RDKit
Open-source cheminformatics and machine learning.
|
Std stuff. More...
Namespaces | |
namespace | Abbreviations |
namespace | AtomPair |
namespace | AtomPairs |
namespace | Canon |
namespace | Chirality |
namespace | CIPLabeler |
namespace | CIPLabeler_detail |
namespace | common_properties |
namespace | constants |
namespace | Deprotect |
namespace | Descriptors |
namespace | detail |
namespace | details |
namespace | DGeomHelpers |
namespace | DTags |
namespace | EnumerationStrategyPickler |
namespace | EnumerationTypes |
namespace | FileParserUtils |
namespace | FilterMatchOps |
namespace | FMCS |
namespace | ForceFieldsHelper |
namespace | GeneralizedSubstruct |
namespace | GeneralMolSupplier |
namespace | GenericGroups |
namespace | Local |
namespace | MACCSFingerprints |
namespace | MHFPFingerprints |
namespace | MMFF |
namespace | MMPA |
namespace | MolAlign |
namespace | MolDraw2D_detail |
namespace | MolDraw2DUtils |
namespace | MolEnumerator |
namespace | MolFragmenter |
namespace | MolHash |
namespace | MolInterchange |
namespace | MolOps |
Groups a variety of molecular query and transformation operations. | |
namespace | MolShapes |
namespace | MolStandardize |
namespace | MorganFingerprint |
namespace | MorganFingerprints |
namespace | PicklerOps |
namespace | PNGData |
Tags used for PNG metadata. | |
namespace | QueryOps |
namespace | RascalMCES |
namespace | RDKitFP |
namespace | RDKitFPUtils |
namespace | RDTypeTag |
namespace | ReactionRunnerUtils |
namespace | ReducedGraphs |
namespace | RxnOps |
namespace | ScaffoldNetwork |
namespace | SGroupParsing |
namespace | SGroupWriting |
namespace | SLNParse |
namespace | SmartsWrite |
namespace | SmilesWrite |
namespace | StructureCheck |
namespace | Subgraphs |
namespace | SubstanceGroupChecks |
namespace | TopologicalTorsion |
namespace | UFF |
namespace | 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 | AtomKekulizeException |
class | AtomMonomerInfo |
The abstract base class for atom-level monomer info. More... | |
class | AtomPDBResidueInfo |
Captures atom-level information about peptide residues. More... | |
class | AtomRingQuery |
class | AtomSanitizeException |
class | AtomValenceException |
class | BadFileException |
used by various file parsing classes to indicate a bad file More... | |
class | Bond |
class for representing a bond More... | |
class | BondInvariantsGenerator |
abstract base class for bond invariants generators More... | |
class | BondIterator_ |
iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
class | CachedMolHolder |
Concrete class that holds binary cached molecules in memory. More... | |
class | CachedSmilesMolHolder |
Concrete class that holds smiles strings in memory. More... | |
class | CachedTrustedSmilesMolHolder |
Concrete class that holds trusted smiles strings in memory. More... | |
struct | CartesianProduct |
iterate through all possible permutations of the rgroups More... | |
class | CartesianProductStrategy |
struct | charptr_functor |
functor for comparing two strings More... | |
class | ChemicalReaction |
This is a class for storing and applying general chemical reactions. More... | |
class | ChemicalReactionException |
used to indicate an error in the chemical reaction engine More... | |
class | ChemicalReactionParserException |
used to indicate an error in parsing reaction data More... | |
class | Conformer |
The class for representing 2D or 3D conformation of a molecule. More... | |
class | ConformerException |
used to indicate errors from incorrect conformer access More... | |
class | ConstBondIterator_ |
const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
class | CustomPropHandler |
struct | CXXAtomIterator |
struct | CXXBondIterator |
class | DataStructsExplicitBitVecPropHandler |
class | Dict |
The Dict class can be used to store objects of arbitrary type keyed by strings . More... | |
class | DiscreteDistMat |
class | DiscreteValueVect |
a class for efficiently storing vectors of discrete values More... | |
struct | DrawColour |
class | EnumerateLibrary |
This is a class for running reactions on sets of reagents. More... | |
class | EnumerateLibraryBase |
struct | EnumerationParams |
class | EnumerationStrategyBase |
class | EnumerationStrategyException |
class for flagging enumeration strategy errors More... | |
class | EvenSamplePairsStrategy |
EvenSamplePairsStrategy. More... | |
class | ExclusionList |
class | FeatureFileParseException |
class used to indicate errors in parsing feature definition files. More... | |
class | FileParseException |
used by various file parsing classes to indicate a parse error More... | |
class | FilterCatalog |
class | FilterCatalogEntry |
class | FilterCatalogParams |
struct | FilterData_t |
class | FilterHierarchyMatcher |
struct | FilterMatch |
Holds the atomPairs matched by the underlying matcher. More... | |
class | FilterMatcherBase |
struct | FilterProperty_t |
class | FingerprintArguments |
Abstract base class that holds molecule independent arguments that are common amongst all fingerprint types and classes inherited from this would hold fingerprint type specific arguments. More... | |
struct | FingerprintFuncArguments |
struct that makes calling the fingerprint generation functions easier More... | |
class | FingerprintGenerator |
class that generates same fingerprint style for different output formats More... | |
struct | FingerprintVarianceScoreData |
class | FixedMolSizeMolBundle |
class | ForwardSDMolSupplier |
class | FPBReader |
class for reading and searching FPB files More... | |
class | FPHolderBase |
Base FPI for the fingerprinter used to rule out impossible matches. More... | |
class | FragCatalogEntry |
class | FragCatGenerator |
class | FragCatParams |
container for user parameters used to create a fragment catalog More... | |
class | FragFPGenerator |
struct | GaResult |
class | GasteigerParams |
class | HasPropQuery |
class | HasPropWithValueQuery |
class | HasPropWithValueQuery< TargetPtr, ExplicitBitVect > |
class | HasPropWithValueQuery< TargetPtr, std::string > |
class | HeteroatomIterator_ |
Iterate over heteroatoms, this is bidirectional. More... | |
class | KekulizeException |
class | KeyFromPropHolder |
class | KeyHolderBase |
struct | larger_of |
functor for returning the larger of two values More... | |
struct | ltDouble |
functor to compare two doubles with a tolerance More... | |
class | MarvinArrow |
class | MarvinAtom |
class | MarvinAttachmentPoint |
class | MarvinBond |
class | MarvinBondStereo |
class | MarvinCondition |
class | MarvinDataSgroup |
class | MarvinGenericSgroup |
class | MarvinMol |
class | MarvinMolBase |
class | MarvinMonomerSgroup |
class | MarvinMulticenterSgroup |
class | MarvinMultipleSgroup |
class | MarvinPlus |
class | MarvinReaction |
class | MarvinRectangle |
class | MarvinSruCoModSgroup |
class | MarvinStereoGroup |
class | MarvinSuperatomSgroup |
class | MarvinSuperatomSgroupExpanded |
class | MarvinWriterException |
class | MatchingAtomIterator_ |
Iterate over atoms matching a query function. This is bidirectional. More... | |
struct | MCSAtomCompareParameters |
struct | MCSBondCompareParameters |
struct | MCSParameters |
struct | MCSProgressData |
struct | MCSResult |
class | MolBundle |
MolBundle contains a collection of related ROMols. More... | |
class | MolCatalogEntry |
This class is used to store ROMol objects in a MolCatalog. More... | |
class | MolCatalogParams |
container for user parameters used to create a mol catalog More... | |
class | MolChemicalFeature |
class | MolChemicalFeatureDef |
class | MolChemicalFeatureFactory |
The class for finding chemical features in molecules. More... | |
class | MolDraw2D |
MolDraw2D is the base class for doing 2D renderings of molecules. More... | |
class | MolDraw2DCairo |
class | MolDraw2DJS |
class | MolDraw2DQt |
class | MolDraw2DSVG |
class | MolDraw2Dwx |
struct | MolDrawOptions |
class | MolFileUnhandledFeatureException |
class | MolHolder |
Concrete class that holds molecules in memory. More... | |
class | MolHolderBase |
Base class API for holding molecules to substructure search. More... | |
class | MolMatchFinalCheckFunctor |
class | MolPickler |
handles pickling (serializing) molecules More... | |
class | MolPicklerException |
used to indicate exceptions whilst pickling (serializing) molecules More... | |
class | MolSanitizeException |
class for flagging sanitization errors More... | |
class | MolSupplier |
class | MolWriter |
struct | MolzipParams |
class | MultiFPBReader |
class for reading and searching multiple FPB files More... | |
class | PatternHolder |
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 |
class | RandomSampleStrategy |
struct | RCore |
RCore is the core common to a series of molecules. More... | |
struct | RDAny |
class | RDProps |
struct | RDValue |
struct | ReactionFingerprintParams |
class | ReactionPickler |
handles pickling (serializing) reactions More... | |
class | ReactionPicklerException |
used to indicate exceptions whilst pickling (serializing) reactions More... | |
class | RecursiveStructureQuery |
allows use of recursive structure queries (e.g. recursive SMARTS) More... | |
class | ResonanceMolSupplier |
class | ResonanceMolSupplierCallback |
struct | RGroupData |
A single rgroup attached to a given core. More... | |
struct | RGroupDecompData |
class | RGroupDecomposition |
class | RGroupDecompositionChromosome |
struct | RGroupDecompositionParameters |
struct | RGroupDecompositionProcessResult |
class | RGroupGa |
struct | RGroupMatch |
RGroupMatch is the decomposition for a single molecule. More... | |
class | RGroupScorer |
class | RingInfo |
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 |
struct | SmartsParserParams |
class | SmilesMolSupplier |
lazy file parser for Smiles tables More... | |
class | SmilesParseException |
struct | SmilesParserParams |
struct | SmilesWriteParams |
class | SmilesWriter |
class | Snapshot |
class | SparseIntVect |
a class for efficiently storing sparse vectors of ints More... | |
struct | StereoBondThresholds |
class | StereoGroup |
class | SubstanceGroup |
The class for representing SubstanceGroups. More... | |
class | SubstanceGroupException |
used to indicate errors from incorrect sgroup access More... | |
class | SubstructLibrary |
Substructure Search a library of molecules. More... | |
struct | SubstructMatchParameters |
class | TautomerPatternHolder |
class | TautomerQuery |
class | TDTMolSupplier |
lazy file parser for TDT files More... | |
class | TDTWriter |
class | Trajectory |
class | UnimplementedFPException |
class | UsedLabelMap |
struct | VarianceDataForLabel |
Std stuff.
Includes a bunch of functionality for handling Atom and Bond queries.
Utilities to handle atomic numbers in Mancude (maximum number of noncumulative double bonds) rings
This guarantees that aromatic rings containing heteroatoms are always resolved in the same way
Definition at line 34 of file QueryOps.h.
Definition at line 31 of file QueryOps.h.
Definition at line 43 of file QueryOps.h.
Definition at line 46 of file QueryOps.h.
Definition at line 50 of file QueryOps.h.
Definition at line 54 of file QueryOps.h.
Definition at line 57 of file QueryOps.h.
Definition at line 67 of file QueryOps.h.
Definition at line 37 of file QueryOps.h.
Definition at line 852 of file QueryOps.h.
Definition at line 60 of file QueryOps.h.
Definition at line 63 of file QueryOps.h.
Definition at line 40 of file QueryOps.h.
typedef std::uint32_t RDKit::atomindex_t |
Definition at line 35 of file QueryOps.h.
Definition at line 32 of file QueryOps.h.
Definition at line 44 of file QueryOps.h.
Definition at line 47 of file QueryOps.h.
Definition at line 52 of file QueryOps.h.
Definition at line 55 of file QueryOps.h.
Definition at line 58 of file QueryOps.h.
Definition at line 66 of file QueryOps.h.
Definition at line 38 of file QueryOps.h.
Definition at line 853 of file QueryOps.h.
Definition at line 61 of file QueryOps.h.
Definition at line 64 of file QueryOps.h.
Definition at line 41 of file QueryOps.h.
typedef std::unordered_map<std::size_t, ConjElectrons *> RDKit::CEMap |
Definition at line 32 of file Resonance.h.
typedef std::vector<ConjElectrons *> RDKit::CEVect |
Definition at line 29 of file Resonance.h.
typedef std::vector<CEVect2 *> RDKit::CEVect3 |
Definition at line 30 of file Resonance.h.
typedef std::map<int, DrawColour> RDKit::ColourPalette |
Definition at line 57 of file MolDraw2DHelpers.h.
typedef boost::shared_ptr<Conformer> RDKit::CONFORMER_SPTR |
Definition at line 167 of file Conformer.h.
typedef std::map<unsigned int, AtomElectrons *> RDKit::ConjAtomMap |
Definition at line 28 of file Resonance.h.
typedef std::map<unsigned int, BondElectrons *> RDKit::ConjBondMap |
Definition at line 27 of file Resonance.h.
typedef std::vector<std::uint8_t> RDKit::ConjFP |
Definition at line 31 of file Resonance.h.
Definition at line 705 of file QueryOps.h.
Definition at line 815 of file QueryOps.h.
typedef std::vector<std::shared_ptr<const CustomPropHandler> > RDKit::CustomPropHandlerVec |
Definition at line 382 of file StreamOps.h.
typedef std::vector<double> RDKit::DashPattern |
Definition at line 58 of file MolDraw2DHelpers.h.
typedef std::map<double, int, ltDouble> RDKit::DOUBLE_INT_MAP |
typedef boost::variate_generator<rng_type &, uniform_double> RDKit::double_source_type |
typedef std::vector<double> RDKit::DOUBLE_VECT |
typedef DOUBLE_VECT::const_iterator RDKit::DOUBLE_VECT_CI |
typedef DOUBLE_VECT::iterator RDKit::DOUBLE_VECT_I |
Definition at line 121 of file FilterCatalog.h.
typedef boost::shared_ptr<MolChemicalFeature> RDKit::FeatSPtr |
Definition at line 20 of file MolChemicalFeatureFactory.h.
typedef std::list<FeatSPtr> RDKit::FeatSPtrList |
Definition at line 21 of file MolChemicalFeatureFactory.h.
typedef FeatSPtrList::iterator RDKit::FeatSPtrList_I |
Definition at line 22 of file MolChemicalFeatureFactory.h.
Definition at line 23 of file FragCatGenerator.h.
typedef std::deque<int> RDKit::INT_DEQUE |
typedef INT_DEQUE::const_iterator RDKit::INT_DEQUE_CI |
typedef INT_DEQUE::iterator RDKit::INT_DEQUE_I |
typedef INT_INT_DEQ_MAP::const_iterator RDKit::INT_INT_DEQ_MAP_CI |
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 INT_MAP_INT::const_iterator RDKit::INT_MAP_INT_CI |
typedef INT_MAP_INT::iterator RDKit::INT_MAP_INT_I |
typedef std::map<int, PATH_LIST> RDKit::INT_PATH_LIST_MAP |
Definition at line 46 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::const_iterator RDKit::INT_PATH_LIST_MAP_CI |
Definition at line 47 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::iterator RDKit::INT_PATH_LIST_MAP_I |
Definition at line 48 of file Subgraphs.h.
typedef std::set<int> RDKit::INT_SET |
typedef INT_SET::const_iterator RDKit::INT_SET_CI |
typedef INT_SET::iterator RDKit::INT_SET_I |
typedef boost::variate_generator<rng_type &, uniform_int> RDKit::int_source_type |
typedef std::vector<int> RDKit::INT_VECT |
typedef INT_VECT::const_iterator RDKit::INT_VECT_CI |
typedef INT_VECT::const_reverse_iterator RDKit::INT_VECT_CRI |
typedef INT_VECT::iterator RDKit::INT_VECT_I |
typedef INT_VECT::reverse_iterator RDKit::INT_VECT_RI |
typedef std::vector<double> RDKit::INVAR_VECT |
typedef INVAR_VECT::const_iterator RDKit::INVAR_VECT_CI |
typedef INVAR_VECT::iterator RDKit::INVAR_VECT_I |
typedef std::list<INT_VECT> RDKit::LIST_INT_VECT |
typedef LIST_INT_VECT::const_iterator RDKit::LIST_INT_VECT_CI |
typedef LIST_INT_VECT::iterator RDKit::LIST_INT_VECT_I |
typedef 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::MCSFinalMatchCheckFunction) (const std::uint32_t[], const std::uint32_t[], const ROMol &, const FMCS::Graph &, const ROMol &, const FMCS::Graph &, const MCSParameters *) |
typedef bool(* RDKit::MCSProgressCallback) (const MCSProgressData &stat, const MCSParameters ¶ms, void *userData) |
typedef std::vector<ROMol *> RDKit::MOL_PTR_VECT |
typedef MOL_PTR_VECT::const_iterator RDKit::MOL_PTR_VECT_CI |
typedef MOL_PTR_VECT::iterator RDKit::MOL_PTR_VECT_I |
typedef std::vector< ROMOL_SPTR > RDKit::MOL_SPTR_VECT |
Definition at line 21 of file FragCatParams.h.
typedef std::vector<ROMol> RDKit::MOL_VECT |
a hierarchical catalog for holding molecules
Definition at line 17 of file MolCatalog.h.
typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, Atom *, Bond *> RDKit::MolGraph |
typedef std::list<PATH_TYPE> RDKit::PATH_LIST |
Definition at line 43 of file Subgraphs.h.
typedef PATH_LIST::const_iterator RDKit::PATH_LIST_CI |
Definition at line 44 of file Subgraphs.h.
typedef std::vector<int> RDKit::PATH_TYPE |
Definition at line 42 of file Subgraphs.h.
typedef std::map<int, RData> RDKit::R_DECOMP |
Definition at line 16 of file RGroupMatch.h.
typedef boost::shared_ptr<RGroupData> RDKit::RData |
Definition at line 15 of file RGroupMatch.h.
Definition at line 417 of file RDValue-doublemagic.h.
typedef std::vector<ROMOL_SPTR> RDKit::RGroupColumn |
Definition at line 32 of file RGroupDecomp.h.
typedef std::map<std::string, RGroupColumn> RDKit::RGroupColumns |
Definition at line 35 of file RGroupDecomp.h.
Definition at line 37 of file RGroupGa.h.
typedef std::map<std::string, ROMOL_SPTR> RDKit::RGroupRow |
Definition at line 31 of file RGroupDecomp.h.
typedef std::vector<RGroupRow> RDKit::RGroupRows |
Definition at line 34 of file RGroupDecomp.h.
typedef boost::minstd_rand RDKit::rng_type |
typedef boost::shared_ptr< ROMol > RDKit::ROMOL_SPTR |
Definition at line 23 of file ChemTransforms.h.
typedef boost::shared_ptr<RWMol> RDKit::RWMOL_SPTR |
typedef std::vector< RWMOL_SPTR > RDKit::RWMOL_SPTR_VECT |
Definition at line 48 of file FileParsers.h.
typedef std::vector<Snapshot> RDKit::SnapshotVect |
Definition at line 21 of file Snapshot.h.
typedef std::map<std::string, UINT> RDKit::STR_UINT_MAP |
typedef std::map<std::string,UINT>::const_iterator RDKit::STR_UINT_MAP_CI |
typedef std::vector< std::string > RDKit::STR_VECT |
typedef std::vector<std::string>::const_iterator RDKit::STR_VECT_CI |
typedef std::vector<std::string>::iterator RDKit::STR_VECT_I |
typedef std::map<std::string, std::string> RDKit::STRING_PROPS |
Definition at line 54 of file FilterCatalogEntry.h.
typedef 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 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 |
Enumerator | |
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LITTLE_ENDIAN_ORDER | |
BIG_ENDIAN_ORDER |
Definition at line 28 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 454 of file FingerprintGenerator.h.
