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RDKit
Open-source cheminformatics and machine learning.
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Std stuff. More...
Namespaces | |
AtomPair | |
AtomPairs | |
Canon | |
common_properties | |
constants | |
Descriptors | |
detail | |
DGeomHelpers | |
DTags | |
EnumerationStrategyPickler | |
EnumerationTypes | |
FileParserUtils | |
FilterMatchOps | |
FMCS | |
Local | |
MACCSFingerprints | |
MMFF | |
MMPA | |
MolAlign | |
MolDraw2D_detail | |
MolDraw2DUtils | |
MolFragmenter | |
MolHash | |
MolInterchange | |
MolOps | |
Groups a variety of molecular query and transformation operations. | |
MolShapes | |
MolStandardize | |
MorganFingerprint | |
MorganFingerprints | |
PicklerOps | |
RDKitFP | |
RDKitFPUtils | |
RDTypeTag | |
ReactionRunnerUtils | |
ReducedGraphs | |
RxnOps | |
SLNParse | |
SmartsWrite | |
SmilesWrite | |
StructureCheck | |
Subgraphs | |
TopologicalTorsion | |
UFF | |
Utils | |
Classes | |
struct | AdditionalOutput |
class | AromaticAtomIterator_ |
Iterate over aromatic atoms, this is bidirectional. More... | |
class | Atom |
The class for representing atoms. More... | |
class | AtomEnvironment |
abstract base class that holds atom-environments that will be hashed to generate the fingerprint More... | |
class | AtomEnvironmentGenerator |
abstract base class that generates atom-environments from a molecule More... | |
class | atomicData |
class | AtomInvariantsGenerator |
abstract base class for atom invariants generators More... | |
class | AtomIterator_ |
A general random access iterator. More... | |
class | AtomMonomerInfo |
The abstract base class for atom-level monomer info. More... | |
class | AtomPDBResidueInfo |
Captures atom-level information about peptide residues. More... | |
class | AtomRingQuery |
class | BadFileException |
used by various file parsing classes to indicate a bad file More... | |
class | Bond |
class for representing a bond More... | |
class | BondInvariantsGenerator |
abstract base class for bond invariants generators More... | |
class | BondIterator_ |
iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
class | CachedMolHolder |
Concrete class that holds binary cached molecules in memory. More... | |
class | CachedSmilesMolHolder |
Concrete class that holds smiles strings in memory. More... | |
class | CachedTrustedSmilesMolHolder |
Concrete class that holds trusted smiles strings in memory. More... | |
class | CartesianProductStrategy |
This is a class for enumerating reagents using Cartesian Products of. More... | |
struct | charptr_functor |
functor for comparing two strings More... | |
class | ChemicalReaction |
This is a class for storing and applying general chemical reactions. More... | |
class | ChemicalReactionException |
used to indicate an error in the chemical reaction engine More... | |
class | ChemicalReactionParserException |
used to indicate an error in parsing reaction data More... | |
class | Conformer |
The class for representing 2D or 3D conformation of a molecule. More... | |
class | ConformerException |
used to indicate errors from incorrect confomer access More... | |
class | ConstBondIterator_ |
const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
struct | CXXAtomIterator |
struct | CXXBondIterator |
class | Dict |
The Dict class can be used to store objects of arbitrary type keyed by strings . More... | |
class | DiscreteDistMat |
class | DiscreteValueVect |
a class for efficiently storing vectors of discrete values More... | |
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... | |
struct | EnumerationParams |
This is a class for providing enumeration options that control. More... | |
class | EnumerationStrategyBase |
class | EnumerationStrategyException |
class for flagging enumeration strategy errors More... | |
class | EvenSamplePairsStrategy |
EvenSamplePairsStrategy. More... | |
class | ExclusionList |
class | FeatureFileParseException |
class used to indicate errors in parsing feature definition files. More... | |
class | FileParseException |
used by various file parsing classes to indicate a parse error More... | |
class | FilterCatalog |
class | FilterCatalogEntry |
class | FilterCatalogParams |
struct | FilterData_t |
class | FilterHierarchyMatcher |
struct | FilterMatch |
Holds the atomPairs matched by the underlying matcher. More... | |
class | FilterMatcherBase |
struct | FilterProperty_t |
class | FingerprintArguments |
Abstract base class that holds molecule independent arguments that are common amongst all fingerprint types and classes inherited from this would hold fingerprint type specific arguments. More... | |
class | FingerprintGenerator |
class that generates same fingerprint style for different output formats More... | |
class | ForwardSDMolSupplier |
class | FPBReader |
class for reading and searching FPB files More... | |
class | FPHolderBase |
Base FPI for the fingerprinter used to rule out impossible matches. More... | |
class | FragCatalogEntry |
class | FragCatGenerator |
class | FragCatParams |
container for user parameters used to create a fragment catalog More... | |
class | FragFPGenerator |
class | GasteigerParams |
class | HasPropQuery |
class | HasPropWithValueQuery |
class | HasPropWithValueQuery< TargetPtr, std::string > |
class | HeteroatomIterator_ |
Iterate over heteroatoms, this is bidirectional. More... | |
struct | larger_of |
functor for returning the larger of two values More... | |
struct | ltDouble |
functor to compare two doubles with a tolerance More... | |
class | MatchingAtomIterator_ |
Iterate over atoms matching a query function. This is bidirectional. More... | |
struct | MCSAtomCompareParameters |
struct | MCSBondCompareParameters |
struct | MCSParameters |
struct | MCSProgressData |
struct | MCSResult |
class | MolBundle |
class | MolCatalogEntry |
This class is used to store ROMol objects in a MolCatalog. More... | |
class | MolCatalogParams |
container for user parameters used to create a mol catalog More... | |
class | MolChemicalFeature |
class | MolChemicalFeatureDef |
class | MolChemicalFeatureFactory |
The class for finding chemical features in molecules. More... | |
class | MolDraw2D |
MolDraw2D is the base class for doing 2D renderings of molecules. More... | |
class | MolDraw2DCairo |
class | MolDraw2DQt |
class | MolDraw2DSVG |
class | MolDraw2Dwx |
struct | MolDrawOptions |
class | MolHolder |
Concrete class that holds molecules in memory. More... | |
class | MolHolderBase |
Base class API for holding molecules to substructure search. More... | |
class | MolPickler |
handles pickling (serializing) molecules More... | |
class | MolPicklerException |
used to indicate exceptions whilst pickling (serializing) molecules More... | |
class | MolSanitizeException |
class for flagging sanitization errors More... | |
class | MolSupplier |
class | MolWriter |
class | MultiFPBReader |
class for reading and searching multiple FPB files More... | |
class | MultiMolDraw2D |
class | PatternHolder |
Uses the pattern fingerprinter to rule out matches. More... | |
class | PDBMolSupplier |
lazy file parser for PDB files More... | |
class | PDBWriter |
class | PeriodicTable |
singleton class for retrieving information about atoms More... | |
class | QueryAtom |
Class for storing atomic queries. More... | |
class | QueryAtomIterator_ |
Iterate over atoms matching a query. This is bidirectional. More... | |
class | QueryBond |
Class for storing Bond queries. More... | |
class | RandomSampleAllBBsStrategy |
This is a class for randomly enumerating reagents that ensures all reagents. More... | |
class | RandomSampleStrategy |
This is a class for fully randomly sampling reagents. More... | |
struct | RDAny |
class | RDProps |
struct | RDValue |
struct | ReactionFingerprintParams |
class | ReactionPickler |
handles pickling (serializing) reactions More... | |
class | ReactionPicklerException |
used to indicate exceptions whilst pickling (serializing) reactions More... | |
class | RecursiveStructureQuery |
allows use of recursive structure queries (e.g. recursive SMARTS) More... | |
class | ResonanceMolSupplier |
class | RGroupDecomposition |
struct | RGroupDecompositionParameters |
class | RingInfo |
A class to store information about a molecule's rings. More... | |
class | ROMol |
class | RWMol |
RWMol is a molecule class that is intended to be edited. More... | |
class | RxnSanitizeException |
class for flagging sanitization errors More... | |
class | SDMolSupplier |
class | SDWriter |
class | SLNParseException |
class | SmartsMatcher |
class | SmilesMolSupplier |
lazy file parser for Smiles tables More... | |
class | SmilesParseException |
struct | SmilesParserParams |
class | SmilesWriter |
class | Snapshot |
class | SparseIntVect |
a class for efficiently storing sparse vectors of ints More... | |
class | StereoGroup |
class | SubstructLibrary |
Substructure Search a library of molecules. More... | |
class | TDTMolSupplier |
lazy file parser for TDT files More... | |
class | TDTWriter |
class | Trajectory |
class | UnimplementedFPException |
used to indicate errors for unimplemented fp types in convenience functions More... | |
Typedefs | |
typedef boost::shared_ptr< Conformer > | CONFORMER_SPTR |
typedef boost::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 short unsigned c1[], const short unsigned 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 boost::tuple< float, float, float > | DrawColour |
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< boost::uint8_t > | ConjFP |
typedef boost::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::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 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 |
Enumerations | |
enum | FingerprintType { AtomPairFP = 1, TopologicalTorsion, MorganFP, RDKitFP, PatternFP } |
enum | ReactionMoleculeType { Reactant, Product, Agent } |
enum | Mol2Type { CORINA = 0 } |
enum | FPType { FPType::AtomPairFP, FPType::MorganFP, FPType::RDKitFP, FPType::TopologicalTorsionFP } |
enum | AtomComparator { AtomCompareAny, AtomCompareElements, AtomCompareIsotopes } |
enum | BondComparator { BondCompareAny, BondCompareOrder, BondCompareOrderExact } |
enum | RGroupLabels { IsotopeLabels = 0x01, AtomMapLabels = 0x02, AtomIndexLabels = 0x04, RelabelDuplicateLabels = 0x08, AutoDetect = 0x0F } |
enum | RGroupMatching { Greedy = 0x01, GreedyChunks = 0x02, Exhaustive = 0x04 } |
enum | RGroupLabelling { AtomMap = 0x01, Isotope = 0x02, MDLRGroup = 0x04 } |
enum | RGroupCoreAlignment { None = 0x0, MCS = 0x01 } |
enum | StereoGroupType { StereoGroupType::STEREO_ABSOLUTE = 0, StereoGroupType::STEREO_OR = 1, StereoGroupType::STEREO_AND = 2 } |
enum | EEndian { LITTLE_ENDIAN_ORDER, BIG_ENDIAN_ORDER } |
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_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) |
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) |
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) |
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=NULL) |
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< boost::uint32_t > * | DifferenceFingerprintChemReaction (const ChemicalReaction &rxn, const ReactionFingerprintParams ¶ms=DefaultDifferenceFPParams) |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * | RxnBlockToChemicalReaction (const std::string &rxnBlock) |
Parse a text block in MDL rxn format into a ChemicalReaction. More... | |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * | RxnFileToChemicalReaction (const std::string &fileName) |
Parse a file in MDL rxn format into a ChemicalReaction. More... | |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * | RxnDataStreamToChemicalReaction (std::istream &rxnStream, unsigned int &line) |
Parse a text stream in MDL rxn format into a ChemicalReaction. More... | |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * | RxnSmartsToChemicalReaction (const std::string &text, std::map< std::string, std::string > *replacements=0, bool useSmiles=false) |
