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RDKit
Open-source cheminformatics and machine learning.
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Std stuff. More...
Classes | |
class | Atom |
The class for representing atoms. More... | |
class | atomicData |
class | AtomIterator_ |
A general random access iterator. More... | |
class | HeteroatomIterator_ |
Iterate over heteroatoms, this is bidirectional. More... | |
class | AromaticAtomIterator_ |
Iterate over aromatic atoms, this is bidirectional. More... | |
class | QueryAtomIterator_ |
Iterate over atoms matching a query. This is bidirectional. More... | |
class | MatchingAtomIterator_ |
Iterate over atoms matching a query function. This is bidirectional. More... | |
class | Bond |
class for representing a bond More... | |
class | BondIterator_ |
iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
class | ConstBondIterator_ |
const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
class | CartesianProductStrategy |
This is a class for enumerating reagents using Cartesian Products of. More... | |
struct | EnumerationParams |
This is a class for providing enumeration options that control. More... | |
class | EnumerateLibrary |
This is a class for running reactions on sets of reagents. More... | |
class | EnumerateLibraryBase |
Base class for enumerating chemical reactions from collections of. More... | |
class | EnumerationStrategyException |
class for flagging enumeration strategy errors More... | |
class | EnumerationStrategyBase |
class | EvenSamplePairsStrategy |
EvenSamplePairsStrategy. More... | |
class | RandomSampleStrategy |
This is a class for fully randomly sampling reagents. More... | |
class | RandomSampleAllBBsStrategy |
This is a class for randomly enumerating reagents that ensures all reagents. More... | |
class | ChemicalReactionException |
used to indicate an error in the chemical reaction engine More... | |
class | ChemicalReaction |
This is a class for storing and applying general chemical reactions. More... | |
struct | ReactionFingerprintParams |
class | ChemicalReactionParserException |
used to indicate an error in parsing reaction data More... | |
class | ReactionPicklerException |
used to indicate exceptions whilst pickling (serializing) reactions More... | |
class | ReactionPickler |
handles pickling (serializing) reactions More... | |
class | RxnSanitizeException |
class for flagging sanitization errors More... | |
class | ConformerException |
used to indicate errors from incorrect conformer access More... | |
class | Conformer |
The class for representing 2D or 3D conformation of a molecule. More... | |
class | MolFileUnhandledFeatureException |
class | MolSupplier |
class | ForwardSDMolSupplier |
class | SDMolSupplier |
class | SmilesMolSupplier |
lazy file parser for Smiles tables More... | |
class | TDTMolSupplier |
lazy file parser for TDT files More... | |
class | PDBMolSupplier |
lazy file parser for PDB files More... | |
class | MolWriter |
class | SmilesWriter |
class | SDWriter |
class | TDTWriter |
class | PDBWriter |
class | FilterCatalogParams |
class | FilterCatalog |
class | FilterCatalogEntry |
struct | FilterMatch |
Holds the atomPairs matched by the underlying matcher. More... | |
class | FilterMatcherBase |
class | SmartsMatcher |
class | ExclusionList |
class | FilterHierarchyMatcher |
struct | FilterData_t |
struct | FilterProperty_t |
struct | AdditionalOutput |
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... | |
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 | AtomInvariantsGenerator |
abstract base class for atom invariants generators More... | |
class | BondInvariantsGenerator |
abstract base class for bond invariants generators More... | |
class | FingerprintGenerator |
class that generates same fingerprint style for different output formats More... | |
class | UnimplementedFPException |
used to indicate errors for unimplemented fp types in convenience functions More... | |
struct | MCSAtomCompareParameters |
struct | MCSBondCompareParameters |
struct | MCSProgressData |
struct | MCSParameters |
struct | MCSResult |
class | FragCatalogEntry |
class | FragCatGenerator |
class | FragCatParams |
container for user parameters used to create a fragment catalog More... | |
class | FragFPGenerator |
class | MolBundle |
MolBundle contains a collection of related ROMols. More... | |
class | FixedMolSizeMolBundle |
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 | FeatureFileParseException |
class used to indicate errors in parsing feature definition files. More... | |
class | MolChemicalFeature |
class | MolChemicalFeatureDef |
class | MolChemicalFeatureFactory |
The class for finding chemical features in molecules. More... | |
class | DrawText |
class | DrawTextCairo |
class | DrawTextFT |
class | DrawTextFTCairo |
class | DrawTextFTJS |
class | DrawTextFTQt |
class | DrawTextFTSVG |
class | DrawTextJS |
class | DrawTextQt |
class | DrawTextSVG |
struct | DrawColour |
struct | StringRect |
struct | MolDrawOptions |
class | MolDraw2D |
MolDraw2D is the base class for doing 2D renderings of molecules. More... | |
class | MolDraw2DCairo |
class | MolDraw2DJS |
class | MolDraw2DQt |
class | MolDraw2DSVG |
class | MolDraw2Dwx |
class | MultiMolDraw2D |
class | MolPicklerException |
used to indicate exceptions whilst pickling (serializing) molecules More... | |
class | MolPickler |
handles pickling (serializing) molecules More... | |
class | AtomMonomerInfo |
The abstract base class for atom-level monomer info. More... | |
class | AtomPDBResidueInfo |
Captures atom-level information about peptide residues. More... | |
class | GasteigerParams |
class | PeriodicTable |
singleton class for retrieving information about atoms More... | |
class | QueryAtom |
Class for storing atomic queries. More... | |
class | QueryBond |
Class for storing Bond queries. More... | |
class | AtomRingQuery |
class | RecursiveStructureQuery |
allows use of recursive structure queries (e.g. recursive SMARTS) More... | |
class | HasPropQuery |
class | HasPropWithValueQuery |
class | HasPropWithValueQuery< TargetPtr, std::string > |
class | HasPropWithValueQuery< TargetPtr, ExplicitBitVect > |
class | ResonanceMolSupplierCallback |
class | ResonanceMolSupplier |
struct | RCore |
RCore is the core common to a series of molecules. More... | |
struct | RGroupData |
A single rgroup attached to a given core. More... | |
struct | RGroupDecompositionParameters |
class | RGroupDecomposition |
struct | RGroupDecompData |
struct | RGroupMatch |
RGroupMatch is the decomposition for a single molecule. More... | |
struct | CartesianProduct |
iterate through all possible permutations of the rgroups More... | |
class | RingInfo |
A class to store information about a molecule's rings. More... | |
struct | CXXAtomIterator |
struct | CXXBondIterator |
class | ROMol |
class | RWMol |
RWMol is a molecule class that is intended to be edited. More... | |
class | MolSanitizeException |
class for flagging sanitization errors More... | |
class | AtomSanitizeException |
class | AtomValenceException |
class | AtomKekulizeException |
class | KekulizeException |
class | SLNParseException |
struct | SmilesParserParams |
class | SmilesParseException |
class | StereoGroup |
class | SubstanceGroupException |
used to indicate errors from incorrect sgroup access More... | |
class | SubstanceGroup |
The class for representing SubstanceGroups. More... | |
struct | SubstructMatchParameters |
class | MolHolderBase |
Base class API for holding molecules to substructure search. More... | |
class | MolHolder |
Concrete class that holds molecules in memory. 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... | |
class | FPHolderBase |
Base FPI for the fingerprinter used to rule out impossible matches. More... | |
class | PatternHolder |
Uses the pattern fingerprinter to rule out matches. More... | |
class | SubstructLibrary |
Substructure Search a library of molecules. More... | |
class | TautomerQuery |
class | Snapshot |
class | Trajectory |
class | DataStructsExplicitBitVecPropHandler |
class | DiscreteDistMat |
class | DiscreteValueVect |
a class for efficiently storing vectors of discrete values More... | |
class | FPBReader |
class for reading and searching FPB files More... | |
class | MultiFPBReader |
class for reading and searching multiple FPB files More... | |
class | SparseIntVect |
a class for efficiently storing sparse vectors of ints More... | |
class | BadFileException |
used by various file parsing classes to indicate a bad file More... | |
class | Dict |
The Dict class can be used to store objects of arbitrary type keyed by strings . More... | |
class | FileParseException |
used by various file parsing classes to indicate a parse error More... | |
struct | RDAny |
class | RDProps |
struct | RDValue |
class | CustomPropHandler |
struct | ltDouble |
functor to compare two doubles with a tolerance More... | |
struct | larger_of |
functor for returning the larger of two values More... | |
struct | charptr_functor |
functor for comparing two strings More... | |
Typedefs | |
typedef boost::shared_ptr< Conformer > | CONFORMER_SPTR |
typedef std::uint32_t | atomindex_t |
typedef std::vector< RWMOL_SPTR > | RWMOL_SPTR_VECT |
typedef RDCatalog::Catalog< FilterCatalogEntry, FilterCatalogParams > | FCatalog |
typedef std::map< std::string, std::string > | STRING_PROPS |
typedef bool(* | MCSFinalMatchCheckFunction) (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) |
typedef bool(* | MCSAtomCompareFunction) (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
typedef bool(* | MCSBondCompareFunction) (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
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) More... | |
typedef RDCatalog::HierarchCatalog< MolCatalogEntry, MolCatalogParams, int > | MolCatalog |
a hierarchical catalog for holding molecules More... | |
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< unsigned int > | 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, boost::shared_ptr< ROMol > > | RGroupRow |
typedef std::vector< boost::shared_ptr< ROMol > > | RGroupColumn |
typedef std::vector< RGroupRow > | RGroupRows |
typedef std::map< std::string, RGroupColumn > | RGroupColumns |
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: More... | |
typedef boost::shared_ptr< RWMol > | RWMOL_SPTR |
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. More... | |
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:
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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) |
Set the atom's MDL integer RLabel. More... | |
RDKIT_GRAPHMOL_EXPORT int | getAtomRLabel (const Atom *atm) |
RDKIT_GRAPHMOL_EXPORT void | setAtomAlias (Atom *atom, const std::string &alias) |
Set the atom's MDL atom alias. More... | |
RDKIT_GRAPHMOL_EXPORT std::string | getAtomAlias (const Atom *atom) |
RDKIT_GRAPHMOL_EXPORT void | setAtomValue (Atom *atom, const std::string &value) |
Set the atom's MDL atom value. More... | |
RDKIT_GRAPHMOL_EXPORT std::string | getAtomValue (const Atom *atom) |
RDKIT_GRAPHMOL_EXPORT void | setSupplementalSmilesLabel (Atom *atom, const std::string &label) |
Sets the supplemental label that will follow the atom when writing. More... | |
RDKIT_GRAPHMOL_EXPORT std::string | getSupplementalSmilesLabel (const Atom *atom) |
RDKIT_GRAPHMOL_EXPORT bool | isEarlyAtom (int atomicNum) |
returns whether or not the atom is to the left of C More... | |