Enumerator | |
---|---|
SgroupInAtomSet | |
SgroupNotInAtomSet | |
SgroupBothInAndNotInAtomSet |
Definition at line 56 of file MarvinDefs.h.
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strong |
Enumerator | |
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RGROUP_LABELS | |
ISOTOPE_LABELS | |
ATOMMAP_LABELS | |
INDEX_LABELS | |
DUMMY_LABELS | |
INTERNAL_LABELS |
Definition at line 31 of file RGroupUtils.h.
Enumerator | |
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CORINA | supports output from Corina and some dbtranslate output |
Definition at line 236 of file FileParsers.h.
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strong |
Enumerator | |
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AtomMapNumber | |
Isotope | |
FragmentOnBonds | |
AtomType | |
AtomProperty |
Definition at line 106 of file MolFragmenter.h.
Enumerator | |
---|---|
CIRCLEANDLINE | |
LASSO |
Definition at line 146 of file MolDraw2DHelpers.h.
Enumerator | |
---|---|
RgroupMutate | |
Crossover | |
Create |
Definition at line 39 of file RGroupGa.h.
Enumerator | |
---|---|
Reactant | |
Product | |
Agent |
Definition at line 41 of file ReactionUtils.h.
Enumerator | |
---|---|
None | |
NoAlignment | |
MCS |
Definition at line 44 of file RGroupDecompParams.h.
Enumerator | |
---|---|
AtomMap | |
Isotope | |
MDLRGroup |
Definition at line 38 of file RGroupDecompParams.h.
Enumerator | |
---|---|
IsotopeLabels | |
AtomMapLabels | |
AtomIndexLabels | |
RelabelDuplicateLabels | |
MDLRGroupLabels | |
DummyAtomLabels | |
AutoDetect |
Definition at line 20 of file RGroupDecompParams.h.
Enumerator | |
---|---|
Greedy | |
GreedyChunks | |
Exhaustive | |
NoSymmetrization | |
GA |
Definition at line 30 of file RGroupDecompParams.h.
Enumerator | |
---|---|
Match | |
FingerprintVariance |
Definition at line 51 of file RGroupDecompParams.h.
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strong |
Enumerator | |
---|---|
STEREO_ABSOLUTE | |
STEREO_OR | |
STEREO_AND |
Definition at line 30 of file StereoGroup.h.
|
inline |
adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.
Definition at line 239 of file ReactionParser.h.
References addChemicalReactionToPNGFile(), and addChemicalReactionToPNGStream().
Referenced by addChemicalReactionToPNGFile().
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::addChemicalReactionToPNGStream | ( | const ChemicalReaction & | rxn, |
std::istream & | iStream, | ||
bool | includePkl = true , |
||
bool | includeSmiles = true , |
||
bool | includeSmarts = false , |
||
bool | includeRxn = false |
||
) |
adds metadata for a ChemicalReaction to the data from a PNG stream. The modified PNG data is returned.
rxn | the reaction to add |
iStream | the stream to read from |
includePkl | include a reaction pickle |
includeSmiles | include reaction SMILES for the reaction |
includeSmarts | include reaction SMARTS for the reaction |
includeRxn | include an RXN block for the reaction |
References addChemicalReactionToPNGStream().
Referenced by addChemicalReactionToPNGFile(), addChemicalReactionToPNGStream(), and addChemicalReactionToPNGString().
|
inline |
adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStream() for more details.
Definition at line 227 of file ReactionParser.h.
References addChemicalReactionToPNGStream(), and addChemicalReactionToPNGString().
Referenced by addChemicalReactionToPNGString().
|
inline |
adds metadata to a PNG file. The modified PNG data is returned.
Definition at line 84 of file PNGParser.h.
References addMetadataToPNGStream(), and rdvalue_is().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::addMetadataToPNGStream | ( | std::istream & | iStream, |
const std::vector< std::pair< std::string, std::string > > & | metadata, | ||
bool | compressed = true |
||
) |
adds metadata to a PNG stream. The modified PNG data is returned.
The compressed flag is ignored if the RDKit is not built with boost::iostreams support
Referenced by addMetadataToPNGFile(), and addMetadataToPNGString().
|
inline |
adds metadata to a PNG string. The modified PNG data is returned.
Definition at line 74 of file PNGParser.h.
References addMetadataToPNGStream(), and rdvalue_is().
|
inline |
adds metadata for an ROMol to the data from a PNG file. The modified PNG data is returned. See addMolToPNGStream()
for more details.
Definition at line 191 of file PNGParser.h.
References addMolToPNGStream(), and rdvalue_is().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::addMolToPNGStream | ( | const ROMol & | mol, |
std::istream & | iStream, | ||
bool | includePkl = true , |
||
bool | includeSmiles = true , |
||
bool | includeMol = false |
||
) |
adds metadata for an ROMol to the data from a PNG stream. The modified PNG data is returned.
mol | the molecule to add |
iStream | the stream to read from |
includePkl | include a molecule pickle |
includeSmiles | include CXSMILES for the molecule |
includeMol | include a mol block for the molecule |
Referenced by addMolToPNGFile(), and addMolToPNGString().
|
inline |
adds metadata for an ROMol to a PNG string. The modified PNG data is returned. See addMolToPNGStream()
for more details.
Definition at line 179 of file PNGParser.h.
References addMolToPNGStream(), and rdvalue_is().
RDKIT_SUBSTRUCTLIBRARY_EXPORT void RDKit::addPatterns | ( | SubstructLibrary & | sslib, |
boost::shared_ptr< FPHolderBase > | patterns, | ||
int | numThreads = 1 |
||
) |
Create pattern fingerprints for the given substructure library The substructure library must not already have fingerprints
RDKIT_SUBSTRUCTLIBRARY_EXPORT void RDKit::addPatterns | ( | SubstructLibrary & | sslib, |
int | numThreads = 1 |
||
) |
Create default pattern fingerprints for the given substructure library The substructure library must not already have fingerprints
RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::addRecursiveQueries | ( | ROMol & | mol, |
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
const std::string & | propName, | ||
std::vector< std::pair< unsigned int, std::string > > * | reactantLabels = nullptr |
||
) |
Adds named recursive queries to a molecule's atoms based on atom labels.
mol | - the molecule to be modified |
queries | - the dictionary of named queries to add |
propName | - the atom property to use to get query names |
reactantLabels | - to store pairs of (atom index, query string) |
NOTES:
queries
RDKIT_CHEMREACTIONS_EXPORT void RDKit::addRecursiveQueriesToReaction | ( | ChemicalReaction & | rxn, |
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
const std::string & | propName, | ||
std::vector< std::vector< std::pair< unsigned int, std::string > > > * | reactantLabels = nullptr |
||
) |
add the recursive queries to the reactants of a reaction
This does its work using RDKit::addRecursiveQueries()
rxn | the reaction we are interested in |
queries | - the dictionary of named queries to add |
propName | - the atom property to use to get query names optional: |
reactantLabels | - to store pairs of (atom index, query string) per reactant |
NOTES:
queries
References addRecursiveQueriesToReaction().
Referenced by addRecursiveQueriesToReaction().
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::addSubstanceGroup | ( | ROMol & | mol, |
SubstanceGroup | sgroup | ||
) |
Add a new SubstanceGroup. A copy is added, so we can be sure that no other references to the SubstanceGroup exist.
sgroup | - SubstanceGroup to be added to the molecule. |
RDKIT_FILEPARSERS_EXPORT void RDKit::addWavyBondsForStereoAny | ( | ROMol & | mol, |
bool | clearDoubleBondFlags = true , |
||
unsigned | addWhenImpossible = StereoBondThresholds::DBL_BOND_NO_STEREO |
||
) |
set wavy bonds around double bonds with STEREOANY stereo
mol | molecule to be modified |
clearDoubleBondFlags | when this is true flags for unknown double bond stereo will also be removed. |
addWhenImpossible | if nonzero a neighboring single bond will be made wavy even if it connects to a chiral center or double bond with specified stereo. one example of this would be the middle double bond in C/C=C/C=C/C=C/C (if that's set to STEREOANY after constructing the molecule) Otherwise, no wavy bond will be set |
|
inline |
Packs an integer and outputs it to a stream.
Definition at line 106 of file StreamOps.h.
References CHECK_INVARIANT, and rdvalue_is().
|
inline |
use the color palette from the Avalon renderer
Definition at line 85 of file MolDraw2DHelpers.h.
References rdvalue_is().
|
inline |
Definition at line 141 of file MolDraw2DHelpers.h.
References rdvalue_is().
|
inline |
use (part of) the CDK color palette
Definition at line 107 of file MolDraw2DHelpers.h.
References rdvalue_is().
|
inline |
Definition at line 125 of file MolDraw2DHelpers.h.
References rdvalue_is().
Referenced by setDarkMode().
|
inline |
use the RDKit's default palette r
Definition at line 67 of file MolDraw2DHelpers.h.
References rdvalue_is().
Referenced by RDKit::MolDrawOptions::MolDrawOptions().
RDKIT_GRAPHMOL_EXPORT void RDKit::assignStereoGroupIds | ( | std::vector< StereoGroup > & | groups | ) |
Assign Group output IDs to all AND and OR StereoGroups in the vector that don't already have one. The IDs are assigned based on the order of the groups.
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::atomCompat | ( | const Atom * | a1, |
const Atom * | a2, | ||
const SubstructMatchParameters & | ps | ||
) |
RDKIT_RDGENERAL_EXPORT std::string RDKit::augmentTagName | ( | const std::string & | tag | ) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::bondCompat | ( | const Bond * | b1, |
const Bond * | b2, | ||
const SubstructMatchParameters & | ps | ||
) |
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * RDKit::buildFeatureFactory | ( | const std::string & | featureData | ) |
constructs a MolChemicalFeatureFactory from the data in a string
RDKIT_MOLCHEMICALFEATURES_EXPORT MolChemicalFeatureFactory * RDKit::buildFeatureFactory | ( | std::istream & | inStream | ) |
constructs a MolChemicalFeatureFactory from the data in a stream
RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > > RDKit::CDXMLDataStreamToChemicalReactions | ( | std::istream & | rxnStream, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
Parse a text stream in CDXML rxn format into a vector of ChemicalReactions.
References CDXMLDataStreamToChemicalReactions().
Referenced by CDXMLDataStreamToChemicalReactions().
RDKIT_FILEPARSERS_EXPORT std::vector< std::unique_ptr< RWMol > > RDKit::CDXMLDataStreamToMols | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true |
||
) |
construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.
inStream | - 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 correctness of the contents. |
RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > > RDKit::CDXMLFileToChemicalReactions | ( | const std::string & | fileName, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
Parse a file in CDXML rxn format into a vector of ChemicalReactions.
References CDXMLFileToChemicalReactions().
Referenced by CDXMLFileToChemicalReactions().
RDKIT_FILEPARSERS_EXPORT std::vector< std::unique_ptr< RWMol > > RDKit::CDXMLFileToMols | ( | const std::string & | filename, |
bool | sanitize = true , |
||
bool | removeHs = true |
||
) |
construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.
fileName | - cdxml fileName |
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 correctness of the contents. |
RDKIT_CHEMREACTIONS_EXPORT std::vector< std::unique_ptr< ChemicalReaction > > RDKit::CDXMLToChemicalReactions | ( | const std::string & | rxnBlock, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
Parse text in CDXML rxn format into a vector of ChemicalReactions.
References CDXMLToChemicalReactions().
Referenced by CDXMLToChemicalReactions().
RDKIT_FILEPARSERS_EXPORT std::vector< std::unique_ptr< RWMol > > RDKit::CDXMLToMols | ( | const std::string & | cdxml, |
bool | sanitize = true , |
||
bool | removeHs = true |
||
) |
construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.
cdxml | - 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 correctness of the contents. |
RDKIT_FMCS_EXPORT bool RDKit::checkAtomCharge | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2 | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::checkAtomChirality | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2 | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::checkAtomDistance | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2 | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::checkAtomRingMatch | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2 | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::checkBondRingMatch | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2 | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::checkBondStereo | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2 | ||
) |
|
inline |
Definition at line 123 of file RGroupDecomp.h.
References rdvalue_is().
RDKIT_MARVINPARSER_EXPORT std::string RDKit::ChemicalReactionToMrvBlock | ( | const ChemicalReaction & | rxn, |
bool | prettyPrint = false |
||
) |
RDKIT_MARVINPARSER_EXPORT void RDKit::ChemicalReactionToMrvFile | ( | const ChemicalReaction & | rxn, |
const std::string & | fName, | ||
bool | prettyPrint = false |
||
) |
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnBlock | ( | const ChemicalReaction & | rxn, |
bool | separateAgents = false , |
||
bool | forceV3000 = false |
||
) |
returns an rxn block for a reaction
rxn | chemical reaction |
separateAgents | flag to decide if agents are put in a separate block, otherwise they are included in the reactants block (default) |
forceV3000 | flag to cause the V3000 format to be used instead of V2000 |
RDKIT_CHEMREACTIONS_EXPORT ROMol * RDKit::ChemicalReactionToRxnMol | ( | const ChemicalReaction & | rxn | ) |
returns a ROMol with RXN roles used to describe the reaction
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmarts | ( | const ChemicalReaction & | rxn | ) |
returns the reaction SMARTS for a reaction
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToRxnSmiles | ( | const ChemicalReaction & | rxn, |
bool | canonical = true |
||
) |
returns the reaction SMILES for a reaction
RDKIT_CHEMREACTIONS_EXPORT std::string RDKit::ChemicalReactionToV3KRxnBlock | ( | const ChemicalReaction & | rxn, |
bool | separateAgents = false |
||
) |
returns an V3000 rxn block for a reaction
rxn | chemical reaction |
separateAgents | flag to decide if agents are put in a separate block, otherwise they are included in the reactants block (default) |
RDKIT_FILEPARSERS_EXPORT void RDKit::clearMolBlockWedgingInfo | ( | ROMol & | mol | ) |
RDKIT_FILEPARSERS_EXPORT void RDKit::ClearSingleBondDirFlags | ( | ROMol & | mol | ) |
void RDKit::clearVarianceData | ( | FingerprintVarianceScoreData & | fingerprintVarianceScoreData | ) |
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::combineMols | ( | const ROMol & | mol1, |
const ROMol & | mol2, | ||
RDGeom::Point3D | offset = RDGeom::Point3D(0, 0, 0) |
||
) |
Combined two molecules to create a new one.
mol1 | - the first ROMol to be combined |
mol2 | - the second ROMol to be combined |
offset | - a constant offset to be added to every atom position in mol2 |
RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges | ( | const ROMol & | mol, |
int | nIter = 12 , |
||
bool | throwOnParamFailure = false |
||
) |
RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges | ( | const ROMol & | mol, |
std::vector< double > & | charges, | ||
int | nIter = 12 , |
||
bool | throwOnParamFailure = false |
||
) |
RDKIT_PARTIALCHARGES_EXPORT void RDKit::computeGasteigerCharges | ( | const ROMol * | mol, |
int | nIter = 12 , |
||
bool | throwOnParamFailure = false |
||
) |
RDKIT_RDGENERAL_EXPORT double RDKit::computeIntVectPrimesProduct | ( | const INT_VECT & | ring | ) |
compute the product of the set of primes corresponding to the values in an INT_VECT
RDKIT_DATASTRUCTS_EXPORT unsigned int RDKit::computeL1Norm | ( | const DiscreteValueVect & | v1, |
const DiscreteValueVect & | v2 | ||
) |
RDKIT_CHEMREACTIONS_EXPORT boost::uint64_t RDKit::computeNumProducts | ( | const EnumerationTypes::RGROUPS & | sizes | ) |
computeNumProducts Returns the number of possible product combination from The given numbers of building blocks for each rgroup or EnumerationStrategyBase::EnumerationOverflow if the number will not fit into the machines integer type. n.b. An overflow simply means there are a lot of products not that they cannot be enumerated
References computeNumProducts().
Referenced by computeNumProducts(), RDKit::EnumerationStrategyBase::initialize(), and RDKit::EnumerationStrategyBase::internalInitialize().
RDKIT_FILEPARSERS_EXPORT void RDKit::ConnectTheDots | ( | RWMol * | mol, |
unsigned int | flags = 0 |
||
) |
RDKIT_GRAPHMOL_EXPORT void RDKit::convertComplexNameToQuery | ( | Atom * | query, |
std::string_view | symb | ||
) |
Definition at line 339 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::AnyTag, rdvalue_is(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
Referenced by RDKit::Dict::Dict(), RDKit::Dict::operator=(), RDKit::RDAny::operator=(), RDKit::RDAny::RDAny(), and RDKit::Dict::update().
void RDKit::copyVarianceData | ( | const FingerprintVarianceScoreData & | fromData, |
FingerprintVarianceScoreData & | toData | ||
) |
Definition at line 54 of file utils.h.
References CHECK_INVARIANT, PRECONDITION, and rdvalue_is().
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. Definition at line 150 of file QueryAtom.h.
References RDKit::Atom::getQuery(), RDKit::Atom::hasQuery(), PRECONDITION, and rdvalue_is().
Definition at line 136 of file QueryBond.h.
References RDKit::Bond::getQuery(), RDKit::Bond::hasQuery(), PRECONDITION, and rdvalue_is().
