Definition at line 707 of file QueryOps.h.
typedef Bond const* RDKit::ConstBondPtr |
Definition at line 817 of file QueryOps.h.
typedef std::vector<std::shared_ptr<const CustomPropHandler> > RDKit::CustomPropHandlerVec |
Definition at line 388 of file StreamOps.h.
typedef std::vector<double> RDKit::DashPattern |
Definition at line 68 of file MolDraw2DHelpers.h.
typedef std::map<double, int, ltDouble> RDKit::DOUBLE_INT_MAP |
typedef boost::variate_generator<rng_type &, uniform_double> RDKit::double_source_type |
typedef std::vector<double> RDKit::DOUBLE_VECT |
typedef DOUBLE_VECT::const_iterator RDKit::DOUBLE_VECT_CI |
typedef DOUBLE_VECT::iterator RDKit::DOUBLE_VECT_I |
Definition at line 121 of file FilterCatalog.h.
typedef boost::shared_ptr<MolChemicalFeature> RDKit::FeatSPtr |
Definition at line 20 of file MolChemicalFeatureFactory.h.
typedef std::list<FeatSPtr> RDKit::FeatSPtrList |
Definition at line 21 of file MolChemicalFeatureFactory.h.
typedef FeatSPtrList::iterator RDKit::FeatSPtrList_I |
Definition at line 22 of file MolChemicalFeatureFactory.h.
typedef RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int > RDKit::FragCatalog |
Definition at line 23 of file FragCatGenerator.h.
typedef std::deque<int> RDKit::INT_DEQUE |
typedef INT_DEQUE::const_iterator RDKit::INT_DEQUE_CI |
typedef INT_DEQUE::iterator RDKit::INT_DEQUE_I |
typedef std::map<int, INT_DEQUE> RDKit::INT_INT_DEQ_MAP |
typedef INT_INT_DEQ_MAP::const_iterator RDKit::INT_INT_DEQ_MAP_CI |
typedef std::map<int, INT_VECT> RDKit::INT_INT_VECT_MAP |
typedef INT_INT_VECT_MAP::const_iterator RDKit::INT_INT_VECT_MAP_CI |
typedef std::list<int> RDKit::INT_LIST |
typedef INT_LIST::const_iterator RDKit::INT_LIST_CI |
typedef INT_LIST::iterator RDKit::INT_LIST_I |
typedef std::map<int, int> RDKit::INT_MAP_INT |
typedef INT_MAP_INT::const_iterator RDKit::INT_MAP_INT_CI |
typedef INT_MAP_INT::iterator RDKit::INT_MAP_INT_I |
typedef std::map<int, PATH_LIST> RDKit::INT_PATH_LIST_MAP |
Definition at line 46 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::const_iterator RDKit::INT_PATH_LIST_MAP_CI |
Definition at line 47 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::iterator RDKit::INT_PATH_LIST_MAP_I |
Definition at line 48 of file Subgraphs.h.
typedef std::set<int> RDKit::INT_SET |
typedef INT_SET::const_iterator RDKit::INT_SET_CI |
typedef INT_SET::iterator RDKit::INT_SET_I |
typedef boost::variate_generator<rng_type &, uniform_int> RDKit::int_source_type |
typedef std::vector<int> RDKit::INT_VECT |
typedef INT_VECT::const_iterator RDKit::INT_VECT_CI |
typedef INT_VECT::const_reverse_iterator RDKit::INT_VECT_CRI |
typedef INT_VECT::iterator RDKit::INT_VECT_I |
typedef INT_VECT::reverse_iterator RDKit::INT_VECT_RI |
typedef std::vector<double> RDKit::INVAR_VECT |
typedef INVAR_VECT::const_iterator RDKit::INVAR_VECT_CI |
typedef INVAR_VECT::iterator RDKit::INVAR_VECT_I |
typedef std::list<INT_VECT> RDKit::LIST_INT_VECT |
typedef LIST_INT_VECT::const_iterator RDKit::LIST_INT_VECT_CI |
typedef LIST_INT_VECT::iterator RDKit::LIST_INT_VECT_I |
typedef long long int RDKit::LONGINT |
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.
typedef bool(* RDKit::MCSAcceptanceFunction) (const ROMol &, const ROMol &, const std::vector< std::pair< int, int > > &, const std::vector< std::pair< int, int > > &, const MCSParameters *) |
typedef bool(* RDKit::MCSAtomCompareFunction) (const MCSAtomCompareParameters &, const ROMol &, unsigned int, const ROMol &, unsigned int, void *) |
typedef bool(* RDKit::MCSBondCompareFunction) (const MCSBondCompareParameters &, const ROMol &, unsigned int, const ROMol &, unsigned int, void *) |
typedef bool(* RDKit::MCSFinalMatchCheckFunction) (const std::uint32_t[], const std::uint32_t[], const ROMol &, const FMCS::Graph &, const ROMol &, const FMCS::Graph &, const MCSParameters *) |
typedef bool(* RDKit::MCSProgressCallback) (const MCSProgressData &stat, const MCSParameters ¶ms, void *userData) |
typedef std::vector<ROMol *> RDKit::MOL_PTR_VECT |
typedef MOL_PTR_VECT::const_iterator RDKit::MOL_PTR_VECT_CI |
typedef MOL_PTR_VECT::iterator RDKit::MOL_PTR_VECT_I |
typedef std::vector< boost::shared_ptr< ROMol > > RDKit::MOL_SPTR_VECT |
Definition at line 21 of file FragCatParams.h.
typedef std::vector<ROMol> RDKit::MOL_VECT |
a hierarchical catalog for holding molecules
Definition at line 17 of file MolCatalog.h.
typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, Atom *, Bond *> RDKit::MolGraph |
typedef std::list<PATH_TYPE> RDKit::PATH_LIST |
Definition at line 43 of file Subgraphs.h.
typedef PATH_LIST::const_iterator RDKit::PATH_LIST_CI |
Definition at line 44 of file Subgraphs.h.
typedef std::vector<int> RDKit::PATH_TYPE |
Definition at line 42 of file Subgraphs.h.
typedef std::map<int, RData> RDKit::R_DECOMP |
Definition at line 16 of file RGroupMatch.h.
typedef boost::shared_ptr<RGroupData> RDKit::RData |
Definition at line 15 of file RGroupMatch.h.
typedef RDValue RDKit::RDValue_cast_t |
Definition at line 417 of file RDValue-doublemagic.h.
typedef std::vector<ROMOL_SPTR> RDKit::RGroupColumn |
Definition at line 32 of file RGroupDecomp.h.
typedef std::map<std::string, RGroupColumn> RDKit::RGroupColumns |
Definition at line 35 of file RGroupDecomp.h.
typedef LinkedPopLinearSel<RGroupDecompositionChromosome, RGroupGa> RDKit::RGroupGaPopulation |
Definition at line 37 of file RGroupGa.h.
typedef std::map<std::string, ROMOL_SPTR> RDKit::RGroupRow |
Definition at line 31 of file RGroupDecomp.h.
typedef std::vector<RGroupRow> RDKit::RGroupRows |
Definition at line 34 of file RGroupDecomp.h.
typedef boost::minstd_rand RDKit::rng_type |
typedef boost::shared_ptr< ROMol > RDKit::ROMOL_SPTR |
Definition at line 23 of file ChemTransforms.h.
typedef boost::shared_ptr<RWMol> RDKit::RWMOL_SPTR |
typedef std::vector<RWMOL_SPTR> RDKit::RWMOL_SPTR_VECT |
typedef std::vector<Snapshot> RDKit::SnapshotVect |
Definition at line 21 of file Snapshot.h.
typedef std::map<std::string, UINT> RDKit::STR_UINT_MAP |
typedef std::map<std::string,UINT>::const_iterator RDKit::STR_UINT_MAP_CI |
typedef std::vector< std::string > RDKit::STR_VECT |
typedef std::vector<std::string>::const_iterator RDKit::STR_VECT_CI |
typedef std::vector<std::string>::iterator RDKit::STR_VECT_I |
typedef std::map<std::string, std::string> RDKit::STRING_PROPS |
Definition at line 54 of file FilterCatalogEntry.h.
typedef unsigned char RDKit::UCHAR |
typedef unsigned int RDKit::UINT |
typedef std::vector<UINT> RDKit::UINT_VECT |
typedef std::vector<UINT>::const_iterator RDKit::UINT_VECT_CI |
typedef boost::uniform_real RDKit::uniform_double |
typedef boost::uniform_int RDKit::uniform_int |
typedef unsigned short RDKit::USHORT |
typedef std::vector<DOUBLE_VECT> RDKit::VECT_DOUBLE_VECT |
typedef VECT_DOUBLE_VECT::const_iterator RDKit::VECT_DOUBLE_VECT_CI |
typedef VECT_DOUBLE_VECT::iterator RDKit::VECT_DOUBLE_VECT_I |
typedef std::vector<INT_VECT> RDKit::VECT_INT_VECT |
typedef VECT_INT_VECT::const_iterator RDKit::VECT_INT_VECT_CI |
typedef VECT_INT_VECT::iterator RDKit::VECT_INT_VECT_I |
enum RDKit::EEndian |
Enumerator | |
---|---|
LITTLE_ENDIAN_ORDER | |
BIG_ENDIAN_ORDER |
Definition at line 28 of file StreamOps.h.
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.
|
strong |
Enumerator | |
---|---|
AtomPairFP | |
TopologicalTorsionFP | |
MorganFP | |
RDKitFP | |
PatternFP |
Definition at line 43 of file ReactionFingerprints.h.
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Enumerator | |
---|---|
AtomPairFP | |
MorganFP | |
RDKitFP | |
TopologicalTorsionFP |
Definition at line 454 of file FingerprintGenerator.h.
