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RDKit
Open-source cheminformatics and machine learning.
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Includes a bunch of functionality for handling Atom and Bond queries. More...
Namespaces | |
AtomPairs | |
Canon | |
common_properties | |
Descriptors | |
DGeomHelpers | |
Drawing | |
FileParserUtils | |
Fingerprints | |
FMCS | |
Local | |
MACCSFingerprints | |
MMFF | |
MolAlign | |
MolDraw2D_detail | |
MolFragmenter | |
MolHash | |
MolOps | |
Groups a variety of molecular query and transformation operations. | |
MolShapes | |
MorganFingerprints | |
SLNParse | |
SmartsWrite | |
SmilesWrite | |
Subgraphs | |
UFF | |
Utils | |
Classes | |
class | AromaticAtomIterator_ |
Iterate over aromatic atoms, this is bidirectional. More... | |
class | Atom |
The class for representing atoms. More... | |
class | atomicData |
class | AtomIterator_ |
A general random access iterator. More... | |
class | AtomMonomerInfo |
The abstract base class for atom-level monomer info. More... | |
class | AtomPDBResidueInfo |
Captures atom-level information about peptide residues. More... | |
class | AtomRingQuery |
class | BadFileException |
used by various file parsing classes to indicate a bad file More... | |
class | Bond |
class for representing a bond More... | |
class | BondIterator_ |
iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
struct | charptr_functor |
functor for comparing two strings More... | |
class | ChemicalReaction |
This is a class for storing and applying general chemical reactions. More... | |
class | ChemicalReactionException |
used to indicate an error in the chemical reaction engine More... | |
class | ChemicalReactionParserException |
used to indicate an error in parsing reaction data More... | |
class | Conformer |
The class for representing 2D or 3D conformation of a molecule. More... | |
class | ConformerException |
used to indicate errors from incorrect confomer access More... | |
class | ConstBondIterator_ |
const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
class | Dict |
The Dict class can be used to store objects of arbitrary type keyed by strings . More... | |
class | DiscreteDistMat |
class | DiscreteValueVect |
a class for efficiently storing vectors of discrete values More... | |
class | 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 | ForwardSDMolSupplier |
class | FragCatalogEntry |
class | FragCatGenerator |
class | FragCatParams |
container for user parameters used to create a fragment catalog More... | |
class | FragFPGenerator |
class | GasteigerParams |
class | HasPropQuery |
class | HasPropWithValueQuery |
class | HasPropWithValueQuery< TargetPtr, std::string > |
class | HeteroatomIterator_ |
Iterate over heteroatoms, this is bidirectional. More... | |
struct | larger_of |
functor for returning the larger of two values More... | |
struct | ltDouble |
functor to compare two doubles with a tolerance More... | |
class | MatchingAtomIterator_ |
Iterate over atoms matching a query function. This is bidirectional. More... | |
struct | MCSAtomCompareParameters |
struct | MCSBondCompareParameters |
struct | MCSParameters |
struct | MCSProgressData |
struct | MCSResult |
class | 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 |
class | MolDraw2DCairo |
class | MolDraw2DQt |
class | MolDraw2DSVG |
class | MolDraw2Dwx |
struct | MolDrawOptions |
class | MolPickler |
handles pickling (serializing) molecules More... | |
class | MolPicklerException |
used to indicate exceptions whilst pickling (serializing) molecules More... | |
class | MolSanitizeException |
class for flagging sanitization errors More... | |
class | MolSupplier |
class | MolWriter |
class | 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... | |
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 | RingInfo |
A class to store information about a molecule's rings. More... | |
class | ROMol |
ROMol is a molecule class that is intended to have a fixed topology. More... | |
class | RWMol |
RWMol is a molecule class that is intended to be edited. More... | |
class | SDMolSupplier |
class | SDWriter |
class | SLNParseException |
class | SmilesMolSupplier |
lazy file parser for Smiles tables More... | |
class | SmilesParseException |
class | SmilesWriter |
class | SparseIntVect |
a class for efficiently storing sparse vectors of ints More... | |
class | TDTMolSupplier |
lazy file parser for TDT files More... | |
class | TDTWriter |
Typedefs | |
typedef boost::shared_ptr< Atom > | ATOM_SPTR |
typedef boost::shared_ptr< ROMol > | ROMOL_SPTR |
typedef boost::shared_ptr< Conformer > | CONFORMER_SPTR |
typedef boost::uint16_t | atomindex_t |
typedef std::vector< RWMOL_SPTR > | RWMOL_SPTR_VECT |
typedef bool(* | MCSFinalMatchCheckFunction) (const short unsigned c1[], const short unsigned c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p) |
typedef bool(* | MCSAtomCompareFunction) (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
typedef bool(* | MCSBondCompareFunction) (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
typedef bool(* | MCSProgressCallback) (const MCSProgressData &stat, const MCSParameters ¶ms, void *userData) |
typedef RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int > | FragCatalog |
typedef std::vector< boost::shared_ptr< ROMol > > | MOL_SPTR_VECT |
typedef std::vector< std::pair< int, int > > | MatchVectType |
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx) More... | |
typedef RDCatalog::HierarchCatalog< MolCatalogEntry, MolCatalogParams, int > | MolCatalog |
a hierarchical catalog for holding molecules More... | |
typedef boost::shared_ptr< MolChemicalFeature > | FeatSPtr |
typedef std::list< FeatSPtr > | FeatSPtrList |
typedef FeatSPtrList::iterator | FeatSPtrList_I |
typedef boost::tuple< float, float, float > | DrawColour |
typedef std::vector< unsigned int > | DashPattern |
typedef std::vector< double > | INVAR_VECT |
typedef INVAR_VECT::iterator | INVAR_VECT_I |
typedef INVAR_VECT::const_iterator | INVAR_VECT_CI |
typedef Queries::Query< bool, Atom const *, true > | ATOM_BOOL_QUERY |
typedef Queries::Query< bool, Bond const *, true > | BOND_BOOL_QUERY |
typedef Queries::AndQuery< int, Atom const *, true > | ATOM_AND_QUERY |
typedef Queries::AndQuery< int, Bond const *, true > | BOND_AND_QUERY |
typedef Queries::OrQuery< int, Atom const *, true > | ATOM_OR_QUERY |
typedef Queries::OrQuery< int, Bond const *, true > | BOND_OR_QUERY |
typedef Queries::XOrQuery< int, Atom const *, true > | ATOM_XOR_QUERY |
typedef Queries::XOrQuery< int, Bond const *, true > | BOND_XOR_QUERY |
typedef Queries::EqualityQuery< int, Atom const *, true > | ATOM_EQUALS_QUERY |
typedef Queries::EqualityQuery< int, Bond const *, true > | BOND_EQUALS_QUERY |
typedef Queries::GreaterQuery< int, Atom const *, true > | ATOM_GREATER_QUERY |
typedef Queries::GreaterQuery< int, Bond const *, true > | BOND_GREATER_QUERY |
typedef Queries::GreaterEqualQuery< int, Atom const *, true > | ATOM_GREATEREQUAL_QUERY |
typedef Queries::GreaterEqualQuery< int, Bond const *, true > | BOND_GREATEREQUAL_QUERY |
typedef Queries::LessQuery< int, Atom const *, true > | ATOM_LESS_QUERY |
typedef Queries::LessQuery< int, Bond const *, true > | BOND_LESS_QUERY |
typedef Queries::LessEqualQuery< int, Atom const *, true > | ATOM_LESSEQUAL_QUERY |
typedef Queries::LessEqualQuery< int, Bond const *, true > | BOND_LESSEQUAL_QUERY |
typedef Queries::RangeQuery< int, Atom const *, true > | ATOM_RANGE_QUERY |
typedef Queries::RangeQuery< int, Bond const *, true > | BOND_RANGE_QUERY |
typedef Queries::SetQuery< int, Atom const *, true > | ATOM_SET_QUERY |
typedef Queries::SetQuery< int, Bond const *, true > | BOND_SET_QUERY |
typedef Queries::Query< int, Bond const *, true > | BOND_NULL_QUERY |
typedef Queries::Query< int, Atom const *, true > | ATOM_NULL_QUERY |
typedef Atom const * | ConstAtomPtr |