RDKIT_FILEPARSERS_EXPORT void RDKit::DetectAtomStereoChemistry | ( | RWMol & | mol, |
const Conformer * | conf | ||
) |
deprecated, please use MolOps::assignChiralTypesFromBondDirs instead
RDKIT_FILEPARSERS_EXPORT void RDKit::DetectBondStereoChemistry | ( | ROMol & | mol, |
const Conformer * | conf | ||
) |
deprecated, please use MolOps::detectBondStereoChemistry instead
RDKIT_DETERMINEBONDS_EXPORT void RDKit::determineBondOrders | ( | RWMol & | mol, |
int | charge = 0 , |
||
bool | allowChargedFragments = true , |
||
bool | embedChiral = true , |
||
bool | useAtomMap = false |
||
) |
This is based on xyz2mol: https://github.com/jensengroup/xyz2mol
mol | is the molecule of interest; it must have single bonds corresponding to the atomic connectivity |
charge | (optional) the charge of the molecule; it must be provided if charge is non-zero |
allowChargedFragments | (optional) if this is true , formal charges will be placed on atoms according to their valency; otherwise, radical electrons will be placed on the atoms |
embedChiral | (optional) if this is true , chirality information will be embedded into the molecule; the function calls sanitizeMol() when this is true |
useAtomMap | (optional) if this is true , an atom map will be created for the molecule |
RDKIT_DETERMINEBONDS_EXPORT void RDKit::determineBonds | ( | RWMol & | mol, |
bool | useHueckel = false , |
||
int | charge = 0 , |
||
double | covFactor = 1.3 , |
||
bool | allowChargedFragments = true , |
||
bool | embedChiral = true , |
||
bool | useAtomMap = false , |
||
bool | useVdw = false |
||
) |
This is based on xyz2mol: https://github.com/jensengroup/xyz2mol
mol | is the molecule of interest; it must have a 3D conformer |
useHueckel | (optional) if this is true , extended Hueckel theory will be used to determine connectivity rather than the van der Waals or connect-the-dots method |
charge | (optional) the charge of the molecule; it must be provided if charge is non-zero |
covFactor | (optional) the factor with which to multiply each covalent radius if the van der Waals method is used |
allowChargedFragments | (optional) if this is true , formal charges will be placed on atoms according to their valency; otherwise, radical electrons will be placed on the atoms |
embedChiral | (optional) if this is true , chirality information will be embedded into the molecule; the function calls sanitizeMol() when this is true |
useAtomMap | (optional) if this is true , an atom map will be created for the molecule |
useVdw | (optional) if this is false , the connect-the-dots method will be used instead of the van der Waals method |
RDKIT_FILEPARSERS_EXPORT Bond::BondDir RDKit::DetermineBondWedgeState | ( | const Bond * | bond, |
const INT_MAP_INT & | wedgeBonds, | ||
const Conformer * | conf | ||
) |
RDKIT_FILEPARSERS_EXPORT Bond::BondDir RDKit::DetermineBondWedgeState | ( | const Bond * | bond, |
unsigned int | fromAtomIdx, | ||
const Conformer * | conf | ||
) |
RDKIT_DETERMINEBONDS_EXPORT void RDKit::determineConnectivity | ( | RWMol & | mol, |
bool | useHueckel = false , |
||
int | charge = 0 , |
||
double | covFactor = 1.3 , |
||
bool | useVdw = false |
||
) |
This is based on xyz2mol: https://github.com/jensengroup/xyz2mol
mol | is the molecule of interest; it must have a 3D conformer |
useHueckel | (optional) if this is true , extended Hueckel theory will be used to determine connectivity rather than the van der Waals or connect-the-dots method |
charge | (optional) the charge of the molecule; it must be provided if the Hueckel method is used and charge is non-zero |
covFactor | (optional) the factor with which to multiply each covalent radius if the van der Waals method is used |
useVdw | (optional) if this is false , the connect-the-dots method will be used instead of the van der Waals method |
double RDKit::DiceSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
||
double | bounds = 0.0 |
||
) |
Definition at line 492 of file SparseIntVect.h.
References rdvalue_is().
|
inline |
Definition at line 346 of file Dict.h.
References rdvalue_is().
RDKIT_CHEMREACTIONS_EXPORT SparseIntVect< std::uint32_t > * RDKit::DifferenceFingerprintChemReaction | ( | const ChemicalReaction & | rxn, |
const ReactionFingerprintParams & | params = DefaultDifferenceFPParams |
||
) |
Generates a difference fingerprint for a reaction to use in similarity search of reactions
A difference fingerprint is generated as a SparseIntVect to use for similarity search of reactions. By default the fingerprint is generated as 2048 bit hashed fingerprint subtracting AtompairFP of the reactants from the products' AtompairFP and tentatively the agent AtompairFP is added
rxn | the reaction to be fingerprinted |
params | specific settings to manipulate fingerprint generation |
Notes:
delete
ing the result Definition at line 92 of file StreamOps.h.
Definition at line 100 of file StreamOps.h.
Definition at line 73 of file StreamOps.h.
References rdvalue_is().
Definition at line 96 of file StreamOps.h.
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::EnumerateLibraryCanSerialize | ( | ) |
void RDKit::eraseUniquePtr | ( | std::vector< std ::unique_ptr< T > > & | vector, |
T * | itemToErase | ||
) |
Definition at line 236 of file MarvinDefs.h.
References rdvalue_is().
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
lowerD | - if set, lower case letters will be parsed as the d form of the corresponding amino acid |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::FASTAToMol | ( | const char * | seq, |
bool | sanitize = true , |
||
int | flavor = 0 |
||
) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
flavor | - 0 Protein, L amino acids (default) 1 Protein, D amino acids 2 RNA, no cap 3 RNA, 5' cap 4 RNA, 3' cap 5 RNA, both caps 6 DNA, no cap 7 DNA, 5' cap 8 DNA, 3' cap 9 DNA, both caps |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::FASTAToMol | ( | const std::string & | seq, |
bool | sanitize, | ||
bool | lowerD | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::FASTAToMol | ( | const std::string & | seq, |
bool | sanitize = true , |
||
int | flavor = 0 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
floating point comparison with a tolerance
RDKIT_FILTERCATALOG_EXPORT bool RDKit::FilterCatalogCanSerialize | ( | ) |
|
inline |
bool RDKit::FinalMatchCheckFunction | ( | const std::uint32_t | c1[], |
const std::uint32_t | c2[], | ||
const ROMol & | mol1, | ||
const FMCS::Graph & | query, | ||
const ROMol & | mol2, | ||
const FMCS::Graph & | target, | ||
const MCSParameters * | p | ||
) |
RDKIT_SUBGRAPHS_EXPORT PATH_LIST RDKit::findAllPathsOfLengthN | ( | const ROMol & | mol, |
unsigned int | targetLen, | ||
bool | useBonds = true , |
||
bool | useHs = false , |
||
int | rootedAtAtom = -1 , |
||
bool | onlyShortestPaths = false |
||
) |
find all paths of a particular size
mol | - the molecule to be considered |
targetLen | - the length of the paths to be returned |
useBonds | - if set, the path indices will be bond indices, not atom indices |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
rootedAtAtom | - if non-negative, only subgraphs that start at this atom will be returned. |
onlyShortestPaths | - if set then only paths which are <= the shortest path between the begin and end atoms will be included in the results |
The result is a list of paths (i.e. list of list of bond indices)
RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP RDKit::findAllPathsOfLengthsMtoN | ( | const ROMol & | mol, |
unsigned int | lowerLen, | ||
unsigned int | upperLen, | ||
bool | useBonds = true , |
||
bool | useHs = false , |
||
int | rootedAtAtom = -1 , |
||
bool | onlyShortestPaths = false |
||
) |
RDKIT_SUBGRAPHS_EXPORT PATH_LIST RDKit::findAllSubgraphsOfLengthN | ( | const ROMol & | mol, |
unsigned int | targetLen, | ||
bool | useHs = false , |
||
int | rootedAtAtom = -1 |
||
) |
find all bond subgraphs of a particular size
mol | - the molecule to be considered |
targetLen | - the length of the subgraphs to be returned |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
rootedAtAtom | - if non-negative, only subgraphs that start at this atom will be returned. |
The result is a list of paths (i.e. list of list of bond indices)
RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP RDKit::findAllSubgraphsOfLengthsMtoN | ( | const ROMol & | mol, |
unsigned int | lowerLen, | ||
unsigned int | upperLen, | ||
bool | useHs = false , |
||
int | rootedAtAtom = -1 |
||
) |
find all bond subgraphs in a range of sizes
mol | - the molecule to be considered |
lowerLen | - the minimum subgraph size to find |
upperLen | - the maximum subgraph size to find |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
rootedAtAtom | - if non-negative, only subgraphs that start at this atom will be returned. |
The result is a map from subgraph size -> list of paths (i.e. list of list of bond indices)
RDKIT_SUBGRAPHS_EXPORT PATH_TYPE RDKit::findAtomEnvironmentOfRadiusN | ( | const ROMol & | mol, |
unsigned int | radius, | ||
unsigned int | rootedAtAtom, | ||
bool | useHs = false , |
||
bool | enforceSize = true , |
||
std::unordered_map< unsigned int, unsigned int > * | atomMap = nullptr |
||
) |
Find bond subgraphs of a particular radius around an atom. Return empty result if there is no bond at the requested radius.
mol | - the molecule to be considered |
radius | - the radius of the subgraphs to be considered |
rootedAtAtom | - the atom to consider |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
enforceSize | - If false, all the bonds within the requested radius (<= radius) is collected. Otherwise, at least one bond located at the requested radius must be found and added. |
atomMap | - Optional: If provided, it will measure the minimum distance of the atom from the rooted atom (start with 0 from the rooted atom). The result is a pair of the atom ID and the distance. The result is a path (a vector of bond indices) |
RDKIT_FRAGCATALOG_EXPORT MatchVectType RDKit::findFuncGroupsOnMol | ( | const ROMol & | mol, |
const FragCatParams * | params, | ||
INT_VECT & | fgBonds | ||
) |
RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS | ( | const std::vector< ROMOL_SPTR > & | mols, |
bool | maximizeBonds, | ||
double | threshold, | ||
unsigned int | timeout, | ||
bool | verbose, | ||
bool | matchValences, | ||
bool | ringMatchesRingOnly, | ||
bool | completeRingsOnly, | ||
bool | matchChiralTag, | ||
AtomComparator | atomComp, | ||
BondComparator | bondComp, | ||
RingComparator | ringComp | ||
) |
RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS | ( | const std::vector< ROMOL_SPTR > & | mols, |
bool | maximizeBonds, | ||
double | threshold = 1.0 , |
||
unsigned int | timeout = 3600 , |
||
bool | verbose = false , |
||
bool | matchValences = false , |
||
bool | ringMatchesRingOnly = false , |
||
bool | completeRingsOnly = false , |
||
bool | matchChiralTag = false , |
||
AtomComparator | atomComp = AtomCompareElements , |
||
BondComparator | bondComp = BondCompareOrder |
||
) |
RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS | ( | const std::vector< ROMOL_SPTR > & | mols, |
const MCSParameters * | params = nullptr |
||
) |
RDKIT_FMCS_EXPORT MCSResult RDKit::findMCS_P | ( | const std::vector< ROMOL_SPTR > & | mols, |
const char * | params_json | ||
) |
std::vector< std::unique_ptr< T > >::iterator RDKit::findUniquePtr | ( | std::vector< std ::unique_ptr< T > > & | vector, |
T * | itemToFind | ||
) |
Definition at line 221 of file MarvinDefs.h.
References rdvalue_is().
RDKIT_SUBGRAPHS_EXPORT PATH_LIST RDKit::findUniqueSubgraphsOfLengthN | ( | const ROMol & | mol, |
unsigned int | targetLen, | ||
bool | useHs = false , |
||
bool | useBO = true , |
||
int | rootedAtAtom = -1 |
||
) |
find unique bond subgraphs of a particular size
mol | - the molecule to be considered |
targetLen | - the length of the subgraphs to be returned |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
useBO | - if set, bond orders will be considered when uniquifying the paths |
rootedAtAtom | - if non-negative, only subgraphs that start at this atom will be returned. |
The result is a list of paths (i.e. list of list of bond indices)
RDKIT_RGROUPDECOMPOSITION_EXPORT double RDKit::fingerprintVarianceScore | ( | const std::vector< size_t > & | permutation, |
const std::vector< std::vector< RGroupMatch > > & | matches, | ||
const std::set< int > & | labels, | ||
FingerprintVarianceScoreData * | fingerprintVarianceScoreData = nullptr |
||
) |
RDKIT_GRAPHMOL_EXPORT void RDKit::forwardStereoGroupIds | ( | ROMol & | mol | ) |
Copy StereoGroup "read" IDs to "write" IDs so that they will be preserved when the mol is exported.
boost::enable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdany | ( | const RDAny & | arg | ) |
Definition at line 190 of file RDAny.h.
References rdvalue_is(), and RDKit::RDTypeTag::StringTag.
boost::disable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdany | ( | const RDAny & | arg | ) |
Definition at line 211 of file RDAny.h.
References rdvalue_is().
boost::enable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
Definition at line 265 of file RDValue.h.
References rdvalue_cast< std::string >(), rdvalue_is(), and RDKit::RDTypeTag::StringTag.
boost::disable_if< boost::is_arithmetic< T >, T >::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
Definition at line 286 of file RDValue.h.
References rdvalue_is().
RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomAlias | ( | const Atom * | atom | ) |
RDKIT_GRAPHMOL_EXPORT void RDKit::getAtomListQueryVals | ( | const Atom::QUERYATOM_QUERY * | q, |
std::vector< int > & | vals | ||
) |
RDKIT_GRAPHMOL_EXPORT int RDKit::getAtomRLabel | ( | const Atom * | atm | ) |
Definition at line 145 of file QueryOps.h.
Definition at line 144 of file QueryOps.h.
RDKIT_GRAPHMOL_EXPORT std::string RDKit::getAtomValue | ( | const Atom * | atom | ) |
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint32_t > * RDKit::getCountFP | ( | const ROMol & | mol, |
FPType | fPType | ||
) |
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint32_t > * > * RDKit::getCountFPBulk | ( | const std::vector< const ROMol * > | molVector, |
FPType | fPType | ||
) |
|
extern |
RDKIT_RDGENERAL_EXPORT double_source_type & RDKit::getDoubleRandomSource | ( | ) |
return a reference to the global (Boost) random source
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT::const_iterator RDKit::getEndIterator | ( | const ChemicalReaction & | rxn, |
ReactionMoleculeType | t | ||
) |
const FilterData_t * RDKit::GetFilterData | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
const FilterProperty_t * RDKit::GetFilterProperties | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
RDKIT_FILTERCATALOG_EXPORT const std::map< std::string, ROMOL_SPTR > & RDKit::GetFlattenedFunctionalGroupHierarchy | ( | bool | normalized = false | ) |
Return the flattened functional group hierarchy as a string->ROMOL_SPTR map The label is the name of the functional group in the hiearchy e.g. Halogen.Bromine.Aliphatic
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::getFP | ( | const ROMol & | mol, |
FPType | fPType | ||
) |
Referenced by RDKit::FPBReader::operator[]().
RDKIT_FINGERPRINTS_EXPORT std::vector< ExplicitBitVect * > * RDKit::getFPBulk | ( | const std::vector< const ROMol * > | molVector, |
FPType | fPType | ||
) |
RDKIT_FILTERCATALOG_EXPORT const FilterCatalog & RDKit::GetFunctionalGroupHierarchy | ( | ) |
Return the functional group hierarchy as a FilterCatalog.
|
inline |
grabs the next line from an instream and returns it.
Definition at line 347 of file StreamOps.h.
References getLine(), and rdvalue_is().
|
inline |
grabs the next line from an instream and returns it.
Definition at line 338 of file StreamOps.h.
References rdvalue_is().
Referenced by getLine().
RDKIT_SUBSTRUCTMATCH_EXPORT const MatchVectType & RDKit::getMostSubstitutedCoreMatch | ( | const ROMol & | mol, |
const ROMol & | core, | ||
const std::vector< MatchVectType > & | matches | ||
) |
This postprocesses the passed substruct matches and returns the match that has the largest number of non-hydrogen atoms in correspondence of terminal dummy atoms
unsigned int RDKit::GetNumEntries | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
unsigned int RDKit::GetNumPropertyEntries | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
Definition at line 37 of file RDThreads.h.
References RDUNUSED_PARAM, and rdvalue_is().
Referenced by RDPickers::LeaderPicker::lazyPick(), and RDKit::ForceFieldsHelper::OptimizeMoleculeConfs().
RDKIT_RDGENERAL_EXPORT rng_type & RDKit::getRandomGenerator | ( | int | seed = -1 | ) |
Optionally seed and return a reference to the global (Boost) random generator
RDKIT_RDGENERAL_EXPORT double RDKit::getRandomVal | ( | int | seed = -1 | ) |
Return a random double value between 0.0 and 1.0 Optionally seed the random number generator
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT RDKit::getReactantsFromRGroups | ( | const std::vector< MOL_SPTR_VECT > & | bbs, |
const EnumerationTypes::RGROUPS & | rgroups | ||
) |
getReactantsFromRGroups Helper function for enumeration, bbs are stored in a std::vector< std::vector<boost:shared_ptr<ROMol> >
References getReactantsFromRGroups().
Referenced by getReactantsFromRGroups().
RDKIT_CHEMREACTIONS_EXPORT VECT_INT_VECT RDKit::getReactingAtoms | ( | const ChemicalReaction & | rxn, |
bool | mappedAtomsOnly = false |
||
) |
returns indices of the atoms in each reactant that are changed in the reaction
rxn | the reaction we are interested in |
mappedAtomsOnly | if set, atoms that are not mapped will not be included in the list of changed atoms (otherwise they are automatically included) |
How are changed atoms recognized? 1) Atoms whose degree changes 2) Atoms whose bonding pattern changes 3) unmapped atoms (unless the mappedAtomsOnly flag is set) 4) Atoms connected to unmapped atoms 5) Atoms whose atomic number changes (unless the corresponding product atom is a dummy) 6) Atoms with more than one atomic number query (unless the corresponding product atom is a dummy)
Note that the atomic number of a query atom depends on how it's constructed. When coming from SMARTS: if the first query is an atomic label/number that sets the atomic number, otherwise it's zero. For example [O;] is atomic number 8 while [;O] is atomic number 0. When coming from RXN: the atomic number of the atom in the rxn file sets the value.
References getReactingAtoms().
Referenced by getReactingAtoms().
Get the RLabels,atom mapping for the current molecule.
EnumerationTypes::RGROUPS RDKit::getSizesFromBBs | ( | const std::vector< std::vector< T > > & | bbs | ) |
Return the number of elements per input vector.
bbs | vector<vector<T> > |
Definition at line 75 of file EnumerationStrategyBase.h.
Referenced by RDKit::EnumerationStrategyBase::initialize().
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::RGROUPS RDKit::getSizesFromReactants | ( | const std::vector< MOL_SPTR_VECT > & | bbs | ) |
getSizesFromReactants Helper function for enumeration, bbs are stored in a std::vector< std::vector<boost:shared_ptr<ROMol> >
References getSizesFromReactants().
Referenced by getSizesFromReactants().
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::uint64_t > * RDKit::getSparseCountFP | ( | const ROMol & | mol, |
FPType | fPType | ||
) |
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseIntVect< std::uint64_t > * > * RDKit::getSparseCountFPBulk | ( | const std::vector< const ROMol * > | molVector, |
FPType | fPType | ||
) |
RDKIT_FINGERPRINTS_EXPORT SparseBitVect * RDKit::getSparseFP | ( | const ROMol & | mol, |
FPType | fPType | ||
) |
RDKIT_FINGERPRINTS_EXPORT std::vector< SparseBitVect * > * RDKit::getSparseFPBulk | ( | const std::vector< const ROMol * > | molVector, |
FPType | fPType | ||
) |
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT::const_iterator RDKit::getStartIterator | ( | const ChemicalReaction & | rxn, |
ReactionMoleculeType | t | ||
) |
RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & RDKit::getSubstanceGroups | ( | const ROMol & | mol | ) |
RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & RDKit::getSubstanceGroups | ( | ROMol & | mol | ) |
RDKIT_GRAPHMOL_EXPORT std::string RDKit::getSupplementalSmilesLabel | ( | const Atom * | atom | ) |
|
extern |
returns twice the bondType
(e.g. SINGLE->2, AROMATIC->3, etc.)
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< boost::uint64_t > * RDKit::getUnfoldedRDKFingerprintMol | ( | const ROMol & | mol, |
unsigned int | minPath = 1 , |
||
unsigned int | maxPath = 7 , |
||
bool | useHs = true , |
||
bool | branchedPaths = true , |
||
bool | useBondOrder = true , |
||
std::vector< std::uint32_t > * | atomInvariants = nullptr , |
||
const std::vector< std::uint32_t > * | fromAtoms = nullptr , |
||
std::vector< std::vector< boost::uint64_t > > * | atomBits = nullptr , |
||
std::map< boost::uint64_t, std::vector< std::vector< int > > > * | bitInfo = nullptr |
||
) |
bool RDKit::hanoi | ( | int * | base, |
int | nel, | ||
int * | temp, | ||
int * | count, | ||
int * | changed, | ||
CompareFunc | compar | ||
) |
changed ||
changed ||
Definition at line 27 of file hanoiSort.h.