Enumerator | |
---|---|
SgroupInAtomSet | |
SgroupNotInAtomSet | |
SgroupBothInAndNotInAtomSet |
Definition at line 48 of file MarvinDefs.h.
|
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Enumerator | |
---|---|
RGROUP_LABELS | |
ISOTOPE_LABELS | |
ATOMMAP_LABELS | |
INDEX_LABELS | |
DUMMY_LABELS | |
INTERNAL_LABELS |
Definition at line 32 of file RGroupUtils.h.
|
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Enumerator | |
---|---|
AtomMapNumber | |
Isotope | |
FragmentOnBonds | |
AtomType | |
AtomProperty |
Definition at line 106 of file MolFragmenter.h.
|
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Enumerator | |
---|---|
CIRCLEANDLINE | |
LASSO |
Definition at line 156 of file MolDraw2DHelpers.h.
enum RDKit::OperationName |
Enumerator | |
---|---|
RgroupMutate | |
Crossover | |
Create |
Definition at line 39 of file RGroupGa.h.
Enumerator | |
---|---|
Reactant | |
Product | |
Agent |
Definition at line 41 of file ReactionUtils.h.
Enumerator | |
---|---|
RESTOREBONDDIROPTION_ENUM_ITEMS |
Definition at line 281 of file SmilesWrite.h.
Enumerator | |
---|---|
RGROUPCOREALIGNMENT_ENUM_ITEMS |
Definition at line 57 of file RGroupDecompParams.h.
Enumerator | |
---|---|
RGROUPLABELLING_ENUM_ITEMS |
Definition at line 55 of file RGroupDecompParams.h.
enum RDKit::RGroupLabels |
Enumerator | |
---|---|
RGROUPLABELS_ENUM_ITEMS |
Definition at line 51 of file RGroupDecompParams.h.
Enumerator | |
---|---|
RGROUPMATCHING_ENUM_ITEMS |
Definition at line 53 of file RGroupDecompParams.h.
enum RDKit::RGroupScore |
Enumerator | |
---|---|
RGROUPSCORE_ENUM_ITEMS |
Definition at line 59 of file RGroupDecompParams.h.
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Enumerator | |
---|---|
OnlyIncludeWhenOtherGroupsExist | |
NeverInclude | |
AlwaysInclude |
Definition at line 22 of file CanonicalizeStereoGroups.h.
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Enumerator | |
---|---|
STEREO_ABSOLUTE | |
STEREO_OR | |
STEREO_AND |
Definition at line 31 of file StereoGroup.h.
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inline |
adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.
Definition at line 379 of file ReactionParser.h.
References addChemicalReactionToPNGFile(), and addChemicalReactionToPNGStream().
Referenced by addChemicalReactionToPNGFile().
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.
rxn | the reaction to add |
iStream | the stream to read from |
includePkl | include a reaction pickle |
includeSmiles | include reaction SMILES for the reaction |
includeSmarts | include reaction SMARTS for the reaction |
includeRxn | include an RXN block for the reaction |
References addChemicalReactionToPNGStream().
Referenced by addChemicalReactionToPNGFile(), addChemicalReactionToPNGStream(), and addChemicalReactionToPNGString().
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adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.
Definition at line 367 of file ReactionParser.h.
References addChemicalReactionToPNGStream(), and addChemicalReactionToPNGString().
Referenced by addChemicalReactionToPNGString().
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adds metadata to a PNG file. The modified PNG data is returned.
Definition at line 84 of file PNGParser.h.
References addMetadataToPNGStream().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::addMetadataToPNGStream | ( | std::istream & | iStream, |
const std::vector< std::pair< std::string, std::string > > & | metadata, | ||
bool | compressed = true ) |
adds metadata to a PNG stream. The modified PNG data is returned.
The compressed flag is ignored if the RDKit is not built with boost::iostreams support
Referenced by addMetadataToPNGFile(), and addMetadataToPNGString().
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adds metadata to a PNG string. The modified PNG data is returned.
Definition at line 74 of file PNGParser.h.
References addMetadataToPNGStream().
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adds metadata for an ROMol to the data from a PNG file. The modified PNG data is returned. See addMolToPNGStream()
for more details.
Definition at line 191 of file PNGParser.h.
References addMolToPNGStream().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::addMolToPNGStream | ( | const ROMol & | mol, |
std::istream & | iStream, | ||
bool | includePkl = true, | ||
bool | includeSmiles = true, | ||
bool | includeMol = false ) |
adds metadata for an ROMol to the data from a PNG stream. The modified PNG data is returned.
mol | the molecule to add |
iStream | the stream to read from |
includePkl | include a molecule pickle |
includeSmiles | include CXSMILES for the molecule |
includeMol | include a mol block for the molecule |
Referenced by addMolToPNGFile(), and addMolToPNGString().
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adds metadata for an ROMol to a PNG string. The modified PNG data is returned. See addMolToPNGStream()
for more details.
Definition at line 179 of file PNGParser.h.
References addMolToPNGStream().
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
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
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.
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:
queries
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()
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:
queries
References addRecursiveQueriesToReaction().
Referenced by addRecursiveQueriesToReaction().
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.
sgroup | - SubstanceGroup to be added to the molecule. |
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
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 |
|
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Packs an integer and outputs it to a stream.
Definition at line 110 of file StreamOps.h.
References CHECK_INVARIANT.
|
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use the color palette from the Avalon renderer
Definition at line 95 of file MolDraw2DHelpers.h.
|
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Definition at line 151 of file MolDraw2DHelpers.h.
|
inline |
use (part of) the CDK color palette
Definition at line 117 of file MolDraw2DHelpers.h.
|
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Definition at line 135 of file MolDraw2DHelpers.h.
Referenced by setDarkMode().
|
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use the RDKit's default palette r
Definition at line 77 of file MolDraw2DHelpers.h.
Referenced by RDKit::MolDrawOptions::MolDrawOptions().
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.
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::atomCompat | ( | const Atom * | a1, |
const Atom * | a2, | ||
const SubstructMatchParameters & | ps ) |
RDKIT_RDGENERAL_EXPORT std::string RDKit::augmentTagName | ( | const std::string & | tag | ) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::bondCompat | ( | const Bond * | b1, |
const Bond * | b2, | ||
const SubstructMatchParameters & | ps ) |
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * RDKit::buildFeatureFactory | ( | const std::string & | featureData | ) |
constructs a MolChemicalFeatureFactory from the data in a string
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * RDKit::buildFeatureFactory | ( | std::istream & | inStream | ) |
constructs a MolChemicalFeatureFactory from the data in a stream
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inline |
Definition at line 401 of file Bond.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.
RDKIT_SMILESPARSE_EXPORT void RDKit::canonicalizeStereoGroups | ( | std::unique_ptr< ROMol > & | mol, |
StereoGroupAbsOptions | outputAbsoluteGroups = StereoGroupAbsOptions::OnlyIncludeWhenOtherGroupsExist ) |
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inline |
Definition at line 395 of file Bond.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::getBondType(), isDative(), and RDKit::Bond::SINGLE.
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().
RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > > RDKit::CDXMLFileToChemicalReactions | ( | const std::string & | fileName, |
bool | sanitize = false, | ||
bool | removeHs = false ) |
Parse a file in CDXML rxn format into a vector of ChemicalReactions.
References CDXMLFileToChemicalReactions().
Referenced by CDXMLFileToChemicalReactions().
RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > > RDKit::CDXMLToChemicalReactions | ( | const std::string & | rxnBlock, |
bool | sanitize = false, | ||
bool | removeHs = false ) |
Parse text in CDXML rxn format into a vector of ChemicalReactions.
References CDXMLToChemicalReactions().
Referenced by CDXMLToChemicalReactions().
RDKIT_FMCS_EXPORT bool RDKit::checkAtomCharge | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2 ) |
RDKIT_FMCS_EXPORT bool RDKit::checkAtomChirality | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2 ) |
RDKIT_FMCS_EXPORT bool RDKit::checkAtomDistance | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2 ) |
RDKIT_FMCS_EXPORT bool RDKit::checkAtomRingMatch | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2 ) |
RDKIT_FMCS_EXPORT bool RDKit::checkBondRingMatch | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2 ) |
RDKIT_FMCS_EXPORT bool RDKit::checkBondStereo | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2 ) |
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Definition at line 125 of file RGroupDecomp.h.
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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().
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().
Referenced by ChemicalReactionToCXRxnSmarts(), and ChemicalReactionToCXRxnSmarts().
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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 166 of file ReactionParser.h.
References RDKit::SmilesWriteParams::canonical, and ChemicalReactionToCXRxnSmiles().
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().
Referenced by ChemicalReactionToCXRxnSmiles(), and ChemicalReactionToCXRxnSmiles().
RDKIT_MARVINPARSER_EXPORT std::string RDKit::ChemicalReactionToMrvBlock | ( | const ChemicalReaction & | rxn, |
bool | prettyPrint = false ) |
RDKIT_MARVINPARSER_EXPORT void RDKit::ChemicalReactionToMrvFile | ( | const ChemicalReaction & | rxn, |
const std::string & | fName, | ||
bool | prettyPrint = false ) |
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnBlock | ( | const ChemicalReaction & | rxn, |
bool | separateAgents = false, | ||
bool | forceV3000 = false ) |
returns an rxn block for a reaction
rxn | chemical reaction |
separateAgents | flag to decide if agents are put in a separate block, otherwise they are included in the reactants block (default) |
forceV3000 | flag to cause the V3000 format to be used instead of V2000 |
References ChemicalReactionToRxnBlock().
Referenced by ChemicalReactionToRxnBlock().