typedef Bond const * | ConstBondPtr |
typedef Queries::EqualityQuery< int, Atom const *, true > | ATOM_PROP_QUERY |
typedef Queries::EqualityQuery< int, Bond const *, true > | BOND_PROP_QUERY |
typedef boost::shared_ptr< Bond > | BOND_SPTR |
typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, ATOM_SPTR, BOND_SPTR > | MolGraph |
This is the BGL type used to store the topology: More... | |
typedef std::vector< ROMol > | MOL_VECT |
typedef std::vector< ROMol * > | MOL_PTR_VECT |
typedef MOL_PTR_VECT::const_iterator | MOL_PTR_VECT_CI |
typedef MOL_PTR_VECT::iterator | MOL_PTR_VECT_I |
typedef boost::shared_ptr< RWMol > | RWMOL_SPTR |
typedef std::vector< int > | PATH_TYPE |
typedef std::list< PATH_TYPE > | PATH_LIST |
typedef PATH_LIST::const_iterator | PATH_LIST_CI |
typedef std::map< int, PATH_LIST > | INT_PATH_LIST_MAP |
typedef INT_PATH_LIST_MAP::const_iterator | INT_PATH_LIST_MAP_CI |
typedef INT_PATH_LIST_MAP::iterator | INT_PATH_LIST_MAP_I |
typedef std::vector< std::string > | STR_VECT |
typedef long long int | LONGINT |
typedef unsigned int | UINT |
typedef unsigned short | USHORT |
typedef unsigned char | UCHAR |
typedef std::vector< int > | INT_VECT |
typedef INT_VECT::iterator | INT_VECT_I |
typedef INT_VECT::const_iterator | INT_VECT_CI |
typedef INT_VECT::reverse_iterator | INT_VECT_RI |
typedef INT_VECT::const_reverse_iterator | INT_VECT_CRI |
typedef std::list< int > | INT_LIST |
typedef INT_LIST::iterator | INT_LIST_I |
typedef INT_LIST::const_iterator | INT_LIST_CI |
typedef std::list< INT_VECT > | LIST_INT_VECT |
typedef LIST_INT_VECT::iterator | LIST_INT_VECT_I |
typedef LIST_INT_VECT::const_iterator | LIST_INT_VECT_CI |
typedef std::vector< INT_VECT > | VECT_INT_VECT |
typedef VECT_INT_VECT::iterator | VECT_INT_VECT_I |
typedef VECT_INT_VECT::const_iterator | VECT_INT_VECT_CI |
typedef std::vector< UINT >::const_iterator | UINT_VECT_CI |
typedef std::vector< UINT > | UINT_VECT |
typedef std::vector< std::string >::const_iterator | STR_VECT_CI |
typedef std::vector< std::string >::iterator | STR_VECT_I |
typedef std::vector< double > | DOUBLE_VECT |
typedef DOUBLE_VECT::iterator | DOUBLE_VECT_I |
typedef DOUBLE_VECT::const_iterator | DOUBLE_VECT_CI |
typedef std::vector< DOUBLE_VECT > | VECT_DOUBLE_VECT |
typedef VECT_DOUBLE_VECT::iterator | VECT_DOUBLE_VECT_I |
typedef VECT_DOUBLE_VECT::const_iterator | VECT_DOUBLE_VECT_CI |
typedef std::map< std::string, UINT > | STR_UINT_MAP |
typedef std::map< std::string, UINT >::const_iterator | STR_UINT_MAP_CI |
typedef std::map< int, INT_VECT > | INT_INT_VECT_MAP |
typedef INT_INT_VECT_MAP::const_iterator | INT_INT_VECT_MAP_CI |
typedef std::map< int, int > | INT_MAP_INT |
typedef INT_MAP_INT::iterator | INT_MAP_INT_I |
typedef INT_MAP_INT::const_iterator | INT_MAP_INT_CI |
typedef std::deque< int > | INT_DEQUE |
typedef INT_DEQUE::iterator | INT_DEQUE_I |
typedef INT_DEQUE::const_iterator | INT_DEQUE_CI |
typedef std::map< int, INT_DEQUE > | INT_INT_DEQ_MAP |
typedef INT_INT_DEQ_MAP::const_iterator | INT_INT_DEQ_MAP_CI |
typedef std::set< int > | INT_SET |
typedef INT_SET::iterator | INT_SET_I |
typedef INT_SET::const_iterator | INT_SET_CI |
typedef std::map< double, int, ltDouble > | DOUBLE_INT_MAP |
std::map from double to integer. More... | |
typedef boost::minstd_rand | rng_type |
typedef boost::uniform_int | uniform_int |
typedef boost::uniform_real | uniform_double |
typedef boost::variate_generator< rng_type &, uniform_int > | int_source_type |
typedef boost::variate_generator< rng_type &, uniform_double > | double_source_type |
Enumerations | |
enum | FingerprintType { AtomPairFP = 1, TopologicalTorsion, MorganFP, RDKitFP, PatternFP } |
enum | ReactionMoleculeType { Reactant, Product, Agent } |
enum | Mol2Type { CORINA =0 } |
enum | AtomComparator { AtomCompareAny, AtomCompareElements, AtomCompareIsotopes } |
enum | BondComparator { BondCompareAny, BondCompareOrder, BondCompareOrderExact } |
enum | EEndian { LITTLE_ENDIAN_ORDER, BIG_ENDIAN_ORDER } |
Functions | |
bool | isMoleculeReactantOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which) |
bool | isMoleculeReactantOfReaction (const ChemicalReaction &rxn, const ROMol &mol) |
bool | isMoleculeProductOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which) |
bool | isMoleculeProductOfReaction (const ChemicalReaction &rxn, const ROMol &mol) |
bool | isMoleculeAgentOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which) |
bool | isMoleculeAgentOfReaction (const ChemicalReaction &rxn, const ROMol &mol) |
VECT_INT_VECT | getReactingAtoms (const ChemicalReaction &rxn, bool mappedAtomsOnly=false) |
void | addRecursiveQueriesToReaction (ChemicalReaction &rxn, const std::map< std::string, ROMOL_SPTR > &queries, std::string propName, std::vector< std::vector< std::pair< unsigned int, std::string > > > *reactantLabels=NULL) |
add the recursive queries to the reactants of a reaction More... | |
const ReactionFingerprintParams | DefaultStructuralFPParams (true, 0.2, 1, 1, 4096, PatternFP) |
const ReactionFingerprintParams | DefaultDifferenceFPParams (true, 0.0, 10, 1, 2048, AtomPairFP) |
ExplicitBitVect * | StructuralFingerprintChemReaction (const ChemicalReaction &rxn, const ReactionFingerprintParams ¶ms=DefaultStructuralFPParams) |
SparseIntVect< boost::uint32_t > * | DifferenceFingerprintChemReaction (const ChemicalReaction &rxn, const ReactionFingerprintParams ¶ms=DefaultDifferenceFPParams) |
ChemicalReaction * | RxnBlockToChemicalReaction (const std::string &rxnBlock) |
Parse a text block in MDL rxn format into a ChemicalReaction. More... | |
ChemicalReaction * | RxnFileToChemicalReaction (const std::string &fileName) |
Parse a file in MDL rxn format into a ChemicalReaction. More... | |
ChemicalReaction * | RxnDataStreamToChemicalReaction (std::istream &rxnStream, unsigned int &line) |
Parse a text stream in MDL rxn format into a ChemicalReaction. More... | |
ChemicalReaction * | RxnSmartsToChemicalReaction (const std::string &text, std::map< std::string, std::string > *replacements=0, bool useSmiles=false) |
Parse a string containing "Reaction SMARTS" into a ChemicalReaction. More... | |
ChemicalReaction * | RxnMolToChemicalReaction (const ROMol &mol) |
Parse a ROMol into a ChemicalReaction, RXN role must be set before. More... | |
std::string | ChemicalReactionToRxnSmarts (const ChemicalReaction &rxn) |
returns the reaction SMARTS for a reaction More... | |
std::string | ChemicalReactionToRxnSmiles (const ChemicalReaction &rxn, bool canonical=true) |
returns the reaction SMILES for a reaction More... | |
std::string | ChemicalReactionToRxnBlock (const ChemicalReaction &rxn, bool separateAgents=false) |
returns an RXN block for a reaction More... | |
ROMol * | ChemicalReactionToRxnMol (const ChemicalReaction &rxn) |
returns a ROMol with RXN roles used to describe the reaction More... | |
std::vector< MOL_SPTR_VECT > | run_Reactants (const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants) |
Runs the reaction on a set of reactants. More... | |
MOL_SPTR_VECT::const_iterator | getStartIterator (const ChemicalReaction &rxn, ReactionMoleculeType t) |
MOL_SPTR_VECT::const_iterator | getEndIterator (const ChemicalReaction &rxn, ReactionMoleculeType t) |
bool | hasReactantTemplateSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn) |
bool | hasProductTemplateSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn) |
bool | hasAgentTemplateSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn) |
bool | hasReactionSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn, bool includeAgents=false) |
bool | hasReactionAtomMapping (const ChemicalReaction &rxn) |
bool | isReactionTemplateMoleculeAgent (const ROMol &mol, double agentThreshold) |
void | updateProductsStereochem (ChemicalReaction *rxn) |
ROMol * | deleteSubstructs (const ROMol &mol, const ROMol &query, bool onlyFrags=false) |
Returns a copy of an ROMol with the atoms and bonds that match a pattern removed. More... | |