References hanoi(), and rdvalue_is().
Referenced by hanoi(), and hanoisort().
void RDKit::hanoisort | ( | int * | base, |
int | nel, | ||
int * | count, | ||
int * | changed, | ||
CompareFunc | compar | ||
) |
Definition at line 151 of file hanoiSort.h.
References hanoi(), and rdvalue_is().
Referenced by RDKit::Canon::RefinePartitions().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasAgentTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
Returns true if any of the z coords are non zero, false otherwise.
conf | Conformer object to analyze |
Definition at line 173 of file Conformer.h.
References RDKit::Conformer::getPositions(), and hasNonZeroZCoords().
Referenced by hasNonZeroZCoords().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasProductTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactantTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactionAtomMapping | ( | const ChemicalReaction & | rxn | ) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::hasReactionSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn, | ||
bool | includeAgents = false |
||
) |
RDKIT_FMCS_EXPORT bool RDKit::havePairOfCompatibleRings | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2 | ||
) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::HELMToMol | ( | const std::string & | helm, |
bool | sanitize = true |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_RDGENERAL_EXPORT void RDKit::Intersect | ( | const INT_VECT & | r1, |
const INT_VECT & | r2, | ||
INT_VECT & | res | ||
) |
calculate the intersection of two INT_VECTs and put the results in a third vector
RDKIT_FILEPARSERS_EXPORT void RDKit::invertMolBlockWedgingInfo | ( | ROMol & | mol | ) |
Returns true if the core atom is either a dummy atom with multiple connections or a dummy atom with a single connection that has no user defined rgroup label
Definition at line 72 of file RGroupUtils.h.
References RDKit::Atom::getAtomicNum(), and isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment().
RDKIT_GRAPHMOL_EXPORT bool RDKit::isAromaticAtom | ( | const Atom & | atom | ) |
returns true if the atom is aromatic or has an aromatic bond
RDKIT_GRAPHMOL_EXPORT bool RDKit::isAtomAromatic | ( | const Atom * | a | ) |
Definition at line 1093 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::getDescription(), Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::getNegation(), RDKit::Atom::getQuery(), and RDKit::Atom::hasQuery().
RDKIT_GRAPHMOL_EXPORT bool RDKit::isAtomListQuery | ( | const Atom * | a | ) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::isAtomTerminalRGroupOrQueryHydrogen | ( | const Atom * | atom | ) |
Returns true if the core atom is either an atom with multiple connections or an atom with a single connection that has no user defined rgroup label
Referenced by isAnyAtomWithMultipleNeighborsOrNotUserRLabel().
RDKIT_FILEPARSERS_EXPORT bool RDKit::IsBlacklistedPair | ( | Atom * | beg_atom, |
Atom * | end_atom | ||
) |
RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery | ( | const Atom * | a | ) |
RDKIT_GRAPHMOL_EXPORT bool RDKit::isComplexQuery | ( | const Bond * | b | ) |
RDKIT_GRAPHMOL_EXPORT bool RDKit::isEarlyAtom | ( | int | atomicNum | ) |
returns true if the atom is to the left of C
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeAgentOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
References isMoleculeAgentOfReaction().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeAgentOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which | ||
) |
tests whether or not the molecule has a substructure match to any of the reaction's agents the which
argument is used to return which of the agents the molecule matches. If there's no match, it is equal to the number of agents on return
References isMoleculeAgentOfReaction().
Referenced by isMoleculeAgentOfReaction(), and isMoleculeAgentOfReaction().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeProductOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
References isMoleculeProductOfReaction().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeProductOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
std::vector< unsigned int > & | which, | ||
bool | stopAtFirstMatch = false |
||
) |
tests whether or not the molecule has a substructure match to the reaction's products the which
argument is used to return which of the products the molecule matches.
References isMoleculeProductOfReaction().
Referenced by isMoleculeProductOfReaction(), isMoleculeProductOfReaction(), and isMoleculeProductOfReaction().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeProductOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
References isMoleculeProductOfReaction().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeReactantOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
References isMoleculeReactantOfReaction().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeReactantOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
std::vector< unsigned int > & | which, | ||
bool | stopAtFirstMatch = false |
||
) |
tests whether or not the molecule has a substructure match to the reaction's reactants the which
argument is used to return which of the reactants the molecule matches.
References isMoleculeReactantOfReaction().
Referenced by isMoleculeReactantOfReaction(), isMoleculeReactantOfReaction(), and isMoleculeReactantOfReaction().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isMoleculeReactantOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
References isMoleculeReactantOfReaction().
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::isReactionTemplateMoleculeAgent | ( | const ROMol & | mol, |
double | agentThreshold | ||
) |
|
inline |
Definition at line 384 of file StreamOps.h.
Return true if the atom has a user-defined R group label.
std::string RDKit::labellingToString | ( | Labelling | type | ) |
return the user friendly name for the given labelling
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::LayeredFingerprintMol | ( | const ROMol & | mol, |
unsigned int | layerFlags = 0xFFFFFFFF , |
||
unsigned int | minPath = 1 , |
||
unsigned int | maxPath = 7 , |
||
unsigned int | fpSize = 2048 , |
||
std::vector< unsigned int > * | atomCounts = nullptr , |
||
ExplicitBitVect * | setOnlyBits = nullptr , |
||
bool | branchedPaths = true , |
||
const std::vector< std::uint32_t > * | fromAtoms = nullptr |
||
) |
Generates a topological (Daylight like) fingerprint for a molecule using a layer-based hashing algorithm.
Experimental: This function is experimental. The API or results may change from release to release.
mol | the molecule to be fingerprinted |
layerFlags | the layers to be included (see below) |
minPath | the minimum path length (in bonds) to be included |
maxPath | the minimum path length (in bonds) to be included |
fpSize | the size of the fingerprint |
atomCounts | if provided, this will be used to provide the count of the number of paths that set bits each atom is involved in. The vector should have at least as many entries as the molecule has atoms and is not zeroed out here. |
setOnlyBits | if provided, only bits that are set in this bit vector will be set in the result. This is essentially the same as doing: (*res) &= (*setOnlyBits); but also has an impact on the atomCounts (if being used) |
branchedPaths | toggles generation of branched subgraphs, not just linear paths |
Notes:
delete
ing the resultLayer definitions:
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAAtomQuery | ( | ) |
returns a Query for matching generic A atoms (heavy atoms)
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * RDKit::makeAHAtomQuery | ( | ) |
returns a Query for matching generic AH atoms (any atom)
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomAliphaticQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
returns a Query for matching aliphatic atoms
Definition at line 461 of file QueryOps.h.
References queryAtomAliphatic(), and rdvalue_is().
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.
returns a Query for matching the isAromatic
flag
Definition at line 453 of file QueryOps.h.
References queryAtomAromatic(), and rdvalue_is().
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.
returns a Query for matching explicit degree
Definition at line 405 of file QueryOps.h.
References queryAtomExplicitDegree(), and rdvalue_is().
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.
returns a Query for matching explicit valence
Definition at line 389 of file QueryOps.h.
References queryAtomExplicitValence(), and rdvalue_is().
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.
returns a Query for matching formal charge
Definition at line 486 of file QueryOps.h.
References queryAtomFormalCharge(), and rdvalue_is().
Referenced by RDKit::QueryAtom::QueryAtom().
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.
returns a Query for matching atoms that have heteroatom neighbors
Definition at line 640 of file QueryOps.h.
References queryAtomHasAliphaticHeteroatomNbrs(), and rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomHasChiralTagQuery | ( | ) |
\overloadquery
returns a Query for matching whether or not chirality has been set on the atom
Definition at line 522 of file QueryOps.h.
References queryAtomHasChiralTag(), and rdvalue_is().
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.
returns a Query for matching atoms that have heteroatom neighbors
Definition at line 622 of file QueryOps.h.
References queryAtomHasHeteroatomNbrs(), and rdvalue_is().
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.
returns a Query for matching ring atoms
Definition at line 437 of file QueryOps.h.
References queryAtomHasImplicitH(), and rdvalue_is().
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.
returns a Query for matching atoms that have ring bonds
Definition at line 605 of file QueryOps.h.
References queryAtomHasRingBond(), and rdvalue_is().
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.
returns a Query for matching hydrogen count
Definition at line 429 of file QueryOps.h.
References queryAtomHCount(), and rdvalue_is().
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.
returns a Query for matching heavy atom degree
Definition at line 421 of file QueryOps.h.
References queryAtomHeavyAtomDegree(), and rdvalue_is().
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.
returns a Query for matching hybridization
Definition at line 504 of file QueryOps.h.
References queryAtomHybridization(), and rdvalue_is().
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.
returns a Query for matching implicit hydrogen count
Definition at line 445 of file QueryOps.h.
References queryAtomImplicitHCount(), and rdvalue_is().
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.
returns a Query for matching implicit valence
Definition at line 381 of file QueryOps.h.
References queryAtomImplicitValence(), and rdvalue_is().
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.
returns a Query for matching atoms in a particular number of rings
Definition at line 555 of file QueryOps.h.
References queryIsAtomInNRings(), and rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomInRingOfSizeQuery | ( | int | tgt | ) |
returns a Query for matching atoms in rings of a particular size
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomInRingQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
returns a Query for matching ring atoms
Definition at line 547 of file QueryOps.h.
References queryIsAtomInRing(), and rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomIsBridgeheadQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
returns a Query for matching bridgehead atoms
Definition at line 658 of file QueryOps.h.
References queryIsAtomBridgehead(), and rdvalue_is().
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.
returns a Query for matching atoms with a particular isotope
Definition at line 478 of file QueryOps.h.
References queryAtomIsotope(), and rdvalue_is().
Referenced by RDKit::QueryAtom::QueryAtom().
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.
returns a Query for matching atoms with a particular mass
Definition at line 469 of file QueryOps.h.
References massIntegerConversionFactor, queryAtomMass(), and rdvalue_is().
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.
returns a Query for matching an atom's minimum ring size
Definition at line 566 of file QueryOps.h.
References queryAtomMinRingSize(), and rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomMissingChiralTagQuery | ( | ) |
\overloadquery
returns a Query for matching whether or not a potentially chiral atom is missing a chiral tag
Definition at line 531 of file QueryOps.h.
References queryAtomMissingChiralTag(), and rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNegativeFormalChargeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T * RDKit::makeAtomNegativeFormalChargeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching negative formal charges (i.e. a query val of 1 matches a formal charge of -1)
Definition at line 495 of file QueryOps.h.
References queryAtomNegativeFormalCharge(), and rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNonHydrogenDegreeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T * RDKit::makeAtomNonHydrogenDegreeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching the number of non-hydrogen neighbors
Definition at line 649 of file QueryOps.h.
References queryAtomNonHydrogenDegree(), and rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_NULL_QUERY * RDKit::makeAtomNullQuery | ( | ) |
returns a Query for matching any atom
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNumAliphaticHeteroatomNbrsQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T * RDKit::makeAtomNumAliphaticHeteroatomNbrsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching the number of aliphatic heteroatom neighbors
Definition at line 630 of file QueryOps.h.
References queryAtomNumAliphaticHeteroatomNbrs(), and rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNumHeteroatomNbrsQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T * RDKit::makeAtomNumHeteroatomNbrsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching the number of heteroatom neighbors
Definition at line 613 of file QueryOps.h.
References queryAtomNumHeteroatomNbrs(), and rdvalue_is().
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.
returns a Query for matching atomic number
Definition at line 363 of file QueryOps.h.
References queryAtomNum(), and rdvalue_is().
Referenced by RDKit::QueryAtom::QueryAtom(), and RDKit::QueryAtom::QueryAtom().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomNumRadicalElectronsQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T * RDKit::makeAtomNumRadicalElectronsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching the number of radical electrons
Definition at line 512 of file QueryOps.h.
References queryAtomNumRadicalElectrons(), and rdvalue_is().
Referenced by RDKit::QueryAtom::QueryAtom().
|
inlinestatic |
Definition at line 351 of file QueryOps.h.
References rdvalue_is().
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.
returns a Query for matching atoms with a particular number of ring bonds
Definition at line 574 of file QueryOps.h.
References queryAtomRingBondCount(), and rdvalue_is().
T * RDKit::makeAtomSimpleQuery | ( | int | what, |
int | funcAtom const *, | ||
const std::string & | description = "Atom Simple" |
||
) |
Definition at line 342 of file QueryOps.h.
References rdvalue_is().
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.
returns a Query for matching atomic degree
Definition at line 413 of file QueryOps.h.
References queryAtomTotalDegree(), and rdvalue_is().
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.
returns a Query for matching total valence
Definition at line 397 of file QueryOps.h.
References queryAtomTotalValence(), and rdvalue_is().
Definition at line 132 of file QueryOps.h.
References rdvalue_is().
Referenced by makeAtomTypeQuery(), and queryAtomType().
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeAtomTypeQuery | ( | int | num, |
int | aromatic | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T * RDKit::makeAtomTypeQuery | ( | int | num, |
int | aromatic, | ||
const std::string & | descr | ||
) |
returns a Query for matching atomic number and aromaticity
Definition at line 371 of file QueryOps.h.
References makeAtomType(), queryAtomType(), and rdvalue_is().
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.
returns a Query for matching atoms with unsaturation:
Definition at line 539 of file QueryOps.h.
References queryAtomUnsaturated(), and rdvalue_is().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondDirEqualsQuery | ( | Bond::BondDir | what | ) |
returns a Query for matching bond directions
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondHasStereoQuery | ( | ) |
returns a Query for matching bonds with stereo set
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondInNRingsQuery | ( | int | tgt | ) |
returns a Query for matching bonds in a particular number of rings
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondInRingOfSizeQuery | ( | int | what | ) |
returns a Query for matching bonds in rings of a particular size
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondIsInRingQuery | ( | ) |
returns a Query for matching ring bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondMinRingSizeQuery | ( | int | what | ) |
returns a Query for matching a bond's minimum ring size
RDKIT_GRAPHMOL_EXPORT BOND_NULL_QUERY * RDKit::makeBondNullQuery | ( | ) |
returns a Query for matching any bond
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeBondOrderEqualsQuery | ( | Bond::BondType | what | ) |
returns a Query for matching bond orders
Referenced by RDKit::QueryBond::QueryBond().
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeDoubleOrAromaticBondQuery | ( | ) |
returns a Query for double|aromatic bonds
FilterCatalogEntry * RDKit::MakeFilterCatalogEntry | ( | const FilterData_t & | , |
unsigned int | num_props = 0 , |
||
const FilterProperty_t * | props = nullptr |
||
) |
Queries::EqualityQuery< int, const Target *, true > * RDKit::makeHasPropQuery | ( | const std::string & | property | ) |
returns a Query for matching atoms that have a particular property
Definition at line 857 of file QueryOps.h.
References rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeMAtomQuery | ( | ) |
returns a Query for matching generic M atoms (metals)
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeMHAtomQuery | ( | ) |
returns a Query for matching generic MH atoms (metals or H)
Queries::EqualityQuery< int, const Target *, true > * RDKit::makePropQuery | ( | const std::string & | propname, |
const ExplicitBitVect & | val, | ||
float | tolerance = 0.0 |
||
) |
Definition at line 1073 of file QueryOps.h.
References rdvalue_is().
Queries::EqualityQuery< int, const Target *, true > * RDKit::makePropQuery | ( | const std::string & | propname, |
const T & | val, | ||
const T & | tolerance = T() |
||
) |
Definition at line 1067 of file QueryOps.h.
References rdvalue_is().
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeQAtomQuery | ( | ) |
returns a Query for matching generic Q atoms (heteroatoms)
RDKIT_GRAPHMOL_EXPORT ATOM_EQUALS_QUERY * RDKit::makeQHAtomQuery | ( | ) |
returns a Query for matching generic QH atoms (heteroatom or H)
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrAromaticBondQuery | ( | ) |
returns a Query for unspecified SMARTS bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrDoubleBondQuery | ( | ) |
returns a Query for single|double bonds
RDKIT_GRAPHMOL_EXPORT BOND_EQUALS_QUERY * RDKit::makeSingleOrDoubleOrAromaticBondQuery | ( | ) |
returns a Query for tautomeric bonds
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeXAtomQuery | ( | ) |
returns a Query for matching generic X atoms (halogens)
RDKIT_GRAPHMOL_EXPORT ATOM_OR_QUERY * RDKit::makeXHAtomQuery | ( | ) |
returns a Query for matching generic XH atoms (halogen or H)
RDKIT_FILEPARSERS_EXPORT void RDKit::markUnspecifiedStereoAsUnknown | ( | ROMol & | mol, |
int | confId = -1 |
||
) |
Set double bonds with unspecified stereo to STEREOANY and add wavy bonds to potential stereocenters with unspecified chirality
RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareAny | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareAnyHeavyAtom | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareElements | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::MCSAtomCompareIsotopes | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::MCSBondCompareAny | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::MCSBondCompareOrder | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::MCSBondCompareOrderExact | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData | ||
) |
RDKIT_FMCS_EXPORT bool RDKit::MCSProgressCallbackTimeout | ( | const MCSProgressData & | stat, |
const MCSParameters & | params, | ||
void * | userData | ||
) |
void RDKit::mergeNullQueries | ( | T *& | returnQuery, |
bool | isQueryNull, | ||
T *& | otherQuery, | ||
bool | isOtherQNull, | ||
Queries::CompositeQueryType | how | ||
) |
Definition at line 67 of file NullQueryAlgebra.h.
References Queries::COMPOSITE_AND, Queries::COMPOSITE_OR, Queries::COMPOSITE_XOR, PRECONDITION, and rdvalue_is().
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 |
References Mol2BlockToMol().
Referenced by Mol2BlockToMol(), and operator""_mol2().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::Mol2DataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA , |
||
bool | cleanupSubstructures = true |
||
) |
References Mol2DataStreamToMol().
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 |
References Mol2DataStreamToMol().
Referenced by Mol2DataStreamToMol(), and Mol2DataStreamToMol().
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 |
References Mol2FileToMol().
Referenced by Mol2FileToMol().
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 to false, the parser is more lax about correctness of the contents. |
Referenced by operator""_ctab().
|
inline |
Definition at line 46 of file MolBundle.h.
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::MolDataStreamToMol | ( | std::istream & | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::MolDataStreamToMol | ( | std::istream * | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
inStream | - stream containing the data |
line | - current line number (used for error reporting) |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
line | - current line number (used for error reporting) |
strictParsing | - if set to false, the parser is more lax about correctness of the contents. |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::MolFileToMol | ( | const std::string & | fName, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
fName | - string containing the file name |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
strictParsing | - if set to false, the parser is more lax about correctness of the contents. |
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToCXSmarts | ( | const ROMol & | mol, |
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr , |
||
bool | doIsomericSmarts = true |
||
) |
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToCXSmiles | ( | const ROMol & | mol, |
const SmilesWriteParams & | params, | ||
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr , |
||
const std::vector< std::string > * | atomSymbols = nullptr , |
||
const std::vector< std::string > * | bondSymbols = nullptr |
||
) |
returns canonical CXSMILES for part of a molecule
Referenced by MolFragmentToCXSmiles().
|
inline |
returns canonical CXSMILES for part of a molecule
mol | : the molecule in question. |
atomsToUse | : indices of the atoms in the fragment |
bondsToUse | : indices of the bonds in the fragment. If this is not provided, all bonds between the atoms in atomsToUse will be included |
atomSymbols | : symbols to use for the atoms in the output SMILES |
bondSymbols | : symbols to use for the bonds in the output SMILES |
doIsomericSmiles | : include stereochemistry and isotope information in the SMILES |
doKekule | : do Kekule smiles (i.e. don't use aromatic bonds) |
rootedAtAtom | : make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical. |
canonical | : if false, no attempt will be made to canonicalize the SMILES |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
NOTE: the bondSymbols are not currently used in the canonicalization.