RDKIT_CHEMREACTIONS_EXPORT ROMol * RDKit::ChemicalReactionToRxnMol | ( | const ChemicalReaction & | rxn | ) |
returns a ROMol with RXN roles used to describe the reaction
References ChemicalReactionToRxnMol().
Referenced by ChemicalReactionToRxnMol().
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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 134 of file ReactionParser.h.
References RDKit::SmilesWriteParams::canonical, and ChemicalReactionToRxnSmarts().
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmarts | ( | const ChemicalReaction & | rxn, |
const SmilesWriteParams & | params ) |
returns the reaction SMARTS for a reaction
References ChemicalReactionToRxnSmarts().
Referenced by ChemicalReactionToRxnSmarts(), and ChemicalReactionToRxnSmarts().
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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 145 of file ReactionParser.h.
References RDKit::SmilesWriteParams::canonical, and ChemicalReactionToRxnSmiles().
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmiles | ( | const ChemicalReaction & | rxn, |
const SmilesWriteParams & | params = SmilesWriteParams() ) |
returns the reaction SMILES for a reaction
References ChemicalReactionToRxnSmiles().
Referenced by ChemicalReactionToRxnSmiles(), and ChemicalReactionToRxnSmiles().
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToV3KRxnBlock | ( | const ChemicalReaction & | rxn, |
bool | separateAgents = false ) |
returns an V3000 rxn block for a reaction
rxn | chemical reaction |
separateAgents | flag to decide if agents are put in a separate block, otherwise they are included in the reactants block (default) |
References ChemicalReactionToV3KRxnBlock().
Referenced by ChemicalReactionToV3KRxnBlock().
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::chiralAtomCompat | ( | const Atom * | a1, |
const Atom * | a2 ) |
void RDKit::clearInputLabels | ( | Atom * | atom | ) |
Remove the user labels from the atom.
RDKIT_FILEPARSERS_EXPORT void RDKit::clearMolBlockWedgingInfo | ( | ROMol & | mol | ) |
RDKIT_FILEPARSERS_EXPORT void RDKit::ClearSingleBondDirFlags | ( | ROMol & | mol | ) |
void RDKit::clearVarianceData | ( | FingerprintVarianceScoreData & | fingerprintVarianceScoreData | ) |
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.
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 |
RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges | ( | const ROMol & | mol, |
int | nIter = 12, | ||
bool | throwOnParamFailure = false ) |
RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges | ( | const ROMol & | mol, |
std::vector< double > & | charges, | ||
int | nIter = 12, | ||
bool | throwOnParamFailure = false ) |
RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges | ( | const ROMol * | mol, |
int | nIter = 12, | ||
bool | throwOnParamFailure = false ) |
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
RDKIT_DATASTRUCTS_EXPORT unsigned int RDKit::computeL1Norm | ( | const DiscreteValueVect & | v1, |
const DiscreteValueVect & | v2 ) |
RDKIT_DATASTRUCTS_EXPORT double RDKit::computeL1Norm | ( | const RealValueVect & | v1, |
const RealValueVect & | v2 ) |
returns L1 Norm of vectors
RDKIT_CHEMREACTIONS_EXPORT boost::uint64_t RDKit::computeNumProducts | ( | const EnumerationTypes::RGROUPS & | sizes | ) |
computeNumProducts Returns the number of possible product combination from The given numbers of building blocks for each rgroup or EnumerationStrategyBase::EnumerationOverflow if the number will not fit into the machines integer type. n.b. An overflow simply means there are a lot of products not that they cannot be enumerated
References computeNumProducts().
Referenced by computeNumProducts(), RDKit::EnumerationStrategyBase::initialize(), and RDKit::EnumerationStrategyBase::internalInitialize().
RDKIT_FILEPARSERS_EXPORT void RDKit::ConnectTheDots | ( | RWMol * | mol, |
unsigned int | flags = 0 ) |
RDKIT_GRAPHMOL_EXPORT void RDKit::convertComplexNameToQuery | ( | Atom * | query, |
std::string_view | symb ) |
Definition at line 339 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::AnyTag, 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().
void RDKit::copyVarianceData | ( | const FingerprintVarianceScoreData & | fromData, |
FingerprintVarianceScoreData & | toData ) |
unsigned int RDKit::countSwapsToInterconvert | ( | const T & | ref, |
T | probe ) |
Definition at line 54 of file utils.h.
References CHECK_INVARIANT, and PRECONDITION.
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.
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 |
mol
with the matching atoms and bonds (if any) removed.
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inline |
Definition at line 150 of file QueryAtom.h.
References RDKit::Atom::getQuery(), RDKit::Atom::hasQuery(), PRECONDITION, and RDKit::detail::qhelper().
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inline |
Definition at line 136 of file QueryBond.h.
References RDKit::Bond::getQuery(), RDKit::Bond::hasQuery(), PRECONDITION, and RDKit::detail::qhelper().
RDKIT_FILEPARSERS_EXPORT void RDKit::DetectAtomStereoChemistry | ( | RWMol & | mol, |
const Conformer * | conf ) |
deprecated, please use MolOps::assignChiralTypesFromBondDirs instead
RDKIT_FILEPARSERS_EXPORT void RDKit::DetectBondStereoChemistry | ( | ROMol & | mol, |
const Conformer * | conf ) |
deprecated, please use MolOps::detectBondStereoChemistry instead
RDKIT_DETERMINEBONDS_EXPORT void RDKit::determineBondOrders | ( | RWMol & | mol, |
int | charge = 0, | ||
bool | allowChargedFragments = true, | ||
bool | embedChiral = true, | ||
bool | useAtomMap = false ) |
This is based on xyz2mol: https://github.com/jensengroup/xyz2mol
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 |
RDKIT_DETERMINEBONDS_EXPORT void RDKit::determineBonds | ( | RWMol & | mol, |
bool | useHueckel = false, | ||
int | charge = 0, | ||
double | covFactor = 1.3, | ||
bool | allowChargedFragments = true, | ||
bool | embedChiral = true, | ||
bool | useAtomMap = false, | ||
bool | useVdw = false ) |
This is based on xyz2mol: https://github.com/jensengroup/xyz2mol
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 |
RDKIT_FILEPARSERS_EXPORT Bond::BondDir RDKit::DetermineBondWedgeState | ( | const Bond * | bond, |
const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > & | wedgeBonds, | ||
const Conformer * | conf ) |
RDKIT_FILEPARSERS_EXPORT Bond::BondDir RDKit::DetermineBondWedgeState | ( | const Bond * | bond, |
unsigned int | fromAtomIdx, | ||
const Conformer * | conf ) |
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
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 |
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.
References RDKit::SparseIntVect< IndexType >::getLength(), and RDKit::SparseIntVect< IndexType >::getTotalVal().
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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
rxn | the reaction to be fingerprinted |
params | specific settings to manipulate fingerprint generation |
Notes:
delete
ing the result Definition at line 93 of file StreamOps.h.
Definition at line 103 of file StreamOps.h.
Definition at line 73 of file StreamOps.h.
References SwapBytes().
Referenced by streamRead(), and streamWrite().
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inline |
Definition at line 98 of file StreamOps.h.
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::EnumerateLibraryCanSerialize | ( | ) |
void RDKit::eraseUniquePtr | ( | std::vector< std ::unique_ptr< T > > & | vector, |
T * | itemToErase ) |
Definition at line 227 of file MarvinDefs.h.
References findUniquePtr().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::FASTAToMol | ( | const char * | seq, |
bool | sanitize, | ||
bool | lowerD ) |
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 |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::FASTAToMol | ( | const char * | seq, |
bool | sanitize = true, | ||
int | flavor = 0 ) |
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 |
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.
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.
RDKIT_RDGENERAL_EXPORT bool RDKit::feq | ( | double | v1, |
double | v2, | ||
double | tol = 1e-4 ) |
floating point comparison with a tolerance
RDKIT_FILTERCATALOG_EXPORT bool RDKit::FilterCatalogCanSerialize | ( | ) |
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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 ) |
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
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)
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 ) |
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
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)
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
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)
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.
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) |
RDKIT_FRAGCATALOG_EXPORT MatchVectType RDKit::findFuncGroupsOnMol | ( | const ROMol & | mol, |
const FragCatParams * | params, | ||
INT_VECT & | fgBonds ) |
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 ) |
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 ) |
RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS | ( | const std::vector< ROMOL_SPTR > & | mols, |
const MCSParameters * | params = nullptr ) |
RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS_P | ( | const std::vector< ROMOL_SPTR > & | mols, |
const char * | params_json ) |
std::vector< std::unique_ptr< T > >::iterator RDKit::findUniquePtr | ( | std::vector< std ::unique_ptr< T > > & | vector, |
T * | itemToFind ) |
Definition at line 212 of file MarvinDefs.h.
Referenced by eraseUniquePtr().
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
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)
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 ) |
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.
boost::enable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdany | ( | const RDAny & | arg | ) |
Definition at line 190 of file RDAny.h.
References RDKit::RDValue::getTag(), RDKit::RDAny::m_value, rdany_cast(), and RDKit::RDTypeTag::StringTag.
boost::disable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdany | ( | const RDAny & | arg | ) |
Definition at line 211 of file RDAny.h.
References rdany_cast().
boost::enable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
Definition at line 268 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().
boost::disable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
Definition at line 289 of file RDValue.h.
References rdvalue_cast().
RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomAlias | ( | const Atom * | atom | ) |
RDKIT_GRAPHMOL_EXPORT void RDKit::getAtomListQueryVals | ( | const Atom::QUERYATOM_QUERY * | q, |
std::vector< int > & | vals ) |
RDKIT_GRAPHMOL_EXPORT int RDKit::getAtomRLabel | ( | const Atom * | atm | ) |
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Definition at line 146 of file QueryOps.h.