std::vector< ROMOL_SPTR > | replaceSubstructs (const ROMol &mol, const ROMol &query, const ROMol &replacement, bool replaceAll=false, unsigned int replacementConnectionPoint=0) |
Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule. More... | |
ROMol * | replaceSidechains (const ROMol &mol, const ROMol &coreQuery) |
Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed. More... | |
ROMol * | replaceCore (const ROMol &mol, const ROMol &coreQuery, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false) |
Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed. More... | |
ROMol * | MurckoDecompose (const ROMol &mol) |
Carries out a Murcko decomposition on the molecule provided. More... | |
ROMol * | combineMols (const ROMol &mol1, const ROMol &mol2, RDGeom::Point3D offset=RDGeom::Point3D(0, 0, 0)) |
Combined two molecules to create a new one. More... | |
void | addRecursiveQueries (ROMol &mol, const std::map< std::string, ROMOL_SPTR > &queries, std::string propName, std::vector< std::pair< unsigned int, std::string > > *reactantLabels=NULL) |
Adds named recursive queries to a molecule's atoms based on atom labels. More... | |
void | parseQueryDefFile (std::string filename, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, std::string delimiter="\t", std::string comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1) |
parses a query definition file and sets up a set of definitions suitable for use by addRecursiveQueries() More... | |
void | parseQueryDefFile (std::istream *inStream, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, std::string delimiter="\t", std::string comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1) |
void | parseQueryDefText (const std::string &queryDefText, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, std::string delimiter="\t", std::string comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1) |
equivalent to parseQueryDefFile() but the query definitions are explicitly passed in More... | |
std::string | strip (const std::string &orig) |
RWMol * | MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | MolFileToMol (std::string fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
std::string | MolToMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false) |
void | MolToMolFile (const ROMol &mol, std::string fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false) |
RWMol * | TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false) |
translate TPL data (BioCad format) into a multi-conf molecule More... | |
RWMol * | TPLFileToMol (std::string fName, bool sanitize=true, bool skipFirstConf=false) |
construct a multi-conf molecule from a TPL (BioCad format) file More... | |
std::string | MolToTPLText (const ROMol &mol, std::string partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false) |
void | MolToTPLFile (const ROMol &mol, std::string fName, std::string partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false) |
RWMol * | Mol2FileToMol (std::string fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA) |
RWMol * | Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA) |
RWMol * | Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA) |
RWMol * | Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA) |
RWMol * | PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
RWMol * | PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
RWMol * | PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
RWMol * | PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
RWMol * | PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
std::string | MolToPDBBlock (const ROMol &mol, int confId=-1, unsigned int flavor=0) |
void | MolToPDBFile (const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) |
void | DetectAtomStereoChemistry (RWMol &mol, const Conformer *conf) |
void | DetectBondStereoChemistry (ROMol &mol, const Conformer *conf) |
void | WedgeMolBonds (ROMol &mol, const Conformer *conf) |
INT_MAP_INT | pickBondsToWedge (const ROMol &mol) |
void | ClearSingleBondDirFlags (ROMol &mol) |
Bond::BondDir | DetermineBondWedgeState (const Bond *bond, const INT_MAP_INT &wedgeBonds, const Conformer *conf) |
void | ConnectTheDots (RWMol *mol) |
void | StandardPDBResidueBondOrders (RWMol *mol) |
ExplicitBitVect * | RDKFingerprintMol (const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< boost::uint32_t > *atomInvariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, std::vector< std::vector< boost::uint32_t > > *atomBits=0) |
Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm. More... | |
ExplicitBitVect * | LayeredFingerprintMol (const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=0, ExplicitBitVect *setOnlyBits=0, bool branchedPaths=true, const std::vector< boost::uint32_t > *fromAtoms=0) |
Generates a topological (Daylight like) fingerprint for a molecule using a layer-based hashing algorithm. More... | |
ExplicitBitVect * | PatternFingerprintMol (const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=0, ExplicitBitVect *setOnlyBits=0) |
Generates a topological fingerprint for a molecule using a series of pre-defined structural patterns. More... | |
bool | MCSAtomCompareAny (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
bool | MCSAtomCompareElements (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
bool | MCSAtomCompareIsotopes (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
bool | MCSBondCompareAny (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
bool | MCSBondCompareOrder (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
bool | MCSBondCompareOrderExact (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
bool | MCSProgressCallbackTimeout (const MCSProgressData &stat, const MCSParameters ¶ms, void *userData) |
void | parseMCSParametersJSON (const char *json, MCSParameters *params) |
MCSResult | findMCS (const std::vector< ROMOL_SPTR > &mols, const MCSParameters *params=0) |
MCSResult | findMCS_P (const std::vector< ROMOL_SPTR > &mols, const char *params_json) |
MCSResult | findMCS (const std::vector< ROMOL_SPTR > &mols, bool maximizeBonds, double threshold=1.0, unsigned timeout=3600, bool verbose=false, bool matchValences=false, bool ringMatchesRingOnly=false, bool completeRingsOnly=false, bool matchChiralTag=false, AtomComparator atomComp=AtomCompareElements, BondComparator bondComp=BondCompareOrder) |
bool | FinalChiralityCheckFunction (const short unsigned c1[], const short unsigned c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p) |
MOL_SPTR_VECT | readFuncGroups (std::string fileName) |
MOL_SPTR_VECT | readFuncGroups (std::istream &inStream, int nToRead=-1) |
MatchVectType | findFuncGroupsOnMol (const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds) |
ROMol * | prepareMol (const ROMol &mol, const FragCatParams *fparams, MatchVectType &aToFmap) |
int | parseFeatureData (const std::string &defnText, MolChemicalFeatureDef::CollectionType &featDefs) |
int | parseFeatureData (std::istream &istream, MolChemicalFeatureDef::CollectionType &featDefs) |
int | parseFeatureFile (const std::string &fileName, MolChemicalFeatureDef::CollectionType &featDefs) |
MolChemicalFeatureFactory * | buildFeatureFactory (std::istream &inStream) |
constructs a MolChemicalFeatureFactory from the data in a stream More... | |
MolChemicalFeatureFactory * | buildFeatureFactory (const std::string &featureData) |
constructs a MolChemicalFeatureFactory from the data in a string More... | |
void | computeGasteigerCharges (const ROMol *mol, int nIter=12, bool throwOnParamFailure=false) |
void | computeGasteigerCharges (const ROMol &mol, int nIter=12, bool throwOnParamFailure=false) |
void | computeGasteigerCharges (const ROMol &mol, std::vector< double > &charges, int nIter=12, bool throwOnParamFailure=false) |
static int | queryAtomAromatic (Atom const *at) |
static int | queryAtomAliphatic (Atom const *at) |