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::BBS | removeNonmatchingReagents (const ChemicalReaction &rxn, EnumerationTypes::BBS bbs, const EnumerationParams ¶ms=EnumerationParams()) |
Helper function, remove reagents that are incompatible. More... | |
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. More... | |
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, unsigned int &which) |
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. More... | |
RDKIT_CHEMREACTIONS_EXPORT bool | isMoleculeProductOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which) |
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. More... | |
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. More... | |
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 More... | |
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::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. More... | |
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. More... | |
RDKIT_CHEMREACTIONS_EXPORT ROMol * | reduceProductToSideChains (const ROMOL_SPTR &product, bool addDummyAtoms=true) |
Reduce the product generated by run_Reactants or run_Reactant to. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * | MurckoDecompose (const ROMol &mol) |
Carries out a Murcko decomposition on the molecule provided. More... | |
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. More... | |
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. More... | |
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() More... | |
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. More... | |
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 More... | |
bool | hasNonZeroZCoords (const Conformer &conf) |
Returns true if any of the z coords are non zero, false otherwise. More... | |
RDKIT_FILEPARSERS_EXPORT std::string | strip (const std::string &orig) |
RDKIT_FILEPARSERS_EXPORT RWMol * | MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | MolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RDKIT_FILEPARSERS_EXPORT std::string | MolToMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false) |
std::string | MolToV3KMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true) |
RDKIT_FILEPARSERS_EXPORT void | MolToMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false) |
void | MolToV3KMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true) |
RDKIT_FILEPARSERS_EXPORT std::string | MolToXYZBlock (const ROMol &mol, int confId=-1) |
RDKIT_FILEPARSERS_EXPORT void | MolToXYZFile (const ROMol &mol, const std::string &fName, int confId=-1) |
RDKIT_FILEPARSERS_EXPORT RWMol * | TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false) |
translate TPL data (BioCad format) into a multi-conf molecule More... | |
RDKIT_FILEPARSERS_EXPORT RWMol * | TPLFileToMol (const std::string &fName, bool sanitize=true, bool skipFirstConf=false) |
construct a multi-conf molecule from a TPL (BioCad format) file More... | |
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 RWMol * | Mol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true) |
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 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 void | DetectAtomStereoChemistry (RWMol &mol, const Conformer *conf) |
deprecated, please use MolOps::assignChiralTypesFromBondDirs instead More... | |
RDKIT_FILEPARSERS_EXPORT void | DetectBondStereoChemistry (ROMol &mol, const Conformer *conf) |
deprecated, please use MolOps::detectBondStereoChemistry instead More... | |
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 INT_MAP_INT | pickBondsToWedge (const ROMol &mol) |
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 INT_MAP_INT &wedgeBonds, const Conformer *conf) |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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 | 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 | checkBondRingMatch (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *v_ringMatchMatrixSet) |
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 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 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) |
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 More... | |
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * | buildFeatureFactory (const std::string &featureData) |
constructs a MolChemicalFeatureFactory from the data in a string More... | |
std::ostream & | operator<< (std::ostream &oss, const TextAlignType &tat) |
std::ostream & | operator<< (std::ostream &oss, const TextDrawType &tdt) |
std::ostream & | operator<< (std::ostream &oss, const OrientType &o) |
bool | setStringDrawMode (const std::string &instring, TextDrawType &draw_mode, size_t &i) |
std::vector< std::string > | atomLabelToPieces (const std::string &label, OrientType orient) |
int | moveToFunction (const FT_Vector *to, void *user) |
int | lineToFunction (const FT_Vector *to, void *user) |
int | conicToFunction (const FT_Vector *control, const FT_Vector *to, void *user) |
int | cubicToFunction (const FT_Vector *controlOne, const FT_Vector *controlTwo, const FT_Vector *to, void *user) |
void | assignDefaultPalette (ColourPalette &palette) |
void | assignBWPalette (ColourPalette &palette) |
RDKIT_MOLDRAW2D_EXPORT bool | doLinesIntersect (const Point2D &l1s, const Point2D &l1f, const Point2D &l2s, const Point2D &l2f, Point2D *ip=nullptr) |
RDKIT_MOLDRAW2D_EXPORT bool | doesLineIntersectLabel (const Point2D &ls, const Point2D &lf, const StringRect &lab_rect, double padding=0.0) |
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. More... | |
static int | queryAtomHeavyAtomDegree (Atom const *at) |
D and T are not treated as heavy atoms here. More... | |
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 | 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) |
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 More... | |
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. More... | |
template<class T > | |
T * | makeAtomTypeQuery (int num, int aromatic, const std::string &descr) |
returns a Query for matching atomic number and aromaticity More... | |
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. More... | |
template<class T > | |
T * | makeAtomImplicitValenceQuery (int what, const std::string &descr) |
returns a Query for matching implicit valence More... | |
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. More... | |
template<class T > | |
T * | makeAtomExplicitValenceQuery (int what, const std::string &descr) |
returns a Query for matching explicit valence More... | |
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. More... | |
template<class T > | |
T * | makeAtomTotalValenceQuery (int what, const std::string &descr) |
returns a Query for matching total valence More... | |
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. More... | |
template<class T > | |
T * | makeAtomExplicitDegreeQuery (int what, const std::string &descr) |
returns a Query for matching explicit degree More... | |
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. More... | |
template<class T > | |
T * | makeAtomTotalDegreeQuery (int what, const std::string &descr) |
returns a Query for matching atomic degree More... | |
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. More... | |
template<class T > | |
T * | makeAtomHeavyAtomDegreeQuery (int what, const std::string &descr) |
returns a Query for matching heavy atom degree More... | |
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. More... | |
template<class T > | |
T * | makeAtomHCountQuery (int what, const std::string &descr) |
returns a Query for matching hydrogen count More... | |
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. More... | |
template<class T > | |
T * | makeAtomHasImplicitHQuery (const std::string &descr) |
returns a Query for matching ring atoms More... | |
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. More... | |
template<class T > | |
T * | makeAtomImplicitHCountQuery (int what, const std::string &descr) |
returns a Query for matching implicit hydrogen count More... | |
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. More... | |
template<class T > | |
T * | makeAtomAromaticQuery (const std::string &descr) |
returns a Query for matching the isAromatic flag More... | |
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. More... | |
template<class T > | |
T * | makeAtomAliphaticQuery (const std::string &descr) |
returns a Query for matching aliphatic atoms More... | |
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. More... | |
template<class T > | |
T * | makeAtomMassQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular mass More... | |
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. More... | |
template<class T > | |
T * | makeAtomIsotopeQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular isotope More... | |
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. More... | |
template<class T > | |
T * | makeAtomFormalChargeQuery (int what, const std::string &descr) |
returns a Query for matching formal charge More... | |
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. More... | |
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. More... | |
template<class T > | |
T * | makeAtomHybridizationQuery (int what, const std::string &descr) |
returns a Query for matching hybridization More... | |
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. More... | |
template<class T > | |
T * | makeAtomNumRadicalElectronsQuery (int what, const std::string &descr) |
returns a Query for matching the number of radical electrons More... | |
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. More... | |
template<class T > | |
T * | makeAtomHasChiralTagQuery (const std::string &descr) |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHasChiralTagQuery () |
\overloadquery More... | |
template<class T > | |
T * | makeAtomMissingChiralTagQuery (const std::string &descr) |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomMissingChiralTagQuery () |
\overloadquery More... | |
template<class T > | |
T * | makeAtomUnsaturatedQuery (const std::string &descr) |
returns a Query for matching atoms with unsaturation: More... | |
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. More... | |
template<class T > | |
T * | makeAtomInRingQuery (const std::string &descr) |
returns a Query for matching ring atoms More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomInRingQuery () |
template<class T > | |
T * | makeAtomInNRingsQuery (int what, const std::string &descr) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More... | |
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. More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomInRingOfSizeQuery (int tgt) |
returns a Query for matching atoms in rings of a particular size More... | |
template<class T > | |
T * | makeAtomMinRingSizeQuery (int tgt, const std::string &descr) |
returns a Query for matching an atom's minimum ring size More... | |
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. More... | |
template<class T > | |
T * | makeAtomRingBondCountQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular number of ring bonds More... | |
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. More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAAtomQuery () |
returns a Query for matching generic A atoms (heavy atoms) More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * | makeAHAtomQuery () |
returns a Query for matching generic AH atoms (any atom) More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeQAtomQuery () |