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Definition at line 145 of file QueryOps.h.
RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomValue | ( | const Atom * | atom | ) |
bool RDKit::getCleanNumber | ( | std::string | strToParse, |
T & | outInt ) |
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint32_t > * RDKit::getCountFP | ( | const ROMol & | mol, |
FPType | fPType ) |
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint32_t > * > * RDKit::getCountFPBulk | ( | const std::vector< const ROMol * > | molVector, |
FPType | fPType ) |
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RDKIT_RDGENERAL_EXPORT double_source_type & RDKit::getDoubleRandomSource | ( | ) |
return a reference to the global (Boost) random source
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT::const_iterator RDKit::getEndIterator | ( | const ChemicalReaction & | rxn, |
ReactionMoleculeType | t ) |
const FilterData_t * RDKit::GetFilterData | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
const FilterProperty_t * RDKit::GetFilterProperties | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
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
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::getFP | ( | const ROMol & | mol, |
FPType | fPType ) |
Referenced by RDKit::FPBReader::operator[]().
RDKIT_FINGERPRINTS_EXPORT std::vector< ExplicitBitVect * > * RDKit::getFPBulk | ( | const std::vector< const ROMol * > | molVector, |
FPType | fPType ) |
RDKIT_FILTERCATALOG_EXPORT const FilterCatalog & RDKit::GetFunctionalGroupHierarchy | ( | ) |
Return the functional group hierarchy as a FilterCatalog.
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grabs the next line from an instream and returns it.
Definition at line 348 of file StreamOps.h.
References getLine().
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grabs the next line from an instream and returns it.
Definition at line 338 of file StreamOps.h.
Referenced by getLine().
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
unsigned int RDKit::GetNumEntries | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
unsigned int RDKit::GetNumPropertyEntries | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
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Definition at line 37 of file RDThreads.h.
References RDUNUSED_PARAM.
Referenced by RDKit::GeneralMolSupplier::getSupplier(), RDPickers::LeaderPicker::lazyPick(), and RDKit::ForceFieldsHelper::OptimizeMoleculeConfs().
RDKIT_RDGENERAL_EXPORT rng_type & RDKit::getRandomGenerator | ( | int | seed = -1 | ) |
Optionally seed and return a reference to the global (Boost) random generator
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
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().
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
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().
Get the RLabels,atom mapping for the current molecule.
EnumerationTypes::RGROUPS RDKit::getSizesFromBBs | ( | const std::vector< std::vector< T > > & | bbs | ) |
Return the number of elements per input vector.
bbs | vector<vector<T> > |
Definition at line 75 of file EnumerationStrategyBase.h.
Referenced by RDKit::EnumerationStrategyBase::initialize().
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::RGROUPS RDKit::getSizesFromReactants | ( | const std::vector< MOL_SPTR_VECT > & | bbs | ) |
getSizesFromReactants Helper function for enumeration, bbs are stored in a std::vector< std::vector<boost:shared_ptr<ROMol> >
References getSizesFromReactants().
Referenced by getSizesFromReactants().
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint64_t > * RDKit::getSparseCountFP | ( | const ROMol & | mol, |
FPType | fPType ) |
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint64_t > * > * RDKit::getSparseCountFPBulk | ( | const std::vector< const ROMol * > | molVector, |
FPType | fPType ) |
RDKIT_FINGERPRINTS_EXPORT SparseBitVect * RDKit::getSparseFP | ( | const ROMol & | mol, |
FPType | fPType ) |
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseBitVect * > * RDKit::getSparseFPBulk | ( | const std::vector< const ROMol * > | molVector, |
FPType | fPType ) |
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT::const_iterator RDKit::getStartIterator | ( | const ChemicalReaction & | rxn, |
ReactionMoleculeType | t ) |
RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & RDKit::getSubstanceGroups | ( | const ROMol & | mol | ) |
RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & RDKit::getSubstanceGroups | ( | ROMol & | mol | ) |
RDKIT_GRAPHMOL_EXPORT std::string RDKit::getSupplementalSmilesLabel | ( | const Atom * | atom | ) |
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returns twice the bondType
(e.g. SINGLE->2, AROMATIC->3, etc.)
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 ) |
bool RDKit::hanoi | ( | int * | base, |
int | nel, | ||
int * | temp, | ||
int * | count, | ||
int * | changed, | ||
CompareFunc | compar ) |
changed ||
changed ||
Definition at line 27 of file hanoiSort.h.
References hanoi().
Referenced by hanoi(), and hanoisort().
void RDKit::hanoisort | ( | int * | base, |
int | nel, | ||
int * | count, | ||
int * | changed, | ||
CompareFunc | compar ) |
Definition at line 151 of file hanoiSort.h.
References hanoi().
Referenced by RDKit::Canon::RefinePartitions().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasAgentTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn ) |
bool RDKit::hasDummy | ( | const RWMol & | core | ) |
Returns true if the core has a dummy atom.
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Returns true if any of the z coords are non zero, false otherwise.
conf | Conformer object to analyze |
Definition at line 166 of file Conformer.h.
References RDKit::Conformer::getPositions(), and hasNonZeroZCoords().
Referenced by hasNonZeroZCoords().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasProductTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn ) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactantTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn ) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactionAtomMapping | ( | const ChemicalReaction & | rxn | ) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactionSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn, | ||
bool | includeAgents = false ) |
RDKIT_FMCS_EXPORT bool RDKit::havePairOfCompatibleRings | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2 ) |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::HELMToMol | ( | const char * | helm, |
bool | sanitize = true ) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
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.
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
RDKIT_FILEPARSERS_EXPORT void RDKit::invertMolBlockWedgingInfo | ( | ROMol & | mol | ) |
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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().
RDKIT_GRAPHMOL_EXPORT bool RDKit::isAromaticAtom | ( | const Atom & | atom | ) |
returns true if the atom is aromatic or has an aromatic bond
RDKIT_GRAPHMOL_EXPORT bool RDKit::isAtomAromatic | ( | const Atom * | a | ) |
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inline |
Definition at line 1119 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().
RDKIT_GRAPHMOL_EXPORT bool RDKit::isAtomListQuery | ( | const Atom * | a | ) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::isAtomTerminalRGroupOrQueryHydrogen | ( | const Atom * | atom | ) |
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().
RDKIT_FILEPARSERS_EXPORT bool RDKit::IsBlacklistedPair | ( | Atom * | beg_atom, |
Atom * | end_atom ) |
RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery | ( | const Atom * | a | ) |
RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery | ( | const Bond * | b | ) |
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inline |
Definition at line 389 of file Bond.h.
References RDKit::Bond::DATIVE, RDKit::Bond::DATIVEL, RDKit::Bond::DATIVEONE, RDKit::Bond::DATIVER, and RDKit::Bond::getBondType().
Referenced by canSetDoubleBondStereo().
bool RDKit::isDummyRGroupAttachment | ( | const Atom & | atom | ) |
RDKIT_GRAPHMOL_EXPORT bool RDKit::isEarlyAtom | ( | int | atomicNum | ) |
returns true if the atom is to the left of C
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().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeAgentOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which ) |
tests whether or not the molecule has a substructure match to any of the reaction's agents the which
argument is used to return which of the agents the molecule matches. If there's no match, it is equal to the number of agents on return
References isMoleculeAgentOfReaction().
Referenced by isMoleculeAgentOfReaction(), and isMoleculeAgentOfReaction().
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().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeProductOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
std::vector< unsigned int > & | which, | ||
bool | stopAtFirstMatch = false ) |
tests whether or not the molecule has a substructure match to the reaction's products the which
argument is used to return which of the products the molecule matches.
References isMoleculeProductOfReaction().
Referenced by isMoleculeProductOfReaction(), isMoleculeProductOfReaction(), and isMoleculeProductOfReaction().
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().
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().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeReactantOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
std::vector< unsigned int > & | which, | ||
bool | stopAtFirstMatch = false ) |
tests whether or not the molecule has a substructure match to the reaction's reactants the which
argument is used to return which of the reactants the molecule matches.
References isMoleculeReactantOfReaction().
Referenced by isMoleculeReactantOfReaction(), isMoleculeReactantOfReaction(), and isMoleculeReactantOfReaction().
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().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isReactionTemplateMoleculeAgent | ( | const ROMol & | mol, |
double | agentThreshold ) |
|
inline |
Definition at line 390 of file StreamOps.h.
bool RDKit::isUserRLabel | ( | const Atom & | atom | ) |
Return true if the atom has a user-defined R group label.
std::string RDKit::labellingToString | ( | Labelling | type | ) |
return the user friendly name for the given labelling
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.
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 |
Notes:
delete
ing the resultLayer definitions:
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAAtomQuery | ( | ) |
returns a Query for matching generic A atoms (heavy atoms)
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * RDKit::makeAHAtomQuery | ( | ) |
returns a Query for matching generic AH atoms (any atom)
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.
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().
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.
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().
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.
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().
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.
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().
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.
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().
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.
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().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHasChiralTagQuery | ( | ) |
\overloadquery
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().
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.
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().
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.
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().
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.
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().
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.
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().
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.
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().
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.
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().
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.
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().
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.
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().
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.
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().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomInRingOfSizeQuery | ( | int | tgt | ) |
returns a Query for matching atoms in rings of a particular size
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.
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().
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.
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().
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.
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().
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.
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().
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.
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().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomMissingChiralTagQuery | ( | ) |
\overloadquery
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().
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.
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().
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.
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().
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * RDKit::makeAtomNullQuery | ( | ) |
returns a Query for matching any atom
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.
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().
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.
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().
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.
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().
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.
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().
|
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().
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.
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().
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().
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.
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().