Parse a string containing "Reaction SMARTS" into a ChemicalReaction. More... | |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * | RxnMolToChemicalReaction (const ROMol &mol) |
Parse a ROMol into a ChemicalReaction, RXN role must be set before. 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... | |
RDKIT_CHEMREACTIONS_EXPORT std::string | ChemicalReactionToRxnBlock (const ChemicalReaction &rxn, bool separateAgents=false) |
returns an RXN block for a reaction More... | |
RDKIT_CHEMREACTIONS_EXPORT ROMol * | ChemicalReactionToRxnMol (const ChemicalReaction &rxn) |
returns a ROMol with RXN roles used to describe the reaction More... | |
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=NULL) |
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="\, 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="\, const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1) |
RDKIT_CHEMTRANSFORMS_EXPORT void | parseQueryDefText (const std::string &queryDefText, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\, 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) |
RDKIT_FILEPARSERS_EXPORT void | MolToMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false) |
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) |
RDKIT_FILEPARSERS_EXPORT void | DetectAtomStereoChemistry (RWMol &mol, const Conformer *conf) |
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) |
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) |
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) |
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) |
RDKIT_FILEPARSERS_EXPORT RWMol * | HELMToMol (const char *helm, bool sanitize=true) |
RDKIT_FILEPARSERS_EXPORT RWMol * | HELMToMol (const std::string &helm, bool sanitize=true) |
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 () |
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=0) |
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< boost::uint32_t > *atomInvariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, std::vector< std::vector< boost::uint32_t > > *atomBits=0, std::map< boost::uint32_t, std::vector< std::vector< int > > > *bitInfo=0) |
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=0, ExplicitBitVect *setOnlyBits=0, bool branchedPaths=true, const std::vector< boost::uint32_t > *fromAtoms=0) |
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=0, ExplicitBitVect *setOnlyBits=0) |
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< boost::uint32_t > *atomInvariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, std::vector< std::vector< boost::uint64_t > > *atomBits=0, std::map< boost::uint64_t, std::vector< std::vector< int > > > *bitInfo=0) |
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 | 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 | 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=0) |
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=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 short unsigned c1[], const short unsigned 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... | |
void | assignDefaultPalette (ColourPalette &palette) |
void | assignBWPalette (ColourPalette &palette) |
RDKIT_PARTIALCHARGES_EXPORT void | computeGasteigerCharges (const ROMol *mol, int nIter=12, bool throwOnParamFailure=false) |
RDKIT_PARTIALCHARGES_EXPORT void | computeGasteigerCharges (const ROMol &mol, int nIter=12, bool throwOnParamFailure=false) |
RDKIT_PARTIALCHARGES_EXPORT void | computeGasteigerCharges (const ROMol &mol, std::vector< double > &charges, int nIter=12, bool throwOnParamFailure=false) |
std::string | describeQuery (const Atom *atom) |
std::string | describeQuery (const Bond *bond) |
static int | queryAtomAromatic (Atom const *at) |
static int | queryAtomAliphatic (Atom const *at) |
static int | queryAtomExplicitDegree (Atom const *at) |
static int | queryAtomTotalDegree (Atom const *at) |
static int | queryAtomNonHydrogenDegree (Atom const *at) |
static int | queryAtomHeavyAtomDegree (Atom const *at) |
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 | 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 | 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) |
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) |
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) |
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) |
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) |
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) |
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) |
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) |
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) |
template<class T > | |
T * | makeAtomHasImplicitHQuery (const std::string &descr) |
returns a Query for matching ring atoms More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHasImplicitHQuery () |
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) |
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 () |
template<class T > | |
T * | makeAtomAliphaticQuery (const std::string &descr) |
returns a Query for matching aliphatic atoms More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomAliphaticQuery () |
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) |
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) |
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) |
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) |
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) |
template<class T > | |
T * | makeAtomHasChiralTagQuery (const std::string &descr) |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomHasChiralTagQuery () |
template<class T > | |
T * | makeAtomMissingChiralTagQuery (const std::string &descr) |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomMissingChiralTagQuery () |
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 () |
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) |
returns a Query for matching atoms in a particular number of rings More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAtomInNRingsQuery (int what) |
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) |
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) |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * | makeAAtomQuery () |
returns a Query for matching generic A atoms (heavy atoms) More... | |
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_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 () |
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) |
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 () |
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) |
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 () |
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 * | 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()) |
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=0, 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=0, const RGroupDecompositionParameters &options=RGroupDecompositionParameters()) |
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 (ROMol &mol, bool doIsomericSmarts=true) |
returns the SMARTS for a molecule More... | |
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=0) |
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=0) |
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::string | MolFragmentToSmiles (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=0, const std::vector< std::string > *atomSymbols=0, const std::vector< std::string > *bondSymbols=0, 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_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 bool | SubstructMatch (const ROMol &mol, const ROMol &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
Find a substructure match for a query in a molecule. More... | |
RDKIT_SUBSTRUCTMATCH_EXPORT bool | SubstructMatch (ResonanceMolSupplier &resMolSuppl, const ROMol &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
Find a substructure match for a query in a ResonanceMolSupplier object. More... | |
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int | SubstructMatch (const ROMol &mol, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000) |
Find all substructure matches for a query in a molecule. More... | |
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int | SubstructMatch (ResonanceMolSupplier &resMolSuppl, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify=false, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000, int numThreads=1) |
Find all substructure matches for a query in a ResonanceMolSupplier object. More... | |
RDKIT_SUBSTRUCTMATCH_EXPORT bool | SubstructMatch (const MolBundle &bundle, const ROMol &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool | SubstructMatch (const ROMol &bundle, const MolBundle &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool | SubstructMatch (const MolBundle &bundle, const MolBundle &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int | SubstructMatch (const MolBundle &mol, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000) |
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int | SubstructMatch (const MolBundle &mol, const MolBundle &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000) |
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int | SubstructMatch (const ROMol &mol, const MolBundle &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000) |
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, bool useQueryQueryMatches=false) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool | chiralAtomCompat (const Atom *a1, const Atom *a2) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool | bondCompat (const Bond *b1, const Bond *b2, bool useQueryQueryMatches=false) |
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<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 (RDValue v) |
template<> | |
bool | rdvalue_is< double > (RDValue v) |
template<> | |
bool | rdvalue_is< const double & > (RDValue v) |
template<class T > | |
T | rdvalue_cast (RDValue v) |
template<> | |
double | rdvalue_cast< double > (RDValue v) |
template<> | |
float | rdvalue_cast< float > (RDValue v) |
template<> | |
int | rdvalue_cast< int > (RDValue v) |
template<> | |
unsigned int | rdvalue_cast< unsigned int > (RDValue v) |
template<> | |
bool | rdvalue_cast< bool > (RDValue 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) |
bool | streamWriteProp (std::ostream &ss, const Dict::Pair &pair) |
bool | streamWriteProps (std::ostream &ss, const RDProps &props, bool savePrivate=false, bool saveComputed=false) |
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) |
unsigned int | streamReadProps (std::istream &ss, RDProps &props) |
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=NULL) |
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 | round (double v) |
rounds a value to the closest int 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) |
typedef Queries::AndQuery<int, Atom const *, true> RDKit::ATOM_AND_QUERY |
Definition at line 31 of file QueryOps.h.
typedef Queries::Query<bool, Atom const *, true> RDKit::ATOM_BOOL_QUERY |
Definition at line 28 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_EQUALS_QUERY |
Definition at line 40 of file QueryOps.h.
typedef Queries::GreaterQuery<int, Atom const *, true> RDKit::ATOM_GREATER_QUERY |
Definition at line 43 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int, Atom const *, true> RDKit::ATOM_GREATEREQUAL_QUERY |
Definition at line 47 of file QueryOps.h.
typedef Queries::LessQuery<int, Atom const *, true> RDKit::ATOM_LESS_QUERY |
Definition at line 51 of file QueryOps.h.
typedef Queries::LessEqualQuery<int, Atom const *, true> RDKit::ATOM_LESSEQUAL_QUERY |
Definition at line 54 of file QueryOps.h.
typedef Queries::Query<int, Atom const *, true> RDKit::ATOM_NULL_QUERY |
Definition at line 64 of file QueryOps.h.
typedef Queries::OrQuery<int, Atom const *, true> RDKit::ATOM_OR_QUERY |
Definition at line 34 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_PROP_QUERY |
Definition at line 782 of file QueryOps.h.
typedef Queries::RangeQuery<int, Atom const *, true> RDKit::ATOM_RANGE_QUERY |
Definition at line 57 of file QueryOps.h.