returns a Query for matching generic Q atoms (heteroatoms) More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeQHAtomQuery () |
returns a Query for matching generic QH atoms (heteroatom or H) More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeXAtomQuery () |
returns a Query for matching generic X atoms (halogens) More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeXHAtomQuery () |
returns a Query for matching generic XH atoms (halogen or H) More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeMAtomQuery () |
returns a Query for matching generic M atoms (metals) More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * | makeMHAtomQuery () |
returns a Query for matching generic MH atoms (metals or H) More... | |
template<class T > | |
T * | makeAtomHasRingBondQuery (const std::string &descr) |
returns a Query for matching atoms that have ring bonds More... | |
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. More... | |
template<class T > | |
T * | makeAtomNumHeteroatomNbrsQuery (int what, const std::string &descr) |
returns a Query for matching the number of heteroatom neighbors More... | |
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. More... | |
template<class T > | |
T * | makeAtomHasHeteroatomNbrsQuery (const std::string &descr) |
returns a Query for matching atoms that have heteroatom neighbors More... | |
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. More... | |
template<class T > | |
T * | makeAtomNumAliphaticHeteroatomNbrsQuery (int what, const std::string &descr) |
returns a Query for matching the number of aliphatic heteroatom neighbors More... | |
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. More... | |
template<class T > | |
T * | makeAtomHasAliphaticHeteroatomNbrsQuery (const std::string &descr) |
returns a Query for matching atoms that have heteroatom neighbors More... | |
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. More... | |
template<class T > | |
T * | makeAtomNonHydrogenDegreeQuery (int what, const std::string &descr) |
returns a Query for matching the number of non-hydrogen neighbors More... | |
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. More... | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondOrderEqualsQuery (Bond::BondType what) |
returns a Query for matching bond orders More... | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeSingleOrAromaticBondQuery () |
returns a Query for unspecified SMARTS bonds More... | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeSingleOrDoubleOrAromaticBondQuery () |
returns a Query for tautomeric bonds More... | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondDirEqualsQuery (Bond::BondDir what) |
returns a Query for matching bond directions More... | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondHasStereoQuery () |
returns a Query for matching bonds with stereo set More... | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondIsInRingQuery () |
returns a Query for matching ring bonds More... | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondInRingOfSizeQuery (int what) |
returns a Query for matching bonds in rings of a particular size More... | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondMinRingSizeQuery (int what) |
returns a Query for matching a bond's minimum ring size More... | |
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * | makeBondInNRingsQuery (int tgt) |
returns a Query for matching bonds in a particular number of rings More... | |
RDKIT_GRAPHMOL_EXPORT BOND_NULL_QUERY * | makeBondNullQuery () |
returns a Query for matching any bond More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * | makeAtomNullQuery () |
returns a Query for matching any atom More... | |
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 More... | |
template<class Target , class T > | |
Queries::EqualityQuery< int, const Target *, true > * | makePropQuery (const std::string &propname, const T &val, const T &tolerance=T()) |
template<class Target > | |
Queries::EqualityQuery< int, const Target *, true > * | makePropQuery (const std::string &propname, const ExplicitBitVect &val, float tolerance=0.0) |
RDKIT_GRAPHMOL_EXPORT bool | isComplexQuery (const Bond *b) |
RDKIT_GRAPHMOL_EXPORT bool | isComplexQuery (const Atom *a) |
RDKIT_GRAPHMOL_EXPORT bool | isAtomAromatic (const Atom *a) |
RDKIT_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) |
double | score (const std::vector< size_t > &permutation, const std::vector< std::vector< RGroupMatch >> &matches, const std::set< int > &labels) |
std::string | labellingToString (Labelling type) |
return the user friendly name for the given labelling More... | |
std::map< int, Atom * > | getRlabels (const RWMol &mol) |
Get the RLabels,atom mapping for the current molecule. More... | |
void | clearInputLabels (Atom *atom) |
Remove the user labels from the atom. More... | |
bool | 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. More... | |
bool | hasDummy (const RWMol &core) |
Returns true if the core has a dummy atom. More... | |
RDKIT_SLNPARSE_EXPORT RWMol * | SLNToMol (const std::string &smi, bool sanitize=true, int debugParse=0) |
RDKIT_SLNPARSE_EXPORT RWMol * | SLNQueryToMol (const std::string &smi, bool mergeHs=true, int debugParse=0) |
RDKIT_SMILESPARSE_EXPORT std::string | MolToSmarts (const ROMol &mol, bool doIsomericSmarts=true) |
returns the SMARTS for a molecule More... | |
RDKIT_SMILESPARSE_EXPORT std::string | MolFragmentToSmarts (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, bool doIsomericSmarts=true) |
RDKIT_SMILESPARSE_EXPORT RWMol * | SmilesToMol (const std::string &smi, const SmilesParserParams ¶ms) |
RDKIT_SMILESPARSE_EXPORT Atom * | SmilesToAtom (const std::string &smi) |
RDKIT_SMILESPARSE_EXPORT 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. More... | |
RDKIT_SMILESPARSE_EXPORT 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. More... | |
RDKIT_SMILESPARSE_EXPORT Atom * | SmartsToAtom (const std::string &sma) |
RDKIT_SMILESPARSE_EXPORT 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, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false) |
returns canonical SMILES for a molecule More... | |
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) More... | |
RDKIT_SMILESPARSE_EXPORT 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 More... | |
RDKIT_SMILESPARSE_EXPORT 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 More... | |
RDKIT_SMILESPARSE_EXPORT 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 More... | |
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_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 More... | |
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 More... | |
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 More... | |
RDKIT_SUBGRAPHS_EXPORT PATH_LIST | findAllPathsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1) |
find all paths of a particular size More... | |
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) |
RDKIT_SUBGRAPHS_EXPORT PATH_TYPE | findAtomEnvironmentOfRadiusN (const ROMol &mol, unsigned int radius, unsigned int rootedAtAtom, bool useHs=false) |
find bond subgraphs of a particular radius around an atom More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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 | 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_SUBSTRUCTLIBRARY_EXPORT void | addPatterns (SubstructLibrary &sslib, int numThreads=1) |
RDKIT_SUBSTRUCTLIBRARY_EXPORT bool | SubstructLibraryCanSerialize () |
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. More... | |
RDKIT_TRAJECTORY_EXPORT unsigned int | readGromosTrajectory (const std::string &fName, Trajectory &traj) |
Reads coordinates from a GROMOS trajectory file into the traj Trajectory object. More... | |
DiscreteDistMat * | getDiscreteDistMat () |
RDKIT_DATASTRUCTS_EXPORT unsigned int | computeL1Norm (const DiscreteValueVect &v1, const DiscreteValueVect &v2) |
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect | operator+ (const DiscreteValueVect &p1, const DiscreteValueVect &p2) |
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect | operator- (const DiscreteValueVect &p1, const DiscreteValueVect &p2) |
template<typename IndexType , typename SequenceType > | |
void | updateFromSequence (SparseIntVect< IndexType > &vect, const SequenceType &seq) |
template<typename IndexType > | |
double | DiceSimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, bool returnDistance=false, double bounds=0.0) |
template<typename IndexType > | |
double | TverskySimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, double a, double b, bool returnDistance=false, double bounds=0.0) |
template<typename IndexType > | |
double | TanimotoSimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, bool returnDistance=false, double bounds=0.0) |
template<class T > | |
void | mergeNullQueries (T *&returnQuery, bool isQueryNull, T *&otherQuery, bool isOtherQNull, Queries::CompositeQueryType how) |
template<> | |
std::string | Dict::getVal< std::string > (const std::string &what) const |
template<typename CompareFunc > | |
bool | hanoi (int *base, int nel, int *temp, int *count, int *changed, CompareFunc compar) |
template<typename CompareFunc > | |
void | hanoisort (int *base, int nel, int *count, int *changed, CompareFunc compar) |
template<class T > | |
const T | rdany_cast (const RDAny &d) |
template<class T > | |
T | rdany_cast (RDAny &d) |
template<class T > | |
boost::enable_if< boost::is_arithmetic< T >, T >::type | from_rdany (const RDAny &arg) |
template<class T > | |
boost::disable_if< boost::is_arithmetic< T >, T >::type | from_rdany (const RDAny &arg) |
unsigned int | getNumThreadsToUse (int target) |
void | copy_rdvalue (RDValue &dest, const RDValue &src) |
template<class T > | |
bool | rdvalue_is (const RDValue_cast_t) |
template<> | |
bool | rdvalue_is< double > (const RDValue_cast_t) |
template<> | |
bool | rdvalue_is< const double & > (const RDValue_cast_t) |
template<class T > | |
T | rdvalue_cast (RDValue_cast_t v) |
template<> | |
double | rdvalue_cast< double > (RDValue_cast_t v) |
template<> | |
float | rdvalue_cast< float > (RDValue_cast_t v) |
template<> | |
int | rdvalue_cast< int > (RDValue_cast_t v) |
template<> | |
unsigned int | rdvalue_cast< unsigned int > (RDValue_cast_t v) |
template<> | |
bool | rdvalue_cast< bool > (RDValue_cast_t v) |
template<> | |
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<> | |
boost::any | rdvalue_cast< boost::any > (RDValue_cast_t v) |
template<> | |
boost::any & | rdvalue_cast< boost::any & > (RDValue_cast_t v) |
template<> | |
const boost::any & | rdvalue_cast< const boost::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. More... | |
boost::uint32_t | readPackedIntFromStream (std::stringstream &ss) |
Reads an integer from a stream in packed format and returns the result. More... | |
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 More... | |
void | streamWrite (std::ostream &ss, const std::string &what) |
special case for string More... | |
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 More... | |
template<class T > | |
void | streamRead (std::istream &ss, T &obj, int version) |
special case for string More... | |
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. More... | |
std::string | getLine (std::istream &inStream) |
grabs the next line from an instream and returns it. More... | |
bool | isSerializable (const Dict::Pair &pair, const CustomPropHandlerVec &handlers={}) |