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.
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().
|
inlinestatic |
Definition at line 133 of file QueryOps.h.
Referenced by makeAtomTypeQuery(), and queryAtomType().
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.
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().
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.
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().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondDirEqualsQuery | ( | Bond::BondDir | what | ) |
returns a Query for matching bond directions
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondHasStereoQuery | ( | ) |
returns a Query for matching bonds with stereo set
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondInNRingsQuery | ( | int | tgt | ) |
returns a Query for matching bonds in a particular number of rings
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondInRingOfSizeQuery | ( | int | what | ) |
returns a Query for matching bonds in rings of a particular size
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondIsInRingQuery | ( | ) |
returns a Query for matching ring bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondMinRingSizeQuery | ( | int | what | ) |
returns a Query for matching a bond's minimum ring size
RDKIT_GRAPHMOL_EXPORT BOND_NULL_QUERY * RDKit::makeBondNullQuery | ( | ) |
returns a Query for matching any bond
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondOrderEqualsQuery | ( | Bond::BondType | what | ) |
returns a Query for matching bond orders
Referenced by RDKit::QueryBond::QueryBond().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeDoubleOrAromaticBondQuery | ( | ) |
returns a Query for double|aromatic bonds
FilterCatalogEntry * RDKit::MakeFilterCatalogEntry | ( | const FilterData_t & | , |
unsigned int | num_props = 0, | ||
const FilterProperty_t * | props = nullptr ) |
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.
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeMAtomQuery | ( | ) |
returns a Query for matching generic M atoms (metals)
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeMHAtomQuery | ( | ) |
returns a Query for matching generic MH atoms (metals or H)
Queries::EqualityQuery< int, const Target *, true > * RDKit::makePropQuery | ( | const std::string & | propname, |
const ExplicitBitVect & | val, | ||
double | tolerance = 0.0 ) |
Definition at line 1099 of file QueryOps.h.
Queries::EqualityQuery< int, const Target *, true > * RDKit::makePropQuery | ( | const std::string & | propname, |
const T & | val, | ||
double | tolerance = 0.0 ) |
Definition at line 1093 of file QueryOps.h.
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeQAtomQuery | ( | ) |
returns a Query for matching generic Q atoms (heteroatoms)
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeQHAtomQuery | ( | ) |
returns a Query for matching generic QH atoms (heteroatom or H)
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrAromaticBondQuery | ( | ) |
returns a Query for unspecified SMARTS bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrDoubleBondQuery | ( | ) |
returns a Query for single|double bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrDoubleOrAromaticBondQuery | ( | ) |
returns a Query for tautomeric bonds
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeXAtomQuery | ( | ) |
returns a Query for matching generic X atoms (halogens)
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeXHAtomQuery | ( | ) |
returns a Query for matching generic XH atoms (halogen or H)
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
RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareAny | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData ) |
RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareAnyHeavyAtom | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData ) |
RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareElements | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData ) |
RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareIsotopes | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData ) |
RDKIT_FMCS_EXPORT bool RDKit::MCSBondCompareAny | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData ) |
RDKIT_FMCS_EXPORT bool RDKit::MCSBondCompareOrder | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData ) |
RDKIT_FMCS_EXPORT bool RDKit::MCSBondCompareOrderExact | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData ) |
RDKIT_FMCS_EXPORT bool RDKit::MCSProgressCallbackTimeout | ( | const MCSProgressData & | stat, |
const MCSParameters & | params, | ||
void * | userData ) |
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.
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Definition at line 46 of file MolBundle.h.
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToCXSmarts | ( | const ROMol & | mol, |
const SmilesWriteParams & | params, | ||
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr ) |
Referenced by MolFragmentToCXSmarts().
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Definition at line 87 of file SmartsWrite.h.
References RDKit::SmilesWriteParams::doIsomericSmiles, and MolFragmentToCXSmarts().
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToCXSmiles | ( | const ROMol & | mol, |
const SmilesWriteParams & | params, | ||
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr, | ||
const std::vector< std::string > * | atomSymbols = nullptr, | ||
const std::vector< std::string > * | bondSymbols = nullptr ) |
returns canonical CXSMILES for part of a molecule
Referenced by MolFragmentToCXSmiles().
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returns canonical CXSMILES for part of a molecule
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 361 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.
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToSmarts | ( | const ROMol & | mol, |
const SmilesWriteParams & | params, | ||
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr ) |
Referenced by MolFragmentToSmarts().
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Definition at line 70 of file SmartsWrite.h.
References RDKit::SmilesWriteParams::doIsomericSmiles, and MolFragmentToSmarts().
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToSmiles | ( | const ROMol & | mol, |
const SmilesWriteParams & | params, | ||
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr, | ||
const std::vector< std::string > * | atomSymbols = nullptr, | ||
const std::vector< std::string > * | bondSymbols = nullptr ) |
returns canonical SMILES for part of a molecule
Referenced by MolFragmentToSmiles().
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returns canonical SMILES for part of a molecule
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 255 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.
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToCMLBlock | ( | const ROMol & | mol, |
int | confId = -1, | ||
bool | kekulize = true ) |
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToCMLFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
int | confId = -1, | ||
bool | kekulize = true ) |
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returns the CXSMARTS for a molecule
Definition at line 80 of file SmartsWrite.h.
References RDKit::SmilesWriteParams::doIsomericSmiles, and MolToCXSmarts().
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToCXSmarts | ( | const ROMol & | mol, |
const SmilesWriteParams & | params ) |
returns the CXSMARTS for a molecule
Referenced by MolToCXSmarts().
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returns canonical CXSMILES for a molecule
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 313 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.
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToCXSmiles | ( | const ROMol & | mol, |
const SmilesWriteParams & | ps, | ||
std::uint32_t | flags = SmilesWrite::CXSmilesFields::CX_ALL, | ||
RestoreBondDirOption | restoreBondDirs = RestoreBondDirOptionClear ) |
returns canonical CXSMILES for a molecule
Referenced by MolToCXSmiles().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToFASTA | ( | const ROMol & | mol | ) |
mol | - the molecule to work with |
mol
should contain monomer information in AtomMonomerInfo
structures RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToHELM | ( | const ROMol & | mol | ) |
mol | - the molecule to work with |
mol
should contain monomer information in AtomMonomerInfo
structures
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mol | - the molecule in question |
includeStereo | - toggles inclusion of stereochemistry information (default=true) |
confId | - selects the conformer to be used (default=-1 - find first in mol) |
kekulize | - triggers kekulization of the molecule before it is written (default=true) |
forceV3000 | - force generation a V3000 mol block (happens automatically with more than 999 atoms or bonds)(default=false) |
Definition at line 57 of file FileWriters.h.
References MolToMolBlock().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToMolBlock | ( | const ROMol & | mol, |
const MolWriterParams & | params, | ||
int | confId = -1 ) |
mol | - the molecule in question |
MolWriterParams | - parmeter struct with write options |
confId | - selects the conformer to be used (default=-1 - find first in mol) |
Referenced by MolToMolBlock(), MolToV3KMolBlock(), and MolToV3KMolBlock().
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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 133 of file FileWriters.h.
References MolToMolFile().
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToMolFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
const MolWriterParams & | params, | ||
int | confId = -1 ) |
mol | - the molecule in question |
fName | - the name of the file to use |
MolWriterParams | - parameter struct with write options |
confId | - selects the conformer to be used |
Referenced by MolToMolFile(), MolToV3KMolFile(), and MolToV3KMolFile().
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\param mol - the molecule \param includeStereo - toggles inclusion of stereochemical information in
the output
confId | - selects which conformation to output |
kekulize | - triggers kekulization of the molecule before it's written |
prettyPrint | - makes the output more human readable |
Definition at line 187 of file MarvinParser.h.
References MolToMrvBlock().
RDKIT_MARVINPARSER_EXPORT std::string RDKit::MolToMrvBlock | ( | const ROMol & | mol, |
const MrvWriterParams & | params, | ||
int | confId = -1 ) |
mol | - the molecule |
params | - marvin write params |
confId | - selects which conformation to output |
Referenced by MolToMrvBlock().
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\param mol - the molecule \param fName - the file to write to \param includeStereo - toggles inclusion of stereochemical information in
the output
confId | - selects which conformation to output |
kekulize | - triggers kekulization of the molecule before it's written |
prettyPrint | - makes the output more human readable |
Definition at line 163 of file MarvinParser.h.
References MolToMrvFile().
RDKIT_MARVINPARSER_EXPORT void RDKit::MolToMrvFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
const MrvWriterParams & | params, | ||
int | confId = -1 ) |
mol | - the molecule |
fName | - the file to write to |
params | - marvin write params |
confId | - selects which conformation to output |
Referenced by MolToMrvFile().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToPDBBlock | ( | const ROMol & | mol, |
int | confId = -1, | ||
unsigned int | flavor = 0 ) |
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 |
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToPDBFile | ( | const ROMol & | mol, |
const std::string & | fname, | ||
int | confId = -1, | ||
unsigned int | flavor = 0 ) |
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 |
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)
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. |
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToSequence | ( | const ROMol & | mol | ) |
mol | - the molecule to work with |
mol
should contain monomer information in AtomMonomerInfo
structures
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returns the SMARTS for a molecule
Definition at line 48 of file SmartsWrite.h.
References RDKit::SmilesWriteParams::doIsomericSmiles, MolToSmarts(), and RDKit::SmilesWriteParams::rootedAtAtom.
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToSmarts | ( | const ROMol & | mol, |
const SmilesWriteParams & | params ) |
Referenced by MolToSmarts().
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returns SMILES for a molecule, canonical by default
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 185 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.