typedef Queries::SetQuery<int, Atom const *, true> RDKit::ATOM_SET_QUERY |
Definition at line 60 of file QueryOps.h.
typedef Queries::XOrQuery<int, Atom const *, true> RDKit::ATOM_XOR_QUERY |
Definition at line 37 of file QueryOps.h.
typedef boost::uint32_t RDKit::atomindex_t |
typedef Queries::AndQuery<int, Bond const *, true> RDKit::BOND_AND_QUERY |
Definition at line 32 of file QueryOps.h.
typedef Queries::Query<bool, Bond const *, true> RDKit::BOND_BOOL_QUERY |
Definition at line 29 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_EQUALS_QUERY |
Definition at line 41 of file QueryOps.h.
typedef Queries::GreaterQuery<int, Bond const *, true> RDKit::BOND_GREATER_QUERY |
Definition at line 44 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int, Bond const *, true> RDKit::BOND_GREATEREQUAL_QUERY |
Definition at line 49 of file QueryOps.h.
typedef Queries::LessQuery<int, Bond const *, true> RDKit::BOND_LESS_QUERY |
Definition at line 52 of file QueryOps.h.
typedef Queries::LessEqualQuery<int, Bond const *, true> RDKit::BOND_LESSEQUAL_QUERY |
Definition at line 55 of file QueryOps.h.
typedef Queries::Query<int, Bond const *, true> RDKit::BOND_NULL_QUERY |
Definition at line 63 of file QueryOps.h.
typedef Queries::OrQuery<int, Bond const *, true> RDKit::BOND_OR_QUERY |
Definition at line 35 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_PROP_QUERY |
Definition at line 783 of file QueryOps.h.
typedef Queries::RangeQuery<int, Bond const *, true> RDKit::BOND_RANGE_QUERY |
Definition at line 58 of file QueryOps.h.
typedef Queries::SetQuery<int, Bond const *, true> RDKit::BOND_SET_QUERY |
Definition at line 61 of file QueryOps.h.
typedef Queries::XOrQuery<int, Bond const *, true> RDKit::BOND_XOR_QUERY |
Definition at line 38 of file QueryOps.h.
typedef boost::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 40 of file MolDraw2D.h.
typedef boost::shared_ptr<Conformer> RDKit::CONFORMER_SPTR |
Definition at line 136 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 26 of file Resonance.h.
typedef std::vector<boost::uint8_t> RDKit::ConjFP |
Definition at line 31 of file Resonance.h.
typedef Atom const* RDKit::ConstAtomPtr |
Definition at line 634 of file QueryOps.h.
typedef Bond const* RDKit::ConstBondPtr |
Definition at line 745 of file QueryOps.h.
typedef std::vector<unsigned int> RDKit::DashPattern |
Definition at line 41 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 |
typedef boost::tuple<float, float, float> RDKit::DrawColour |
Definition at line 39 of file MolDraw2D.h.
Definition at line 110 of file FilterCatalog.h.
typedef boost::shared_ptr<MolChemicalFeature> RDKit::FeatSPtr |
Definition at line 19 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 20 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 short unsigned c1[], const short unsigned 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 20 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 37 of file Subgraphs.h.
typedef RDValue RDKit::RDValue_cast_t |
Definition at line 360 of file RDValue-doublemagic.h.
typedef std::vector<boost::shared_ptr<ROMol> > RDKit::RGroupColumn |
Definition at line 88 of file RGroupDecomp.h.
typedef std::map<std::string, RGroupColumn> RDKit::RGroupColumns |
Definition at line 91 of file RGroupDecomp.h.
typedef std::map<std::string, boost::shared_ptr<ROMol> > RDKit::RGroupRow |
Definition at line 87 of file RGroupDecomp.h.
typedef std::vector<RGroupRow> RDKit::RGroupRows |
Definition at line 90 of file RGroupDecomp.h.
typedef boost::minstd_rand RDKit::rng_type |
typedef boost::shared_ptr< ROMol > RDKit::ROMOL_SPTR |
Definition at line 22 of file ChemTransforms.h.
typedef boost::shared_ptr<RWMol> RDKit::RWMOL_SPTR |
typedef std::vector< RWMOL_SPTR > RDKit::RWMOL_SPTR_VECT |
Definition at line 31 of file FileParsers.h.
typedef std::vector<Snapshot> RDKit::SnapshotVect |
Definition at line 19 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 295 of file FingerprintGenerator.h.
enum RDKit::Mol2Type |
Enumerator | |
---|---|
CORINA |
Definition at line 174 of file FileParsers.h.
Enumerator | |
---|---|
Reactant | |
Product | |
Agent |
Definition at line 41 of file ReactionUtils.h.
Enumerator | |
---|---|
None | |
MCS |
Definition at line 48 of file RGroupDecomp.h.
Enumerator | |
---|---|
AtomMap | |
Isotope | |
MDLRGroup |
Definition at line 42 of file RGroupDecomp.h.
enum RDKit::RGroupLabels |
Compute the isomporphic degenerative points in the molecule. These are points that are symmetrically equivalent.
mol | Molecule to compute the degenerative points |
Enumerator | |
---|---|
IsotopeLabels | |
AtomMapLabels | |
AtomIndexLabels | |
RelabelDuplicateLabels | |
AutoDetect |
Definition at line 28 of file RGroupDecomp.h.
Enumerator | |
---|---|
Greedy | |
GreedyChunks | |
Exhaustive |
Definition at line 36 of file RGroupDecomp.h.
|
strong |
Enumerator | |
---|---|
STEREO_ABSOLUTE | |
STEREO_OR | |
STEREO_AND |
Definition at line 28 of file StereoGroup.h.
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 = NULL |
||
) |
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 = NULL |
||
) |
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
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
|
inline |
Packs an integer and outputs it to a stream.
Definition at line 98 of file StreamOps.h.
References CHECK_INVARIANT.
|
inline |
Definition at line 58 of file MolDraw2D.h.
|
inline |
Definition at line 43 of file MolDraw2D.h.
Referenced by RDKit::MolDrawOptions::MolDrawOptions().
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::atomCompat | ( | const Atom * | a1, |
const Atom * | a2, | ||
bool | useQueryQueryMatches = false |
||
) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::bondCompat | ( | const Bond * | b1, |
const Bond * | b2, | ||
bool | useQueryQueryMatches = false |
||
) |
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory* RDKit::buildFeatureFactory | ( | std::istream & | inStream | ) |
constructs a MolChemicalFeatureFactory from the data in a stream
Referenced by RDKit::MolChemicalFeatureFactory::addFeatureDef().
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory* RDKit::buildFeatureFactory | ( | const std::string & | featureData | ) |
constructs a MolChemicalFeatureFactory from the data in a string
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 seperate block, otherwise they were included in the reactants block (default) |
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RDKIT_CHEMREACTIONS_EXPORT ROMol* RDKit::ChemicalReactionToRxnMol | ( | const ChemicalReaction & | rxn | ) |
returns a ROMol with RXN roles used to describe the reaction
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmarts | ( | const ChemicalReaction & | rxn | ) |
returns the reaction SMARTS for a reaction
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmiles | ( | const ChemicalReaction & | rxn, |
bool | canonical = true |
||
) |
returns the reaction SMILES for a reaction
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::chiralAtomCompat | ( | const Atom * | a1, |
const Atom * | a2 | ||
) |
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 |
RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges | ( | const ROMol * | mol, |
int | nIter = 12 , |
||
bool | throwOnParamFailure = false |
||
) |
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_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 | ||
) |
Referenced by RDKit::DiscreteValueVect::getNumInts().
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 getSizesFromBBs(), RDKit::EnumerationStrategyBase::initialize(), and RDKit::EnumerationStrategyBase::internalInitialize().
RDKIT_FILEPARSERS_EXPORT void RDKit::ConnectTheDots | ( | RWMol * | mol, |
unsigned int | flags = 0 |
||
) |
Definition at line 290 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::RDValue::cleanup_rdvalue(), RDKit::Dict::Dict(), RDKit::RDAny::operator=(), RDKit::Dict::operator=(), RDKit::RDAny::RDAny(), and RDKit::Dict::update().
unsigned int RDKit::countSwapsToInterconvert | ( | const T & | ref, |
T | probe | ||
) |
Definition at line 54 of file utils.h.
References CHECK_INVARIANT, and PRECONDITION.
RDKIT_CHEMTRANSFORMS_EXPORT ROMol* RDKit::deleteSubstructs | ( | const ROMol & | mol, |
const ROMol & | query, | ||
bool | onlyFrags = false , |
||
bool | useChirality = false |
||
) |
Returns a copy of an ROMol with the atoms and bonds that match a pattern removed.
mol | the ROMol of interest |
query | the query ROMol |
onlyFrags | if this is set, atoms will only be removed if the entire fragment in which they are found is matched by the query. |
useChirality | - if set, match the coreQuery using chirality |
mol
with the matching atoms and bonds (if any) removed.
|
inline |
Definition at line 97 of file QueryAtom.h.
References RDKit::Atom::getQuery(), RDKit::Atom::hasQuery(), PRECONDITION, and RDKit::detail::qhelper().
|
inline |
Definition at line 108 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 | ||
) |
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, |
unsigned int | fromAtomIdx, | ||
const Conformer * | conf | ||
) |
RDKIT_FILEPARSERS_EXPORT Bond::BondDir RDKit::DetermineBondWedgeState | ( | const Bond * | bond, |
const INT_MAP_INT & | wedgeBonds, | ||
const Conformer * | conf | ||
) |
double RDKit::DiceSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
||
double | bounds = 0.0 |
||
) |
Definition at line 470 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getLength(), and RDKit::SparseIntVect< IndexType >::getTotalVal().
RDKIT_CHEMREACTIONS_EXPORT SparseIntVect<boost::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
|
inline |
Definition at line 69 of file StreamOps.h.
|
inline |
Definition at line 84 of file StreamOps.h.
|
inline |
Definition at line 88 of file StreamOps.h.
|
inline |
Definition at line 92 of file StreamOps.h.