bool | streamWriteProp (std::ostream &ss, const Dict::Pair &pair, const CustomPropHandlerVec &handlers={}) |
bool | streamWriteProps (std::ostream &ss, const RDProps &props, bool savePrivate=false, bool saveComputed=false, const CustomPropHandlerVec &handlers={}) |
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={}) |
unsigned int | streamReadProps (std::istream &ss, RDProps &props, const CustomPropHandlerVec &handlers={}) |
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 More... | |
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 More... | |
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 More... | |
RDKIT_RDGENERAL_EXPORT int | nextCombination (INT_VECT &comb, int tot) |
given a current combination of numbers change it to the next possible More... | |
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 More... | |
RDKIT_RDGENERAL_EXPORT bool | feq (double v1, double v2, double tol=1e-4) |
floating point comparison with a tolerance More... | |
RDKIT_RDGENERAL_EXPORT rng_type & | getRandomGenerator (int seed=-1) |
Optionally seed and return a reference to the global (Boost) random. More... | |
RDKIT_RDGENERAL_EXPORT double | getRandomVal (int seed=-1) |
RDKIT_RDGENERAL_EXPORT double_source_type & | getDoubleRandomSource () |
return a reference to the global (Boost) random source More... | |
template<class T > | |
unsigned int | countSwapsToInterconvert (const T &ref, T probe) |
RDKIT_RDGENERAL_EXPORT std::string | augmentTagName (const std::string &tag) |
Reaction SMARTS/SMILES Support | |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * | RxnSmartsToChemicalReaction (const std::string &text, std::map< std::string, std::string > *replacements=nullptr, bool useSmiles=false) |
Parse a string containing "Reaction SMARTS" into a ChemicalReaction. More... | |
RDKIT_CHEMREACTIONS_EXPORT std::string | ChemicalReactionToRxnSmarts (const ChemicalReaction &rxn) |
returns the reaction SMARTS for a reaction More... | |
RDKIT_CHEMREACTIONS_EXPORT std::string | ChemicalReactionToRxnSmiles (const ChemicalReaction &rxn, bool canonical=true) |
returns the reaction SMILES for a reaction More... | |
Reaction Mol Support | |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * | RxnMolToChemicalReaction (const ROMol &mol) |
Parse a ROMol into a ChemicalReaction, RXN role must be set before. More... | |
RDKIT_CHEMREACTIONS_EXPORT ROMol * | ChemicalReactionToRxnMol (const ChemicalReaction &rxn) |
returns a ROMol with RXN roles used to describe the reaction More... | |
MDL rxn Support | |
RDKIT_CHEMREACTIONS_EXPORT 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. More... | |
RDKIT_CHEMREACTIONS_EXPORT 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. More... | |
RDKIT_CHEMREACTIONS_EXPORT 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. More... | |
RDKIT_CHEMREACTIONS_EXPORT std::string | ChemicalReactionToRxnBlock (const ChemicalReaction &rxn, bool separateAgents=false) |
returns an rxn block for a reaction More... | |
PNG Support | |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * | PNGStreamToChemicalReaction (std::istream &pngStream) |
constructs a ChemicalReaction from the metadata in a PNG stream More... | |
ChemicalReaction * | PNGStringToChemicalReaction (const std::string &data) |
constructs a ChemicalReaction from the metadata in a PNG string See PNGStreamToChemicalReaction() for more details More... | |
ChemicalReaction * | PNGFileToChemicalReaction (const std::string &fname) |
constructs a ChemicalReaction from the metadata in a PNG file See PNGStreamToChemicalReaction() for more details More... | |
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. More... | |
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. More... | |
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. More... | |
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 More... | |
std::vector< std::pair< std::string, std::string > > | PNGFileToMetadata (const std::string &fname) |
returns the metadata (tEXt and zTXt chunks) from PNG data More... | |
std::vector< std::pair< std::string, std::string > > | PNGStringToMetadata (const std::string &data) |
returns the metadata (tEXt and zTXt chunks) from PNG data More... | |
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. More... | |
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. More... | |
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. More... | |
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 More... | |
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. More... | |
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. More... | |
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 More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
RDKIT_GRAPHMOL_EXPORT void | removeSubstanceGroupsReferencingBond (RWMol &mol, unsigned int idx) |
Removes SubstanceGroups which reference a particular bond index. More... | |
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 33 of file QueryOps.h.
typedef Queries::Query<bool, Atom const *, true> RDKit::ATOM_BOOL_QUERY |
Definition at line 30 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_EQUALS_QUERY |
Definition at line 42 of file QueryOps.h.
typedef Queries::GreaterQuery<int, Atom const *, true> RDKit::ATOM_GREATER_QUERY |
Definition at line 45 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int, Atom const *, true> RDKit::ATOM_GREATEREQUAL_QUERY |
Definition at line 49 of file QueryOps.h.
typedef Queries::LessQuery<int, Atom const *, true> RDKit::ATOM_LESS_QUERY |
Definition at line 53 of file QueryOps.h.
typedef Queries::LessEqualQuery<int, Atom const *, true> RDKit::ATOM_LESSEQUAL_QUERY |
Definition at line 56 of file QueryOps.h.
typedef Queries::Query<int, Atom const *, true> RDKit::ATOM_NULL_QUERY |
Definition at line 66 of file QueryOps.h.
typedef Queries::OrQuery<int, Atom const *, true> RDKit::ATOM_OR_QUERY |
Definition at line 36 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_PROP_QUERY |
Definition at line 823 of file QueryOps.h.
typedef Queries::RangeQuery<int, Atom const *, true> RDKit::ATOM_RANGE_QUERY |
Definition at line 59 of file QueryOps.h.
typedef Queries::SetQuery<int, Atom const *, true> RDKit::ATOM_SET_QUERY |
Definition at line 62 of file QueryOps.h.
typedef Queries::XOrQuery<int, Atom const *, true> RDKit::ATOM_XOR_QUERY |
Definition at line 39 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 34 of file QueryOps.h.
typedef Queries::Query<bool, Bond const *, true> RDKit::BOND_BOOL_QUERY |
Definition at line 31 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_EQUALS_QUERY |
Definition at line 43 of file QueryOps.h.
typedef Queries::GreaterQuery<int, Bond const *, true> RDKit::BOND_GREATER_QUERY |
Definition at line 46 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int, Bond const *, true> RDKit::BOND_GREATEREQUAL_QUERY |
Definition at line 51 of file QueryOps.h.
typedef Queries::LessQuery<int, Bond const *, true> RDKit::BOND_LESS_QUERY |
Definition at line 54 of file QueryOps.h.
typedef Queries::LessEqualQuery<int, Bond const *, true> RDKit::BOND_LESSEQUAL_QUERY |
Definition at line 57 of file QueryOps.h.
typedef Queries::Query<int, Bond const *, true> RDKit::BOND_NULL_QUERY |
Definition at line 65 of file QueryOps.h.
typedef Queries::OrQuery<int, Bond const *, true> RDKit::BOND_OR_QUERY |
Definition at line 37 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_PROP_QUERY |
Definition at line 824 of file QueryOps.h.
typedef Queries::RangeQuery<int, Bond const *, true> RDKit::BOND_RANGE_QUERY |
Definition at line 60 of file QueryOps.h.
typedef Queries::SetQuery<int, Bond const *, true> RDKit::BOND_SET_QUERY |
Definition at line 63 of file QueryOps.h.
typedef Queries::XOrQuery<int, Bond const *, true> RDKit::BOND_XOR_QUERY |
Definition at line 40 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 148 of file MolDraw2D.h.
typedef boost::shared_ptr<Conformer> RDKit::CONFORMER_SPTR |
Definition at line 146 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 676 of file QueryOps.h.
typedef Bond const* RDKit::ConstBondPtr |
Definition at line 786 of file QueryOps.h.
typedef std::vector<std::shared_ptr<const CustomPropHandler> > RDKit::CustomPropHandlerVec |
Definition at line 369 of file StreamOps.h.
typedef std::vector<unsigned int> RDKit::DashPattern |
Definition at line 149 of file MolDraw2D.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 111 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 45 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::const_iterator RDKit::INT_PATH_LIST_MAP_CI |
Definition at line 46 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::iterator RDKit::INT_PATH_LIST_MAP_I |
Definition at line 47 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::MCSAtomCompareFunction) (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
typedef bool(* RDKit::MCSBondCompareFunction) (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
typedef bool(* RDKit::MCSFinalMatchCheckFunction) (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) |
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< ROMOL_SPTR > 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 42 of file Subgraphs.h.
typedef PATH_LIST::const_iterator RDKit::PATH_LIST_CI |
Definition at line 43 of file Subgraphs.h.
typedef std::vector<int> RDKit::PATH_TYPE |
Definition at line 41 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<boost::shared_ptr<ROMol> > RDKit::RGroupColumn |
Definition at line 82 of file RGroupDecomp.h.
typedef std::map<std::string, RGroupColumn> RDKit::RGroupColumns |
Definition at line 85 of file RGroupDecomp.h.
typedef std::map<std::string, boost::shared_ptr<ROMol> > RDKit::RGroupRow |
Definition at line 81 of file RGroupDecomp.h.
typedef std::vector<RGroupRow> RDKit::RGroupRows |
Definition at line 84 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 |
Definition at line 46 of file FileParsers.h.
typedef std::vector<Snapshot> RDKit::SnapshotVect |
Definition at line 20 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 53 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 27 of file StreamOps.h.
Enumerator | |
---|---|
AtomPairFP | |
TopologicalTorsion | |
MorganFP | |
RDKitFP | |
PatternFP |
Definition at line 43 of file ReactionFingerprints.h.
|
strong |
Enumerator | |
---|---|
AtomPairFP | |
MorganFP | |
RDKitFP | |
TopologicalTorsionFP |
Definition at line 297 of file FingerprintGenerator.h.
|
strong |
Enumerator | |
---|---|
RGROUP_LABELS | |
ISOTOPE_LABELS | |
ATOMMAP_LABELS | |
INDEX_LABELS | |
DUMMY_LABELS | |
INTERNAL_LABELS |
Definition at line 24 of file RGroupUtils.h.
enum RDKit::Mol2Type |
Enumerator | |
---|---|
CORINA |
Definition at line 225 of file FileParsers.h.
|
strong |
Enumerator | |
---|---|
C | |
N | |
E | |
S | |
W |
Definition at line 28 of file DrawText.h.
Enumerator | |
---|---|
Reactant | |
Product | |
Agent |
Definition at line 41 of file ReactionUtils.h.
Enumerator | |
---|---|
None | |
NoAlignment | |
MCS |
Definition at line 52 of file RGroupDecomp.h.
Enumerator | |
---|---|
AtomMap | |
Isotope | |
MDLRGroup |
Definition at line 46 of file RGroupDecomp.h.
enum RDKit::RGroupLabels |
Compute the isomorphic degenerative points in the molecule. These are points that are symmetrically equivalent.
mol | Molecule to compute the degenerative points |
Enumerator | |
---|---|
IsotopeLabels | |
AtomMapLabels | |
AtomIndexLabels | |
RelabelDuplicateLabels | |
MDLRGroupLabels | |
DummyAtomLabels | |
AutoDetect |
Definition at line 29 of file RGroupDecomp.h.