static int | queryAtomExplicitDegree (Atom const *at) |
static int | queryAtomTotalDegree (Atom const *at) |
static int | queryAtomHeavyAtomDegree (Atom const *at) |
static int | queryAtomHCount (Atom const *at) |
static int | queryAtomImplicitHCount (Atom const *at) |
static int | queryAtomHasImplicitH (Atom const *at) |
static int | queryAtomImplicitValence (Atom const *at) |
static int | queryAtomExplicitValence (Atom const *at) |
static int | queryAtomTotalValence (Atom const *at) |
static int | queryAtomUnsaturated (Atom const *at) |
static int | queryAtomNum (Atom const *at) |
static int | queryAtomMass (Atom const *at) |
static int | queryAtomIsotope (Atom const *at) |
static int | queryAtomFormalCharge (Atom const *at) |
static int | queryAtomHybridization (Atom const *at) |
unsigned int | queryAtomBondProduct (Atom const *at) |
unsigned int | queryAtomAllBondProduct (Atom const *at) |
static int | queryBondOrder (Bond const *bond) |
static int | queryBondDir (Bond const *bond) |
static int | queryIsBondInNRings (Bond const *at) |
static int | queryIsAtomInNRings (Atom const *at) |
static int | queryIsAtomInRing (Atom const *at) |
static int | queryAtomHasRingBond (Atom const *at) |
static int | queryIsBondInRing (Bond const *bond) |
static int | queryAtomMinRingSize (Atom const *at) |
static int | queryBondMinRingSize (Bond const *bond) |
static int | queryAtomRingBondCount (Atom const *at) |
template<int tgt> | |
int | queryAtomIsInRingOfSize (Atom const *at) |
template<int tgt> | |
int | queryBondIsInRingOfSize (Bond const *bond) |
template<class T > | |
T * | makeAtomSimpleQuery (int what, int func(Atom const *), const std::string &description="Atom Simple") |
template<class T > | |
T * | makeAtomNumQuery (int what, const std::string &descr) |
returns a Query for matching atomic number More... | |
ATOM_EQUALS_QUERY * | makeAtomNumQuery (int what) |
template<class T > | |
T * | makeAtomImplicitValenceQuery (int what, const std::string &descr) |
returns a Query for matching implicit valence More... | |
ATOM_EQUALS_QUERY * | makeAtomImplicitValenceQuery (int what) |
template<class T > | |
T * | makeAtomExplicitValenceQuery (int what, const std::string &descr) |
returns a Query for matching explicit valence More... | |
ATOM_EQUALS_QUERY * | makeAtomExplicitValenceQuery (int what) |
template<class T > | |
T * | makeAtomTotalValenceQuery (int what, const std::string &descr) |
returns a Query for matching total valence More... | |
ATOM_EQUALS_QUERY * | makeAtomTotalValenceQuery (int what) |
template<class T > | |
T * | makeAtomExplicitDegreeQuery (int what, const std::string &descr) |
returns a Query for matching explicit degree More... | |
ATOM_EQUALS_QUERY * | makeAtomExplicitDegreeQuery (int what) |
template<class T > | |
T * | makeAtomTotalDegreeQuery (int what, const std::string &descr) |
returns a Query for matching atomic degree More... | |
ATOM_EQUALS_QUERY * | makeAtomTotalDegreeQuery (int what) |
template<class T > | |
T * | makeAtomHCountQuery (int what, const std::string &descr) |
returns a Query for matching hydrogen count More... | |
ATOM_EQUALS_QUERY * | makeAtomHCountQuery (int what) |
template<class T > | |
T * | makeAtomHasImplicitHQuery (const std::string &descr) |
returns a Query for matching ring atoms More... | |
ATOM_EQUALS_QUERY * | makeAtomHasImplicitHQuery () |
template<class T > | |
T * | makeAtomImplicitHCountQuery (int what, const std::string &descr) |
returns a Query for matching implicit hydrogen count More... | |
ATOM_EQUALS_QUERY * | makeAtomImplicitHCountQuery (int what) |
template<class T > | |
T * | makeAtomAromaticQuery (const std::string &descr) |
returns a Query for matching the isAromatic flag More... | |
ATOM_EQUALS_QUERY * | makeAtomAromaticQuery () |
template<class T > | |
T * | makeAtomAliphaticQuery (const std::string &descr) |
returns a Query for matching aliphatic atoms More... | |
ATOM_EQUALS_QUERY * | makeAtomAliphaticQuery () |
template<class T > | |
T * | makeAtomMassQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular mass More... | |
ATOM_EQUALS_QUERY * | makeAtomMassQuery (int what) |
template<class T > | |
T * | makeAtomIsotopeQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular isotope More... | |
ATOM_EQUALS_QUERY * | makeAtomIsotopeQuery (int what) |
template<class T > | |
T * | makeAtomFormalChargeQuery (int what, const std::string &descr) |
returns a Query for matching formal charge More... | |
ATOM_EQUALS_QUERY * | makeAtomFormalChargeQuery (int what) |
template<class T > | |
T * | makeAtomHybridizationQuery (int what, const std::string &descr) |
returns a Query for matching hybridization More... | |
ATOM_EQUALS_QUERY * | makeAtomHybridizationQuery (int what) |
template<class T > | |
T * | makeAtomUnsaturatedQuery (const std::string &descr) |
returns a Query for matching atoms with unsaturation: More... | |
ATOM_EQUALS_QUERY * | makeAtomUnsaturatedQuery () |
template<class T > | |
T * | makeAtomInRingQuery (const std::string &descr) |
returns a Query for matching ring atoms More... | |
ATOM_EQUALS_QUERY * | makeAtomInRingQuery () |
template<class T > | |
T * | makeAtomInNRingsQuery (int what, const std::string &descr) |
returns a Query for matching atoms in a particular number of rings More... | |
ATOM_EQUALS_QUERY * | makeAtomInNRingsQuery (int what) |
ATOM_EQUALS_QUERY * | makeAtomInRingOfSizeQuery (int tgt) |
returns a Query for matching atoms in rings of a particular size More... | |
template<class T > | |
T * | makeAtomMinRingSizeQuery (int tgt, const std::string &descr) |
returns a Query for matching an atom's minimum ring size More... | |
ATOM_EQUALS_QUERY * | makeAtomMinRingSizeQuery (int tgt) |
template<class T > | |
T * | makeAtomRingBondCountQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular number of ring bonds More... | |
ATOM_EQUALS_QUERY * | makeAtomRingBondCountQuery (int what) |
template<class T > | |
T * | makeAtomHasRingBondQuery (const std::string &descr) |
returns a Query for matching atoms with a particular number of ring bonds More... | |
ATOM_EQUALS_QUERY * | makeAtomHasRingBondQuery () |
BOND_EQUALS_QUERY * | makeBondOrderEqualsQuery (Bond::BondType what) |
returns a Query for matching bond orders More... | |
BOND_EQUALS_QUERY * | makeBondDirEqualsQuery (Bond::BondDir what) |
returns a Query for matching bond directions More... | |
BOND_EQUALS_QUERY * | makeBondIsInRingQuery () |
returns a Query for matching ring bonds More... | |
BOND_EQUALS_QUERY * | makeBondInRingOfSizeQuery (int what) |
returns a Query for matching bonds in rings of a particular size More... | |
BOND_EQUALS_QUERY * | makeBondMinRingSizeQuery (int what) |
returns a Query for matching a bond's minimum ring size More... | |
BOND_EQUALS_QUERY * | makeBondInNRingsQuery (int tgt) |
returns a Query for matching bonds in a particular number of rings More... | |
BOND_NULL_QUERY * | makeBondNullQuery () |
returns a Query for matching any bond More... | |
ATOM_NULL_QUERY * | makeAtomNullQuery () |
returns a Query for matching any atom More... | |
static int | queryAtomRingMembership (Atom const *at) |
template<typename T > | |
int | nullDataFun (T arg) |
template<typename T > | |
bool | nullQueryFun (T arg) |
template<class Target > | |
Queries::EqualityQuery< int, const Target *, true > * | makeHasPropQuery (const std::string &property) |
returns a Query for matching atoms that have a particular property More... | |
template<class Target , class T > | |
Queries::EqualityQuery< int, const Target *, true > * | makePropQuery (const std::string &propname, const T &val, const T &tolerance=T()) |
RWMol * | SLNToMol (std::string smi, bool sanitize=true, int debugParse=0) |
RWMol * | SLNQueryToMol (std::string smi, bool mergeHs=true, int debugParse=0) |
std::string | MolToSmarts (ROMol &mol, bool doIsomericSmarts=false) |
returns the SMARTS for a molecule More... | |