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToSmiles | ( | const ROMol & | mol, |
const SmilesWriteParams & | params ) |
returns canonical SMILES for a molecule
Referenced by MolToSmiles().
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToTPLFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
const std::string & | partialChargeProp = "_GasteigerCharge", | ||
bool | writeFirstConfTwice = false ) |
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToTPLText | ( | const ROMol & | mol, |
const std::string & | partialChargeProp = "_GasteigerCharge", | ||
bool | writeFirstConfTwice = false ) |
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToV2KMolBlock | ( | const ROMol & | mol, |
const MolWriterParams & | params = MolWriterParams(), | ||
int | confId = -1 ) |
mol | - the molecule in question |
MolWriterParams | - parameter struct with write options |
confId | - selects the conformer to be used (default=-1 - find first in mol) |
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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
|
Definition at line 89 of file FileWriters.h.
References MolToMolBlock().
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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 71 of file FileWriters.h.
References RDKit::MolWriterParams::forceV3000, and MolToMolBlock().
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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 164 of file FileWriters.h.
References MolToMolFile().
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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 147 of file FileWriters.h.
References RDKit::MolWriterParams::forceV3000, and MolToMolFile().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToXYZBlock | ( | const ROMol & | mol, |
int | confId = -1, | ||
unsigned int | precision = 6 ) |
mol | - the molecule in question |
confId | - selects which conformation to output |
precision | - precision of the coordinates |
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToXYZFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
int | confId = -1, | ||
unsigned int | precision = 6 ) |
mol | - the molecule in question |
fName | - the file to write to |
confId | - selects which conformation to output |
precision | - precision of the coordinates |
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > RDKit::molzip | ( | const ROMol & | a, |
const MolzipParams & | params = MolzipParams() ) |
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > RDKit::molzip | ( | const ROMol & | a, |
const ROMol & | b, | ||
const MolzipParams & | params = MolzipParams() ) |
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.
row | - rgroup row as returned by the rgroup decompisition |
optional:
params | - molzip parameters |
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.
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:
params | - molzip parameters |
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::MurckoDecompose | ( | const ROMol & | mol | ) |
RDKIT_RDGENERAL_EXPORT int RDKit::nextCombination | ( | INT_VECT & | comb, |
int | tot ) |
given a current combination of numbers change it to the next possible
comb | the sorted vector to consider |
tot | the maximum number possible in the vector |
int RDKit::nullDataFun | ( | T | ) |
Definition at line 809 of file QueryOps.h.
bool RDKit::nullQueryFun | ( | T | ) |
Definition at line 813 of file QueryOps.h.
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::numPiElectrons | ( | const Atom & | atom | ) |
returns the number of pi electrons on the atom
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Definition at line 447 of file FileParsers.h.
References RDKit::v2::FileParsers::MolFromMolBlock().
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Definition at line 456 of file FileParsers.h.
References RDKit::v2::FileParsers::MolFromMol2Block().
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Definition at line 466 of file FileParsers.h.
References RDKit::v2::FileParsers::MolFromPDBBlock().
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Definition at line 391 of file ReactionParser.h.
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Definition at line 402 of file ReactionParser.h.
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Definition at line 246 of file SmilesParse.h.
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Definition at line 237 of file SmilesParse.h.
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]
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect RDKit::operator+ | ( | const DiscreteValueVect & | p1, |
const DiscreteValueVect & | p2 ) |
RDKIT_DATASTRUCTS_EXPORT RealValueVect RDKit::operator+ | ( | const RealValueVect & | p1, |
const RealValueVect & | p2 ) |
returns the sum of vectors
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect RDKit::operator- | ( | const DiscreteValueVect & | p1, |
const DiscreteValueVect & | p2 ) |
RDKIT_DATASTRUCTS_EXPORT RealValueVect RDKit::operator- | ( | const RealValueVect & | p1, |
const RealValueVect & | p2 ) |
returns the difference of vectors
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]
|
inlinestatic |
Definition at line 136 of file QueryOps.h.
RDKIT_MOLCHEMICALFEATURES_EXPORT int RDKit::parseFeatureData | ( | const std::string & | defnText, |
MolChemicalFeatureDef::CollectionType & | featDefs ) |
RDKIT_MOLCHEMICALFEATURES_EXPORT int RDKit::parseFeatureData | ( | std::istream & | istream, |
MolChemicalFeatureDef::CollectionType & | featDefs ) |
RDKIT_MOLCHEMICALFEATURES_EXPORT int RDKit::parseFeatureFile | ( | const std::string & | fileName, |
MolChemicalFeatureDef::CollectionType & | featDefs ) |
RDKIT_FMCS_EXPORT void RDKit::parseMCSParametersJSON | ( | const char * | json, |
MCSParameters * | params ) |
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()
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 |
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.
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
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.
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.
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) |
Notes:
delete
ing the result Referenced by RDKit::PatternHolder::makeFingerprint(), and RDKit::TautomerPatternHolder::makeFingerprint().
|
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returns the metadata (tEXt and zTXt chunks) from PNG data
Definition at line 43 of file PNGParser.h.
References PNGStreamToMetadata().
|
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constructs an ROMol from the metadata in a PNG file. See PNGStreamToMol()
for more details.
Definition at line 112 of file PNGParser.h.
References PNGStreamToMol().
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constructs a vector of ROMol from the metadata in a PNG file. See PNGStreamToMols()
for more details.
Definition at line 143 of file PNGParser.h.
References PNGStreamToMols().
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().
RDKIT_FILEPARSERS_EXPORT ROMol * RDKit::PNGStreamToMol | ( | std::istream & | inStream, |
const SmilesParserParams & | params = SmilesParserParams() ) |
constructs an ROMol from the metadata in a PNG stream
Looks through the metadata in the PNG to find the first tag that matches one of the tags in RDKit::PNGData
. A molecule is constructed from this chunk.
Throws a FileParseException
if no suitable tag is found.
The caller is responsible for the returned pointer.
Referenced by PNGFileToMol(), and PNGStringToMol().
RDKIT_FILEPARSERS_EXPORT std::vector< std::unique_ptr< ROMol > > RDKit::PNGStreamToMols | ( | std::istream & | inStream, |
const std::string & | tagToUse = PNGData::pklTag, | ||
const SmilesParserParams & | params = SmilesParserParams() ) |
constructs a vector of ROMol from the metadata in a PNG stream
Looks through the metadata in the PNG to find tags that start with tagToUse (must be one of the tags in RDKit::PNGData
). The molecules constructed from these data are returned.
Referenced by PNGFileToMols(), and PNGStringToMols().
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returns the metadata (tEXt and zTXt chunks) from PNG data
Definition at line 53 of file PNGParser.h.
References PNGStreamToMetadata().
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constructs an ROMol from the metadata in a PNG string. See PNGStreamToMol()
for more details.
Definition at line 123 of file PNGParser.h.
References PNGStreamToMol().
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constructs a vector of ROMol from the metadata in a PNG string. See PNGStreamToMols()
for more details.
Definition at line 154 of file PNGParser.h.
References PNGStreamToMols().
RDKIT_FRAGCATALOG_EXPORT ROMol * RDKit::prepareMol | ( | const ROMol & | mol, |
const FragCatParams * | fparams, | ||
MatchVectType & | aToFmap ) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
const std::string & | propName = common_properties::molFileValue ) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
const std::string & | propName = common_properties::molFileValue ) |
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 ) |
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 ) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::propertyCompat | ( | const RDProps * | r1, |
const RDProps * | r2, | ||
const std::vector< std::string > & | properties ) |
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Reads an integer from a char * in packed format and returns the result. The argument is advanced
Definition at line 220 of file StreamOps.h.
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Definition at line 76 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAliphaticQuery().
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomAllBondProduct | ( | Atom const * | at | ) |
|
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Definition at line 73 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAromaticQuery().
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomBondProduct | ( | Atom const * | at | ) |
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Definition at line 79 of file QueryOps.h.
References RDKit::Atom::getDegree().
Referenced by makeAtomExplicitDegreeQuery().
|
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Definition at line 123 of file QueryOps.h.
References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getNumExplicitHs().
Referenced by makeAtomExplicitValenceQuery().
|
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Definition at line 164 of file QueryOps.h.
References RDKit::Atom::getFormalCharge().
Referenced by makeAtomFormalChargeQuery().
|
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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().
|
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Definition at line 176 of file QueryOps.h.
References RDKit::Atom::CHI_UNSPECIFIED, and RDKit::Atom::getChiralTag().
Referenced by makeAtomHasChiralTagQuery().
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Definition at line 184 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomHasHeteroatomNbrsQuery().
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Definition at line 117 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHasImplicitHQuery().
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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().
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Definition at line 111 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHCountQuery().
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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().
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Definition at line 170 of file QueryOps.h.
References RDKit::Atom::getHybridization().
Referenced by makeAtomHybridizationQuery().
|
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Definition at line 114 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomImplicitHCountQuery().
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Definition at line 120 of file QueryOps.h.
References RDKit::Atom::getImplicitValence().
Referenced by makeAtomImplicitValenceQuery().
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().
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Definition at line 161 of file QueryOps.h.
References RDKit::Atom::getIsotope().
Referenced by makeAtomIsotopeQuery().
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Definition at line 157 of file QueryOps.h.
References RDKit::Atom::getMass(), and massIntegerConversionFactor.
Referenced by makeAtomMassQuery().
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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().
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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().
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Definition at line 167 of file QueryOps.h.
References RDKit::Atom::getFormalCharge().
Referenced by makeAtomNegativeFormalChargeQuery().
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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().
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Definition at line 132 of file QueryOps.h.
References RDKit::Atom::getAtomicNum().
Referenced by makeAtomNumQuery().