Enumerator | |
---|---|
Greedy | |
GreedyChunks | |
Exhaustive | |
NoSymmetrization |
Definition at line 39 of file RGroupDecomp.h.
|
strong |
Enumerator | |
---|---|
STEREO_ABSOLUTE | |
STEREO_OR | |
STEREO_AND |
Definition at line 28 of file StereoGroup.h.
|
strong |
Enumerator | |
---|---|
START | |
MIDDLE | |
END |
Definition at line 29 of file DrawText.h.
|
strong |
Enumerator | |
---|---|
TextDrawNormal | |
TextDrawSuperscript | |
TextDrawSubscript |
Definition at line 30 of file DrawText.h.
|
inline |
adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.
Definition at line 216 of file ReactionParser.h.
References addChemicalReactionToPNGStream().
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::addChemicalReactionToPNGStream | ( | const ChemicalReaction & | rxn, |
std::istream & | iStream, | ||
bool | includePkl = true , |
||
bool | includeSmiles = true , |
||
bool | includeSmarts = false , |
||
bool | includeRxn = false |
||
) |
adds metadata for a ChemicalReaction to the data from a PNG stream. The modified PNG data is returned.
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 |
Referenced by addChemicalReactionToPNGFile(), and addChemicalReactionToPNGString().
|
inline |
adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.
Definition at line 204 of file ReactionParser.h.
References addChemicalReactionToPNGStream().
|
inline |
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().
|
inline |
adds metadata to a PNG string. The modified PNG data is returned.
Definition at line 74 of file PNGParser.h.
References addMetadataToPNGStream().
|
inline |
adds metadata for an ROMol to the data from a PNG file. The modified PNG data is returned. See addMolToPNGStream()
for more details.
Definition at line 191 of file PNGParser.h.
References addMolToPNGStream().
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().
|
inline |
adds metadata for an ROMol to a PNG string. The modified PNG data is returned. See addMolToPNGStream()
for more details.
Definition at line 179 of file PNGParser.h.
References addMolToPNGStream().
RDKIT_SUBSTRUCTLIBRARY_EXPORT void RDKit::addPatterns | ( | SubstructLibrary & | sslib, |
int | numThreads = 1 |
||
) |
Create pattern fingerprints for the given substructure library The substructure library must not already have fingepints
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.
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
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. |
|
inline |
Packs an integer and outputs it to a stream.
Definition at line 99 of file StreamOps.h.
References CHECK_INVARIANT.
|
inline |
Definition at line 166 of file MolDraw2D.h.
|
inline |
Definition at line 151 of file MolDraw2D.h.
Referenced by RDKit::MolDrawOptions::MolDrawOptions().
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::atomCompat | ( | const Atom * | a1, |
const Atom * | a2, | ||
const SubstructMatchParameters & | ps | ||
) |
std::vector<std::string> RDKit::atomLabelToPieces | ( | const std::string & | label, |
OrientType | orient | ||
) |
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
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::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, | ||
void * | v_ringMatchMatrixSet | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::checkBondStereo | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2 | ||
) |
|
inline |
Definition at line 129 of file RGroupDecomp.h.
Referenced by RDKit::RGroupDecompData::process().
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnBlock | ( | const ChemicalReaction & | rxn, |
bool | separateAgents = false |
||
) |
returns an rxn block for a reaction
rxn | chemical reaction |
separateAgents | flag to decide if agents were put in a separate block, otherwise they were included in the reactants block (default) |
RDKIT_CHEMREACTIONS_EXPORT ROMol* RDKit::ChemicalReactionToRxnMol | ( | const ChemicalReaction & | rxn | ) |
returns a ROMol with RXN roles used to describe the reaction
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmarts | ( | const ChemicalReaction & | rxn | ) |
returns the reaction SMARTS for a reaction
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmiles | ( | const ChemicalReaction & | rxn, |
bool | canonical = true |
||
) |
returns the reaction SMILES for a reaction
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::ClearSingleBondDirFlags | ( | ROMol & | mol | ) |
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 |
Referenced by RDKit::RGroupData::add().
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_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
Referenced by RDKit::EnumerationStrategyBase::initialize(), and RDKit::EnumerationStrategyBase::internalInitialize().
int RDKit::conicToFunction | ( | const FT_Vector * | control, |
const FT_Vector * | to, | ||
void * | user | ||
) |
RDKIT_FILEPARSERS_EXPORT void RDKit::ConnectTheDots | ( | RWMol * | mol, |
unsigned int | flags = 0 |
||
) |
Definition at line 339 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::AnyTag, RDKit::RDValue::destroy(), RDKit::RDValue::getTag(), RDKit::RDValue::ptrCast(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
Referenced by RDKit::Dict::Dict(), RDKit::Dict::operator=(), RDKit::RDAny::operator=(), RDKit::RDAny::RDAny(), and RDKit::Dict::update().
unsigned int RDKit::countSwapsToInterconvert | ( | const T & | ref, |
T | probe | ||
) |
Definition at line 56 of file utils.h.
References CHECK_INVARIANT, and PRECONDITION.
int RDKit::cubicToFunction | ( | const FT_Vector * | controlOne, |
const FT_Vector * | controlTwo, | ||
const FT_Vector * | to, | ||
void * | user | ||
) |
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.
|
inline |
Definition at line 121 of file QueryAtom.h.
References RDKit::Atom::getQuery(), RDKit::Atom::hasQuery(), PRECONDITION, and RDKit::detail::qhelper().
|
inline |
Definition at line 111 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_FILEPARSERS_EXPORT Bond::BondDir RDKit::DetermineBondWedgeState | ( | const Bond * | bond, |
const INT_MAP_INT & | wedgeBonds, | ||
const Conformer * | conf | ||
) |
RDKIT_FILEPARSERS_EXPORT Bond::BondDir RDKit::DetermineBondWedgeState | ( | const Bond * | bond, |
unsigned int | fromAtomIdx, | ||
const Conformer * | conf | ||
) |
double RDKit::DiceSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
||
double | bounds = 0.0 |
||
) |
Definition at line 479 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getLength(), and RDKit::SparseIntVect< IndexType >::getTotalVal().
|
inline |
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 RDKIT_MOLDRAW2D_EXPORT bool RDKit::doesLineIntersectLabel | ( | const Point2D & | ls, |
const Point2D & | lf, | ||
const StringRect & | lab_rect, | ||
double | padding = 0.0 |
||
) |
RDKIT_MOLDRAW2D_EXPORT bool RDKit::doLinesIntersect | ( | const Point2D & | l1s, |
const Point2D & | l1f, | ||
const Point2D & | l2s, | ||
const Point2D & | l2f, | ||
Point2D * | ip = nullptr |
||
) |
|
inline |
Definition at line 85 of file StreamOps.h.
|
inline |
Definition at line 93 of file StreamOps.h.
|
inline |
Definition at line 70 of file StreamOps.h.
|
inline |
Definition at line 89 of file StreamOps.h.
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::EnumerateLibraryCanSerialize | ( | ) |
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 | ( | ) |
|
inline |
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 |
||
) |
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. |
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 |
||
) |
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 |
||
) |
find bond subgraphs of a particular radius around an atom
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. |
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 | 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 | 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 | ||
) |
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)
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, and RDKit::RDTypeTag::StringTag.
boost::disable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdany | ( | const RDAny & | arg | ) |
boost::enable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
Definition at line 243 of file RDValue.h.
References RDKit::RDValue::getTag(), and RDKit::RDTypeTag::StringTag.
boost::disable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomAlias | ( | const Atom * | atom | ) |
RDKIT_GRAPHMOL_EXPORT int RDKit::getAtomRLabel | ( | const Atom * | atm | ) |
|
inlinestatic |
Definition at line 147 of file QueryOps.h.
|
inlinestatic |
Definition at line 143 of file QueryOps.h.
RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomValue | ( | const Atom * | atom | ) |
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 | ||
) |
DiscreteDistMat* RDKit::getDiscreteDistMat | ( | ) |
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.
|
inline |
grabs the next line from an instream and returns it.
Definition at line 334 of file StreamOps.h.
References getLine().
|
inline |
grabs the next line from an instream and returns it.
Definition at line 325 of file StreamOps.h.
Referenced by getLine().
unsigned int RDKit::GetNumEntries | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
unsigned int RDKit::GetNumPropertyEntries | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
|
inline |
Definition at line 37 of file RDThreads.h.
References RDUNUSED_PARAM.
Referenced by RDKit::ForceFieldsHelper::OptimizeMoleculeConfs().
RDKIT_RDGENERAL_EXPORT rng_type& RDKit::getRandomGenerator | ( | int | seed = -1 | ) |
Optionally seed and return a reference to the global (Boost) random.
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> >
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.
Get the RLabels,atom mapping for the current molecule.
Referenced by RDKit::RGroupDecompData::GetCurrentBestPermutation(), and RDKit::RGroupDecompData::relabelCore().
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 74 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> >
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 | ) |
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 | ||
) |
void RDKit::hanoisort | ( | int * | base, |
int | nel, | ||
int * | count, | ||
int * | changed, | ||
CompareFunc | compar | ||
) |
Definition at line 145 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.
|
inline |
Returns true if any of the z coords are non zero, false otherwise.
conf | Conformer object to analyze |
Definition at line 152 of file Conformer.h.
References RDKit::Conformer::getPositions().
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_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_GRAPHMOL_EXPORT bool RDKit::isAtomAromatic | ( | const Atom * | a | ) |
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 | ) |
RDKIT_GRAPHMOL_EXPORT bool RDKit::isEarlyAtom | ( | int | atomicNum | ) |
returns whether or not 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.
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
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.
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeProductOfReaction | ( | 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 products the which
argument is used to return which of the products the molecule matches. If there's no match, it is equal to the number of products on return
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.