Definition at line 276 of file SmilesWrite.h.
References RDKit::SmilesWriteParams::doIsomericSmiles, MolFragmentToCXSmiles(), and rdvalue_is().
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToSmarts | ( | const ROMol & | mol, |
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr , |
||
bool | doIsomericSmarts = true |
||
) |
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolFragmentToSmiles | ( | const ROMol & | mol, |
const SmilesWriteParams & | params, | ||
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = nullptr , |
||
const std::vector< std::string > * | atomSymbols = nullptr , |
||
const std::vector< std::string > * | bondSymbols = nullptr |
||
) |
returns canonical SMILES for part of a molecule
Referenced by MolFragmentToSmiles().
|
inline |
returns canonical SMILES for part of a molecule
mol | : the molecule in question. |
atomsToUse | : indices of the atoms in the fragment |
bondsToUse | : indices of the bonds in the fragment. If this is not provided, all bonds between the atoms in atomsToUse will be included |
atomSymbols | : symbols to use for the atoms in the output SMILES |
bondSymbols | : symbols to use for the bonds in the output SMILES |
doIsomericSmiles | : include stereochemistry and isotope information in the SMILES |
doKekule | : do Kekule smiles (i.e. don't use aromatic bonds) |
rootedAtAtom | : make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical. |
canonical | : if false, no attempt will be made to canonicalize the SMILES |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
doRandom | : generate a randomized smiles string by randomly choosing the priority to follow in the DFS traversal. [default false] |
NOTE: the bondSymbols are not currently used in the canonicalization.
Definition at line 190 of file SmilesWrite.h.
References RDKit::SmilesWriteParams::doIsomericSmiles, MolFragmentToSmiles(), and rdvalue_is().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToCMLBlock | ( | const ROMol & | mol, |
int | confId = -1 , |
||
bool | kekulize = true |
||
) |
References MolToCMLBlock().
Referenced by MolToCMLBlock().
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToCMLFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
int | confId = -1 , |
||
bool | kekulize = true |
||
) |
References MolToCMLFile().
Referenced by MolToCMLFile().
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToCXSmarts | ( | const ROMol & | mol, |
bool | doIsomericSmarts = true |
||
) |
returns the CXSMARTS for a molecule
|
inline |
returns canonical CXSMILES for a molecule
mol | : the molecule in question. |
doIsomericSmiles | : include stereochemistry and isotope information in the SMILES |
doKekule | : do Kekule smiles (i.e. don't use aromatic bonds) |
rootedAtAtom | : make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical. |
canonical | : if false, no attempt will be made to canonicalize the SMILES |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
Definition at line 228 of file SmilesWrite.h.
References RDKit::SmilesWriteParams::doIsomericSmiles, MolToCXSmiles(), and rdvalue_is().
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToCXSmiles | ( | const ROMol & | mol, |
const SmilesWriteParams & | ps, | ||
std::uint32_t | flags = SmilesWrite::CXSmilesFields::CX_ALL |
||
) |
returns canonical CXSMILES for a molecule
Referenced by MolToCXSmiles().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToFASTA | ( | const ROMol & | mol | ) |
mol | - the molecule to work with |
mol
should contain monomer information in AtomMonomerInfo
structures RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToHELM | ( | const ROMol & | mol | ) |
mol | - the molecule to work with |
mol
should contain monomer information in AtomMonomerInfo
structures RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToMolBlock | ( | const ROMol & | mol, |
bool | includeStereo = true , |
||
int | confId = -1 , |
||
bool | kekulize = true , |
||
bool | forceV3000 = false |
||
) |
mol | - the molecule in question |
includeStereo | - toggles inclusion of stereochemistry information |
confId | - selects the conformer to be used |
kekulize | - triggers kekulization of the molecule before it is written |
forceV3000 | - force generation a V3000 mol block (happens automatically with more than 999 atoms or bonds) |
Referenced by MolToV3KMolBlock().
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToMolFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
bool | includeStereo = true , |
||
int | confId = -1 , |
||
bool | kekulize = true , |
||
bool | forceV3000 = false |
||
) |
mol | - the molecule in question |
fName | - the name of the file to use |
includeStereo | - toggles inclusion of stereochemistry information |
confId | - selects the conformer to be used |
kekulize | - triggers kekulization of the molecule before it is written |
forceV3000 | - force generation a V3000 mol block (happens automatically with more than 999 atoms or bonds) |
References MolToMolFile().
Referenced by MolToMolFile(), and MolToV3KMolFile().
RDKIT_MARVINPARSER_EXPORT std::string RDKit::MolToMrvBlock | ( | const ROMol & | mol, |
bool | includeStereo = true , |
||
int | confId = -1 , |
||
bool | kekulize = true , |
||
bool | prettyPrint = false |
||
) |
RDKIT_MARVINPARSER_EXPORT void RDKit::MolToMrvFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
bool | includeStereo = true , |
||
int | confId = -1 , |
||
bool | kekulize = true , |
||
bool | prettyPrint = false |
||
) |
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToPDBBlock | ( | const ROMol & | mol, |
int | confId = -1 , |
||
unsigned int | flavor = 0 |
||
) |
mol | - the molecule in question |
confId | - selects the conformer to be used |
flavor | - controls what gets written: flavor & 1 : Write MODEL/ENDMDL lines around each record flavor & 2 : Don't write single CONECT records flavor & 4 : Write CONECT records in both directions flavor & 8 : Don't use multiple CONECTs to encode bond order flavor & 16 : Write MASTER record flavor & 32 : Write TER record |
References MolToPDBBlock().
Referenced by MolToPDBBlock().
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToPDBFile | ( | const ROMol & | mol, |
const std::string & | fname, | ||
int | confId = -1 , |
||
unsigned int | flavor = 0 |
||
) |
mol | - the molecule in question |
fName | - the name of the file to use |
confId | - selects the conformer to be used |
flavor | - controls what gets written: flavor & 1 : Write MODEL/ENDMDL lines around each record flavor & 2 : Don't write single CONECT records flavor & 4 : Write CONECT records in both directions flavor & 8 : Don't use multiple CONECTs to encode bond order flavor & 16 : Write MASTER record flavor & 32 : Write TER record |
References MolToPDBFile().
Referenced by MolToPDBFile().
RDKIT_SMILESPARSE_EXPORT std::vector< std::string > RDKit::MolToRandomSmilesVect | ( | const ROMol & | mol, |
unsigned int | numSmiles, | ||
unsigned int | randomSeed = 0 , |
||
bool | doIsomericSmiles = true , |
||
bool | doKekule = false , |
||
bool | allBondsExplicit = false , |
||
bool | allHsExplicit = false |
||
) |
returns a vector of random SMILES for a molecule (may contain duplicates)
mol | : the molecule in question. |
numSmiles | : the number of SMILES to return |
randomSeed | : if >0, will be used to seed the random number generator |
doIsomericSmiles | : include stereochemistry and isotope information in the SMILES |
doKekule | : do Kekule smiles (i.e. don't use aromatic bonds) |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToSequence | ( | const ROMol & | mol | ) |
mol | - the molecule to work with |
mol
should contain monomer information in AtomMonomerInfo
structures RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToSmarts | ( | const ROMol & | mol, |
bool | doIsomericSmarts = true , |
||
int | rootedAtAtom = -1 |
||
) |
returns the SMARTS for a molecule
|
inline |
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) NOTE that this will throw an exception if the molecule cannot be kekulized. |
rootedAtAtom | : make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical. |
canonical | : if false, no attempt will be made to canonicalize the SMILES |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
Definition at line 122 of file SmilesWrite.h.
References RDKit::SmilesWriteParams::doIsomericSmiles, MolToSmiles(), and rdvalue_is().
RDKIT_SMILESPARSE_EXPORT std::string RDKit::MolToSmiles | ( | const ROMol & | mol, |
const SmilesWriteParams & | params | ||
) |
returns canonical SMILES for a molecule
Referenced by MolToSmiles().
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToTPLFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
const std::string & | partialChargeProp = "_GasteigerCharge" , |
||
bool | writeFirstConfTwice = false |
||
) |
References MolToTPLFile().
Referenced by MolToTPLFile().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToTPLText | ( | const ROMol & | mol, |
const std::string & | partialChargeProp = "_GasteigerCharge" , |
||
bool | writeFirstConfTwice = false |
||
) |
References MolToTPLText().
Referenced by MolToTPLText().
|
inline |
mol | - the molecule in question |
includeStereo | - toggles inclusion of stereochemistry information |
confId | - selects the conformer to be used |
kekulize | - triggers kekulization of the molecule before it is written |
Definition at line 128 of file FileParsers.h.
References MolToMolBlock().
|
inline |
mol | - the molecule in question |
fName | - the name of the file to use |
includeStereo | - toggles inclusion of stereochemistry information |
confId | - selects the conformer to be used |
kekulize | - triggers kekulization of the molecule before it is written |
Definition at line 158 of file FileParsers.h.
References MolToMolFile(), and MolToV3KMolFile().
Referenced by MolToV3KMolFile().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToXYZBlock | ( | const ROMol & | mol, |
int | confId = -1 |
||
) |
References MolToXYZBlock().
Referenced by MolToXYZBlock().
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToXYZFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
int | confId = -1 |
||
) |
References MolToXYZFile().
Referenced by MolToXYZFile().
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > RDKit::molzip | ( | const ROMol & | a, |
const MolzipParams & | params = MolzipParams() |
||
) |
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > RDKit::molzip | ( | const ROMol & | a, |
const ROMol & | b, | ||
const MolzipParams & | params = MolzipParams() |
||
) |
RDKIT_CHEMTRANSFORMS_EXPORT std::unique_ptr< ROMol > RDKit::molzip | ( | std::vector< ROMOL_SPTR > & | decomposition, |
const MolzipParams & | params = MolzipParams() |
||
) |
Creates a molecule from an R group decomposition.
decomposition | - A list of molecules that comprises an R group decomposition. The core must be the first molecule in the list. If generateCoordinates is set in the parameters then aligned depiction coordinates will be set on the returned molecule and the input decomposition |
optional:
params | - molzip parameters |
RDKIT_MARVINPARSER_EXPORT bool RDKit::MrvBlockIsReaction | ( | const std::string & | molmrvText | ) |
RDKIT_MARVINPARSER_EXPORT ChemicalReaction * RDKit::MrvBlockToChemicalReaction | ( | const std::string & | molmrvText, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
RDKIT_MARVINPARSER_EXPORT RWMol * RDKit::MrvBlockToMol | ( | const std::string & | molmrvText, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
RDKIT_MARVINPARSER_EXPORT bool RDKit::MrvDataStreamIsReaction | ( | std::istream & | inStream | ) |
RDKIT_MARVINPARSER_EXPORT bool RDKit::MrvDataStreamIsReaction | ( | std::istream * | inStream | ) |
RDKIT_MARVINPARSER_EXPORT ChemicalReaction * RDKit::MrvDataStreamToChemicalReaction | ( | std::istream & | inStream, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
RDKIT_MARVINPARSER_EXPORT ChemicalReaction * RDKit::MrvDataStreamToChemicalReaction | ( | std::istream * | inStream, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
RDKIT_MARVINPARSER_EXPORT RWMol * RDKit::MrvDataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
RDKIT_MARVINPARSER_EXPORT RWMol * RDKit::MrvDataStreamToMol | ( | std::istream * | inStream, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
RDKIT_MARVINPARSER_EXPORT bool RDKit::MrvFileIsReaction | ( | const std::string & | fname | ) |
RDKIT_MARVINPARSER_EXPORT ChemicalReaction * RDKit::MrvFileToChemicalReaction | ( | const std::string & | fName, |
bool | sanitize = false , |
||
bool | removeHs = false |
||
) |
RDKIT_MARVINPARSER_EXPORT RWMol * RDKit::MrvFileToMol | ( | const std::string & | fName, |
bool | sanitize = false , |
||
bool | removeHs = 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 |
Definition at line 807 of file QueryOps.h.
Definition at line 811 of file QueryOps.h.
|
inline |
Definition at line 375 of file FileParsers.h.
References MolBlockToMol().
|
inline |
Definition at line 386 of file FileParsers.h.
References Mol2BlockToMol().
|
inline |
Definition at line 398 of file FileParsers.h.
References PDBBlockToMol().
|
inline |
Definition at line 251 of file ReactionParser.h.
References RxnSmartsToChemicalReaction().
|
inline |
Definition at line 262 of file ReactionParser.h.
References RxnSmartsToChemicalReaction().
|
inline |
Definition at line 147 of file SmilesParse.h.
References SmartsToMol().
|
inline |
Definition at line 136 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 | ||
) |
Definition at line 135 of file QueryOps.h.
References rdvalue_is().
RDKIT_MOLCHEMICALFEATURES_EXPORT int RDKit::parseFeatureData | ( | const std::string & | defnText, |
MolChemicalFeatureDef::CollectionType & | featDefs | ||
) |
RDKIT_MOLCHEMICALFEATURES_EXPORT int RDKit::parseFeatureData | ( | std::istream & | istream, |
MolChemicalFeatureDef::CollectionType & | featDefs | ||
) |
RDKIT_MOLCHEMICALFEATURES_EXPORT int RDKit::parseFeatureFile | ( | const std::string & | fileName, |
MolChemicalFeatureDef::CollectionType & | featDefs | ||
) |
RDKIT_FMCS_EXPORT void RDKit::parseMCSParametersJSON | ( | const char * | json, |
MCSParameters * | params | ||
) |
RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::parseQueryDefFile | ( | const std::string & | filename, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true , |
||
const std::string & | delimiter = "\t" , |
||
const std::string & | comment = "//" , |
||
unsigned int | nameColumn = 0 , |
||
unsigned int | smartsColumn = 1 |
||
) |
parses a query definition file and sets up a set of definitions suitable for use by addRecursiveQueries()
filename | - the name of the file to be read |
queryDefs | - the dictionary of named queries (return value) |
standardize | - if true, query names will be converted to lower case |
delimiter | - the line delimiter in the file |
comment | - text used to recognize comment lines |
nameColumn | - column with the names of queries |
smartsColumn | - column with the SMARTS definitions of the queries |
RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::parseQueryDefFile | ( | std::istream * | inStream, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true , |
||
const std::string & | delimiter = "\t" , |
||
const std::string & | comment = "//" , |
||
unsigned int | nameColumn = 0 , |
||
unsigned int | smartsColumn = 1 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::parseQueryDefText | ( | const std::string & | queryDefText, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true , |
||
const std::string & | delimiter = "\t" , |
||
const std::string & | comment = "//" , |
||
unsigned int | nameColumn = 0 , |
||
unsigned int | smartsColumn = 1 |
||
) |
equivalent to parseQueryDefFile() but the query definitions are explicitly passed in
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::PatternFingerprintMol | ( | const MolBundle & | bundle, |
unsigned int | fpSize = 2048 , |
||
ExplicitBitVect * | setOnlyBits = nullptr , |
||
bool | tautomericFingerprint = false |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::PatternFingerprintMol | ( | const ROMol & | mol, |
unsigned int | fpSize = 2048 , |
||
std::vector< unsigned int > * | atomCounts = nullptr , |
||
ExplicitBitVect * | setOnlyBits = nullptr , |
||
bool | tautomericFingerprint = false |
||
) |
Generates a topological fingerprint for a molecule using a series of pre-defined structural patterns.
Experimental: This function is experimental. The API or results may change from release to release.
mol | the molecule to be fingerprinted |
fpSize | the size of the fingerprint |
atomCounts | if provided, this will be used to provide the count of the number of paths that set bits each atom is involved in. The vector should have at least as many entries as the molecule has atoms and is not zeroed out here. |
setOnlyBits | if provided, only bits that are set in this bit vector will be set in the result. This is essentially the same as doing: (*res) &= (*setOnlyBits); but also has an impact on the atomCounts (if being used) |
Notes:
delete
ing the result Referenced by RDKit::PatternHolder::makeFingerprint(), and RDKit::TautomerPatternHolder::makeFingerprint().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::PDBBlockToMol | ( | const char * | str, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
References PDBBlockToMol().
Referenced by operator""_pdb(), PDBBlockToMol(), and PDBBlockToMol().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::PDBBlockToMol | ( | const std::string & | str, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
References PDBBlockToMol().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::PDBDataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
References PDBDataStreamToMol().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::PDBDataStreamToMol | ( | std::istream * | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
References PDBDataStreamToMol().
Referenced by PDBDataStreamToMol(), and PDBDataStreamToMol().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::PDBFileToMol | ( | const std::string & | fname, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 , |
||
bool | proximityBonding = true |
||
) |
References PDBFileToMol().
Referenced by PDBFileToMol().
RDKIT_FILEPARSERS_EXPORT INT_MAP_INT RDKit::pickBondsToWedge | ( | const ROMol & | mol | ) |
|
inline |
constructs a ChemicalReaction from the metadata in a PNG file See PNGStreamToChemicalReaction()
for more details
Definition at line 201 of file ReactionParser.h.
References PNGFileToChemicalReaction(), and PNGStreamToChemicalReaction().
Referenced by PNGFileToChemicalReaction().
|
inline |
returns the metadata (tEXt and zTXt chunks) from PNG data
Definition at line 43 of file PNGParser.h.
References PNGStreamToMetadata(), and rdvalue_is().
|
inline |
constructs an ROMol from the metadata in a PNG file. See PNGStreamToMol()
for more details.
Definition at line 112 of file PNGParser.h.
References PNGStreamToMol(), and rdvalue_is().
|
inline |
constructs a vector of ROMol from the metadata in a PNG file. See PNGStreamToMols()
for more details.
Definition at line 143 of file PNGParser.h.
References PNGStreamToMols(), and rdvalue_is().
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RDKit::PNGStreamToChemicalReaction | ( | std::istream & | pngStream | ) |
constructs a ChemicalReaction from the metadata in a PNG stream
Looks through the metadata in the PNG to find the first tag that matches one of the tags in RDKit::PNGData
. A molecule is constructed from this chunk.
Throws a FileParseException
if no suitable tag is found.
The caller is responsible for the returned pointer.
References PNGStreamToChemicalReaction().
Referenced by PNGFileToChemicalReaction(), PNGStreamToChemicalReaction(), and PNGStringToChemicalReaction().
RDKIT_FILEPARSERS_EXPORT std::vector< std::pair< std::string, std::string > > RDKit::PNGStreamToMetadata | ( | std::istream & | inStream | ) |
returns the metadata (tEXt and zTXt chunks) from PNG data
Referenced by PNGFileToMetadata(), and PNGStringToMetadata().
RDKIT_FILEPARSERS_EXPORT ROMol * RDKit::PNGStreamToMol | ( | std::istream & | inStream, |
const SmilesParserParams & | params = SmilesParserParams() |
||
) |
constructs an ROMol from the metadata in a PNG stream
Looks through the metadata in the PNG to find the first tag that matches one of the tags in RDKit::PNGData
. A molecule is constructed from this chunk.