RWMol * | SmilesToMol (std::string smi, int debugParse=0, bool sanitize=1, std::map< std::string, std::string > *replacements=0) |
Construct a molecule from a SMILES string. More... | |
RWMol * | SmartsToMol (std::string sma, int debugParse=0, bool mergeHs=false, std::map< std::string, std::string > *replacements=0) |
Construct a molecule from a SMARTS string. More... | |
std::string | MolToSmiles (const ROMol &mol, bool doIsomericSmiles=false, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) |
returns canonical SMILES for a molecule More... | |
std::string | MolFragmentToSmiles (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=0, const std::vector< std::string > *atomSymbols=0, const std::vector< std::string > *bondSymbols=0, bool doIsomericSmiles=false, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) |
returns canonical SMILES for part of a molecule More... | |
INT_PATH_LIST_MAP | findAllSubgraphsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useHs=false, int rootedAtAtom=-1) |
find all bond subgraphs in a range of sizes More... | |
PATH_LIST | findAllSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, int rootedAtAtom=-1) |
find all bond subgraphs of a particular size More... | |
PATH_LIST | findUniqueSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, bool useBO=true, int rootedAtAtom=-1) |
find unique bond subgraphs of a particular size More... | |
PATH_LIST | findAllPathsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1) |
find all paths of a particular size More... | |
INT_PATH_LIST_MAP | findAllPathsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1) |
PATH_TYPE | findAtomEnvironmentOfRadiusN (const ROMol &mol, unsigned int radius, unsigned int rootedAtAtom, bool useHs=false) |
find bond subgraphs of a particular radius around an atom More... | |
bool | SubstructMatch (const ROMol &mol, const ROMol &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
Find a substructure match for a query in a molecule. More... | |
unsigned int | SubstructMatch (const ROMol &mol, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000) |
Find all substructure matches for a query in a molecule. More... | |
double | toPrime (const MatchVectType &v) |
void | removeDuplicates (std::vector< MatchVectType > &v, unsigned int nAtoms) |
bool | atomCompat (const ATOM_SPTR &a1, const ATOM_SPTR &a2, bool useQueryQueryMatches=false) |
bool | chiralAtomCompat (const ATOM_SPTR &a1, const ATOM_SPTR &a2) |
bool | bondCompat (const BOND_SPTR &b1, const BOND_SPTR &b2, bool useQueryQueryMatches=false) |
DiscreteDistMat * | getDiscreteDistMat () |
unsigned int | computeL1Norm (const DiscreteValueVect &v1, const DiscreteValueVect &v2) |
DiscreteValueVect | operator+ (const DiscreteValueVect &p1, const DiscreteValueVect &p2) |
DiscreteValueVect | operator- (const DiscreteValueVect &p1, const DiscreteValueVect &p2) |
template<typename IndexType , typename SequenceType > | |
void | updateFromSequence (SparseIntVect< IndexType > &vect, const SequenceType &seq) |
template<typename IndexType > | |
double | DiceSimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, bool returnDistance=false, double bounds=0.0) |
template<typename IndexType > | |
double | TverskySimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, double a, double b, bool returnDistance=false, double bounds=0.0) |
template<typename IndexType > | |
double | TanimotoSimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, bool returnDistance=false, double bounds=0.0) |
template<typename CompareFunc > | |
bool | hanoi (int *base, int nel, int *temp, int *count, int *changed, CompareFunc compar) |
template<typename CompareFunc > | |
void | hanoisort (int *base, int nel, int *count, int *changed, CompareFunc compar) |
template<class T , unsigned int size> | |
T | SwapBytes (T value) |
template<EEndian from, EEndian to, class T > | |
T | EndianSwapBytes (T value) |
template<EEndian from, EEndian to> | |
char | EndianSwapBytes (char value) |
template<EEndian from, EEndian to> | |
unsigned char | EndianSwapBytes (unsigned char value) |
template<EEndian from, EEndian to> | |
signed char | EndianSwapBytes (signed char value) |
void | appendPackedIntToStream (std::stringstream &ss, boost::uint32_t num) |
Packs an integer and outputs it to a stream. More... | |
boost::uint32_t | readPackedIntFromStream (std::stringstream &ss) |
Reads an integer from a stream in packed format and returns the result. More... | |
boost::uint32_t | pullPackedIntFromString (const char *&text) |
template<typename T > | |
void | streamWrite (std::ostream &ss, const T &val) |
does a binary write of an object to a stream More... | |
template<typename T > | |
void | streamRead (std::istream &ss, T &loc) |
does a binary read of an object from a stream More... | |
std::string | getLine (std::istream *inStream) |
grabs the next line from an instream and returns it. More... | |
std::string | getLine (std::istream &inStream) |
grabs the next line from an instream and returns it. More... | |
void | Union (const INT_VECT &r1, const INT_VECT &r2, INT_VECT &res) |
calculate the union of two INT_VECTs and put the results in a third vector More... | |
void | Intersect (const INT_VECT &r1, const INT_VECT &r2, INT_VECT &res) |
calculate the intersection of two INT_VECTs and put the results in a third vector More... | |
void | Union (const VECT_INT_VECT &rings, INT_VECT &res, const INT_VECT *exclude=NULL) |
calculating the union of the INT_VECT's in a VECT_INT_VECT More... | |
int | nextCombination (INT_VECT &comb, int tot) |
given a current combination of numbers change it to the next possible combination More... | |
double | round (double v) |
rounds a value to the closest int More... | |
double | computeIntVectPrimesProduct (const INT_VECT &ring) |
compute the product of the set of primes corresponding to the values in an INT_VECT More... | |
bool | feq (double v1, double v2, double tol=1e-4) |
floating point comparison with a tolerance More... | |
rng_type & | getRandomGenerator (int seed=-1) |
Optionally seed and return a reference to the global (Boost) random generator. More... | |
double | getRandomVal (int seed=-1) |
double_source_type & | getDoubleRandomSource () |
return a reference to the global (Boost) random source More... | |
template<class T > | |
unsigned int | countSwapsToInterconvert (const T &ref, T probe) |
Variables | |
const std::string | periodicTableAtomData |
const std::string | isotopesAtomData [] |
const int | MOLFILE_MAXLINE =256 |
static int | defaultConfId =-1 |
const std::string | RDKFingerprintMolVersion ="2.0.0" |
const unsigned int | maxFingerprintLayers =10 |
const std::string | LayeredFingerprintMolVersion ="0.7.0" |
const unsigned int | substructLayers =0x07 |
std::string | paramData |
std::string | additionalParamData |
const double | IONXH = 20.02 |
const double | DAMP_SCALE = 0.5 |
const double | DAMP = 0.5 |
static int | massIntegerConversionFactor =1000 |
const int | ci_RIGHTMOST_ATOM |
const int | ci_LEADING_BOND |
const int | ci_ATOM_HOLDER |
const int | NUM_PRIMES_AVAIL = 1000 |
the number of primes available and stored More... | |
int | firstThousandPrimes [NUM_PRIMES_AVAIL] |
const unsigned int | BITS_PER_INT =32 |
const double | MAX_DOUBLE = std::numeric_limits<double>::max() |
const double | EPS_DOUBLE = std::numeric_limits<double>::epsilon() |
const double | SMALL_DOUBLE = 1.0e-8 |
const double | MAX_INT = static_cast<double>(std::numeric_limits<int>::max()) |
const double | MAX_LONGINT = static_cast<double>(std::numeric_limits<LONGINT>::max()) |
const int | FILE_MAXLINE =256 |
an assumed maximum length for lines read from files More... | |
const char * | rdkitVersion ="2015.03.1" |
const char * | boostVersion ="1_60" |
typedef Queries::AndQuery<int,Atom const *,true> RDKit::ATOM_AND_QUERY |
Definition at line 30 of file QueryOps.h.
typedef Queries::Query<bool,Atom const *,true> RDKit::ATOM_BOOL_QUERY |
Definition at line 27 of file QueryOps.h.