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeReactantOfReaction | ( | 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 reactants the which
argument is used to return which of the reactants the molecule matches. If there's no match, it is equal to the number of reactants on return
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isReactionTemplateMoleculeAgent | ( | const ROMol & | mol, |
double | agentThreshold | ||
) |
|
inline |
Definition at line 371 of file StreamOps.h.
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:
int RDKit::lineToFunction | ( | const FT_Vector * | to, |
void * | user | ||
) |
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 451 of file QueryOps.h.
References 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 443 of file QueryOps.h.
References 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 395 of file QueryOps.h.
References 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 379 of file QueryOps.h.
References 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 476 of file QueryOps.h.
References queryAtomFormalCharge().
Referenced by RDKit::QueryAtom::QueryAtom().
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 624 of file QueryOps.h.
References 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 512 of file QueryOps.h.
References 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 606 of file QueryOps.h.
References 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 427 of file QueryOps.h.
References 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 589 of file QueryOps.h.
References 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 419 of file QueryOps.h.
References 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 411 of file QueryOps.h.
References 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 494 of file QueryOps.h.
References 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 435 of file QueryOps.h.
References 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 371 of file QueryOps.h.
References 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 | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
returns a Query for matching atoms in a particular number of rings
Definition at line 545 of file QueryOps.h.
References 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 | ( | ) |
T* RDKit::makeAtomInRingQuery | ( | const std::string & | descr | ) |
returns a Query for matching ring atoms
Definition at line 537 of file QueryOps.h.
References queryIsAtomInRing().
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 468 of file QueryOps.h.
References queryAtomIsotope().
Referenced by RDKit::QueryAtom::QueryAtom().
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 459 of file QueryOps.h.
References 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 556 of file QueryOps.h.
References 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 521 of file QueryOps.h.
References 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 485 of file QueryOps.h.
References 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 633 of file QueryOps.h.
References 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 614 of file QueryOps.h.
References 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 597 of file QueryOps.h.
References 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 353 of file QueryOps.h.
References queryAtomNum().
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 502 of file QueryOps.h.
References queryAtomNumRadicalElectrons().
Referenced by RDKit::QueryAtom::QueryAtom().
|
inlinestatic |
Definition at line 341 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 564 of file QueryOps.h.
References queryAtomRingBondCount().
T* RDKit::makeAtomSimpleQuery | ( | int | what, |
int | funcAtom const *, | ||
const std::string & | description = "Atom Simple" |
||
) |
Definition at line 332 of file QueryOps.h.
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 403 of file QueryOps.h.
References 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 387 of file QueryOps.h.
References queryAtomTotalValence().
|
inlinestatic |
Definition at line 131 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 361 of file QueryOps.h.
References 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 529 of file QueryOps.h.
References 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
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 828 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, | ||
float | tolerance = 0.0 |
||
) |
Definition at line 1042 of file QueryOps.h.
Queries::EqualityQuery<int, const Target *, true>* RDKit::makePropQuery | ( | const std::string & | propname, |
const T & | val, | ||
const T & | tolerance = T() |
||
) |
Definition at line 1036 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::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_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.
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::Mol2BlockToMol | ( | const std::string & | molBlock, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA , |
||
bool | cleanupSubstructures = true |
||
) |
molBlock | - string containing the mol block |
sanitize | - toggles sanitization of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
variant | - the atom type definitions to use |
cleanupSubstructures | - toggles recognition and cleanup of common substructures |
Referenced by operator""_mol2().
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::Mol2DataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA , |
||
bool | cleanupSubstructures = true |
||
) |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::Mol2DataStreamToMol | ( | std::istream * | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA , |
||
bool | cleanupSubstructures = true |
||
) |
inStream | - stream containing the data |
sanitize | - toggles sanitization of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
variant | - the atom type definitions to use |
cleanupSubstructures | - toggles recognition and cleanup of common substructures |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::Mol2FileToMol | ( | const std::string & | fName, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA , |
||
bool | cleanupSubstructures = true |
||
) |
fName | - string containing the file name |
sanitize | - toggles sanitization of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
variant | - the atom type definitions to use |
cleanupSubstructures | - toggles recognition and cleanup of common substructures |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::MolBlockToMol | ( | const std::string & | molBlock, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
molBlock | - string containing the mol block |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
strictParsing | - if set, the parser is more lax about correctness of the contents. |
Referenced by operator""_ctab().
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::MolDataStreamToMol | ( | std::istream & | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::MolDataStreamToMol | ( | std::istream * | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
inStream | - stream containing the data |
line | - current line number (used for error reporting) |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
line | - current line number (used for error reporting) |
strictParsing | - if not set, the parser is more lax about correctness of the contents. |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::MolFileToMol | ( | const std::string & | fName, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
fName | - string containing the file name |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
strictParsing | - if set, the parser is more lax about correctness of the contents. |
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToCXSmiles | ( | const ROMol & | mol, |
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr , |
||
const std::vector< std::string > * | atomSymbols = nullptr , |
||
const std::vector< std::string > * | bondSymbols = nullptr , |
||
bool | doIsomericSmiles = true , |
||
bool | doKekule = false , |
||
int | rootedAtAtom = -1 , |
||
bool | canonical = true , |
||
bool | allBondsExplicit = false , |
||
bool | allHsExplicit = false |
||
) |
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. |
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.
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToSmarts | ( | const ROMol & | mol, |
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr , |
||
bool | doIsomericSmarts = true |
||
) |
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToSmiles | ( | const ROMol & | mol, |
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr , |
||
const std::vector< std::string > * | atomSymbols = nullptr , |
||
const std::vector< std::string > * | bondSymbols = nullptr , |
||
bool | doIsomericSmiles = true , |
||
bool | doKekule = false , |
||
int | rootedAtAtom = -1 , |
||
bool | canonical = true , |
||
bool | allBondsExplicit = false , |
||
bool | allHsExplicit = false |
||
) |
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.
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToCXSmiles | ( | const ROMol & | mol, |
bool | doIsomericSmiles = true , |
||
bool | doKekule = false , |
||
int | rootedAtAtom = -1 , |
||
bool | canonical = true , |
||
bool | allBondsExplicit = false , |
||
bool | allHsExplicit = false , |
||
bool | doRandom = false |
||
) |
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 atom. |
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 RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToMolBlock | ( | const ROMol & | mol, |
bool | includeStereo = true , |
||
int | confId = -1 , |
||
bool | kekulize = true , |
||
bool | forceV3000 = false |
||
) |
mol | - the molecule in question |
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) |
Referenced by MolToV3KMolBlock().
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToMolFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
bool | includeStereo = true , |
||
int | confId = -1 , |
||
bool | kekulize = true , |
||
bool | forceV3000 = false |
||
) |
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) |
Referenced by MolToV3KMolFile().
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 RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToSmarts | ( | const ROMol & | mol, |
bool | doIsomericSmarts = true |
||
) |
returns the SMARTS for a molecule
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToSmiles | ( | const ROMol & | mol, |
bool | doIsomericSmiles = true , |
||
bool | doKekule = false , |
||
int | rootedAtAtom = -1 , |
||
bool | canonical = true , |
||
bool | allBondsExplicit = false , |
||
bool | allHsExplicit = false , |
||
bool | doRandom = false |
||
) |
returns canonical SMILES 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 atom. |
Referenced by RDKit::RGroupData::add(), RDKit::CachedSmilesMolHolder::addMol(), RDKit::CachedTrustedSmilesMolHolder::addMol(), and RDKit::MolStandardize::TautomerEnumerator::pickCanonical().
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 |
||
) |
|
inline |
mol | - the molecule in question |
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 126 of file FileParsers.h.
References MolToMolBlock().
|
inline |
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 156 of file FileParsers.h.
References MolToMolFile().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToXYZBlock | ( | const ROMol & | mol, |
int | confId = -1 |
||
) |
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToXYZFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
int | confId = -1 |
||
) |
int RDKit::moveToFunction | ( | const FT_Vector * | to, |
void * | user | ||
) |
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 778 of file QueryOps.h.
bool RDKit::nullQueryFun | ( | T | ) |
Definition at line 782 of file QueryOps.h.
|
inline |
Definition at line 352 of file FileParsers.h.
References MolBlockToMol().
|
inline |
Definition at line 363 of file FileParsers.h.
References Mol2BlockToMol().
|
inline |
Definition at line 375 of file FileParsers.h.
References PDBBlockToMol().
|
inline |
Definition at line 125 of file SmilesParse.h.
References SmartsToMol().
|
inline |
Definition at line 114 of file SmilesParse.h.
References SmilesToMol().
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect RDKit::operator+ | ( | const DiscreteValueVect & | p1, |
const DiscreteValueVect & | p2 | ||
) |
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect RDKit::operator- | ( | const DiscreteValueVect & | p1, |
const DiscreteValueVect & | p2 | ||
) |
std::ostream& RDKit::operator<< | ( | std::ostream & | oss, |
const OrientType & | o | ||
) |
std::ostream& RDKit::operator<< | ( | std::ostream & | oss, |
const TextAlignType & | tat | ||
) |
std::ostream& RDKit::operator<< | ( | std::ostream & | oss, |
const TextDrawType & | tdt | ||
) |
|
inlinestatic |
Definition at line 134 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
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().
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::PDBBlockToMol | ( | const char * | str, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
Referenced by operator""_pdb().
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::PDBBlockToMol | ( | const std::string & | str, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::PDBDataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::PDBDataStreamToMol | ( | std::istream * | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::PDBFileToMol | ( | const std::string & | fname, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
RDKIT_FILEPARSERS_EXPORT INT_MAP_INT RDKit::pickBondsToWedge | ( | const ROMol & | mol | ) |
|
inline |
constructs a ChemicalReaction from the metadata in a PNG file See PNGStreamToChemicalReaction()
for more details
Definition at line 178 of file ReactionParser.h.
References PNGStreamToChemicalReaction().
|
inline |
returns the metadata (tEXt and zTXt chunks) from PNG data
Definition at line 43 of file PNGParser.h.
References PNGStreamToMetadata().
|
inline |
constructs an ROMol from the metadata in a PNG file. See PNGStreamToMol()
for more details.
Definition at line 112 of file PNGParser.h.