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::EnumerateLibraryCanSerialize | ( | ) |
Referenced by RDKit::EnumerateLibrary::getReagents().
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 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 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 = 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 | ( | ) |
Referenced by RDKit::FilterCatalog::getNumEntries().
bool RDKit::FinalChiralityCheckFunction | ( | const short unsigned | c1[], |
const short unsigned | 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, |
const MCSParameters * | params = 0 |
||
) |
Referenced by RDKit::MCSResult::isCompleted().
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_P | ( | const std::vector< ROMOL_SPTR > & | mols, |
const char * | params_json | ||
) |
Referenced by RDKit::MCSResult::isCompleted().
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 193 of file RDAny.h.
References RDKit::RDValue::getTag(), RDKit::RDAny::m_value, rdany_cast(), and RDKit::RDTypeTag::StringTag.
boost::disable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdany | ( | const RDAny & | arg | ) |
Definition at line 214 of file RDAny.h.
References rdany_cast().
boost::enable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
Definition at line 230 of file RDValue.h.
References RDKit::RDValue::getTag(), rdvalue_cast(), and RDKit::RDTypeTag::StringTag.
boost::disable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
Definition at line 251 of file RDValue.h.
References rdvalue_cast().
RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomAlias | ( | const Atom * | atom | ) |
RDKIT_GRAPHMOL_EXPORT int RDKit::getAtomRLabel | ( | const Atom * | atm | ) |
|
inlinestatic |
Definition at line 136 of file QueryOps.h.
|
inlinestatic |
Definition at line 132 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 | ||
) |
Referenced by RDKit::UnimplementedFPException::~UnimplementedFPException().
RDKIT_FINGERPRINTS_EXPORT std::vector<SparseIntVect<std::uint32_t> *>* RDKit::getCountFPBulk | ( | const std::vector< const ROMol *> | molVector, |
FPType | fPType | ||
) |
Referenced by RDKit::UnimplementedFPException::~UnimplementedFPException().
DiscreteDistMat* RDKit::getDiscreteDistMat | ( | ) |
Referenced by RDKit::DiscreteDistMat::~DiscreteDistMat().
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 | ||
) |
RDKIT_FINGERPRINTS_EXPORT std::vector<ExplicitBitVect *>* RDKit::getFPBulk | ( | const std::vector< const ROMol *> | molVector, |
FPType | fPType | ||
) |
Referenced by RDKit::UnimplementedFPException::~UnimplementedFPException().
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 288 of file StreamOps.h.
Referenced by getLine().
|
inline |
grabs the next line from an instream and returns it.
Definition at line 297 of file StreamOps.h.
References 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::MMFF::MMFFOptimizeMoleculeConfs(), and RDKit::UFF::UFFOptimizeMoleculeConfs().
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> >
Referenced by getSizesFromBBs().
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.
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
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 73 of file EnumerationStrategyBase.h.
References computeNumProducts(), getReactantsFromRGroups(), getSizesFromReactants(), and RDKIT_CHEMREACTIONS_EXPORT.
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> >
Referenced by getSizesFromBBs().
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::uint64_t>* RDKit::getSparseCountFP | ( | const ROMol & | mol, |
FPType | fPType | ||
) |
Referenced by RDKit::UnimplementedFPException::~UnimplementedFPException().
RDKIT_FINGERPRINTS_EXPORT std::vector<SparseIntVect<std::uint64_t> *>* RDKit::getSparseCountFPBulk | ( | const std::vector< const ROMol *> | molVector, |
FPType | fPType | ||
) |
Referenced by RDKit::UnimplementedFPException::~UnimplementedFPException().
RDKIT_FINGERPRINTS_EXPORT SparseBitVect* RDKit::getSparseFP | ( | const ROMol & | mol, |
FPType | fPType | ||
) |
Referenced by RDKit::UnimplementedFPException::~UnimplementedFPException().
RDKIT_FINGERPRINTS_EXPORT std::vector<SparseBitVect *>* RDKit::getSparseFPBulk | ( | const std::vector< const ROMol *> | molVector, |
FPType | fPType | ||
) |
Referenced by RDKit::UnimplementedFPException::~UnimplementedFPException().
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT::const_iterator RDKit::getStartIterator | ( | const ChemicalReaction & | rxn, |
ReactionMoleculeType | t | ||
) |
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< boost::uint32_t > * | atomInvariants = 0 , |
||
const std::vector< boost::uint32_t > * | fromAtoms = 0 , |
||
std::vector< std::vector< boost::uint64_t > > * | atomBits = 0 , |
||
std::map< boost::uint64_t, std::vector< std::vector< int > > > * | bitInfo = 0 |
||
) |
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 141 of file hanoiSort.h.
References hanoi().
Referenced by RDKit::Canon::RefinePartitions().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasAgentTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
|
inline |
Returns true if any of the z coords are non zero, false otherwise.
conf | Conformer object to analyze |
Definition at line 142 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
Referenced by RDKit::charptr_functor::operator()().
RDKIT_GRAPHMOL_EXPORT bool RDKit::isAtomAromatic | ( | const Atom * | a | ) |
Referenced by makePropQuery().
RDKIT_FILEPARSERS_EXPORT bool RDKit::IsBlacklistedPair | ( | Atom * | beg_atom, |
Atom * | end_atom | ||
) |
RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery | ( | const Bond * | b | ) |
Referenced by makePropQuery().
RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery | ( | const Atom * | a | ) |
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
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
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::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
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
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::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
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
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::isReactionTemplateMoleculeAgent | ( | const ROMol & | mol, |
double | agentThreshold | ||
) |
|
inline |
Definition at line 319 of file StreamOps.h.
References RDKit::RDTypeTag::BoolTag, RDKit::RDTypeTag::DoubleTag, RDKit::RDTypeTag::FloatTag, RDKit::RDValue::getTag(), RDKit::RDTypeTag::IntTag, RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::Dict::Pair::val, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
Referenced by streamWriteProp(), and streamWriteProps().
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 = 0 , |
||
ExplicitBitVect * | setOnlyBits = 0 , |
||
bool | branchedPaths = true , |
||
const std::vector< boost::uint32_t > * | fromAtoms = 0 |
||
) |
Generates a topological (Daylight like) fingerprint for a molecule using a layer-based hashing algorithm.
Experimental: This function is experimental. The API or results may change from release to release.
mol | the molecule to be fingerprinted |
layerFlags | the layers to be included (see below) |
minPath | the minimum path length (in bonds) to be included |
maxPath | the minimum path length (in bonds) to be included |
fpSize | the size of the fingerprint |
atomCounts | if provided, this will be used to provide the count of the number of paths that set bits each atom is involved in. The vector should have at least as many entries as the molecule has atoms and is not zeroed out here. |
setOnlyBits | if provided, only bits that are set in this bit vector will be set in the result. This is essentially the same as doing: (*res) &= (*setOnlyBits); but also has an impact on the atomCounts (if being used) |
branchedPaths | toggles generation of branched subgraphs, not just linear paths |
Notes:
delete
ing the resultLayer definitions:
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY* RDKit::makeAAtomQuery | ( | ) |
returns a Query for matching generic A atoms (heavy atoms)
Referenced by makeAtomRingBondCountQuery().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY* RDKit::makeAHAtomQuery | ( | ) |
returns a Query for matching generic AH atoms (any atom)
Referenced by makeAtomRingBondCountQuery().
T* RDKit::makeAtomAliphaticQuery | ( | const std::string & | descr | ) |
returns a Query for matching aliphatic atoms
Definition at line 431 of file QueryOps.h.
References queryAtomAliphatic(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomAromaticQuery | ( | const std::string & | descr | ) |
returns a Query for matching the isAromatic
flag
Definition at line 423 of file QueryOps.h.
References queryAtomAromatic(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomExplicitDegreeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching explicit degree
Definition at line 375 of file QueryOps.h.
References queryAtomExplicitDegree(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomExplicitValenceQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching explicit valence
Definition at line 359 of file QueryOps.h.
References queryAtomExplicitValence(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomFormalChargeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching formal charge
Definition at line 456 of file QueryOps.h.
References queryAtomFormalCharge(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomHasAliphaticHeteroatomNbrsQuery | ( | const std::string & | descr | ) |
returns a Query for matching atoms that have heteroatom neighbors
Definition at line 594 of file QueryOps.h.
References makeAtomNullQuery(), makeBondDirEqualsQuery(), makeBondHasStereoQuery(), makeBondInNRingsQuery(), makeBondInRingOfSizeQuery(), makeBondIsInRingQuery(), makeBondMinRingSizeQuery(), makeBondNullQuery(), makeBondOrderEqualsQuery(), makeSingleOrAromaticBondQuery(), queryAtomHasAliphaticHeteroatomNbrs(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomHasChiralTagQuery | ( | const std::string & | descr | ) |
returns a Query for matching whether or not chirality has been set on the atom
Definition at line 482 of file QueryOps.h.
References queryAtomHasChiralTag(), and RDKIT_GRAPHMOL_EXPORT.
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY* RDKit::makeAtomHasChiralTagQuery | ( | ) |
T* RDKit::makeAtomHasHeteroatomNbrsQuery | ( | const std::string & | descr | ) |
returns a Query for matching atoms that have heteroatom neighbors
Definition at line 576 of file QueryOps.h.
References queryAtomHasHeteroatomNbrs(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomHasImplicitHQuery | ( | const std::string & | descr | ) |
returns a Query for matching ring atoms
Definition at line 407 of file QueryOps.h.
References queryAtomHasImplicitH(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomHasRingBondQuery | ( | const std::string & | descr | ) |
returns a Query for matching atoms that have ring bonds
Definition at line 559 of file QueryOps.h.
References queryAtomHasRingBond(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomHCountQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching hydrogen count
Definition at line 399 of file QueryOps.h.