typedef Queries::EqualityQuery<int,Atom const *,true> RDKit::ATOM_EQUALS_QUERY |
Definition at line 39 of file QueryOps.h.
typedef Queries::GreaterQuery<int,Atom const *,true> RDKit::ATOM_GREATER_QUERY |
Definition at line 42 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int,Atom const *,true> RDKit::ATOM_GREATEREQUAL_QUERY |
Definition at line 45 of file QueryOps.h.
typedef Queries::LessQuery<int,Atom const *,true> RDKit::ATOM_LESS_QUERY |
Definition at line 48 of file QueryOps.h.
typedef Queries::LessEqualQuery<int,Atom const *,true> RDKit::ATOM_LESSEQUAL_QUERY |
Definition at line 51 of file QueryOps.h.
typedef Queries::Query<int,Atom const *,true> RDKit::ATOM_NULL_QUERY |
Definition at line 61 of file QueryOps.h.
typedef Queries::OrQuery<int,Atom const *,true> RDKit::ATOM_OR_QUERY |
Definition at line 33 of file QueryOps.h.
typedef Queries::EqualityQuery< int,Atom const *,true> RDKit::ATOM_PROP_QUERY |
Definition at line 529 of file QueryOps.h.
typedef Queries::RangeQuery<int,Atom const *,true> RDKit::ATOM_RANGE_QUERY |
Definition at line 54 of file QueryOps.h.
typedef Queries::SetQuery<int,Atom const *,true> RDKit::ATOM_SET_QUERY |
Definition at line 57 of file QueryOps.h.
typedef boost::shared_ptr< Atom > RDKit::ATOM_SPTR |
typedef Queries::XOrQuery<int,Atom const *,true> RDKit::ATOM_XOR_QUERY |
Definition at line 36 of file QueryOps.h.
typedef boost::uint16_t RDKit::atomindex_t |
typedef Queries::AndQuery<int,Bond const *,true> RDKit::BOND_AND_QUERY |
Definition at line 31 of file QueryOps.h.
typedef Queries::Query<bool,Bond const *,true> RDKit::BOND_BOOL_QUERY |
Definition at line 28 of file QueryOps.h.
typedef Queries::EqualityQuery<int,Bond const *,true> RDKit::BOND_EQUALS_QUERY |
Definition at line 40 of file QueryOps.h.
typedef Queries::GreaterQuery<int,Bond const *,true> RDKit::BOND_GREATER_QUERY |
Definition at line 43 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int,Bond const *,true> RDKit::BOND_GREATEREQUAL_QUERY |
Definition at line 46 of file QueryOps.h.
typedef Queries::LessQuery<int,Bond const *,true> RDKit::BOND_LESS_QUERY |
Definition at line 49 of file QueryOps.h.
typedef Queries::LessEqualQuery<int,Bond const *,true> RDKit::BOND_LESSEQUAL_QUERY |
Definition at line 52 of file QueryOps.h.
typedef Queries::Query<int,Bond const *,true> RDKit::BOND_NULL_QUERY |
Definition at line 60 of file QueryOps.h.
typedef Queries::OrQuery<int,Bond const *,true> RDKit::BOND_OR_QUERY |
Definition at line 34 of file QueryOps.h.
typedef Queries::EqualityQuery< int,Bond const *,true> RDKit::BOND_PROP_QUERY |
Definition at line 531 of file QueryOps.h.
typedef Queries::RangeQuery<int,Bond const *,true> RDKit::BOND_RANGE_QUERY |
Definition at line 55 of file QueryOps.h.
typedef Queries::SetQuery<int,Bond const *,true> RDKit::BOND_SET_QUERY |
Definition at line 58 of file QueryOps.h.
typedef boost::shared_ptr< Bond > RDKit::BOND_SPTR |
typedef Queries::XOrQuery<int,Bond const *,true> RDKit::BOND_XOR_QUERY |
Definition at line 37 of file QueryOps.h.
typedef boost::shared_ptr<Conformer> RDKit::CONFORMER_SPTR |
Definition at line 135 of file Conformer.h.
typedef Atom const* RDKit::ConstAtomPtr |
Definition at line 374 of file QueryOps.h.
typedef Bond const* RDKit::ConstBondPtr |
Definition at line 486 of file QueryOps.h.
typedef std::vector<unsigned int> RDKit::DashPattern |
Definition at line 38 of file MolDraw2D.h.
typedef std::map<double, int, ltDouble> RDKit::DOUBLE_INT_MAP |
typedef boost::variate_generator<rng_type &,uniform_double> RDKit::double_source_type |
typedef std::vector<double> RDKit::DOUBLE_VECT |
typedef DOUBLE_VECT::const_iterator RDKit::DOUBLE_VECT_CI |
typedef DOUBLE_VECT::iterator RDKit::DOUBLE_VECT_I |
typedef boost::tuple<float,float,float> RDKit::DrawColour |
Definition at line 37 of file MolDraw2D.h.
typedef boost::shared_ptr<MolChemicalFeature> RDKit::FeatSPtr |
Definition at line 18 of file MolChemicalFeatureFactory.h.
typedef std::list< FeatSPtr > RDKit::FeatSPtrList |
Definition at line 20 of file MolChemicalFeatureFactory.h.
typedef FeatSPtrList::iterator RDKit::FeatSPtrList_I |
Definition at line 21 of file MolChemicalFeatureFactory.h.
typedef RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int > RDKit::FragCatalog |
Definition at line 19 of file FragCatGenerator.h.
typedef std::deque<int> RDKit::INT_DEQUE |
typedef INT_DEQUE::const_iterator RDKit::INT_DEQUE_CI |
typedef INT_DEQUE::iterator RDKit::INT_DEQUE_I |
typedef std::map<int, INT_DEQUE> RDKit::INT_INT_DEQ_MAP |
typedef INT_INT_DEQ_MAP::const_iterator RDKit::INT_INT_DEQ_MAP_CI |
typedef std::map<int, INT_VECT> RDKit::INT_INT_VECT_MAP |
typedef INT_INT_VECT_MAP::const_iterator RDKit::INT_INT_VECT_MAP_CI |
typedef std::list<int> RDKit::INT_LIST |
typedef INT_LIST::const_iterator RDKit::INT_LIST_CI |
typedef INT_LIST::iterator RDKit::INT_LIST_I |
typedef std::map<int, int> RDKit::INT_MAP_INT |
typedef INT_MAP_INT::const_iterator RDKit::INT_MAP_INT_CI |
typedef INT_MAP_INT::iterator RDKit::INT_MAP_INT_I |
typedef std::map<int, PATH_LIST> RDKit::INT_PATH_LIST_MAP |
Definition at line 45 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::const_iterator RDKit::INT_PATH_LIST_MAP_CI |
Definition at line 46 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::iterator RDKit::INT_PATH_LIST_MAP_I |
Definition at line 47 of file Subgraphs.h.
typedef std::set<int> RDKit::INT_SET |
typedef INT_SET::const_iterator RDKit::INT_SET_CI |
typedef INT_SET::iterator RDKit::INT_SET_I |
typedef boost::variate_generator<rng_type &,uniform_int> RDKit::int_source_type |
typedef std::vector<int> RDKit::INT_VECT |
typedef INT_VECT::const_iterator RDKit::INT_VECT_CI |
typedef INT_VECT::const_reverse_iterator RDKit::INT_VECT_CRI |
typedef INT_VECT::iterator RDKit::INT_VECT_I |
typedef INT_VECT::reverse_iterator RDKit::INT_VECT_RI |
typedef std::vector<double> RDKit::INVAR_VECT |
typedef INVAR_VECT::const_iterator RDKit::INVAR_VECT_CI |
typedef INVAR_VECT::iterator RDKit::INVAR_VECT_I |
typedef std::list<INT_VECT> RDKit::LIST_INT_VECT |
typedef LIST_INT_VECT::const_iterator RDKit::LIST_INT_VECT_CI |
typedef LIST_INT_VECT::iterator RDKit::LIST_INT_VECT_I |
typedef long long int RDKit::LONGINT |
typedef std::vector< std::pair< int, int > > RDKit::MatchVectType |
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)
Definition at line 22 of file FragFPGenerator.h.