References PNGStreamToMol().
|
inline |
constructs a vector of ROMol from the metadata in a PNG file. See PNGStreamToMols()
for more details.
Definition at line 143 of file PNGParser.h.
References PNGStreamToMols().
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction* RDKit::PNGStreamToChemicalReaction | ( | std::istream & | pngStream | ) |
constructs a ChemicalReaction 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 PNGFileToChemicalReaction(), and PNGStringToChemicalReaction().
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().
|
inline |
constructs a ChemicalReaction from the metadata in a PNG string See PNGStreamToChemicalReaction()
for more details
Definition at line 172 of file ReactionParser.h.
References PNGStreamToChemicalReaction().
|
inline |
returns the metadata (tEXt and zTXt chunks) from PNG data
Definition at line 53 of file PNGParser.h.
References PNGStreamToMetadata().
|
inline |
constructs an ROMol from the metadata in a PNG string. See PNGStreamToMol()
for more details.
Definition at line 123 of file PNGParser.h.
References PNGStreamToMol().
|
inline |
constructs a vector of ROMol from the metadata in a PNG string. See PNGStreamToMols()
for more details.
Definition at line 154 of file PNGParser.h.
References PNGStreamToMols().
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 |
||
) |
|
inline |
Reads an integer from a char * in packed format and returns the result. The argument is advanced
Definition at line 209 of file StreamOps.h.
|
inlinestatic |
Definition at line 74 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAliphaticQuery().
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomAllBondProduct | ( | Atom const * | at | ) |
|
inlinestatic |
Definition at line 71 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAromaticQuery().
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomBondProduct | ( | Atom const * | at | ) |
|
inlinestatic |
Definition at line 77 of file QueryOps.h.
References RDKit::Atom::getDegree().
Referenced by makeAtomExplicitDegreeQuery().
|
inlinestatic |
Definition at line 121 of file QueryOps.h.
References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getNumExplicitHs().
Referenced by makeAtomExplicitValenceQuery().
|
inlinestatic |
Definition at line 163 of file QueryOps.h.
References RDKit::Atom::getFormalCharge().
Referenced by makeAtomFormalChargeQuery().
|
inlinestatic |
Definition at line 210 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getIsAromatic(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
|
inlinestatic |
Definition at line 175 of file QueryOps.h.
References RDKit::Atom::CHI_UNSPECIFIED, and RDKit::Atom::getChiralTag().
Referenced by makeAtomHasChiralTagQuery().
|
inlinestatic |
Definition at line 183 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomHasHeteroatomNbrsQuery().
|
inlinestatic |
Definition at line 115 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHasImplicitHQuery().
|
inlinestatic |
Definition at line 276 of file QueryOps.h.
References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), and RDKit::RingInfo::numBondRings().
Referenced by makeAtomHasRingBondQuery().
|
inlinestatic |
Definition at line 109 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHCountQuery().
|
inlinestatic |
D and T are not treated as heavy atoms here.
Definition at line 97 of file QueryOps.h.
References RDKit::ROMol::getAtomNeighbors(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomHeavyAtomDegreeQuery().
|
inlinestatic |
Definition at line 169 of file QueryOps.h.
References RDKit::Atom::getHybridization().
Referenced by makeAtomHybridizationQuery().
|
inlinestatic |
Definition at line 112 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomImplicitHCountQuery().
|
inlinestatic |
Definition at line 118 of file QueryOps.h.
References RDKit::Atom::getImplicitValence().
Referenced by makeAtomImplicitValenceQuery().
int RDKit::queryAtomIsInRingOfSize | ( | Atom const * | at | ) |
Definition at line 314 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isAtomInRingOfSize().
|
inlinestatic |
Definition at line 160 of file QueryOps.h.
References RDKit::Atom::getIsotope().
Referenced by makeAtomIsotopeQuery().
|
inlinestatic |
Definition at line 156 of file QueryOps.h.
References RDKit::Atom::getMass(), and massIntegerConversionFactor.
Referenced by makeAtomMassQuery().
|
inlinestatic |
Definition at line 291 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minAtomRingSize().
Referenced by makeAtomMinRingSizeQuery().
|
inlinestatic |
Definition at line 178 of file QueryOps.h.
References RDKit::common_properties::_ChiralityPossible, RDKit::Atom::CHI_UNSPECIFIED, RDKit::Atom::getChiralTag(), and RDKit::RDProps::hasProp().
Referenced by makeAtomMissingChiralTagQuery().
|
inlinestatic |
Definition at line 166 of file QueryOps.h.
References RDKit::Atom::getFormalCharge().
Referenced by makeAtomNegativeFormalChargeQuery().
|
inlinestatic |
D and T are treated as "non-hydrogen" here.
Definition at line 84 of file QueryOps.h.
References RDKit::ROMol::getAtomNeighbors(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomNonHydrogenDegreeQuery().
|
inlinestatic |
Definition at line 130 of file QueryOps.h.
References RDKit::Atom::getAtomicNum().
Referenced by makeAtomNumQuery().
|
inlinestatic |
Definition at line 224 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getIsAromatic(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomNumAliphaticHeteroatomNbrsQuery().
|
inlinestatic |
Definition at line 196 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomNumHeteroatomNbrsQuery().
|
inlinestatic |
Definition at line 172 of file QueryOps.h.
References RDKit::Atom::getNumRadicalElectrons().
Referenced by makeAtomNumRadicalElectronsQuery().
|
inlinestatic |
Definition at line 298 of file QueryOps.h.
References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), and RDKit::RingInfo::numBondRings().
Referenced by makeAtomRingBondCountQuery().
|
inlinestatic |
Definition at line 667 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by RDKit::AtomRingQuery::AtomRingQuery().
|
inlinestatic |
Definition at line 80 of file QueryOps.h.
References RDKit::Atom::getTotalDegree().
Referenced by makeAtomTotalDegreeQuery().
|
inlinestatic |
Definition at line 124 of file QueryOps.h.
References RDKit::Atom::getTotalValence().
Referenced by makeAtomTotalValenceQuery().
|
inlinestatic |
Definition at line 152 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::Atom::getIsAromatic(), and makeAtomType().
Referenced by makeAtomTypeQuery().
|
inlinestatic |
Definition at line 127 of file QueryOps.h.
References RDKit::Atom::getTotalDegree(), and RDKit::Atom::getTotalValence().
Referenced by makeAtomUnsaturatedQuery().
|
inlinestatic |
Definition at line 257 of file QueryOps.h.
References RDKit::Bond::getBondDir().
|
inlinestatic |
Definition at line 263 of file QueryOps.h.
References RDKit::Bond::getStereo(), and RDKit::Bond::STEREONONE.
int RDKit::queryBondIsInRingOfSize | ( | Bond const * | bond | ) |
Definition at line 322 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isBondInRingOfSize().
|
inlinestatic |
Definition at line 248 of file QueryOps.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.
|
inlinestatic |
Definition at line 252 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 294 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 245 of file QueryOps.h.
References RDKit::Bond::getBondType().
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Definition at line 270 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 273 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 260 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 288 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.
T RDKit::rdany_cast | ( | RDAny & | d | ) |
Definition at line 185 of file RDAny.h.
References RDKit::RDAny::m_value.
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect* RDKit::RDKFingerprintMol | ( | const ROMol & | mol, |
unsigned int | minPath = 1 , |
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unsigned int | maxPath = 7 , |
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unsigned int | fpSize = 2048 , |
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unsigned int | nBitsPerHash = 2 , |
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bool | useHs = true , |
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double | tgtDensity = 0.0 , |
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unsigned int | minSize = 128 , |
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bool | branchedPaths = true , |
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bool | useBondOrder = true , |
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std::vector< std::uint32_t > * | atomInvariants = nullptr , |
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const std::vector< std::uint32_t > * | fromAtoms = nullptr , |
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std::vector< std::vector< std::uint32_t >> * | atomBits = nullptr , |
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std::map< std::uint32_t, std::vector< std::vector< int >>> * | bitInfo = nullptr |
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) |
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 , |
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bool | removeHs = true |
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) |
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 , |
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bool | removeHs = true |
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) |
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().
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Definition at line 471 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::BoolTag, and RDKit::RDValue::otherBits.
Referenced by rdvalue_tostring().
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Definition at line 142 of file RDValue.h.
References RDKit::RDValue::ptrCast().
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Definition at line 134 of file RDValue.h.
References RDKit::RDValue::ptrCast().
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Definition at line 150 of file RDValue.h.
References RDKit::RDValue::ptrCast().
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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 446 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits.
Referenced by rdvalue_tostring().
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Definition at line 458 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::IntTag, and RDKit::RDValue::otherBits.
Referenced by rdvalue_tostring().
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Definition at line 52 of file RDValue.h.
References RDKit::RDValue::ptrCast().
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Definition at line 46 of file RDValue.h.
References RDKit::RDValue::ptrCast().
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Definition at line 464 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits, and RDKit::RDTypeTag::UnsignedIntTag.
Referenced by rdvalue_tostring().
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Definition at line 372 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::AnyTag.
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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 >(), and rdvalue_is< const double & >().
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Definition at line 171 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< unsigned int >(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
Referenced by RDKit::Dict::getVal(), and RDKit::Dict::getValIfPresent().
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 143 of file StreamOps.h.
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Definition at line 530 of file StreamOps.h.
References streamReadStringVec().
void RDKit::readRDValue | ( | std::istream & | ss, |
RDValue & | value | ||
) |
Definition at line 510 of file StreamOps.h.
References streamRead().
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Definition at line 523 of file StreamOps.h.
References streamRead().
void RDKit::readRDVecValue | ( | std::istream & | ss, |
RDValue & | value | ||
) |
Definition at line 517 of file StreamOps.h.
References streamReadVec().
RDKIT_CHEMREACTIONS_EXPORT ROMol* RDKit::reduceProductToSideChains | ( | const ROMOL_SPTR & | product, |
bool | addDummyAtoms = true |
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) |
Reduce the product generated by run_Reactants or run_Reactant to.
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_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.