References queryAtomHCount(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomHeavyAtomDegreeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching heavy atom degree
Definition at line 391 of file QueryOps.h.
References queryAtomHeavyAtomDegree(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomHybridizationQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching hybridization
Definition at line 464 of file QueryOps.h.
References queryAtomHybridization(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomImplicitHCountQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching implicit hydrogen count
Definition at line 415 of file QueryOps.h.
References queryAtomImplicitHCount(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomImplicitValenceQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching implicit valence
Definition at line 351 of file QueryOps.h.
References queryAtomImplicitValence(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomInNRingsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms in a particular number of rings
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
Definition at line 515 of file QueryOps.h.
References makeAtomInRingOfSizeQuery(), queryIsAtomInNRings(), and RDKIT_GRAPHMOL_EXPORT.
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.
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY* RDKit::makeAtomInRingOfSizeQuery | ( | int | tgt | ) |
returns a Query for matching atoms in rings of a particular size
Referenced by makeAtomInNRingsQuery().
T* RDKit::makeAtomInRingQuery | ( | const std::string & | descr | ) |
returns a Query for matching ring atoms
Definition at line 507 of file QueryOps.h.
References queryIsAtomInRing(), and RDKIT_GRAPHMOL_EXPORT.
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY* RDKit::makeAtomInRingQuery | ( | ) |
T* RDKit::makeAtomIsotopeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms with a particular isotope
Definition at line 448 of file QueryOps.h.
References queryAtomIsotope(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomMassQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms with a particular mass
Definition at line 439 of file QueryOps.h.
References queryAtomMass(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomMinRingSizeQuery | ( | int | tgt, |
const std::string & | descr | ||
) |
returns a Query for matching an atom's minimum ring size
Definition at line 526 of file QueryOps.h.
References queryAtomMinRingSize(), and RDKIT_GRAPHMOL_EXPORT.
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::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 491 of file QueryOps.h.
References queryAtomMissingChiralTag(), and RDKIT_GRAPHMOL_EXPORT.
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY* RDKit::makeAtomMissingChiralTagQuery | ( | ) |
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY* RDKit::makeAtomNullQuery | ( | ) |
returns a Query for matching any atom
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
T* RDKit::makeAtomNumAliphaticHeteroatomNbrsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching the number of aliphatic heteroatom neighbors
Definition at line 584 of file QueryOps.h.
References queryAtomNumAliphaticHeteroatomNbrs(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomNumHeteroatomNbrsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching the number of heteroatom neighbors
Definition at line 567 of file QueryOps.h.
References queryAtomNumHeteroatomNbrs(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomNumQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atomic number
Definition at line 333 of file QueryOps.h.
References queryAtomNum(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomNumRadicalElectronsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching the number of radical electrons
Definition at line 472 of file QueryOps.h.
References queryAtomNumRadicalElectrons(), and RDKIT_GRAPHMOL_EXPORT.
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.
|
inlinestatic |
Definition at line 321 of file QueryOps.h.
References Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::setDataFunc(), Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::setDescription(), and Queries::RangeQuery< MatchFuncArgType, DataFuncArgType, needsConversion >::setEndsOpen().
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 534 of file QueryOps.h.
References makeAAtomQuery(), makeAHAtomQuery(), makeMAtomQuery(), makeMHAtomQuery(), makeQAtomQuery(), makeQHAtomQuery(), makeXAtomQuery(), makeXHAtomQuery(), queryAtomRingBondCount(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomSimpleQuery | ( | int | what, |
int | funcAtom const *, | ||
const std::string & | description = "Atom Simple" |
||
) |
Definition at line 312 of file QueryOps.h.
T* RDKit::makeAtomTotalDegreeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atomic degree
Definition at line 383 of file QueryOps.h.
References queryAtomTotalDegree(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomTotalValenceQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching total valence
Definition at line 367 of file QueryOps.h.
References queryAtomTotalValence(), and RDKIT_GRAPHMOL_EXPORT.
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.
|
inlinestatic |
Definition at line 120 of file QueryOps.h.
Referenced by makeAtomTypeQuery(), and queryAtomType().
T* RDKit::makeAtomTypeQuery | ( | int | num, |
int | aromatic, | ||
const std::string & | descr | ||
) |
returns a Query for matching atomic number and aromaticity
Definition at line 341 of file QueryOps.h.
References makeAtomType(), queryAtomType(), and RDKIT_GRAPHMOL_EXPORT.
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::makeAtomUnsaturatedQuery | ( | const std::string & | descr | ) |
returns a Query for matching atoms with unsaturation:
Definition at line 499 of file QueryOps.h.
References queryAtomUnsaturated(), and RDKIT_GRAPHMOL_EXPORT.
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.
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY* RDKit::makeBondDirEqualsQuery | ( | Bond::BondDir | what | ) |
returns a Query for matching bond directions
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY* RDKit::makeBondHasStereoQuery | ( | ) |
returns a Query for matching bonds with stereo set
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY* RDKit::makeBondInNRingsQuery | ( | int | tgt | ) |
returns a Query for matching bonds in a particular number of rings
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY* RDKit::makeBondInRingOfSizeQuery | ( | int | what | ) |
returns a Query for matching bonds in rings of a particular size
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY* RDKit::makeBondIsInRingQuery | ( | ) |
returns a Query for matching ring bonds
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY* RDKit::makeBondMinRingSizeQuery | ( | int | what | ) |
returns a Query for matching a bond's minimum ring size
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
RDKIT_GRAPHMOL_EXPORT BOND_NULL_QUERY* RDKit::makeBondNullQuery | ( | ) |
returns a Query for matching any bond
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY* RDKit::makeBondOrderEqualsQuery | ( | Bond::BondType | what | ) |
returns a Query for matching bond orders
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
FilterCatalogEntry* RDKit::MakeFilterCatalogEntry | ( | const FilterData_t & | , |
unsigned int | num_props = 0 , |
||
const FilterProperty_t * | props = 0 |
||
) |
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 787 of file QueryOps.h.
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY* RDKit::makeMAtomQuery | ( | ) |
returns a Query for matching generic M atoms (metals)
Referenced by makeAtomRingBondCountQuery().
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY* RDKit::makeMHAtomQuery | ( | ) |
returns a Query for matching generic MH atoms (metals or H)
Referenced by makeAtomRingBondCountQuery().
Queries::EqualityQuery<int, const Target *, true>* RDKit::makePropQuery | ( | const std::string & | propname, |
const T & | val, | ||
const T & | tolerance = T() |
||
) |
Definition at line 926 of file QueryOps.h.
References isAtomAromatic(), isComplexQuery(), and RDKIT_GRAPHMOL_EXPORT.
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY* RDKit::makeQAtomQuery | ( | ) |
returns a Query for matching generic Q atoms (heteroatoms)
Referenced by makeAtomRingBondCountQuery().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY* RDKit::makeQHAtomQuery | ( | ) |
returns a Query for matching generic QH atoms (heteroatom or H)
Referenced by makeAtomRingBondCountQuery().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY* RDKit::makeSingleOrAromaticBondQuery | ( | ) |
returns a Query for unspecified SMARTS bonds
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY* RDKit::makeXAtomQuery | ( | ) |
returns a Query for matching generic X atoms (halogens)
Referenced by makeAtomRingBondCountQuery().
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY* RDKit::makeXHAtomQuery | ( | ) |
returns a Query for matching generic XH atoms (halogen or H)
Referenced by makeAtomRingBondCountQuery().
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::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 | ||
) |
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 |
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::Mol2DataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA , |
||
bool | cleanupSubstructures = true |
||
) |
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. |
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::MolDataStreamToMol | ( | std::istream & | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
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::MolFragmentToSmiles | ( | const ROMol & | mol, |
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = 0 , |
||
const std::vector< std::string > * | atomSymbols = 0 , |
||
const std::vector< std::string > * | bondSymbols = 0 , |
||
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 | : sybmols to use for the bonds in the output SMILES |
doIsomericSmiles | : include stereochemistry and isotope information in the SMILES |
doKekule | : do Kekule smiles (i.e. don't use aromatic bonds) |
rootedAtAtom | : make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical. |
canonical | : if false, no attempt will be made to canonicalize the SMILES |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
NOTE: the bondSymbols are not currently used in the canonicalization.
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) |
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) |
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 any 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 any 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 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 | ( | 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::CachedSmilesMolHolder::addMol(), and RDKit::CachedTrustedSmilesMolHolder::addMol().
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToTPLFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
const std::string & | partialChargeProp = "_GasteigerCharge" , |
||
bool | writeFirstConfTwice = false |
||
) |
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToTPLText | ( | const ROMol & | mol, |
const std::string & | partialChargeProp = "_GasteigerCharge" , |
||
bool | writeFirstConfTwice = false |
||
) |
RDKIT_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 |
Referenced by RDKit::charptr_functor::operator()().
int RDKit::nullDataFun | ( | T | ) |
Definition at line 737 of file QueryOps.h.
bool RDKit::nullQueryFun | ( | T | ) |
Definition at line 741 of file QueryOps.h.
|
inline |
Definition at line 127 of file SmilesParse.h.
References SmartsToMol().
|
inline |
Definition at line 116 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 | ||
) |
|
inlinestatic |
Definition at line 123 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 | ||
) |
Referenced by RDKit::MCSResult::isCompleted().
RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::parseQueryDefFile | ( | const std::string & | filename, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true |
||
) |
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 |
||
) |
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 |
||
) |
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 = 0 , |
||
ExplicitBitVect * | setOnlyBits = 0 |
||
) |
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 |
||
) |
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 | ) |
RDKIT_FRAGCATALOG_EXPORT ROMol* RDKit::prepareMol | ( | const ROMol & | mol, |
const FragCatParams * | fparams, | ||
MatchVectType & | aToFmap | ||
) |
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::string & | propName = common_properties::molFileValue |
||
) |
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, |
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 |
||
) |
|
inline |
Reads an integer from a char * in packed format and returns the result. The argument is advanced
Definition at line 180 of file StreamOps.h.
|
inlinestatic |
Definition at line 72 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAliphaticQuery().