Throws a FileParseException
if no suitable tag is found.
The caller is responsible for the returned pointer.
Referenced by PNGFileToMol(), and PNGStringToMol().
RDKIT_FILEPARSERS_EXPORT std::vector< std::unique_ptr< ROMol > > RDKit::PNGStreamToMols | ( | std::istream & | inStream, |
const std::string & | tagToUse = PNGData::pklTag , |
||
const SmilesParserParams & | params = SmilesParserParams() |
||
) |
constructs a vector of ROMol from the metadata in a PNG stream
Looks through the metadata in the PNG to find tags that start with tagToUse (must be one of the tags in RDKit::PNGData
). The molecules constructed from these data are returned.
Referenced by PNGFileToMols(), and PNGStringToMols().
|
inline |
constructs a ChemicalReaction from the metadata in a PNG string See PNGStreamToChemicalReaction()
for more details
Definition at line 195 of file ReactionParser.h.
References PNGStreamToChemicalReaction(), and PNGStringToChemicalReaction().
Referenced by PNGStringToChemicalReaction().
|
inline |
returns the metadata (tEXt and zTXt chunks) from PNG data
Definition at line 53 of file PNGParser.h.
References PNGStreamToMetadata(), and rdvalue_is().
|
inline |
constructs an ROMol from the metadata in a PNG string. See PNGStreamToMol()
for more details.
Definition at line 123 of file PNGParser.h.
References PNGStreamToMol(), and rdvalue_is().
|
inline |
constructs a vector of ROMol from the metadata in a PNG string. See PNGStreamToMols()
for more details.
Definition at line 154 of file PNGParser.h.
References PNGStreamToMols(), and rdvalue_is().
RDKIT_FRAGCATALOG_EXPORT ROMol * RDKit::prepareMol | ( | const ROMol & | mol, |
const FragCatParams * | fparams, | ||
MatchVectType & | aToFmap | ||
) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
const std::string & | propName = common_properties::molFileValue |
||
) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
const std::string & | propName = common_properties::molFileValue |
||
) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
unsigned int & | numWarnings, | ||
unsigned int & | numErrors, | ||
std::vector< std::vector< std::pair< unsigned int, std::string > > > & | reactantLabels, | ||
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
const std::string & | propName = common_properties::molFileValue |
||
) |
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
unsigned int & | numWarnings, | ||
unsigned int & | numErrors, | ||
std::vector< std::vector< std::pair< unsigned int, std::string > > > & | reactantLabels, | ||
const std::string & | propName = common_properties::molFileValue |
||
) |
RDKIT_SUBSTRUCTMATCH_EXPORT bool RDKit::propertyCompat | ( | const RDProps * | r1, |
const RDProps * | r2, | ||
const std::vector< std::string > & | properties | ||
) |
Reads an integer from a char * in packed format and returns the result. The argument is advanced
Definition at line 216 of file StreamOps.h.
References rdvalue_is().
Definition at line 75 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAliphaticQuery().
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomAllBondProduct | ( | Atom const * | at | ) |
Definition at line 72 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAromaticQuery().
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::queryAtomBondProduct | ( | Atom const * | at | ) |
Definition at line 78 of file QueryOps.h.
References RDKit::Atom::getDegree().
Referenced by makeAtomExplicitDegreeQuery().
Definition at line 122 of file QueryOps.h.
References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getNumExplicitHs().
Referenced by makeAtomExplicitValenceQuery().
Definition at line 163 of file QueryOps.h.
References RDKit::Atom::getFormalCharge().
Referenced by makeAtomFormalChargeQuery().
Definition at line 210 of file QueryOps.h.
References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().
Referenced by makeAtomHasAliphaticHeteroatomNbrsQuery().
Definition at line 175 of file QueryOps.h.
References RDKit::Atom::CHI_UNSPECIFIED, and RDKit::Atom::getChiralTag().
Referenced by makeAtomHasChiralTagQuery().
Definition at line 183 of file QueryOps.h.
References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().
Referenced by makeAtomHasHeteroatomNbrsQuery().
Definition at line 116 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs(), and rdvalue_is().
Referenced by makeAtomHasImplicitHQuery().
Definition at line 284 of file QueryOps.h.
References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), and RDKit::RingInfo::numBondRings().
Referenced by makeAtomHasRingBondQuery().
Definition at line 110 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHCountQuery().
D and T are not treated as heavy atoms here.
Definition at line 98 of file QueryOps.h.
References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().
Referenced by makeAtomHeavyAtomDegreeQuery().
Definition at line 169 of file QueryOps.h.
References RDKit::Atom::getHybridization().
Referenced by makeAtomHybridizationQuery().
Definition at line 113 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomImplicitHCountQuery().
Definition at line 119 of file QueryOps.h.
References RDKit::Atom::getImplicitValence().
Referenced by makeAtomImplicitValenceQuery().
Definition at line 324 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::RingInfo::isAtomInRingOfSize(), and rdvalue_is().
Definition at line 160 of file QueryOps.h.
References RDKit::Atom::getIsotope().
Referenced by makeAtomIsotopeQuery().
Definition at line 156 of file QueryOps.h.
References RDKit::Atom::getMass(), and massIntegerConversionFactor.
Referenced by makeAtomMassQuery().
Definition at line 301 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minAtomRingSize().
Referenced by makeAtomMinRingSizeQuery().
Definition at line 178 of file QueryOps.h.
References RDKit::common_properties::_ChiralityPossible, RDKit::Atom::CHI_UNSPECIFIED, RDKit::Atom::getChiralTag(), and RDKit::RDProps::hasProp().
Referenced by makeAtomMissingChiralTagQuery().
Definition at line 166 of file QueryOps.h.
References RDKit::Atom::getFormalCharge().
Referenced by makeAtomNegativeFormalChargeQuery().
D and T are treated as "non-hydrogen" here.
Definition at line 85 of file QueryOps.h.
References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().
Referenced by makeAtomNonHydrogenDegreeQuery().
Definition at line 131 of file QueryOps.h.
References RDKit::Atom::getAtomicNum().
Referenced by makeAtomNumQuery().
Definition at line 224 of file QueryOps.h.
References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().
Referenced by makeAtomNumAliphaticHeteroatomNbrsQuery().
Definition at line 196 of file QueryOps.h.
References RDKit::ROMol::getAtomNeighbors(), RDKit::Atom::getOwningMol(), and rdvalue_is().
Referenced by makeAtomNumHeteroatomNbrsQuery().
Definition at line 172 of file QueryOps.h.
References RDKit::Atom::getNumRadicalElectrons().
Referenced by makeAtomNumRadicalElectronsQuery().
Definition at line 308 of file QueryOps.h.
References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), RDKit::RingInfo::numBondRings(), and rdvalue_is().
Referenced by makeAtomRingBondCountQuery().
Definition at line 696 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by RDKit::AtomRingQuery::AtomRingQuery(), and RDKit::AtomRingQuery::AtomRingQuery().
Definition at line 81 of file QueryOps.h.
References RDKit::Atom::getTotalDegree().
Referenced by makeAtomTotalDegreeQuery().
Definition at line 125 of file QueryOps.h.
References RDKit::Atom::getTotalValence().
Referenced by makeAtomTotalValenceQuery().
Definition at line 152 of file QueryOps.h.
References RDKit::Atom::getAtomicNum(), RDKit::Atom::getIsAromatic(), and makeAtomType().
Referenced by makeAtomTypeQuery().
Definition at line 128 of file QueryOps.h.
References RDKit::Atom::getTotalDegree(), and RDKit::Atom::getTotalValence().
Referenced by makeAtomUnsaturatedQuery().
Definition at line 265 of file QueryOps.h.
References RDKit::Bond::getBondDir().
Definition at line 271 of file QueryOps.h.
References rdvalue_is(), and RDKit::Bond::STEREONONE.
Definition at line 252 of file QueryOps.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::DOUBLE, and RDKit::Bond::getBondType().
Definition at line 332 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::RingInfo::isBondInRingOfSize(), and rdvalue_is().
Definition at line 248 of file QueryOps.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.
Definition at line 256 of file QueryOps.h.
References RDKit::Bond::DOUBLE, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.
Definition at line 260 of file QueryOps.h.
References RDKit::Bond::AROMATIC, RDKit::Bond::DOUBLE, RDKit::Bond::getBondType(), and RDKit::Bond::SINGLE.
Definition at line 304 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minBondRingSize().
Definition at line 245 of file QueryOps.h.
References RDKit::Bond::getBondType().
RDKIT_GRAPHMOL_EXPORT int RDKit::queryIsAtomBridgehead | ( | Atom const * | at | ) |
Referenced by makeAtomIsBridgeheadQuery().
Definition at line 278 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by makeAtomInNRingsQuery().
Definition at line 281 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by makeAtomInRingQuery().
Definition at line 268 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().
Definition at line 298 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().
Definition at line 179 of file RDAny.h.
References RDKit::RDAny::m_value, and rdvalue_is().
Definition at line 185 of file RDAny.h.
References RDKit::RDAny::m_value, and rdvalue_is().
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * RDKit::RDKFingerprintMol | ( | const ROMol & | mol, |
unsigned int | minPath = 1 , |
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unsigned int | maxPath = 7 , |
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unsigned int | fpSize = 2048 , |
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unsigned int | nBitsPerHash = 2 , |
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bool | useHs = true , |
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double | tgtDensity = 0.0 , |
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unsigned int | minSize = 128 , |
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bool | branchedPaths = true , |
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bool | useBondOrder = true , |
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std::vector< std::uint32_t > * | atomInvariants = nullptr , |
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const std::vector< std::uint32_t > * | fromAtoms = nullptr , |
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std::vector< std::vector< std::uint32_t > > * | atomBits = nullptr , |
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std::map< std::uint32_t, std::vector< std::vector< int > > > * | bitInfo = nullptr |
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) |
Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm.
mol | the molecule to be fingerprinted |
minPath | the minimum path length (in bonds) to be included |
maxPath | the minimum path length (in bonds) to be included |
fpSize | the size of the fingerprint |
nBitsPerHash | the number of bits to be set by each path |
useHs | toggles inclusion of Hs in paths (if the molecule has explicit Hs) |
tgtDensity | if the generated fingerprint is below this density, it will be folded until the density is reached. |
minSize | the minimum size to which the fingerprint will be folded |
branchedPaths | toggles generation of branched subgraphs, not just linear paths |
useBondOrders | toggles inclusion of bond orders in the path hashes |
atomInvariants | a vector of atom invariants to use while hashing the paths |
fromAtoms | only paths starting at these atoms will be included |
atomBits | used to return the bits that each atom is involved in (should be at least mol.numAtoms long) |
Notes:
delete
ing the result RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::RDKitSVGToMol | ( | const std::string & | svg, |
bool | sanitize = true , |
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bool | removeHs = true |
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svg | - string containing the SVG |
sanitize | - toggles sanitization of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
NOTE This functionality should be considered beta.
References RDKitSVGToMol().
Referenced by RDKitSVGToMol(), and RDKitSVGToMol().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::RDKitSVGToMol | ( | std::istream * | instream, |
bool | sanitize = true , |
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bool | removeHs = true |
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
References RDKitSVGToMol().
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Definition at line 420 of file RDValue-doublemagic.h.
References RDKit::RDValue::ptrCast(), rdvalue_is(), and rdvalue_is< std::any >().
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Definition at line 471 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits, and rdvalue_is().
Referenced by rdvalue_tostring().
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Definition at line 520 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::b, rdvalue_is(), and RDKit::RDValue::value.
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Definition at line 166 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().
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Definition at line 440 of file RDValue-doublemagic.h.
References RDKit::RDValue::doubleBits, and rdvalue_is< double >().
Referenced by rdvalue_tostring().
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Definition at line 404 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::d, RDKit::RDTypeTag::detail::Value::f, rdvalue_is(), rdvalue_is< double >(), and RDKit::RDValue::value.
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Definition at line 446 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits, and rdvalue_is().
Referenced by rdvalue_tostring().
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Definition at line 415 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::d, RDKit::RDTypeTag::detail::Value::f, rdvalue_is(), rdvalue_is< double >(), and RDKit::RDValue::value.
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Definition at line 458 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits, and rdvalue_is().
Referenced by rdvalue_tostring().
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Definition at line 426 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 158 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().
Referenced by rdvalue_tostring().
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Definition at line 150 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is< std::any >().
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Definition at line 448 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 459 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, RDKit::RDValue::ptrCast(), rdvalue_is(), rdvalue_is< std::any >(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 437 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 54 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is().
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Definition at line 46 of file RDValue.h.
References RDKit::RDValue::ptrCast(), and rdvalue_is().
Referenced by from_rdvalue(), and rdvalue_tostring().
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Definition at line 495 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 506 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, RDKit::RDValue::ptrCast(), rdvalue_is(), rdvalue_is< std::any >(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 484 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 464 of file RDValue-doublemagic.h.
References RDKit::RDValue::otherBits, and rdvalue_is().
Referenced by rdvalue_tostring().
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Definition at line 473 of file RDValue-taggedunion.h.
References RDKit::RDTypeTag::detail::Value::i, rdvalue_is(), RDKit::RDTypeTag::detail::Value::u, and RDKit::RDValue::value.
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Definition at line 372 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::AnyTag, and rdvalue_is().
Referenced by RDKit::FMCS::DuplicatedSeedCache::add(), RDKit::CIPLabeler::Rules::add(), RDKit::CIPLabeler::PairList::addAll(), RDKit::FMCS::DuplicatedSeedCache::TKey::addAtom(), RDKit::MolDraw2D_detail::addAtomIndices(), RDKit::SLNParse::addAtomToMol(), RDKit::SLNParse::addAtomToMol(), RDKit::FMCS::DuplicatedSeedCache::TKey::addBond(), RDKit::MolDraw2D_detail::addBondIndices(), RDKit::SLNParse::addBranchToMol(), RDKit::SLNParse::addBranchToMol(), RDKit::SLNParse::addFragToMol(), addMetadataToPNGFile(), addMetadataToPNGString(), RDKit::MolBundle::addMol(), RDKit::FixedMolSizeMolBundle::addMol(), addMolToPNGFile(), addMolToPNGString(), appendPackedIntToStream(), RDKit::FileParserUtils::applyMolListPropsToAtoms(), RDKit::FileParserUtils::applyMolListPropToAtoms(), assignAvalonPalette(), assignBWPalette(), assignCDKPalette(), assignDarkModePalette(), assignDefaultPalette(), RDKit::Canon::BreakTies(), RDKit::MolDraw2D_detail::StringRect::calcCentre(), RDKit::MolDraw2D_detail::StringRect::calcCorners(), RDKit::DataStructsExplicitBitVecPropHandler::canSerialize(), checkForTimeout(), RDKit::RDValue::cleanup_rdvalue(), RDKit::RDProps::clearComputedProps(), RDKit::RDProps::clearProp(), RDKit::SLNParse::closeRingBond(), RDKit::SLNParse::closeRingBond(), RDKit::CIPLabeler::Rules::compare(), RDKit::CIPLabeler::PairList::compareTo(), RDKit::MolDraw2DUtils::contourAndDrawGaussians(), RDKit::MolDraw2DUtils::contourAndDrawGrid(), RDKit::SLNParse::convertToString(), RDKit::HasPropQuery< TargetPtr >::copy(), RDKit::HasPropWithValueQuery< TargetPtr, T >::copy(), RDKit::HasPropWithValueQuery< TargetPtr, std::string >::copy(), RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >::copy(), copy_rdvalue(), countSwapsToInterconvert(), RDKit::FileParserUtils::createAtomBoolPropertyList(), RDKit::FileParserUtils::createAtomDoublePropertyList(), RDKit::FileParserUtils::createAtomIntPropertyList(), RDKit::FileParserUtils::createAtomStringPropertyList(), RDKit::ScaffoldNetwork::createScaffoldNetwork(), describeQuery(), describeQuery(), RDKit::RDValue::destroy(), RDKit::GeneralMolSupplier::determineFormat(), DiceSimilarity(), Dict::getVal< std::string >(), RDKit::MolDraw2D_detail::StringRect::doesItIntersect(), RDKit::DGeomHelpers::EmbedMolecule(), RDKit::DGeomHelpers::EmbedMultipleConfs(), RDKit::DGeomHelpers::EmbedMultipleConfs(), RDKit::DGeomHelpers::EmbedMultipleConfs(), EndianSwapBytes(), eraseUniquePtr(), RDKit::DrawColour::feq(), RDKit::FMCS::DuplicatedSeedCache::find(), findUniquePtr(), RDKit::SGroupWriting::FormatV2000DoubleField(), RDKit::SGroupWriting::FormatV2000IntField(), RDKit::SGroupWriting::FormatV2000NumEntriesField(), RDKit::SGroupWriting::FormatV2000StringField(), RDKit::MolStandardize::fragmentRemoverFromParams(), from_rdany(), from_rdvalue(), RDKit::SparseIntVect< IndexType >::fromString(), RDKit::FMCS::Composition2N::generateNext(), RDKit::FileParserUtils::getAtomPropertyList(), RDKit::CIPLabeler::Rules::getComparision(), getLine(), getLine(), RDKit::MolEnumerator::utils::getMolLinkNodes(), getNumThreadsToUse(), RDKit::RDProps::getProp(), RDKit::RDProps::getPropIfPresent(), RDKit::RDProps::getPropList(), RDKit::GeneralMolSupplier::getSupplier(), RDKit::RDValue::getTag(), RDKit::SparseIntVect< IndexType >::getTotalVal(), RDKit::MolStandardize::getV1TautomerEnumerator(), RDKit::SparseIntVect< IndexType >::getVal(), hanoi(), hanoisort(), RDKit::MHFPFingerprints::FNV::hash(), RDKit::GeneralizedSubstruct::hasSubstructMatch(), RDKit::CartesianProduct::increment(), RDKit::FMCS::TargetMatch::init(), RDKit::MolBundle::initFromStream(), RDKit::MolBundle::initFromString(), RDKit::FMCS::Composition2N::is2Power(), RDKit::MolDraw2D_detail::StringRect::isPointInside(), RDKit::FMCS::Composition2N::isSet(), makeAtomAliphaticQuery(), makeAtomAromaticQuery(), makeAtomExplicitDegreeQuery(), makeAtomExplicitValenceQuery(), makeAtomFormalChargeQuery(), makeAtomHasAliphaticHeteroatomNbrsQuery(), makeAtomHasChiralTagQuery(), makeAtomHasHeteroatomNbrsQuery(), makeAtomHasImplicitHQuery(), makeAtomHasRingBondQuery(), makeAtomHCountQuery(), makeAtomHeavyAtomDegreeQuery(), makeAtomHybridizationQuery(), makeAtomImplicitHCountQuery(), makeAtomImplicitValenceQuery(), makeAtomInNRingsQuery(), makeAtomInRingQuery(), makeAtomIsBridgeheadQuery(), makeAtomIsotopeQuery(), makeAtomMassQuery(), makeAtomMinRingSizeQuery(), makeAtomMissingChiralTagQuery(), makeAtomNegativeFormalChargeQuery(), makeAtomNonHydrogenDegreeQuery(), makeAtomNumAliphaticHeteroatomNbrsQuery(), makeAtomNumHeteroatomNbrsQuery(), makeAtomNumQuery(), makeAtomNumRadicalElectronsQuery(), makeAtomRangeQuery(), makeAtomRingBondCountQuery(), makeAtomSimpleQuery(), makeAtomTotalDegreeQuery(), makeAtomTotalValenceQuery(), makeAtomType(), makeAtomTypeQuery(), makeAtomUnsaturatedQuery(), makeHasPropQuery(), RDKit::Descriptors::makePropertyQuery(), makePropQuery(), makePropQuery(), RDKit::HasPropQuery< TargetPtr >::Match(), RDKit::HasPropWithValueQuery< TargetPtr, T >::Match(), RDKit::HasPropWithValueQuery< TargetPtr, std::string >::Match(), RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >::Match(), mergeNullQueries(), RDKit::MMFF::MMFFOptimizeMolecule(), RDKit::MMFF::MMFFOptimizeMoleculeConfs(), RDKit::MolBundle::MolBundle(), RDKit::MolBundle::MolBundle(), MolFragmentToCXSmiles(), MolFragmentToSmiles(), MolToCXSmiles(), RDKit::MolInterchange::MolToJSONData(), MolToSmiles(), RDKit::CIPLabeler::CIPMolSpan< T, U >::CIPMolIter::operator!