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 , |
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bool | labelByIndex = false , |
||
bool | requireDummyMatch = false , |
||
bool | useChirality = false |
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) |
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 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::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.
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction* RDKit::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.
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction* RDKit::RxnFileToChemicalReaction | ( | const std::string & | fileName, |
bool | sanitize = false , |
||
bool | removeHs = false , |
||
bool | strictParsing = true |
||
) |
Parse a file in MDL rxn format into a ChemicalReaction.
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 |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction* RDKit::RxnSmartsToChemicalReaction | ( | const std::string & | text, |
std::map< std::string, std::string > * | replacements = nullptr , |
||
bool | useSmiles = false |
||
) |
Parse a string containing "Reaction SMARTS" into a ChemicalReaction.
Our definition of Reaction SMARTS is something that looks a lot like reaction SMILES, except that SMARTS queries are allowed on the reactant side and that atom-map numbers are required (at least for now)
text | the SMARTS to convert |
replacements | a string->string map of replacement strings. |
useSmiles | if set, the SMILES parser will be used instead of the SMARTS parserfor the individual components |
RDKIT_FILEPARSERS_EXPORT bool RDKit::SamePDBResidue | ( | AtomPDBResidueInfo * | p, |
AtomPDBResidueInfo * | q | ||
) |
double RDKit::score | ( | const std::vector< size_t > & | permutation, |
const std::vector< std::vector< RGroupMatch >> & | matches, | ||
const std::set< int > & | labels | ||
) |
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.
RDKIT_GRAPHMOL_EXPORT void RDKit::setAtomRLabel | ( | Atom * | atm, |
int | rlabel | ||
) |
Set the atom's MDL integer RLabel.
Referenced by RDKit::RGroupDecompData::setRlabel().
RDKIT_GRAPHMOL_EXPORT void RDKit::setAtomValue | ( | Atom * | atom, |
const std::string & | value | ||
) |
Set the atom's MDL atom value.
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.
bool RDKit::setStringDrawMode | ( | const std::string & | instring, |
TextDrawType & | draw_mode, | ||
size_t & | i | ||
) |
establishes whether to put string draw mode into super- or sub-script mode based on contents of instring from i onwards. Increments i appropriately
RDKIT_GRAPHMOL_EXPORT void RDKit::setSupplementalSmilesLabel | ( | Atom * | atom, |
const std::string & | label | ||
) |
Sets the supplemental label that will follow the atom when writing.
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_SMILESPARSE_EXPORT Atom* RDKit::SmartsToAtom | ( | const std::string & | sma | ) |
RDKIT_SMILESPARSE_EXPORT Bond* RDKit::SmartsToBond | ( | const std::string & | sma | ) |
RDKIT_SMILESPARSE_EXPORT RWMol* RDKit::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.
sma | the SMARTS to convert |
debugParse | toggles verbose debugging information from the parser |
mergeHs | toggles merging H atoms in the SMARTS into neighboring atoms |
replacements | a string->string map of replacement strings. |
Referenced by operator""_smarts().
RDKIT_SMILESPARSE_EXPORT Atom* RDKit::SmilesToAtom | ( | const std::string & | smi | ) |
RDKIT_SMILESPARSE_EXPORT Bond* RDKit::SmilesToBond | ( | const std::string & | smi | ) |
RDKIT_SMILESPARSE_EXPORT RWMol* RDKit::SmilesToMol | ( | const std::string & | smi, |
const SmilesParserParams & | params | ||
) |
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Construct a molecule from a SMILES string.
smi | the SMILES to convert |
debugParse | toggles verbose debugging information from the parser |
sanitize | toggles H removal and sanitization of the molecule |
replacements | a string->string map of replacement strings. See below for more information about replacements. |
The optional replacements map can be used to do string substitution of abbreviations in the input SMILES. The set of substitutions is repeatedly looped through until the string no longer changes. It is the responsibility of the caller to make sure that substitutions results in legal and sensible SMILES.
Examples of substitutions:
Definition at line 68 of file SmilesParse.h.
References RDKit::SmilesParserParams::debugParse, RDKit::SmilesParserParams::removeHs, RDKit::SmilesParserParams::replacements, RDKit::SmilesParserParams::sanitize, and SmilesToMol().
RDKIT_FILEPARSERS_EXPORT void RDKit::StandardPDBResidueBondOrders | ( | RWMol * | mol | ) |
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Definition at line 290 of file StreamOps.h.
References RDUNUSED_PARAM.
void RDKit::streamRead | ( | std::istream & | ss, |
T & | loc | ||
) |
does a binary read of an object from a stream
Definition at line 274 of file StreamOps.h.
Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream(), RDKit::DataStructsExplicitBitVecPropHandler::read(), readRDValue(), readRDValueString(), streamRead(), streamReadStringVec(), and streamReadVec().
void RDKit::streamRead | ( | std::istream & | ss, |
T & | obj, | ||
int | version | ||
) |
special case for string
Definition at line 285 of file StreamOps.h.
References RDUNUSED_PARAM, and streamRead().
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Definition at line 537 of file StreamOps.h.
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Definition at line 606 of file StreamOps.h.
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Definition at line 315 of file StreamOps.h.
References streamRead().
Referenced by readRDStringVecValue().
void RDKit::streamReadVec | ( | std::istream & | ss, |
T & | val | ||
) |
Definition at line 307 of file StreamOps.h.
References streamRead().
Referenced by readRDVecValue().
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special case for string
Definition at line 260 of file StreamOps.h.
void RDKit::streamWrite | ( | std::ostream & | ss, |
const T & | val | ||
) |
does a binary write of an object to a stream
Definition at line 254 of file StreamOps.h.
Referenced by streamWriteVec(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream(), RDKit::SparseIntVect< IndexType >::toString(), and RDKit::DataStructsExplicitBitVecPropHandler::write().
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Definition at line 399 of file StreamOps.h.
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Definition at line 471 of file StreamOps.h.
void RDKit::streamWriteVec | ( | std::ostream & | ss, |
const T & | val | ||
) |
Definition at line 267 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 |
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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() |
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RDKIT_SUBSTRUCTMATCH_EXPORT std::vector<MatchVectType> RDKit::SubstructMatch | ( | const MolBundle & | bundle, |
const ROMol & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() |
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RDKIT_SUBSTRUCTMATCH_EXPORT std::vector<MatchVectType> RDKit::SubstructMatch | ( | const ROMol & | mol, |
const MolBundle & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() |
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RDKIT_SUBSTRUCTMATCH_EXPORT std::vector<MatchVectType> RDKit::SubstructMatch | ( | const ROMol & | mol, |
const ROMol & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() |
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) |
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().
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() |
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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 188 of file SubstructMatch.h.
References RDKit::SubstructMatchParameters::maxMatches, RDKit::SubstructMatchParameters::numThreads, RDKit::SubstructMatchParameters::recursionPossible, SubstructMatch(), RDKit::SubstructMatchParameters::uniquify, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.
bool RDKit::SubstructMatch | ( | T1 & | mol, |
const T2 & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
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bool | useChirality = false , |
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bool | useQueryQueryMatches = false |
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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 105 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 , |
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bool | recursionPossible = true , |
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bool | useChirality = false , |
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bool | useQueryQueryMatches = false , |
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unsigned int | maxMatches = 1000 , |
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int | numThreads = 1 |
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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 145 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.
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Definition at line 44 of file StreamOps.h.
double RDKit::TanimotoSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
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double | bounds = 0.0 |
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Definition at line 547 of file SparseIntVect.h.
References TverskySimilarity().
Referenced by RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >::Match().
RDKIT_SUBSTRUCTMATCH_EXPORT double RDKit::toPrime | ( | const MatchVectType & | v | ) |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::TPLDataStreamToMol | ( | std::istream * | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
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bool | skipFirstConf = false |
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translate TPL data (BioCad format) into a multi-conf molecule
inStream | the stream from which to read |
line | used to track the line number of errors |
sanitize | toggles sanitization and stereochemistry perception of the molecule |
skipFirstConf | according to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set. |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::TPLFileToMol | ( | const std::string & | fName, |
bool | sanitize = true , |
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bool | skipFirstConf = false |
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construct a multi-conf molecule from a TPL (BioCad format) file
fName | the name of the file from which to read |
sanitize | toggles sanitization and stereochemistry perception of the molecule |
skipFirstConf | according to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set. |
double RDKit::TverskySimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
double | a, | ||
double | b, | ||
bool | returnDistance = false , |
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double | bounds = 0.0 |
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Definition at line 520 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 |
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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::updateFromSequence | ( | SparseIntVect< IndexType > & | vect, |
const SequenceType & | seq | ||
) |
Definition at line 413 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getVal(), and RDKit::SparseIntVect< IndexType >::setVal().
RDKIT_CHEMREACTIONS_EXPORT void RDKit::updateProductsStereochem | ( | ChemicalReaction * | rxn | ) |
std::string RDKit::vectToString | ( | RDValue | val | ) |
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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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.
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Definition at line 23 of file MolWriters.h.
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Referenced by RDKit::RGroupDecompData::relabelRGroup().
const unsigned int RDKit::EMPTY_CORE_LABEL = -100000 |
Definition at line 20 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 112 of file Fingerprints.h.
const int RDKit::massIntegerConversionFactor = 1000 |
Definition at line 155 of file QueryOps.h.
Referenced by makeAtomMassQuery(), and queryAtomMass().
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const unsigned int RDKit::maxFingerprintLayers = 10 |
Definition at line 111 of file Fingerprints.h.
const int RDKit::MOLFILE_MAXLINE = 256 |
Definition at line 25 of file FileParsers.h.
const int RDKit::NUM_PRIMES_AVAIL = 1000 |
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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::string RDKit::RDKFingerprintMolVersion = "2.0.0" |
Definition at line 62 of file Fingerprints.h.
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Referenced by RDKit::RCore::findIndicesWithRLabel(), and RDKit::RGroupData::getNumBondsToRlabels().
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Referenced by RDKit::RGroupDecompData::relabelRGroup().
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const unsigned int RDKit::substructLayers = 0x07 |
Definition at line 113 of file Fingerprints.h.