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomAllBondProduct | ( | Atom const * | at | ) |
Referenced by queryAtomNumAliphaticHeteroatomNbrs().
|
inlinestatic |
Definition at line 69 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAromaticQuery().
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomBondProduct | ( | Atom const * | at | ) |
Referenced by queryAtomNumAliphaticHeteroatomNbrs().
|
inlinestatic |
Definition at line 75 of file QueryOps.h.
References RDKit::Atom::getDegree().
Referenced by makeAtomExplicitDegreeQuery().
|
inlinestatic |
Definition at line 110 of file QueryOps.h.
References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getNumExplicitHs().
Referenced by makeAtomExplicitValenceQuery().
|
inlinestatic |
Definition at line 151 of file QueryOps.h.
References RDKit::Atom::getFormalCharge().
Referenced by makeAtomFormalChargeQuery().
|
inlinestatic |
Definition at line 195 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 160 of file QueryOps.h.
References RDKit::Atom::CHI_UNSPECIFIED, and RDKit::Atom::getChiralTag().
Referenced by makeAtomHasChiralTagQuery().
|
inlinestatic |
Definition at line 168 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomHasHeteroatomNbrsQuery().
|
inlinestatic |
Definition at line 104 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHasImplicitHQuery().
|
inlinestatic |
Definition at line 256 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 98 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHCountQuery().
|
inlinestatic |
Definition at line 84 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomHeavyAtomDegreeQuery().
|
inlinestatic |
Definition at line 154 of file QueryOps.h.
References RDKit::Atom::getHybridization().
Referenced by makeAtomHybridizationQuery().
|
inlinestatic |
Definition at line 101 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomImplicitHCountQuery().
|
inlinestatic |
Definition at line 107 of file QueryOps.h.
References RDKit::Atom::getImplicitValence().
Referenced by makeAtomImplicitValenceQuery().
int RDKit::queryAtomIsInRingOfSize | ( | Atom const * | at | ) |
Definition at line 294 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isAtomInRingOfSize().
|
inlinestatic |
Definition at line 148 of file QueryOps.h.
References RDKit::Atom::getIsotope().
Referenced by makeAtomIsotopeQuery().
|
inlinestatic |
Definition at line 145 of file QueryOps.h.
References RDKit::Atom::getMass(), and round().
Referenced by makeAtomMassQuery().
|
inlinestatic |
Definition at line 271 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 163 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 81 of file QueryOps.h.
References RDKit::Atom::getTotalDegree(), and RDKit::Atom::getTotalNumHs().
|
inlinestatic |
Definition at line 119 of file QueryOps.h.
References RDKit::Atom::getAtomicNum().
Referenced by makeAtomNumQuery().
|
inlinestatic |
Definition at line 209 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getIsAromatic(), RDKit::Atom::getOwningMol(), queryAtomAllBondProduct(), queryAtomBondProduct(), and RDKIT_GRAPHMOL_EXPORT.
Referenced by makeAtomNumAliphaticHeteroatomNbrsQuery().
|
inlinestatic |
Definition at line 181 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::ROMol::getAtomNeighbors(), and RDKit::Atom::getOwningMol().
Referenced by makeAtomNumHeteroatomNbrsQuery().
|
inlinestatic |
Definition at line 157 of file QueryOps.h.
References RDKit::Atom::getNumRadicalElectrons().
Referenced by makeAtomNumRadicalElectronsQuery().
|
inlinestatic |
Definition at line 278 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 625 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 78 of file QueryOps.h.
References RDKit::Atom::getTotalDegree().
Referenced by makeAtomTotalDegreeQuery().
|
inlinestatic |
Definition at line 113 of file QueryOps.h.
References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getImplicitValence().
Referenced by makeAtomTotalValenceQuery().
|
inlinestatic |
Definition at line 141 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::Atom::getIsAromatic(), and makeAtomType().
Referenced by makeAtomTypeQuery().
|
inlinestatic |
Definition at line 116 of file QueryOps.h.
References RDKit::Atom::getDegree(), and RDKit::Atom::getExplicitValence().
Referenced by makeAtomUnsaturatedQuery().
|
inlinestatic |
Definition at line 237 of file QueryOps.h.
References RDKit::Bond::getBondDir().
|
inlinestatic |
Definition at line 243 of file QueryOps.h.
References RDKit::Bond::getStereo(), and RDKit::Bond::STEREONONE.
int RDKit::queryBondIsInRingOfSize | ( | Bond const * | bond | ) |
Definition at line 302 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isBondInRingOfSize().
|
inlinestatic |
Definition at line 233 of file QueryOps.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.
|
inlinestatic |
Definition at line 274 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minBondRingSize().
|
inlinestatic |
Definition at line 230 of file QueryOps.h.
References RDKit::Bond::getBondType().
|
inlinestatic |
Definition at line 250 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by makeAtomInNRingsQuery().
|
inlinestatic |
Definition at line 253 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by makeAtomInRingQuery().
|
inlinestatic |
Definition at line 240 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().
|
inlinestatic |
Definition at line 268 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 182 of file RDAny.h.
References RDKit::RDAny::m_value, and rdvalue_cast().
Referenced by from_rdany().
T RDKit::rdany_cast | ( | RDAny & | d | ) |
Definition at line 188 of file RDAny.h.
References RDKit::RDAny::m_value, and rdvalue_cast().
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect* RDKit::RDKFingerprintMol | ( | const ROMol & | mol, |
unsigned int | minPath = 1 , |
||
unsigned int | maxPath = 7 , |
||
unsigned int | fpSize = 2048 , |
||
unsigned int | nBitsPerHash = 2 , |
||
bool | useHs = true , |
||
double | tgtDensity = 0.0 , |
||
unsigned int | minSize = 128 , |
||
bool | branchedPaths = true , |
||
bool | useBondOrder = true , |
||
std::vector< boost::uint32_t > * | atomInvariants = 0 , |
||
const std::vector< boost::uint32_t > * | fromAtoms = 0 , |
||
std::vector< std::vector< boost::uint32_t > > * | atomBits = 0 , |
||
std::map< boost::uint32_t, std::vector< std::vector< int > > > * | bitInfo = 0 |
||
) |
Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm.
mol | the molecule to be fingerprinted |
minPath | the minimum path length (in bonds) to be included |
maxPath | the minimum path length (in bonds) to be included |
fpSize | the size of the fingerprint |
nBitsPerHash | the number of bits to be set by each path |
useHs | toggles inclusion of Hs in paths (if the molecule has explicit Hs) |
tgtDensity | if the generated fingerprint is below this density, it will be folded until the density is reached. |
minSize | the minimum size to which the fingerprint will be folded |
branchedPaths | toggles generation of branched subgraphs, not just linear paths |
useBondOrders | toggles inclusion of bond orders in the path hashes |
atomInvariants | a vector of atom invariants to use while hashing the paths |
fromAtoms | only paths starting at these atoms will be included |
atomBits | used to return the bits that each atom is involved in (should be at least mol.numAtoms long) |
Notes:
delete
ing the result RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::RDKitSVGToMol | ( | const std::string & | svg, |
bool | sanitize = true , |
||
bool | removeHs = true |
||
) |
svg | - string containing the SVG |
sanitize | - toggles sanitization of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
NOTE This functionality should be considered beta.
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::RDKitSVGToMol | ( | std::istream * | instream, |
bool | sanitize = true , |
||
bool | removeHs = true |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
|
inline |
Definition at line 363 of file RDValue-doublemagic.h.
References RDKit::RDValue::ptrCast().
Referenced by RDKit::RDValue::cleanup_rdvalue(), from_rdvalue(), rdany_cast(), rdvalue_tostring(), streamWriteProp(), and vectToString().
|
inline |
Definition at line 413 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::BoolTag.
Referenced by streamWriteProp().
|
inline |
|
inline |
|
inline |
|
inline |
Definition at line 382 of file RDValue-doublemagic.h.
References rdvalue_is< double >().
Referenced by streamWriteProp().
|
inline |
Definition at line 388 of file RDValue-doublemagic.h.
Referenced by streamWriteProp().
|
inline |
Definition at line 400 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::IntTag.
Referenced by streamWriteProp().
|
inline |
|
inline |
|
inline |
Definition at line 66 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 59 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 80 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 73 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 108 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 101 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 94 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 87 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 122 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 115 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 406 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::UnsignedIntTag.
Referenced by streamWriteProp().
|
inline |
Definition at line 324 of file RDValue-doublemagic.h.
References RDKit::RDValue::getTag().
Referenced by RDKit::RDValue::cleanup_rdvalue(), rdvalue_cast< std::vector< double > & >(), rdvalue_cast< std::vector< double > >(), rdvalue_cast< std::vector< float > & >(), rdvalue_cast< std::vector< float > >(), rdvalue_cast< std::vector< int > & >(), rdvalue_cast< std::vector< int > >(), rdvalue_cast< std::vector< std::string > & >(), rdvalue_cast< std::vector< std::string > >(), rdvalue_cast< std::vector< unsigned int > & >(), and rdvalue_cast< std::vector< unsigned int > >().
|
inline |
Definition at line 335 of file RDValue-doublemagic.h.
References rdvalue_is< double >().
|
inline |
Definition at line 329 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::MaxDouble, and RDKit::RDTypeTag::NaN.
Referenced by RDKit::RDValue::cleanup_rdvalue(), rdvalue_cast< double >(), and rdvalue_is< const double & >().
|
inline |
Definition at line 167 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(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
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.
Referenced by RDKit::Trajectory::clear().
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::string | fileName | ) |
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::istream & | inStream, |
int | nToRead = -1 |
||
) |
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.
Referenced by RDKit::Trajectory::clear().
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inline |
Reads an integer from a stream in packed format and returns the result.