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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().
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Definition at line 197 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomNumHeteroatomNbrsQuery().
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Definition at line 173 of file QueryOps.h.
References RDKit::Atom::getNumRadicalElectrons().
Referenced by makeAtomNumRadicalElectronsQuery().
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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().
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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().
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Definition at line 82 of file QueryOps.h.
References RDKit::Atom::getTotalDegree().
Referenced by makeAtomTotalDegreeQuery().
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Definition at line 126 of file QueryOps.h.
References RDKit::Atom::getTotalValence().
Referenced by makeAtomTotalValenceQuery().
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Definition at line 153 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::Atom::getIsAromatic(), and makeAtomType().
Referenced by makeAtomTypeQuery().
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Definition at line 129 of file QueryOps.h.
References RDKit::Atom::getTotalDegree(), and RDKit::Atom::getTotalValence().
Referenced by makeAtomUnsaturatedQuery().
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Definition at line 266 of file QueryOps.h.
References RDKit::Bond::getBondDir().
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Definition at line 272 of file QueryOps.h.
References RDKit::Bond::getStereo(), and RDKit::Bond::STEREONONE.
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Definition at line 253 of file QueryOps.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::DOUBLE, and RDKit::Bond::getBondType().
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().
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Definition at line 249 of file QueryOps.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.
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Definition at line 257 of file QueryOps.h.
References RDKit::Bond::DOUBLE, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.
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Definition at line 261 of file QueryOps.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::DOUBLE, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.
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Definition at line 305 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minBondRingSize().
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Definition at line 246 of file QueryOps.h.
References RDKit::Bond::getBondType().
RDKIT_GRAPHMOL_EXPORT int RDKit::queryIsAtomBridgehead | ( | Atom const * | at | ) |
Referenced by makeAtomIsBridgeheadQuery().
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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().
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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().
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Definition at line 269 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().
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Definition at line 299 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().
const T RDKit::rdany_cast | ( | const RDAny & | d | ) |
Definition at line 179 of file RDAny.h.
References RDKit::RDAny::m_value, and rdvalue_cast().
Referenced by from_rdany().
T RDKit::rdany_cast | ( | RDAny & | d | ) |
Definition at line 185 of file RDAny.h.
References RDKit::RDAny::m_value, and rdvalue_cast().
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.
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) |
Notes:
delete
ing the result RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::RDKitSVGToMol | ( | const std::string & | svg, |
bool | sanitize = true, | ||
bool | removeHs = true ) |
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.
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.
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Definition at line 420 of file RDValue-doublemagic.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().
Referenced by from_rdvalue(), rdany_cast(), rdany_cast(), vectToString(), and RDKit::DataStructsExplicitBitVecPropHandler::write().
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Definition at line 471 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits, and rdvalue_is().
Referenced by rdvalue_tostring().
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Definition at line 521 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::b, rdvalue_is(), and RDKit::RDValue::value.
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Definition at line 166 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().
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Definition at line 440 of file RDValue-doublemagic.h.
References RDKit::RDValue::doubleBits, and rdvalue_is< double >().
Referenced by rdvalue_tostring().
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Definition at line 405 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::d, RDKit::RDTypeTag::detail::Value::f, rdvalue_is(), rdvalue_is< double >(), and RDKit::RDValue::value.
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Definition at line 446 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits, and rdvalue_is().
Referenced by rdvalue_tostring().
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Definition at line 416 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::d, RDKit::RDTypeTag::detail::Value::f, rdvalue_is(), rdvalue_is< double >(), and RDKit::RDValue::value.
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Definition at line 458 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits, and rdvalue_is().
Referenced by rdvalue_tostring().
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Definition at line 427 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 158 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().
Referenced by rdvalue_tostring().
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Definition at line 150 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().
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Definition at line 449 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 460 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, RDKit::RDValue::ptrCast(), rdvalue_is(), rdvalue_is< std::any >(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 438 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 54 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is().
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Definition at line 46 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is().
Referenced by from_rdvalue(), and rdvalue_tostring().
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Definition at line 496 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 507 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, RDKit::RDValue::ptrCast(), rdvalue_is(), rdvalue_is< std::any >(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 485 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 464 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits, and rdvalue_is().
Referenced by rdvalue_tostring().
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Definition at line 474 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 372 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::AnyTag.
Referenced by RDKit::DataStructsExplicitBitVecPropHandler::canSerialize(), rdvalue_cast< bool >(), rdvalue_cast< double >(), rdvalue_cast< float >(), rdvalue_cast< int >(), rdvalue_cast< std::int16_t >(), rdvalue_cast< std::int64_t >(), rdvalue_cast< std::int8_t >(), rdvalue_cast< std::string & >(), rdvalue_cast< std::string >(), rdvalue_cast< std::uint16_t >(), rdvalue_cast< std::uint64_t >(), rdvalue_cast< std::uint8_t >(), and rdvalue_cast< unsigned int >().
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Definition at line 392 of file RDValue-doublemagic.h.
References rdvalue_is< double >().
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Definition at line 386 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::MaxDouble, and RDKit::RDTypeTag::NaN.
Referenced by rdvalue_cast< double >(), rdvalue_cast< float >(), and rdvalue_is< const double & >().
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Definition at line 370 of file RDValue-taggedunion.h.
References RDKit::RDValue::getTag(), and RDKit::RDTypeTag::GetTag< std::any >().
Referenced by rdvalue_cast(), rdvalue_cast< const std::any & >(), rdvalue_cast< std::any & >(), rdvalue_cast< std::any >(), rdvalue_cast< std::int64_t >(), and rdvalue_cast< std::uint64_t >().
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Definition at line 190 of file RDValue.h.
References RDKit::RDTypeTag::AnyTag, RDKit::RDTypeTag::BoolTag, RDKit::RDTypeTag::DoubleTag, RDKit::RDTypeTag::FloatTag, RDKit::RDValue::getTag(), RDKit::RDTypeTag::IntTag, rdvalue_cast< bool >(), rdvalue_cast< double >(), rdvalue_cast< float >(), rdvalue_cast< int >(), rdvalue_cast< std::any & >(), rdvalue_cast< std::string >(), rdvalue_cast< unsigned int >(), 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().
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.
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::istream & | inStream, |
int | nToRead = -1 ) |
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::string | fileName | ) |
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.
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Reads an integer from a stream in packed format and returns the result.
Definition at line 154 of file StreamOps.h.
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Definition at line 555 of file StreamOps.h.
References streamReadStringVec().
void RDKit::readRDValue | ( | std::istream & | ss, |
RDValue & | value ) |
Definition at line 535 of file StreamOps.h.
References streamRead().
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Definition at line 548 of file StreamOps.h.
References streamRead().
void RDKit::readRDVecValue | ( | std::istream & | ss, |
RDValue & | value ) |
Definition at line 542 of file StreamOps.h.
References streamReadVec().
RDKIT_FILEPARSERS_EXPORT void RDKit::reapplyMolBlockWedging | ( | ROMol & | mol | ) |
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
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 |
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.
RDKIT_GRAPHMOL_EXPORT void RDKit::removeAtomFromGroups | ( | const Atom * | atom, |
std::vector< StereoGroup > & | groups ) |
RDKIT_SUBSTRUCTMATCH_EXPORT void RDKit::removeDuplicates | ( | std::vector< MatchVectType > & | v, |
unsigned int | nAtoms ) |
RDKIT_GRAPHMOL_EXPORT void RDKit::removeGroupsWithAtom | ( | const Atom * | atom, |
std::vector< StereoGroup > & | groups ) |
RDKIT_GRAPHMOL_EXPORT void RDKit::removeGroupsWithAtoms | ( | const std::vector< Atom * > & | atoms, |
std::vector< StereoGroup > & | groups ) |
RDKIT_CHEMREACTIONS_EXPORT void RDKit::removeMappingNumbersFromReactions | ( | const ChemicalReaction & | rxn | ) |
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
RDKIT_GRAPHMOL_EXPORT void RDKit::removeSubstanceGroupsReferencingAtom | ( | RWMol & | mol, |
unsigned int | idx ) |
Removes SubstanceGroups which reference a particular atom index.
mol | - molecule to be edited. |
idx | - atom index |
RDKIT_GRAPHMOL_EXPORT void RDKit::removeSubstanceGroupsReferencingBond | ( | RWMol & | mol, |
unsigned int | idx ) |
Removes SubstanceGroups which reference a particular bond index.
mol | - molecule to be edited. |
idx | - bond index |
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.
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 |
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. 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.
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 |
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. 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.
mol | the ROMol of interest |
coreQuery | a query ROMol to be used to match the core |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. 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.
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.
replacementConnectionPoint | index of the atom in the replacement that the bond should made to |
mol
with the matching atoms and bonds (if any) replaced 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() ) |
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() ) |
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.
reactant | The single reactant to use |
reactantTemplateIdx | the reactant template to target in the reaction |
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.
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::run_Reactant | ( | const ChemicalReaction & | rxn, |
RWMol & | reactant, | ||
bool | removeUnmatchedAtoms = true ) |
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.
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. |
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.
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.
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)
mol | ROMol with RXN roles set |
References RxnMolToChemicalReaction().
Referenced by RxnMolToChemicalReaction().
RDKIT_FILEPARSERS_EXPORT bool RDKit::SamePDBResidue | ( | AtomPDBResidueInfo * | p, |
AtomPDBResidueInfo * | q ) |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol | ( | const char * | seq, |
bool | sanitize, | ||
bool | lowerD ) |
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 |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol | ( | const char * | seq, |
bool | sanitize = true, | ||
int | flavor = 0 ) |
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 |
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.
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.
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
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]
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
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Definition at line 555 of file MolDraw2D.h.