typedef bool(* RDKit::MCSAtomCompareFunction) (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
typedef bool(* RDKit::MCSBondCompareFunction) (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
typedef bool(* RDKit::MCSFinalMatchCheckFunction) (const short unsigned c1[], const short unsigned c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p) |
typedef bool(* RDKit::MCSProgressCallback) (const MCSProgressData &stat, const MCSParameters ¶ms, void *userData) |
typedef std::vector<ROMol *> RDKit::MOL_PTR_VECT |
typedef MOL_PTR_VECT::const_iterator RDKit::MOL_PTR_VECT_CI |
typedef MOL_PTR_VECT::iterator RDKit::MOL_PTR_VECT_I |
typedef std::vector< ROMOL_SPTR > RDKit::MOL_SPTR_VECT |
Definition at line 20 of file FragCatParams.h.
typedef std::vector<ROMol> RDKit::MOL_VECT |
a hierarchical catalog for holding molecules
Definition at line 15 of file MolCatalog.h.
typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, ATOM_SPTR, BOND_SPTR> RDKit::MolGraph |
typedef std::list< PATH_TYPE > RDKit::PATH_LIST |
Definition at line 42 of file Subgraphs.h.
typedef PATH_LIST::const_iterator RDKit::PATH_LIST_CI |
Definition at line 43 of file Subgraphs.h.
typedef std::vector<int> RDKit::PATH_TYPE |
Definition at line 37 of file Subgraphs.h.
typedef boost::minstd_rand RDKit::rng_type |
typedef boost::shared_ptr< ROMol > RDKit::ROMOL_SPTR |
Definition at line 20 of file ChemTransforms.h.
typedef boost::shared_ptr<RWMol> RDKit::RWMOL_SPTR |
typedef std::vector< RWMOL_SPTR > RDKit::RWMOL_SPTR_VECT |
Definition at line 30 of file FileParsers.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 unsigned char RDKit::UCHAR |
typedef unsigned int RDKit::UINT |
typedef std::vector<UINT> RDKit::UINT_VECT |
typedef std::vector<UINT>::const_iterator RDKit::UINT_VECT_CI |
typedef boost::uniform_real RDKit::uniform_double |
typedef boost::uniform_int RDKit::uniform_int |
typedef unsigned short RDKit::USHORT |
typedef std::vector<DOUBLE_VECT> RDKit::VECT_DOUBLE_VECT |
typedef VECT_DOUBLE_VECT::const_iterator RDKit::VECT_DOUBLE_VECT_CI |
typedef VECT_DOUBLE_VECT::iterator RDKit::VECT_DOUBLE_VECT_I |
typedef std::vector<INT_VECT> RDKit::VECT_INT_VECT |
typedef VECT_INT_VECT::const_iterator RDKit::VECT_INT_VECT_CI |
typedef VECT_INT_VECT::iterator RDKit::VECT_INT_VECT_I |
enum RDKit::EEndian |
Enumerator | |
---|---|
LITTLE_ENDIAN_ORDER | |
BIG_ENDIAN_ORDER |
Definition at line 24 of file StreamOps.h.
Enumerator | |
---|---|
AtomPairFP | |
TopologicalTorsion | |
MorganFP | |
RDKitFP | |
PatternFP |
Definition at line 41 of file ReactionFingerprints.h.
enum RDKit::Mol2Type |
Enumerator | |
---|---|
CORINA |
Definition at line 153 of file FileParsers.h.
Enumerator | |
---|---|
Reactant | |
Product | |
Agent |
Definition at line 39 of file ReactionUtils.h.
void RDKit::addRecursiveQueries | ( | ROMol & | mol, |
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
std::string | propName, | ||
std::vector< std::pair< unsigned int, std::string > > * | reactantLabels = NULL |
||
) |
Adds named recursive queries to a molecule's atoms based on atom 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
void RDKit::addRecursiveQueriesToReaction | ( | ChemicalReaction & | rxn, |
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
std::string | propName, | ||
std::vector< std::vector< std::pair< unsigned int, std::string > > > * | reactantLabels = NULL |
||
) |
add the recursive queries to the reactants of a reaction
This does its work using RDKit::addRecursiveQueries()
rxn | the reaction we are interested in |
queries | - the dictionary of named queries to add |
propName | - the atom property to use to get query names optional: |
reactantLabels | - to store pairs of (atom index, query string) per reactant |
NOTES:
queries
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
|
inline |
Packs an integer and outputs it to a stream.
Definition at line 101 of file StreamOps.h.
References CHECK_INVARIANT.
bool RDKit::atomCompat | ( | const ATOM_SPTR & | a1, |
const ATOM_SPTR & | a2, | ||
bool | useQueryQueryMatches = false |
||
) |
bool RDKit::bondCompat | ( | const BOND_SPTR & | b1, |
const BOND_SPTR & | b2, | ||
bool | useQueryQueryMatches = false |
||
) |
MolChemicalFeatureFactory* RDKit::buildFeatureFactory | ( | std::istream & | inStream | ) |
constructs a MolChemicalFeatureFactory from the data in a stream
Referenced by RDKit::MolChemicalFeatureFactory::addFeatureDef().
MolChemicalFeatureFactory* RDKit::buildFeatureFactory | ( | const std::string & | featureData | ) |
constructs a MolChemicalFeatureFactory from the data in a string
std::string RDKit::ChemicalReactionToRxnBlock | ( | const ChemicalReaction & | rxn, |
bool | separateAgents = false |
||
) |
returns an RXN block for a reaction
rxn | chemical reaction |
separateAgents | flag to decide if agents were put in a seperate block, otherwise they were included in the reactants block (default) |
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ROMol* RDKit::ChemicalReactionToRxnMol | ( | const ChemicalReaction & | rxn | ) |
returns a ROMol with RXN roles used to describe the reaction
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
std::string RDKit::ChemicalReactionToRxnSmarts | ( | const ChemicalReaction & | rxn | ) |
returns the reaction SMARTS for a reaction
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
std::string RDKit::ChemicalReactionToRxnSmiles | ( | const ChemicalReaction & | rxn, |
bool | canonical = true |
||
) |
returns the reaction SMILES for a reaction
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
void RDKit::ClearSingleBondDirFlags | ( | ROMol & | mol | ) |
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 |
void RDKit::computeGasteigerCharges | ( | const ROMol * | mol, |
int | nIter = 12 , |
||
bool | throwOnParamFailure = false |
||
) |
void RDKit::computeGasteigerCharges | ( | const ROMol & | mol, |
int | nIter = 12 , |
||
bool | throwOnParamFailure = false |
||
) |
void RDKit::computeGasteigerCharges | ( | const ROMol & | mol, |
std::vector< double > & | charges, | ||
int | nIter = 12 , |
||
bool | throwOnParamFailure = false |
||
) |
double RDKit::computeIntVectPrimesProduct | ( | const INT_VECT & | ring | ) |
compute the product of the set of primes corresponding to the values in an INT_VECT
unsigned int RDKit::computeL1Norm | ( | const DiscreteValueVect & | v1, |
const DiscreteValueVect & | v2 | ||
) |
Referenced by RDKit::DiscreteValueVect::getNumInts().
void RDKit::ConnectTheDots | ( | RWMol * | mol | ) |
unsigned int RDKit::countSwapsToInterconvert | ( | const T & | ref, |
T | probe | ||
) |
Definition at line 50 of file utils.h.
References CHECK_INVARIANT, and PRECONDITION.
const ReactionFingerprintParams RDKit::DefaultDifferenceFPParams | ( | true | , |
0. | 0, | ||
10 | , | ||
1 | , | ||
2048 | , | ||
AtomPairFP | |||
) |
const ReactionFingerprintParams RDKit::DefaultStructuralFPParams | ( | true | , |
0. | 2, | ||
1 | , | ||
1 | , | ||
4096 | , | ||
PatternFP | |||
) |
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. |
mol
with the matching atoms and bonds (if any) removed. Bond::BondDir RDKit::DetermineBondWedgeState | ( | const Bond * | bond, |
const INT_MAP_INT & | wedgeBonds, | ||
const Conformer * | conf | ||
) |
double RDKit::DiceSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
||
double | bounds = 0.0 |
||
) |
Definition at line 471 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getLength(), and RDKit::SparseIntVect< IndexType >::getTotalVal().