Definition at line 142 of file StreamOps.h.
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inline |
Definition at line 453 of file StreamOps.h.
References streamReadStringVec().
Referenced by streamReadProp().
void RDKit::readRDValue | ( | std::istream & | ss, |
RDValue & | value | ||
) |
Definition at line 433 of file StreamOps.h.
References streamRead().
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inline |
Definition at line 446 of file StreamOps.h.
References streamRead().
Referenced by streamReadProp().
void RDKit::readRDVecValue | ( | std::istream & | ss, |
RDValue & | value | ||
) |
Definition at line 440 of file StreamOps.h.
References streamReadVec().
RDKIT_CHEMREACTIONS_EXPORT ROMol* RDKit::reduceProductToSideChains | ( | const ROMOL_SPTR & | product, |
bool | addDummyAtoms = true |
||
) |
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 | ||
) |
Referenced by RDKit::StereoGroup::operator!=().
RDKIT_GRAPHMOL_EXPORT void RDKit::removeGroupsWithAtoms | ( | const std::vector< Atom *> & | atoms, |
std::vector< StereoGroup > & | groups | ||
) |
Referenced by RDKit::StereoGroup::operator!=().
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.
Referenced by RDKit::EnumerationParams::EnumerationParams().
RDKIT_CHEMTRANSFORMS_EXPORT ROMol* RDKit::replaceCore | ( | const ROMol & | mol, |
const ROMol & | core, | ||
const MatchVectType & | matchVect, | ||
bool | replaceDummies = true , |
||
bool | labelByIndex = false , |
||
bool | requireDummyMatch = false |
||
) |
Returns a copy of an ROMol with the atoms and bonds that are referenced by the MatchVector removed. MatchVector must be defined between mol and the specified core.
dummy atoms are left to indicate attachment points. These dummy atoms can be labeled either by the matching index in the query or by an arbitrary "first match" found. Additional matching options are given below.
Note that this is essentially identical to the replaceSidechains function, except we invert the query and replace the atoms that do match the query.
mol | - the ROMol of interest |
core | - the core being matched against |
matchVect | - a matchVect of the type returned by Substructure Matching |
replaceDummies | - if set, atoms matching dummies in the core will also be replaced |
labelByIndex | - if set, the dummy atoms at attachment points are labelled with the index+1 of the corresponding atom in the core |
requireDummyMatch | - if set, only side chains that are connected to atoms in the core that have attached dummies will be considered. Molecules that have sidechains that are attached at other points will be rejected (NULL returned). |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. The client is responsible for deleting this molecule. If the core query is not matched, NULL is returned. RDKIT_CHEMTRANSFORMS_EXPORT ROMol* RDKit::replaceCore | ( | const ROMol & | mol, |
const ROMol & | coreQuery, | ||
bool | replaceDummies = true , |
||
bool | labelByIndex = false , |
||
bool | requireDummyMatch = false , |
||
bool | useChirality = false |
||
) |
Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed.
dummy atoms are left to indicate attachment points.
Note that this is essentially identical to the replaceSidechains function, except we invert the query and replace the atoms that do match the query.
mol | - the ROMol of interest |
coreQuery | - a query ROMol to be used to match the core |
replaceDummies | - if set, atoms matching dummies in the core will also be replaced |
labelByIndex | - if set, the dummy atoms at attachment points are labelled with the index+1 of the corresponding atom in the core |
requireDummyMatch | - if set, only side chains that are connected to atoms in the core that have attached dummies will be considered. Molecules that have sidechains that are attached at other points will be rejected (NULL returned). |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. The client is responsible for deleting this molecule. If the core query is not matched, NULL is returned. RDKIT_CHEMTRANSFORMS_EXPORT ROMol* RDKit::replaceSidechains | ( | const ROMol & | mol, |
const ROMol & | coreQuery, | ||
bool | useChirality = false |
||
) |
Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed.
dummy atoms are left to indicate attachment points.
mol | the ROMol of interest |
coreQuery | a query ROMol to be used to match the core |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. RDKIT_CHEMTRANSFORMS_EXPORT std::vector<ROMOL_SPTR> RDKit::replaceSubstructs | ( | const ROMol & | mol, |
const ROMol & | query, | ||
const ROMol & | replacement, | ||
bool | replaceAll = false , |
||
unsigned int | replacementConnectionPoint = 0 , |
||
bool | useChirality = false |
||
) |
Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule.
Bonds are created between the joining atom in the existing molecule and the atoms in the new molecule. So, using SMILES instead of molecules: replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]') -> ['[X]NCCNC(=O)O','OC(=O)NCCN[X]'] replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]',true) -> ['[X]NCCN[X]'] Chains should be handled "correctly": replaceSubstructs('CC(=O)C','C(=O)','[X]') -> ['C[X]C'] As should rings: replaceSubstructs('C1C(=O)C1','C(=O)','[X]') -> ['C1[X]C1'] And higher order branches: replaceSubstructs('CC(=O)(C)C','C(=O)','[X]') -> ['C[X](C)C'] Note that the client is responsible for making sure that the resulting molecule actually makes sense - this function does not perform sanitization.
mol | the ROMol of interest |
query | the query ROMol |
replacement | the ROMol to be inserted |
replaceAll | if this is true, only a single result, with all |
useChirality | - if set, match the coreQuery using chirality |
occurances 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, | ||
RGroupRows & | rows, | ||
std::vector< unsigned int > * | unmatched = 0 , |
||
const RGroupDecompositionParameters & | options = RGroupDecompositionParameters() |
||
) |
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 = 0 , |
||
const RGroupDecompositionParameters & | options = RGroupDecompositionParameters() |
||
) |
RDKIT_RDGENERAL_EXPORT double RDKit::round | ( | double | v | ) |
rounds a value to the closest int
Referenced by RDKit::charptr_functor::operator()(), and queryAtomMass().
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_CHEMREACTIONS_EXPORT ChemicalReaction* RDKit::RxnBlockToChemicalReaction | ( | const std::string & | rxnBlock | ) |
Parse a text block in MDL rxn format into a ChemicalReaction.
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction* RDKit::RxnDataStreamToChemicalReaction | ( | std::istream & | rxnStream, |
unsigned int & | line | ||
) |
Parse a text stream in MDL rxn format into a ChemicalReaction.
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction* RDKit::RxnFileToChemicalReaction | ( | const std::string & | fileName | ) |
Parse a file in MDL rxn format into a ChemicalReaction.
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
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 |
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction* RDKit::RxnSmartsToChemicalReaction | ( | const std::string & | text, |
std::map< std::string, std::string > * | replacements = 0 , |
||
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 |
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RDKIT_FILEPARSERS_EXPORT bool RDKit::SamePDBResidue | ( | AtomPDBResidueInfo * | p, |
AtomPDBResidueInfo * | q | ||
) |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::SequenceToMol | ( | const char * | seq, |
bool | sanitize, | ||
bool | lowerD | ||
) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
lowerD | - if set, lower case letters will be parsed as the d form of the corresponding amino acid |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::SequenceToMol | ( | const 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 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 = 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.
RDKIT_GRAPHMOL_EXPORT void RDKit::setAtomValue | ( | Atom * | atom, |
const std::string & | value | ||
) |
Set the atom's MDL atom value.
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 | ) |
Referenced by SmilesToMol().
RDKIT_SMILESPARSE_EXPORT Bond* RDKit::SmartsToBond | ( | const std::string & | sma | ) |
Referenced by SmilesToMol().
RDKIT_SMILESPARSE_EXPORT RWMol* RDKit::SmartsToMol | ( | const std::string & | sma, |
int | debugParse = 0 , |
||
bool | mergeHs = false , |
||
std::map< std::string, std::string > * | replacements = 0 |
||
) |
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(), and SmilesToMol().
RDKIT_SMILESPARSE_EXPORT Atom* RDKit::SmilesToAtom | ( | const std::string & | smi | ) |
Referenced by RDKit::SmilesParserParams::SmilesParserParams().
RDKIT_SMILESPARSE_EXPORT Bond* RDKit::SmilesToBond | ( | const std::string & | smi | ) |
Referenced by RDKit::SmilesParserParams::SmilesParserParams().
RDKIT_SMILESPARSE_EXPORT RWMol* RDKit::SmilesToMol | ( | const std::string & | smi, |
const SmilesParserParams & | params | ||
) |
|
inline |
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 responsiblity of the caller to make sure that substitutions results in legal and sensible SMILES.
Examples of substitutions:
Definition at line 70 of file SmilesParse.h.
References RDKit::SmilesParserParams::debugParse, RDKIT_SMILESPARSE_EXPORT, RDKit::SmilesParserParams::removeHs, RDKit::SmilesParserParams::replacements, RDKit::SmilesParserParams::sanitize, SmartsToAtom(), SmartsToBond(), SmartsToMol(), and SmilesToMol().
RDKIT_FILEPARSERS_EXPORT void RDKit::StandardPDBResidueBondOrders | ( | RWMol * | mol | ) |
void RDKit::streamRead | ( | std::istream & | ss, |
T & | loc | ||
) |
does a binary read of an object from a stream
Definition at line 245 of file StreamOps.h.
Referenced by RDKit::SparseIntVect< IndexType >::fromString(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream(), readRDValue(), readRDValueString(), streamRead(), streamReadProp(), streamReadProps(), streamReadStringVec(), and streamReadVec().
void RDKit::streamRead | ( | std::istream & | ss, |
T & | obj, | ||
int | version | ||
) |
special case for string
Definition at line 253 of file StreamOps.h.
References RDUNUSED_PARAM, and streamRead().
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inline |
Definition at line 258 of file StreamOps.h.
References RDUNUSED_PARAM.
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inline |
Definition at line 460 of file StreamOps.h.