=(), RDKit::CXXAtomIterator< Graph, Vertex, Iterator >::CXXAtomIter::operator!=(), RDKit::CXXBondIterator< Graph, Edge, Iterator >::CXXBondIter::operator!=(), RDKit::DrawColour::operator!=(), RDKit::SparseIntVect< IndexType >::operator!=(), RDKit::SparseIntVect< IndexType >::operator&(), RDKit::SparseIntVect< IndexType >::operator&=(), RDKit::SparseIntVect< IndexType >::operator*(), RDKit::SparseIntVect< IndexType >::operator*=(), RDKit::DrawColour::operator+(), RDKit::SparseIntVect< IndexType >::operator+(), RDKit::SparseIntVect< IndexType >::operator+(), RDKit::SparseIntVect< IndexType >::operator+=(), RDKit::SparseIntVect< IndexType >::operator+=(), RDKit::DrawColour::operator-(), RDKit::SparseIntVect< IndexType >::operator-(), RDKit::SparseIntVect< IndexType >::operator-(), RDKit::SparseIntVect< IndexType >::operator-=(), RDKit::SparseIntVect< IndexType >::operator-=(), RDKit::SparseIntVect< IndexType >::operator/(), RDKit::SparseIntVect< IndexType >::operator/=(), RDKit::CIPLabeler::PairList::operator<(), RDKit::FMCS::DuplicatedSeedCache::TKey::operator<(), RDKit::ScaffoldNetwork::operator<<(), RDKit::ScaffoldNetwork::operator<<(), RDKit::RDAny::operator=(), RDKit::RDProps::operator=(), RDKit::SparseIntVect< IndexType >::operator=(), RDKit::FMCS::TargetMatch::operator=(), RDKit::CXXAtomIterator< Graph, Vertex, Iterator >::CXXAtomIter::operator==(), RDKit::CXXBondIterator< Graph, Edge, Iterator >::CXXBondIter::operator==(), RDKit::DrawColour::operator==(), RDKit::SparseIntVect< IndexType >::operator==(), RDKit::FMCS::DuplicatedSeedCache::TKey::operator==(), RDKit::SparseIntVect< IndexType >::operator|(), RDKit::SparseIntVect< IndexType >::operator|=(), RDKit::ForceFieldsHelper::OptimizeMolecule(), RDKit::ForceFieldsHelper::OptimizeMoleculeConfs(), RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST(), RDKit::CIPLabeler::PairList::PairList(), RDKit::CIPLabeler::Configuration::parity4(), parseAtomType(), RDKit::SGroupParsing::ParseV3000Array(), PNGFileToMetadata(), PNGFileToMol(), PNGFileToMols(), PNGStringToMetadata(), PNGStringToMol(), PNGStringToMols(), RDKit::FileParserUtils::processMolPropertyList(), RDKit::FileParserUtils::processMolPropertyLists(), RDKit::RDValue::ptrCast(), pullPackedIntFromString(), RDKit::detail::qhelper(), queryAtomHasAliphaticHeteroatomNbrs(), queryAtomHasHeteroatomNbrs(), queryAtomHasImplicitH(), queryAtomHeavyAtomDegree(), queryAtomIsInRingOfSize(), queryAtomNonHydrogenDegree(), queryAtomNumAliphaticHeteroatomNbrs(), queryAtomNumHeteroatomNbrs(), queryAtomRingBondCount(), queryBondHasStereo(), queryBondIsInRingOfSize(), RDKit::Canon::rankFragmentAtoms(), RDKit::RDAny::RDAny(), rdany_cast(), rdany_cast(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), RDKit::RDValue::RDValue(), rdvalue_cast(), rdvalue_cast< bool >(), rdvalue_cast< double >(), rdvalue_cast< float >(), rdvalue_cast< int >(), rdvalue_cast< std::int16_t >(), rdvalue_cast< std::int64_t >(), rdvalue_cast< std::int8_t >(), rdvalue_cast< std::string & >(), rdvalue_cast< std::string >(), rdvalue_cast< std::uint16_t >(), rdvalue_cast< std::uint64_t >(), rdvalue_cast< std::uint8_t >(), rdvalue_cast< unsigned int >(), rdvalue_is(), rdvalue_is< std::any >(), rdvalue_tostring(), RDKit::DataStructsExplicitBitVecPropHandler::read(), readPackedIntFromStream(), readRDStringVecValue(), readRDValue(), readRDValueString(), readRDVecValue(), RDKit::Canon::RefinePartitions(), RDKit::CIPLabeler::Rules::Rules(), RDKit::MolBundle::serialize(), setDarkMode(), setDarkMode(), setMonochromeMode(), setMonochromeMode(), RDKit::RDProps::setProp(), RDKit::SparseIntVect< IndexType >::setVal(), RDKit::SGroupParsing::SGroupWarnOrThrow(), SmartsToMol(), SmilesToMol(), RDKit::SparseIntVect< IndexType >::SparseIntVect(), RDKit::SparseIntVect< IndexType >::SparseIntVect(), RDKit::SparseIntVect< IndexType >::SparseIntVect(), RDKit::SLNParse::startMol(), streamRead(), streamRead(), streamRead(), streamReadStringVec(), streamReadVec(), streamWrite(), streamWrite(), streamWriteVec(), RDKit::FileParserUtils::strip(), RDKit::FileParserUtils::stripSpacesAndCast(), RDKit::FileParserUtils::stripSpacesAndCast(), SubstructMatch(), SubstructMatch(), SubstructMatch(), SubstructMatch(), SwapBytes(), TanimotoSimilarity(), RDKit::FMCS::TargetMatch::TargetMatch(), RDKit::CIPLabeler::to_string(), RDKit::MolBundle::toStream(), RDKit::SparseIntVect< IndexType >::toString(), RDKit::CIPLabeler::PairList::toString(), RDKit::RGroupMatch::toString(), TverskySimilarity(), RDKit::UFF::UFFOptimizeMolecule(), RDKit::UFF::UFFOptimizeMoleculeConfs(), updateFromSequence(), RDKit::RDProps::updateProps(), RDKit::UsedLabelMap::UsedLabelMap(), vectToString(), RDKit::DataStructsExplicitBitVecPropHandler::write(), and RDKit::CIPLabeler::Rules::~Rules().
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Definition at line 392 of file RDValue-doublemagic.h.
References rdvalue_is< double >().
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Definition at line 386 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::MaxDouble, and RDKit::RDTypeTag::NaN.
Referenced by rdvalue_cast< double >(), rdvalue_cast< float >(), and rdvalue_is< const double & >().
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Definition at line 369 of file RDValue-taggedunion.h.
References RDKit::RDValue::getTag(), RDKit::RDTypeTag::GetTag< std::any >(), and rdvalue_is().
Referenced by rdvalue_cast(), rdvalue_cast< const std::any & >(), rdvalue_cast< std::any & >(), rdvalue_cast< std::any >(), rdvalue_cast< std::int64_t >(), and rdvalue_cast< std::uint64_t >().
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inline |
Definition at line 187 of file RDValue.h.
References RDKit::RDTypeTag::AnyTag, RDKit::RDTypeTag::BoolTag, RDKit::RDTypeTag::DoubleTag, RDKit::RDTypeTag::FloatTag, RDKit::RDValue::getTag(), RDKit::RDTypeTag::IntTag, rdvalue_cast< bool >(), rdvalue_cast< double >(), rdvalue_cast< float >(), rdvalue_cast< int >(), rdvalue_cast< std::any & >(), rdvalue_cast< std::string >(), rdvalue_cast< unsigned int >(), rdvalue_is(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
Referenced by RDKit::Dict::getVal(), and RDKit::Dict::getValIfPresent().
RDKIT_TRAJECTORY_EXPORT unsigned int RDKit::readAmberTrajectory | ( | const std::string & | fName, |
Trajectory & | traj | ||
) |
Reads coordinates from an AMBER trajectory file into the traj Trajectory object.
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::istream & | inStream, |
int | nToRead = -1 |
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) |
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::string | fileName | ) |
RDKIT_TRAJECTORY_EXPORT unsigned int RDKit::readGromosTrajectory | ( | const std::string & | fName, |
Trajectory & | traj | ||
) |
Reads coordinates from a GROMOS trajectory file into the traj Trajectory object.
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Reads an integer from a stream in packed format and returns the result.
Definition at line 150 of file StreamOps.h.
References rdvalue_is().
Definition at line 549 of file StreamOps.h.
References rdvalue_is(), and streamReadStringVec().
Definition at line 529 of file StreamOps.h.
References rdvalue_is(), and streamRead().
Definition at line 542 of file StreamOps.h.
References rdvalue_is(), and streamRead().
Definition at line 536 of file StreamOps.h.
References rdvalue_is(), and streamReadVec().
RDKIT_FILEPARSERS_EXPORT void RDKit::reapplyMolBlockWedging | ( | ROMol & | mol | ) |
RDKIT_CHEMREACTIONS_EXPORT ROMol * RDKit::reduceProductToSideChains | ( | const ROMOL_SPTR & | product, |
bool | addDummyAtoms = true |
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) |
Reduce the product generated by run_Reactants or run_Reactant to the sidechains that come from the reagents
addDummyAtoms | If true, add dummy atoms to the sidechains for the non-reagent parts of the sidechain. Dummy atoms are annotated with the atom maps from the reaction. If False, then any sidechain atom where a bond was cleaved is annotated with: _rgroupAtomMaps property which indicates the scaffold atommaps that where bonded _rgroupBonds property which indicates the bondtype for each atommap bonded |
RDKIT_RGROUPDECOMPOSITION_EXPORT void RDKit::relabelMappedDummies | ( | ROMol & | mol, |
unsigned int | inputLabels = AtomMap|Isotope|MDLRGroup , |
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unsigned int | outputLabels = MDLRGroup |
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) |
Relabel dummy atoms bearing an R-group mapping (as atom map number, isotope or MDLRGroup label) such that they will be displayed by the rendering code as R# rather than #*, *:#, #*:#, etc. By default, only the MDLRGroup label is retained on output; this may be configured through the outputLabels parameter. In case there are multiple potential R-group mappings, the priority on input is Atom map number > Isotope > MDLRGroup. The inputLabels parameter allows to configure which mappings are taken into consideration.
RDKIT_SUBSTRUCTMATCH_EXPORT void RDKit::removeDuplicates | ( | std::vector< MatchVectType > & | v, |
unsigned int | nAtoms | ||
) |
RDKIT_GRAPHMOL_EXPORT void RDKit::removeGroupsWithAtom | ( | const Atom * | atom, |
std::vector< StereoGroup > & | groups | ||
) |
RDKIT_GRAPHMOL_EXPORT void RDKit::removeGroupsWithAtoms | ( | const std::vector< Atom * > & | atoms, |
std::vector< StereoGroup > & | groups | ||
) |
RDKIT_CHEMREACTIONS_EXPORT void RDKit::removeMappingNumbersFromReactions | ( | const ChemicalReaction & | rxn | ) |
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::BBS RDKit::removeNonmatchingReagents | ( | const ChemicalReaction & | rxn, |
EnumerationTypes::BBS | bbs, | ||
const EnumerationParams & | params = EnumerationParams() |
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) |
Helper function, remove reagents that are incompatible with the reaction. rxn must be sanitized, initialized and preprocessed. this happens automatically in EnumerateLibrary
RDKIT_GRAPHMOL_EXPORT void RDKit::removeSubstanceGroupsReferencingAtom | ( | RWMol & | mol, |
unsigned int | idx | ||
) |
Removes SubstanceGroups which reference a particular atom index.
mol | - molecule to be edited. |
idx | - atom index |
RDKIT_GRAPHMOL_EXPORT void RDKit::removeSubstanceGroupsReferencingBond | ( | RWMol & | mol, |
unsigned int | idx | ||
) |
Removes SubstanceGroups which reference a particular bond index.
mol | - molecule to be edited. |
idx | - bond index |
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::replaceCore | ( | const ROMol & | mol, |
const ROMol & | core, | ||
const MatchVectType & | matchVect, | ||
bool | replaceDummies = true , |
||
bool | labelByIndex = false , |
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bool | requireDummyMatch = false |
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) |
Returns a copy of an ROMol with the atoms and bonds that are referenced by the MatchVector removed. MatchVector must be defined between mol and the specified core.
dummy atoms are left to indicate attachment points. These dummy atoms can be labeled either by the matching index in the query or by an arbitrary "first match" found. Additional matching options are given below.
Note that this is essentially identical to the replaceSidechains function, except we invert the query and replace the atoms that do match the query.
mol | - the ROMol of interest |
core | - the core being matched against |
matchVect | - a matchVect of the type returned by Substructure Matching |
replaceDummies | - if set, atoms matching dummies in the core will also be replaced |
labelByIndex | - if set, the dummy atoms at attachment points are labelled with the index+1 of the corresponding atom in the core |
requireDummyMatch | - if set, only side chains that are connected to atoms in the core that have attached dummies will be considered. Molecules that have sidechains that are attached at other points will be rejected (NULL returned). |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. The client is responsible for deleting this molecule. If the core query is not matched, NULL is returned. RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::replaceCore | ( | const ROMol & | mol, |
const ROMol & | coreQuery, | ||
bool | replaceDummies = true , |
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bool | labelByIndex = false , |
||
bool | requireDummyMatch = false , |
||
bool | useChirality = false |
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) |
Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed.
dummy atoms are left to indicate attachment points.
Note that this is essentially identical to the replaceSidechains function, except we invert the query and replace the atoms that do match the query.
mol | - the ROMol of interest |
coreQuery | - a query ROMol to be used to match the core |
replaceDummies | - if set, atoms matching dummies in the core will also be replaced |
labelByIndex | - if set, the dummy atoms at attachment points are labelled with the index+1 of the corresponding atom in the core |
requireDummyMatch | - if set, only side chains that are connected to atoms in the core that have attached dummies will be considered. Molecules that have sidechains that are attached at other points will be rejected (NULL returned). |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. The client is responsible for deleting this molecule. If the core query is not matched, NULL is returned. RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::replaceSidechains | ( | const ROMol & | mol, |
const ROMol & | coreQuery, | ||
bool | useChirality = false |
||
) |
Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed.
dummy atoms are left to indicate attachment points.
mol | the ROMol of interest |
coreQuery | a query ROMol to be used to match the core |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. RDKIT_CHEMTRANSFORMS_EXPORT std::vector< ROMOL_SPTR > RDKit::replaceSubstructs | ( | const ROMol & | mol, |
const ROMol & | query, | ||
const ROMol & | replacement, | ||
bool | replaceAll = false , |
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unsigned int | replacementConnectionPoint = 0 , |
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bool | useChirality = false |
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) |
Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule.
Bonds are created between the joining atom in the existing molecule and the atoms in the new molecule. So, using SMILES instead of molecules: replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]') -> ['[X]NCCNC(=O)O','OC(=O)NCCN[X]'] replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]',true) -> ['[X]NCCN[X]'] Chains should be handled "correctly": replaceSubstructs('CC(=O)C','C(=O)','[X]') -> ['C[X]C'] As should rings: replaceSubstructs('C1C(=O)C1','C(=O)','[X]') -> ['C1[X]C1'] And higher order branches: replaceSubstructs('CC(=O)(C)C','C(=O)','[X]') -> ['C[X](C)C'] Note that the client is responsible for making sure that the resulting molecule actually makes sense - this function does not perform sanitization.
mol | the ROMol of interest |
query | the query ROMol |
replacement | the ROMol to be inserted |
replaceAll | if this is true, only a single result, with all |
useChirality | - if set, match the coreQuery using chirality |
occurrences of the substructure replaced, will be returned.
replacementConnectionPoint | index of the atom in the replacement that the bond should made to |
mol
with the matching atoms and bonds (if any) replaced RDKIT_RGROUPDECOMPOSITION_EXPORT unsigned int RDKit::RGroupDecompose | ( | const std::vector< ROMOL_SPTR > & | cores, |
const std::vector< ROMOL_SPTR > & | mols, | ||
RGroupColumns & | columns, | ||
std::vector< unsigned int > * | unmatched = nullptr , |
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const RGroupDecompositionParameters & | options = RGroupDecompositionParameters() |
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) |
RDKIT_RGROUPDECOMPOSITION_EXPORT unsigned int RDKit::RGroupDecompose | ( | const std::vector< ROMOL_SPTR > & | cores, |
const std::vector< ROMOL_SPTR > & | mols, | ||
RGroupRows & | rows, | ||
std::vector< unsigned int > * | unmatched = nullptr , |
||
const RGroupDecompositionParameters & | options = RGroupDecompositionParameters() |
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) |
RDKIT_CHEMREACTIONS_EXPORT std::vector< MOL_SPTR_VECT > RDKit::run_Reactant | ( | const ChemicalReaction & | rxn, |
const ROMOL_SPTR & | reactant, | ||
unsigned int | reactantIdx | ||
) |
Runs a single reactant against a single reactant template.
reactant | The single reactant to use |
reactantTemplateIdx | the reactant template to target in the reaction |
We return a vector of vectors of products because each individual template may map multiple times onto its reactant. This leads to multiple possible result sets.
RDKIT_CHEMREACTIONS_EXPORT bool RDKit::run_Reactant | ( | const ChemicalReaction & | rxn, |
RWMol & | reactant, | ||
bool | removeUnmatchedAtoms = true |
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) |
RDKIT_CHEMREACTIONS_EXPORT std::vector< MOL_SPTR_VECT > RDKit::run_Reactants | ( | const ChemicalReaction & | rxn, |
const MOL_SPTR_VECT & | reactants, | ||
unsigned int | maxProducts = 1000 |
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) |
Runs the reaction on a set of reactants.
rxn | the template reaction we are interested |
reactants | the reactants to be used. The length of this must be equal to rxn->getNumReactantTemplates() Caution: The order of the reactant templates determines the order of the reactants! |
maxProducts | if non zero, the maximum number of products to generate before stopping. If hit a warning will be generated. |
We return a vector of vectors of products because each individual template may map multiple times onto its reactant. This leads to multiple possible result sets.
RDKIT_FILTERCATALOG_EXPORT std::vector< std::vector< boost::shared_ptr< const FilterCatalogEntry > > > RDKit::RunFilterCatalog | ( | const FilterCatalog & | filterCatalog, |
const std::vector< std::string > & | smiles, | ||
int | numThreads = 1 |
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) |
Run a filter catalog on a set of smiles strings.