References RDKit::MolDraw2D::drawOptions(), and setDarkMode().
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Definition at line 547 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().
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
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Definition at line 566 of file MolDraw2D.h.
References RDKit::MolDraw2D::drawOptions(), and setMonochromeMode().
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Definition at line 556 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().
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.
RDKIT_SLNPARSE_EXPORT RWMol * RDKit::SLNQueryToMol | ( | const std::string & | smi, |
bool | mergeHs = true, | ||
int | debugParse = 0 ) |
RDKIT_SLNPARSE_EXPORT RWMol * RDKit::SLNToMol | ( | const std::string & | smi, |
bool | sanitize = true, | ||
int | debugParse = 0 ) |
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
RDKIT_FILEPARSERS_EXPORT void RDKit::StandardPDBResidueBondOrders | ( | RWMol * | mol | ) |
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Definition at line 303 of file StreamOps.h.
References RDUNUSED_PARAM, and streamRead().
void RDKit::streamRead | ( | std::istream & | ss, |
T & | loc ) |
does a binary read of an object from a stream
Definition at line 287 of file StreamOps.h.
References EndianSwapBytes().
Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream(), RDKit::DataStructsExplicitBitVecPropHandler::read(), readRDValue(), readRDValueString(), streamRead(), streamRead(), streamReadStringVec(), and streamReadVec().
void RDKit::streamRead | ( | std::istream & | ss, |
T & | obj, | ||
int | version ) |
special case for string
Definition at line 298 of file StreamOps.h.
References RDUNUSED_PARAM, and streamRead().
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Definition at line 562 of file StreamOps.h.
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Definition at line 632 of file StreamOps.h.
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Definition at line 326 of file StreamOps.h.
References streamRead().
Referenced by readRDStringVecValue().
void RDKit::streamReadVec | ( | std::istream & | ss, |
T & | val ) |
Definition at line 316 of file StreamOps.h.
References streamRead().
Referenced by readRDVecValue().
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void RDKit::streamWrite | ( | std::ostream & | ss, |
const T & | val ) |
does a binary write of an object to a stream
Definition at line 265 of file StreamOps.h.
References EndianSwapBytes().
Referenced by streamWrite(), streamWriteVec(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream(), RDKit::SparseIntVect< IndexType >::toString(), and RDKit::DataStructsExplicitBitVecPropHandler::write().
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Definition at line 418 of file StreamOps.h.
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Definition at line 491 of file StreamOps.h.
void RDKit::streamWriteVec | ( | std::ostream & | ss, |
const T & | val ) |
Definition at line 278 of file StreamOps.h.
References streamWrite().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::strip | ( | const std::string & | orig | ) |
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
rxn | the reaction to be fingerprinted |
params | specific settings to manipulate fingerprint generation |
Notes:
delete
ing the result RDKIT_SUBSTRUCTLIBRARY_EXPORT bool RDKit::SubstructLibraryCanSerialize | ( | ) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const MolBundle & | bundle, |
const MolBundle & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() ) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const MolBundle & | bundle, |
const ROMol & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() ) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const ROMol & | mol, |
const MolBundle & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() ) |
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.
mol | The ROMol to be searched |
query | The query ROMol |
matchParams | Parameters controlling the matching |
Referenced by SubstructMatch(), SubstructMatch(), SubstructMatch(), and SubstructMatch().
RDKIT_TAUTOMERQUERY_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const ROMol & | mol, |
const TautomerQuery & | query, | ||
const SubstructMatchParameters & | params ) |
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.
resMolSuppl | The ResonanceMolSupplier object to be searched |
query | The query ROMol |
matchParams | Parameters controlling the matching |
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Definition at line 216 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.
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.
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 |
Definition at line 133 of file SubstructMatch.h.
References RDKit::SubstructMatchParameters::maxMatches, RDKit::SubstructMatchParameters::recursionPossible, SubstructMatch(), RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.
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.
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 |
Definition at line 173 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.
RDKIT_SUBSTRUCTMATCH_EXPORT std::string RDKit::substructMatchParamsToJSON | ( | const SubstructMatchParameters & | params | ) |
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Definition at line 45 of file StreamOps.h.
Referenced by EndianSwapBytes().
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().
RDKIT_TAUTOMERQUERY_EXPORT bool RDKit::TautomerQueryCanSerialize | ( | ) |
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
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
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
RDKIT_SUBSTRUCTMATCH_EXPORT double RDKit::toPrime | ( | const MatchVectType & | v | ) |
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
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 RDKit::SparseIntVect< IndexType >::getLength(), and RDUNUSED_PARAM.
Referenced by TanimotoSimilarity().
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
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
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. |
void RDKit::updateCXSmilesFieldsFromJSON | ( | SmilesWrite::CXSmilesFields & | cxSmilesFields, |
RestoreBondDirOption & | restoreBondDirs, | ||
const char * | details_json ) |
void RDKit::updateCXSmilesFieldsFromJSON | ( | SmilesWrite::CXSmilesFields & | cxSmilesFields, |
RestoreBondDirOption & | restoreBondDirs, | ||
const std::string & | details_json ) |
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().
RDKIT_CHEMREACTIONS_EXPORT void RDKit::updateProductsStereochem | ( | ChemicalReaction * | rxn | ) |
void RDKit::updateRGroupDecompositionParametersFromJSON | ( | RGroupDecompositionParameters & | params, |
const char * | details_json ) |
void RDKit::updateRGroupDecompositionParametersFromJSON | ( | RGroupDecompositionParameters & | params, |
const std::string & | details_json ) |
void RDKit::updateSmilesWriteParamsFromJSON | ( | SmilesWriteParams & | params, |
const char * | details_json ) |
void RDKit::updateSmilesWriteParamsFromJSON | ( | SmilesWriteParams & | params, |
const std::string & | details_json ) |
RDKIT_SUBSTRUCTMATCH_EXPORT void RDKit::updateSubstructMatchParamsFromJSON | ( | SubstructMatchParameters & | params, |
const std::string & | json ) |
std::string RDKit::vectToString | ( | RDValue | val | ) |
Definition at line 176 of file RDValue.h.
References rdvalue_cast().
Referenced by rdvalue_tostring().
RDKIT_FILEPARSERS_EXPORT void RDKit::WedgeBond | ( | Bond * | bond, |
unsigned int | fromAtomIdx, | ||
const Conformer * | conf ) |
RDKIT_FILEPARSERS_EXPORT void RDKit::WedgeMolBonds | ( | ROMol & | mol, |
const Conformer * | conf ) |
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const unsigned int RDKit::BITS_PER_INT = 32 |
Definition at line 21 of file DiscreteValueVect.h.
Referenced by RDKit::DiscreteValueVect::DiscreteValueVect().
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const std::vector<std::string> RDKit::complexQueries |
Definition at line 600 of file QueryOps.h.
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Definition at line 16 of file ProximityBonds.h.
const double RDKit::DAMP = 0.5 |
Definition at line 28 of file GasteigerParams.h.
const double RDKit::DAMP_SCALE = 0.5 |
Definition at line 27 of file GasteigerParams.h.
const DashPattern RDKit::dashes {6.0, 4.0} |
Definition at line 28 of file DrawShape.h.
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Definition at line 35 of file MolWriters.h.
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const DashPattern RDKit::dots {2.0, 6.0} |
Definition at line 27 of file DrawShape.h.
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const unsigned int RDKit::EMPTY_CORE_LABEL = -100000 |
Definition at line 28 of file RGroupUtils.h.
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const int RDKit::FILE_MAXLINE |
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const double RDKit::IONXH = 20.02 |
Definition at line 25 of file GasteigerParams.h.
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const std::string RDKit::LayeredFingerprintMolVersion = "0.7.0" |
Definition at line 113 of file Fingerprints.h.
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Definition at line 73 of file MolDraw2DHelpers.h.
const std::vector<std::string> RDKit::marvinBondOrders {"1", "2", "3", "A"} |
Definition at line 32 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinConventionTypes {"cxn:coord"} |
Definition at line 34 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinQueryBondsTypes {"SD", "SA", "DA", "Any"} |
Definition at line 33 of file MarvinDefs.h.
const std::map<std::string, int> RDKit::marvinRadicalToRadicalElectrons |
Definition at line 41 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinRadicalVals |
Definition at line 38 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinStereoConventionTypes {"1", "3", "4", "6"} |
Definition at line 36 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinStereoDictRefTypes {"cml:W", "cml:H"} |
Definition at line 35 of file MarvinDefs.h.
const int RDKit::massIntegerConversionFactor = 1000 |
Definition at line 156 of file QueryOps.h.
Referenced by makeAtomMassQuery(), and queryAtomMass().
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const unsigned int RDKit::maxFingerprintLayers = 10 |
Definition at line 112 of file Fingerprints.h.
const DashPattern RDKit::noDash |
Definition at line 26 of file DrawShape.h.
const int RDKit::NUM_PRIMES_AVAIL |
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const std::string RDKit::PatternFingerprintMolVersion = "1.0.0" |
Definition at line 149 of file Fingerprints.h.
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const std::map<int, std::string> RDKit::radicalElectronsToMarvinRadical |
Definition at line 45 of file MarvinDefs.h.
const std::string RDKit::RDKFingerprintMolVersion = "2.0.0" |
Definition at line 63 of file Fingerprints.h.
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const DashPattern RDKit::shortDashes {2.0, 2.0} |
Definition at line 29 of file DrawShape.h.
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const std::vector<std::string> RDKit::sruSgroupConnectChoices {"hh", "ht", "eu"} |
Definition at line 31 of file MarvinDefs.h.
const unsigned int RDKit::substructLayers = 0x07 |
Definition at line 114 of file Fingerprints.h.
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