References RDKit::DTags::BoolTag, RDKit::DTags::DoubleTag, RDKit::DTags::FloatTag, RDKit::DTags::IntTag, RDKit::Dict::Pair::key, readRDStringVecValue(), readRDValueString(), streamRead(), RDKit::DTags::StringTag, RDKit::DTags::UnsignedIntTag, RDKit::Dict::Pair::val, RDKit::DTags::VecDoubleTag, RDKit::DTags::VecFloatTag, RDKit::DTags::VecIntTag, RDKit::DTags::VecStringTag, and RDKit::DTags::VecUIntTag.
Referenced by streamReadProps().
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inline |
Definition at line 496 of file StreamOps.h.
References CHECK_INVARIANT, RDKit::Dict::getData(), RDKit::RDProps::getDict(), streamRead(), and streamReadProp().
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inline |
Definition at line 278 of file StreamOps.h.
References streamRead().
Referenced by readRDStringVecValue().
void RDKit::streamReadVec | ( | std::istream & | ss, |
T & | val | ||
) |
Definition at line 270 of file StreamOps.h.
References streamRead().
Referenced by readRDVecValue().
void RDKit::streamWrite | ( | std::ostream & | ss, |
const T & | val | ||
) |
does a binary write of an object to a stream
Definition at line 225 of file StreamOps.h.
Referenced by streamWriteProp(), streamWriteProps(), streamWriteVec(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream(), and RDKit::SparseIntVect< IndexType >::toString().
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inline |
special case for string
Definition at line 231 of file StreamOps.h.
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inline |
Definition at line 340 of file StreamOps.h.
References RDKit::RDTypeTag::BoolTag, RDKit::DTags::BoolTag, RDKit::RDTypeTag::DoubleTag, RDKit::DTags::DoubleTag, RDKit::RDTypeTag::FloatTag, RDKit::DTags::FloatTag, RDKit::RDValue::getTag(), RDKit::RDTypeTag::IntTag, RDKit::DTags::IntTag, isSerializable(), RDKit::Dict::Pair::key, rdvalue_cast(), rdvalue_cast< bool >(), rdvalue_cast< double >(), rdvalue_cast< float >(), rdvalue_cast< int >(), rdvalue_cast< unsigned int >(), streamWrite(), streamWriteVec(), RDKit::RDTypeTag::StringTag, RDKit::DTags::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::DTags::UnsignedIntTag, RDKit::Dict::Pair::val, RDKit::RDTypeTag::VecDoubleTag, RDKit::DTags::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::DTags::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::DTags::VecIntTag, RDKit::RDTypeTag::VecStringTag, RDKit::DTags::VecStringTag, RDKit::DTags::VecUIntTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
Referenced by streamWriteProps().
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inline |
Definition at line 397 of file StreamOps.h.
References RDKit::RDProps::getDict(), RDKit::RDProps::getPropList(), isSerializable(), POSTCONDITION, streamWrite(), and streamWriteProp().
void RDKit::streamWriteVec | ( | std::ostream & | ss, |
const T & | val | ||
) |
Definition at line 238 of file StreamOps.h.
References streamWrite().
Referenced by streamWriteProp().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::strip | ( | const std::string & | orig | ) |
RDKIT_CHEMREACTIONS_EXPORT ExplicitBitVect* RDKit::StructuralFingerprintChemReaction | ( | const ChemicalReaction & | rxn, |
const ReactionFingerprintParams & | params = DefaultStructuralFPParams |
||
) |
Generates a structural fingerprint for a reaction to use in screening
A structural fingerprint is generated as an ExplicitBitVect to use for searching e.g. substructure in reactions. By default the fingerprint is generated as 4096 BitVect using a PatternFP for reactants and products and tentatively agents which were finally concatenated
rxn | the reaction to be fingerprinted |
params | specific settings to manipulate fingerprint generation |
Notes:
delete
ing the result RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::SubstructMatch | ( | const ROMol & | mol, |
const ROMol & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
Find a substructure match for a query in a molecule.
mol | The ROMol to be searched |
query | The query ROMol |
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 |
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::SubstructMatch | ( | ResonanceMolSupplier & | resMolSuppl, |
const ROMol & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
Find a substructure match for a query in a ResonanceMolSupplier object.
resMolSuppl | The ResonanceMolSupplier object to be searched |
query | The query ROMol |
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 |
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int RDKit::SubstructMatch | ( | const ROMol & | mol, |
const ROMol & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = true , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 |
||
) |
Find all substructure matches for a query in a molecule.
mol | The ROMol to be searched |
query | The query ROMol |
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 |
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int RDKit::SubstructMatch | ( | ResonanceMolSupplier & | resMolSuppl, |
const ROMol & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = false , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 , |
||
int | numThreads = 1 |
||
) |
Find all substructure matches for a query in a ResonanceMolSupplier object.
resMolSuppl | The ResonanceMolSupplier object to be searched |
query | The query ROMol |
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 |
numThreads | The number of threads used during the search (defaults to 1; 0 selects the number of concurrent threads supported by the hardware; negative values are added to the number of concurrent threads supported by the hardware) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::SubstructMatch | ( | const MolBundle & | bundle, |
const ROMol & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds the first match in the bundle
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::SubstructMatch | ( | const ROMol & | bundle, |
const MolBundle & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds the first match in the bundle
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::SubstructMatch | ( | const MolBundle & | bundle, |
const MolBundle & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds the first match in the bundle
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int RDKit::SubstructMatch | ( | const MolBundle & | mol, |
const ROMol & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = true , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds all matches in the first molecule of the bundle that matches the query
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int RDKit::SubstructMatch | ( | const MolBundle & | mol, |
const MolBundle & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = true , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds all matches in the first molecule of the bundle that matches
RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int RDKit::SubstructMatch | ( | const ROMol & | mol, |
const MolBundle & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = true , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds all matches against the first molecule of the query bundle that matches
|
inline |
Definition at line 42 of file StreamOps.h.
double RDKit::TanimotoSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
||
double | bounds = 0.0 |
||
) |
Definition at line 541 of file SparseIntVect.h.
References TverskySimilarity().
RDKIT_SUBSTRUCTMATCH_EXPORT double RDKit::toPrime | ( | const MatchVectType & | v | ) |
RDKIT_FILEPARSERS_EXPORT RWMol* RDKit::TPLDataStreamToMol | ( | std::istream * | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | skipFirstConf = false |
||
) |
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 , |
||
bool | skipFirstConf = false |
||
) |
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 , |
||
double | bounds = 0.0 |
||
) |
Definition at line 514 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
Referenced by RDKit::charptr_functor::operator()().
RDKIT_RDGENERAL_EXPORT void RDKit::Union | ( | const VECT_INT_VECT & | rings, |
INT_VECT & | res, | ||
const INT_VECT * | exclude = NULL |
||
) |
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 404 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getLength(), RDKit::SparseIntVect< IndexType >::getNonzeroElements(), RDKit::SparseIntVect< IndexType >::getVal(), and RDKit::SparseIntVect< IndexType >::setVal().
RDKIT_CHEMREACTIONS_EXPORT void RDKit::updateProductsStereochem | ( | ChemicalReaction * | rxn | ) |
std::string RDKit::vectToString | ( | RDValue | val | ) |
Definition at line 156 of file RDValue.h.
References rdvalue_cast().
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 | ||
) |
std::string RDKit::additionalParamData |
const unsigned int RDKit::BITS_PER_INT = 32 |
Definition at line 21 of file DiscreteValueVect.h.
RDKIT_RDGENERAL_EXPORT const char* RDKit::boostVersion |
RDKIT_GRAPHMOL_EXPORT const int RDKit::ci_ATOM_HOLDER |
RDKIT_GRAPHMOL_EXPORT const int RDKit::ci_LEADING_BOND |
RDKIT_GRAPHMOL_EXPORT const int RDKit::ci_RIGHTMOST_ATOM |
|
static |
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.
RDKIT_FILTERCATALOG_EXPORT const char* RDKit::DEFAULT_FILTERMATCHERBASE_NAME |
Referenced by RDKit::FilterMatch::operator!=().
|
static |
Definition at line 23 of file MolWriters.h.
RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams RDKit::DefaultDifferenceFPParams |
RDKIT_CHEMREACTIONS_EXPORT const ReactionFingerprintParams RDKit::DefaultStructuralFPParams |
RDKIT_RDGENERAL_EXPORT const double RDKit::EPS_DOUBLE |
const int RDKit::FILE_MAXLINE |
RDKIT_RDGENERAL_EXPORT int RDKit::firstThousandPrimes |
const double RDKit::IONXH = 20.02 |
Definition at line 25 of file GasteigerParams.h.
RDKIT_GRAPHMOL_EXPORT const std::string RDKit::isotopesAtomData[] |
const std::string RDKit::LayeredFingerprintMolVersion = "0.7.0" |
Definition at line 112 of file Fingerprints.h.
const int RDKit::massIntegerConversionFactor = 1000 |
Definition at line 144 of file QueryOps.h.
RDKIT_RDGENERAL_EXPORT const double RDKit::MAX_DOUBLE |
RDKIT_RDGENERAL_EXPORT const double RDKit::MAX_INT |
RDKIT_RDGENERAL_EXPORT const double RDKit::MAX_LONGINT |
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 |
std::string RDKit::paramData |
RDKIT_GRAPHMOL_EXPORT const std::string RDKit::periodicTableAtomData |
const std::string RDKit::RDKFingerprintMolVersion = "2.0.0" |
Definition at line 62 of file Fingerprints.h.
RDKIT_RDGENERAL_EXPORT const char* RDKit::rdkitBuild |
RDKIT_RDGENERAL_EXPORT const char* RDKit::rdkitVersion |
RDKIT_RDGENERAL_EXPORT const double RDKit::SMALL_DOUBLE |
RDKIT_FILTERCATALOG_EXPORT const char* RDKit::SMARTS_MATCH_NAME_DEFAULT |
Referenced by RDKit::FilterMatchOps::Not::copy().
const unsigned int RDKit::substructLayers = 0x07 |
Definition at line 113 of file Fingerprints.h.