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RDKit::RxnBlockToChemicalReaction | ( | const std::string & | rxnBlock, |
bool | sanitize = false , |
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bool | removeHs = false , |
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bool | strictParsing = true |
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) |
Parse a text block in MDL rxn format into a ChemicalReaction.
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RDKit::RxnDataStreamToChemicalReaction | ( | std::istream & | rxnStream, |
unsigned int & | line, | ||
bool | sanitize = false , |
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bool | removeHs = false , |
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bool | strictParsing = true |
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) |
Parse a text stream in MDL rxn format into a ChemicalReaction.
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RDKit::RxnFileToChemicalReaction | ( | const std::string & | fileName, |
bool | sanitize = false , |
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bool | removeHs = false , |
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bool | strictParsing = true |
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) |
Parse a file in MDL rxn format into a ChemicalReaction.
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RDKit::RxnMolToChemicalReaction | ( | const ROMol & | mol | ) |
Parse a ROMol into a ChemicalReaction, RXN role must be set before.
Alternative to build a reaction from a molecule (fragments) which have RXN roles set as atom properties: common_properties::molRxnRole (1=reactant, 2=product, 3=agent)
mol | ROMol with RXN roles set |
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RDKit::RxnSmartsToChemicalReaction | ( | const std::string & | text, |
std::map< std::string, std::string > * | replacements = nullptr , |
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bool | useSmiles = false , |
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bool | allowCXSMILES = true |
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) |
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 |
allowCXSMILES | if set, any CXSMILES extensions present will be parsed, otherwise it will be ignored |
Referenced by operator""_rxnsmarts(), and operator""_rxnsmiles().
RDKIT_FILEPARSERS_EXPORT bool RDKit::SamePDBResidue | ( | AtomPDBResidueInfo * | p, |
AtomPDBResidueInfo * | q | ||
) |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol | ( | const char * | seq, |
bool | sanitize, | ||
bool | lowerD | ||
) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
lowerD | - if set, lower case letters will be parsed as the d form of the corresponding amino acid |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol | ( | const char * | seq, |
bool | sanitize = true , |
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int | flavor = 0 |
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) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
flavor | - 0 Protein, L amino acids (default) 1 Protein, D amino acids 2 RNA, no cap 3 RNA, 5' cap 4 RNA, 3' cap 5 RNA, both caps 6 DNA, no cap 7 DNA, 5' cap 8 DNA, 3' cap 9 DNA, both caps |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol | ( | const std::string & | seq, |
bool | sanitize, | ||
bool | lowerD | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::SequenceToMol | ( | const std::string & | seq, |
bool | sanitize = true , |
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int | flavor = 0 |
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) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_GRAPHMOL_EXPORT void RDKit::setAtomAlias | ( | Atom * | atom, |
const std::string & | alias | ||
) |
Set the atom's MDL atom alias Setting to an empty string clears the alias
RDKIT_GRAPHMOL_EXPORT void RDKit::setAtomRLabel | ( | Atom * | atm, |
int | rlabel | ||
) |
Set the atom's MDL integer RLabel Setting to 0 clears the rlabel. Rlabel must be in the range [0..99]
RDKIT_GRAPHMOL_EXPORT void RDKit::setAtomValue | ( | Atom * | atom, |
const std::string & | value | ||
) |
Set the atom's MDL atom value Setting to an empty string clears the value This is where recursive smarts get stored in MolBlock Queries
Definition at line 555 of file MolDraw2D.h.
References rdvalue_is(), and setDarkMode().
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Definition at line 547 of file MolDraw2D.h.
References assignDarkModePalette(), and rdvalue_is().
Referenced by setDarkMode().
bool RDKit::setLabel | ( | Atom * | atom, |
int | label, | ||
std::set< int > & | labels, | ||
int & | maxLabel, | ||
bool | relabel, | ||
Labelling | type | ||
) |
Set the rgroup label for the current atom, this also sets the appropriate MDL or other label
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Definition at line 566 of file MolDraw2D.h.
References rdvalue_is(), and setMonochromeMode().
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Definition at line 556 of file MolDraw2D.h.
References rdvalue_is().
Referenced by setMonochromeMode().
RDKIT_GRAPHMOL_EXPORT void RDKit::setSupplementalSmilesLabel | ( | Atom * | atom, |
const std::string & | label | ||
) |
Sets the supplemental label that will follow the atom when writing smiles strings.
RDKIT_SLNPARSE_EXPORT RWMol * RDKit::SLNQueryToMol | ( | const std::string & | smi, |
bool | mergeHs = true , |
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int | debugParse = 0 |
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) |
RDKIT_SLNPARSE_EXPORT RWMol * RDKit::SLNToMol | ( | const std::string & | smi, |
bool | sanitize = true , |
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int | debugParse = 0 |
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) |
RDKIT_SMILESPARSE_EXPORT Atom * RDKit::SmartsToAtom | ( | const std::string & | sma | ) |
RDKIT_SMILESPARSE_EXPORT Bond * RDKit::SmartsToBond | ( | const std::string & | sma | ) |
RDKIT_SMILESPARSE_EXPORT RWMol * RDKit::SmartsToMol | ( | const std::string & | sma, |
const SmartsParserParams & | ps | ||
) |
Referenced by operator""_smarts(), and SmartsToMol().
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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. |
Definition at line 112 of file SmilesParse.h.
References RDKit::SmartsParserParams::debugParse, rdvalue_is(), and SmartsToMol().
RDKIT_SMILESPARSE_EXPORT Atom * RDKit::SmilesToAtom | ( | const std::string & | smi | ) |
RDKIT_SMILESPARSE_EXPORT Bond * RDKit::SmilesToBond | ( | const std::string & | smi | ) |
RDKIT_SMILESPARSE_EXPORT RWMol * RDKit::SmilesToMol | ( | const std::string & | smi, |
const SmilesParserParams & | params | ||
) |
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Construct a molecule from a SMILES string.
smi | the SMILES to convert |
debugParse | toggles verbose debugging information from the parser |
sanitize | toggles H removal and sanitization of the molecule |
replacements | a string->string map of replacement strings. See below for more information about replacements. |
The optional replacements map can be used to do string substitution of abbreviations in the input SMILES. The set of substitutions is repeatedly looped through until the string no longer changes. It is the responsibility of the caller to make sure that substitutions results in legal and sensible SMILES.
Examples of substitutions:
Definition at line 68 of file SmilesParse.h.
References RDKit::SmilesParserParams::debugParse, rdvalue_is(), RDKit::SmilesParserParams::removeHs, RDKit::SmilesParserParams::replacements, RDKit::SmilesParserParams::sanitize, and SmilesToMol().
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::sortMatchesByDegreeOfCoreSubstitution | ( | const ROMol & | mol, |
const ROMol & | core, | ||
const std::vector< MatchVectType > & | matches | ||
) |
This returns a copy of the passed substruct matches sorted by decreasing number of non-hydrogen atoms in correspondence of terminal dummy atoms
RDKIT_FILEPARSERS_EXPORT void RDKit::StandardPDBResidueBondOrders | ( | RWMol * | mol | ) |
Definition at line 299 of file StreamOps.h.
References RDUNUSED_PARAM, and rdvalue_is().
does a binary read of an object from a stream
Definition at line 283 of file StreamOps.h.
References rdvalue_is().
Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream(), RDKit::DataStructsExplicitBitVecPropHandler::read(), readRDValue(), readRDValueString(), streamRead(), streamReadStringVec(), and streamReadVec().
special case for string
Definition at line 294 of file StreamOps.h.
References RDUNUSED_PARAM, rdvalue_is(), and streamRead().
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Definition at line 556 of file StreamOps.h.
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Definition at line 626 of file StreamOps.h.
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Definition at line 326 of file StreamOps.h.
References rdvalue_is(), and streamRead().
Referenced by readRDStringVecValue().
Definition at line 316 of file StreamOps.h.
References rdvalue_is(), and streamRead().
Referenced by readRDVecValue().
does a binary write of an object to a stream
Definition at line 261 of file StreamOps.h.
References rdvalue_is().
Referenced by streamWriteVec(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream(), RDKit::SparseIntVect< IndexType >::toString(), and RDKit::DataStructsExplicitBitVecPropHandler::write().
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Definition at line 412 of file StreamOps.h.
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Definition at line 485 of file StreamOps.h.
Definition at line 274 of file StreamOps.h.
References rdvalue_is(), and streamWrite().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::strip | ( | const std::string & | orig | ) |
RDKIT_CHEMREACTIONS_EXPORT ExplicitBitVect * RDKit::StructuralFingerprintChemReaction | ( | const ChemicalReaction & | rxn, |
const ReactionFingerprintParams & | params = DefaultStructuralFPParams |
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) |
Generates a structural fingerprint for a reaction to use in screening
A structural fingerprint is generated as an ExplicitBitVect to use for searching e.g. substructure in reactions. By default the fingerprint is generated as 4096 BitVect using a PatternFP for reactants and products and tentatively agents which were finally concatenated
rxn | the reaction to be fingerprinted |
params | specific settings to manipulate fingerprint generation |
Notes:
delete
ing the result RDKIT_SUBSTRUCTLIBRARY_EXPORT bool RDKit::SubstructLibraryCanSerialize | ( | ) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const MolBundle & | bundle, |
const MolBundle & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() |
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) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const MolBundle & | bundle, |
const ROMol & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() |
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) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const ROMol & | mol, |
const MolBundle & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() |
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) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const ROMol & | mol, |
const ROMol & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() |
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) |
Find a substructure match for a query in a molecule.
mol | The ROMol to be searched |
query | The query ROMol |
matchParams | Parameters controlling the matching |
Referenced by SubstructMatch(), SubstructMatch(), SubstructMatch(), and SubstructMatch().
RDKIT_TAUTOMERQUERY_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | const ROMol & | mol, |
const TautomerQuery & | query, | ||
const SubstructMatchParameters & | params | ||
) |
RDKIT_SUBSTRUCTMATCH_EXPORT std::vector< MatchVectType > RDKit::SubstructMatch | ( | ResonanceMolSupplier & | resMolSuppl, |
const ROMol & | query, | ||
const SubstructMatchParameters & | params = SubstructMatchParameters() |
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) |
Find all substructure matches for a query in a ResonanceMolSupplier object.
resMolSuppl | The ResonanceMolSupplier object to be searched |
query | The query ROMol |
matchParams | Parameters controlling the matching |
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Definition at line 213 of file SubstructMatch.h.
References RDKit::SubstructMatchParameters::maxMatches, RDKit::SubstructMatchParameters::numThreads, rdvalue_is(), RDKit::SubstructMatchParameters::recursionPossible, SubstructMatch(), RDKit::SubstructMatchParameters::uniquify, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.
bool RDKit::SubstructMatch | ( | T1 & | mol, |
const T2 & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
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bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
Find a substructure match for a query.
mol | The object to be searched |
query | The query |
matchVect | Used to return the match (pre-existing contents will be deleted) |
recursionPossible | flags whether or not recursive matches are allowed |
useChirality | use atomic CIP codes as part of the comparison |
useQueryQueryMatches | if set, the contents of atom and bond queries will be used as part of the matching |
Definition at line 130 of file SubstructMatch.h.
References RDKit::SubstructMatchParameters::maxMatches, rdvalue_is(), RDKit::SubstructMatchParameters::recursionPossible, SubstructMatch(), RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.
unsigned int RDKit::SubstructMatch | ( | T1 & | mol, |
const T2 & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = true , |
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bool | recursionPossible = true , |
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bool | useChirality = false , |
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bool | useQueryQueryMatches = false , |
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unsigned int | maxMatches = 1000 , |
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int | numThreads = 1 |
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Find all substructure matches for a query.
mol | The object to be searched |
query | The query |
matchVect | Used to return the matches (pre-existing contents will be deleted) |
uniquify | Toggles uniquification (by atom index) of the results |
recursionPossible | flags whether or not recursive matches are allowed |
useChirality | use atomic CIP codes as part of the comparison |
useQueryQueryMatches | if set, the contents of atom and bond queries will be used as part of the matching |
maxMatches | The maximum number of matches that will be returned. In high-symmetry cases with medium-sized molecules, it is very easy to end up with a combinatorial explosion in the number of possible matches. This argument prevents that from having unintended consequences |
Definition at line 170 of file SubstructMatch.h.
References RDKit::SubstructMatchParameters::maxMatches, RDKit::SubstructMatchParameters::numThreads, rdvalue_is(), RDKit::SubstructMatchParameters::recursionPossible, SubstructMatch(), RDKit::SubstructMatchParameters::uniquify, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.
RDKIT_SUBSTRUCTMATCH_EXPORT std::string RDKit::substructMatchParamsToJSON | ( | const SubstructMatchParameters & | params | ) |
Definition at line 45 of file StreamOps.h.
References rdvalue_is().
double RDKit::TanimotoSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
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double | bounds = 0.0 |
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Definition at line 564 of file SparseIntVect.h.
References rdvalue_is(), and TverskySimilarity().
Referenced by RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >::Match().
RDKIT_TAUTOMERQUERY_EXPORT bool RDKit::TautomerQueryCanSerialize | ( | ) |
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON | ( | const RGroupColumn & | rgr, |
const std::string & | prefix = "" |
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Returns a JSON form The prefix argument is added to each line in the output
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON | ( | const RGroupRow & | rgr, |
const std::string & | prefix = "" |
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Returns a JSON form The prefix argument is added to each line in the output
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON | ( | const RGroupRows & | rgr, |
const std::string & | prefix = "" |
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Returns a JSON form The prefix argument is added to each line in the output
RDKIT_SUBSTRUCTMATCH_EXPORT double RDKit::toPrime | ( | const MatchVectType & | v | ) |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::TPLDataStreamToMol | ( | std::istream * | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
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bool | skipFirstConf = false |
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translate TPL data (BioCad format) into a multi-conf molecule
inStream | the stream from which to read |
line | used to track the line number of errors |
sanitize | toggles sanitization and stereochemistry perception of the molecule |
skipFirstConf | according to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set. |
References TPLDataStreamToMol().
Referenced by TPLDataStreamToMol().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::TPLFileToMol | ( | const std::string & | fName, |
bool | sanitize = true , |
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bool | skipFirstConf = false |
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construct a multi-conf molecule from a TPL (BioCad format) file
fName | the name of the file from which to read |
sanitize | toggles sanitization and stereochemistry perception of the molecule |
skipFirstConf | according to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set. |
References TPLFileToMol().
Referenced by TPLFileToMol().
RDKIT_FILEPARSERS_EXPORT void RDKit::translateChiralFlagToStereoGroups | ( | ROMol & | mol, |
StereoGroupType | zeroFlagGroupType = StereoGroupType::STEREO_AND |
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generate enhanced stereo groups based on the status of the chiral flag property
double RDKit::TverskySimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
double | a, | ||
double | b, | ||
bool | returnDistance = false , |
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double | bounds = 0.0 |
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Definition at line 535 of file SparseIntVect.h.
References RDUNUSED_PARAM, and rdvalue_is().
Referenced by TanimotoSimilarity().
RDKIT_RDGENERAL_EXPORT void RDKit::Union | ( | const INT_VECT & | r1, |
const INT_VECT & | r2, | ||
INT_VECT & | res | ||
) |
calculate the union of two INT_VECTs and put the results in a third vector
RDKIT_RDGENERAL_EXPORT void RDKit::Union | ( | const VECT_INT_VECT & | rings, |
INT_VECT & | res, | ||
const INT_VECT * | exclude = nullptr |
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calculating the union of the INT_VECT's in a VECT_INT_VECT
rings | the INT_VECT's to consider |
res | used to return results |
exclude | any values in this optional INT_VECT will be excluded from the union. |
void RDKit::updateFromSequence | ( | SparseIntVect< IndexType > & | vect, |
const SequenceType & | seq | ||
) |
Definition at line 416 of file SparseIntVect.h.
References rdvalue_is().
RDKIT_CHEMREACTIONS_EXPORT void RDKit::updateProductsStereochem | ( | ChemicalReaction * | rxn | ) |
RDKIT_SUBSTRUCTMATCH_EXPORT void RDKit::updateSubstructMatchParamsFromJSON | ( | SubstructMatchParameters & | params, |
const std::string & | json | ||
) |
Definition at line 176 of file RDValue.h.
References rdvalue_is().
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 | ||
) |
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::XYZBlockToMol | ( | const std::string & | xyzBlock | ) |
xyzBlock | - string containing the xyz block |
References XYZBlockToMol().
Referenced by XYZBlockToMol().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::XYZDataStreamToMol | ( | std::istream & | inStream | ) |
References XYZDataStreamToMol().
Referenced by XYZDataStreamToMol().
RDKIT_FILEPARSERS_EXPORT RWMol * RDKit::XYZFileToMol | ( | const std::string & | fName | ) |
fName | - string containing the file name |
References XYZFileToMol().
Referenced by XYZFileToMol().
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Definition at line 21 of file DiscreteValueVect.h.
Referenced by RDKit::DiscreteValueVect::DiscreteValueVect().
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const std::vector<std::string> RDKit::complexQueries |
Definition at line 599 of file QueryOps.h.
Definition at line 16 of file ProximityBonds.h.
Definition at line 28 of file GasteigerParams.h.
Definition at line 27 of file GasteigerParams.h.
const DashPattern RDKit::dashes {6.0, 4.0} |
Definition at line 28 of file DrawShape.h.
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Definition at line 35 of file MolWriters.h.
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const DashPattern RDKit::dots {2.0, 6.0} |
Definition at line 27 of file DrawShape.h.
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Definition at line 27 of file RGroupUtils.h.
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Definition at line 25 of file GasteigerParams.h.
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const std::string RDKit::LayeredFingerprintMolVersion = "0.7.0" |
Definition at line 113 of file Fingerprints.h.
Definition at line 63 of file MolDraw2DHelpers.h.
const std::vector<std::string> RDKit::marvinBondOrders {"1", "2", "3", "A"} |
Definition at line 40 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinConventionTypes {"cxn:coord"} |
Definition at line 42 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinQueryBondsTypes {"SD", "SA", "DA", "Any"} |
Definition at line 41 of file MarvinDefs.h.
Definition at line 49 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinRadicalVals |
Definition at line 46 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinStereoConventionTypes {"1", "3", "4", "6"} |
Definition at line 44 of file MarvinDefs.h.
const std::vector<std::string> RDKit::marvinStereoDictRefTypes {"cml:W", "cml:H"} |
Definition at line 43 of file MarvinDefs.h.
Definition at line 155 of file QueryOps.h.
Referenced by makeAtomMassQuery(), and queryAtomMass().
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Definition at line 112 of file Fingerprints.h.
Definition at line 26 of file FileParsers.h.
const DashPattern RDKit::noDash |
Definition at line 26 of file DrawShape.h.
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const std::string RDKit::PatternFingerprintMolVersion = "1.0.0" |
Definition at line 149 of file Fingerprints.h.
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Definition at line 53 of file MarvinDefs.h.
const std::string RDKit::RDKFingerprintMolVersion = "2.0.0" |
Definition at line 63 of file Fingerprints.h.
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const DashPattern RDKit::shortDashes {2.0, 2.0} |
Definition at line 29 of file DrawShape.h.
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const std::vector<std::string> RDKit::sruSgroupConnectChoices {"hh", "ht", "eu"} |
Definition at line 39 of file MarvinDefs.h.
Definition at line 114 of file Fingerprints.h.
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