SparseIntVect<boost::uint32_t>* RDKit::DifferenceFingerprintChemReaction | ( | const ChemicalReaction & | rxn, |
const ReactionFingerprintParams & | params = DefaultDifferenceFPParams |
||
) |
Generates a difference fingerprint for a reaction to use in similarity search of reactions
A difference fingerprint is generated as a SparseIntVect to use for similarity search of reactions. By default the fingerprint is generated as 2048 bit hashed fingerprint subtracting AtompairFP of the reactants from the products' AtompairFP and tentatively the agent AtompairFP is added
rxn | the reaction to be fingerprinted |
params | specific settings to manipulate fingerprint generation |
Notes:
delete
ing the result
|
inline |
Definition at line 68 of file StreamOps.h.
|
inline |
Definition at line 84 of file StreamOps.h.
|
inline |
Definition at line 89 of file StreamOps.h.
|
inline |
Definition at line 94 of file StreamOps.h.
bool RDKit::feq | ( | double | v1, |
double | v2, | ||
double | tol = 1e-4 |
||
) |
floating point comparison with a tolerance
Referenced by RDPickers::MaxMinPicker::lazyPick().
bool RDKit::FinalChiralityCheckFunction | ( | const short unsigned | c1[], |
const short unsigned | c2[], | ||
const ROMol & | mol1, | ||
const FMCS::Graph & | query, | ||
const ROMol & | mol2, | ||
const FMCS::Graph & | target, | ||
const MCSParameters * | p | ||
) |
PATH_LIST RDKit::findAllPathsOfLengthN | ( | const ROMol & | mol, |
unsigned int | targetLen, | ||
bool | useBonds = true , |
||
bool | useHs = false , |
||
int | rootedAtAtom = -1 |
||
) |
find all paths of a particular size
mol | - the molecule to be considered |
targetLen | - the length of the paths to be returned |
useBonds | - if set, the path indices will be bond indices, not atom indices |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
rootedAtAtom | - if non-negative, only subgraphs that start at this atom will be returned. |
The result is a list of paths (i.e. list of list of bond indices)
INT_PATH_LIST_MAP RDKit::findAllPathsOfLengthsMtoN | ( | const ROMol & | mol, |
unsigned int | lowerLen, | ||
unsigned int | upperLen, | ||
bool | useBonds = true , |
||
bool | useHs = false , |
||
int | rootedAtAtom = -1 |
||
) |
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)
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)
PATH_TYPE RDKit::findAtomEnvironmentOfRadiusN | ( | const ROMol & | mol, |
unsigned int | radius, | ||
unsigned int | rootedAtAtom, | ||
bool | useHs = false |
||
) |
find bond subgraphs of a particular radius around an atom
mol | - the molecule to be considered |
radius | - the radius of the subgraphs to be considered |
rootedAtAtom | - the atom to consider |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
The result is a path (a vector of bond indices)
MatchVectType RDKit::findFuncGroupsOnMol | ( | const ROMol & | mol, |
const FragCatParams * | params, | ||
INT_VECT & | fgBonds | ||
) |
MCSResult RDKit::findMCS | ( | const std::vector< ROMOL_SPTR > & | mols, |
const MCSParameters * | params = 0 |
||
) |
Referenced by RDKit::MCSResult::isCompleted().
MCSResult RDKit::findMCS | ( | const std::vector< ROMOL_SPTR > & | mols, |
bool | maximizeBonds, | ||
double | threshold = 1.0 , |
||
unsigned | timeout = 3600 , |
||
bool | verbose = false , |
||
bool | matchValences = false , |
||
bool | ringMatchesRingOnly = false , |
||
bool | completeRingsOnly = false , |
||
bool | matchChiralTag = false , |
||
AtomComparator | atomComp = AtomCompareElements , |
||
BondComparator | bondComp = BondCompareOrder |
||
) |
MCSResult RDKit::findMCS_P | ( | const std::vector< ROMOL_SPTR > & | mols, |
const char * | params_json | ||
) |
Referenced by RDKit::MCSResult::isCompleted().
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)
DiscreteDistMat* RDKit::getDiscreteDistMat | ( | ) |
Referenced by RDKit::DiscreteDistMat::~DiscreteDistMat().
double_source_type& RDKit::getDoubleRandomSource | ( | ) |
return a reference to the global (Boost) random source
MOL_SPTR_VECT::const_iterator RDKit::getEndIterator | ( | const ChemicalReaction & | rxn, |
ReactionMoleculeType | t | ||
) |
|
inline |
grabs the next line from an instream and returns it.
Definition at line 248 of file StreamOps.h.
Referenced by getLine().
|
inline |
grabs the next line from an instream and returns it.
Definition at line 257 of file StreamOps.h.
References getLine().
rng_type& RDKit::getRandomGenerator | ( | int | seed = -1 | ) |
Optionally seed and return a reference to the global (Boost) random generator.
double RDKit::getRandomVal | ( | int | seed = -1 | ) |
Return a random double value between 0.0 and 1.0 Optionally seed the random number generator
VECT_INT_VECT RDKit::getReactingAtoms | ( | const ChemicalReaction & | rxn, |
bool | mappedAtomsOnly = false |
||
) |
returns indices of the atoms in each reactant that are changed in the reaction
rxn | the reaction we are interested in |
mappedAtomsOnly | if set, atoms that are not mapped will not be included in the list of changed atoms (otherwise they are automatically included) |
How are changed atoms recognized? 1) Atoms whose degree changes 2) Atoms whose bonding pattern changes 3) unmapped atoms (unless the mappedAtomsOnly flag is set) 4) Atoms connected to unmapped atoms 5) Atoms whose atomic number changes (unless the corresponding product atom is a dummy) 6) Atoms with more than one atomic number query (unless the corresponding product atom is a dummy)
Note that the atomic number of a query atom depends on how it's constructed. When coming from SMARTS: if the first query is an atomic label/number that sets the atomic number, otherwise it's zero. For example [O;] is atomic number 8 while [;O] is atomic number 0. When coming from RXN: the atomic number of the atom in the rxn file sets the value.
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
MOL_SPTR_VECT::const_iterator RDKit::getStartIterator | ( | const ChemicalReaction & | rxn, |
ReactionMoleculeType | t | ||
) |
bool RDKit::hanoi | ( | int * | base, |
int | nel, | ||
int * | temp, | ||
int * | count, | ||
int * | changed, | ||
CompareFunc | compar | ||
) |
void RDKit::hanoisort | ( | int * | base, |
int | nel, | ||
int * | count, | ||
int * | changed, | ||
CompareFunc | compar | ||
) |
Definition at line 126 of file hanoiSort.h.
References hanoi().
Referenced by RDKit::Canon::RefinePartitions().
bool RDKit::hasAgentTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
bool RDKit::hasProductTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
bool RDKit::hasReactantTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
bool RDKit::hasReactionAtomMapping | ( | const ChemicalReaction & | rxn | ) |
bool RDKit::hasReactionSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn, | ||
bool | includeAgents = false |
||
) |
calculate the intersection of two INT_VECTs and put the results in a third vector
Referenced by RDKit::charptr_functor::operator()().
bool RDKit::isMoleculeAgentOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which | ||
) |
tests whether or not the molecule has a substructure match to any of the reaction's agents the which
argument is used to return which of the agents the molecule matches. If there's no match, it is equal to the number of agents on return
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
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.
bool RDKit::isMoleculeProductOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which | ||
) |
tests whether or not the molecule has a substructure match to any of the reaction's products the which
argument is used to return which of the products the molecule matches. If there's no match, it is equal to the number of products on return
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
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.
bool RDKit::isMoleculeReactantOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which | ||
) |
tests whether or not the molecule has a substructure match to any of the reaction's reactants the which
argument is used to return which of the reactants the molecule matches. If there's no match, it is equal to the number of reactants on return
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
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.
bool RDKit::isReactionTemplateMoleculeAgent | ( | const ROMol & | mol, |
double | agentThreshold | ||
) |
ExplicitBitVect* RDKit::LayeredFingerprintMol | ( | const ROMol & | mol, |
unsigned int | layerFlags = 0xFFFFFFFF , |
||
unsigned int | minPath = 1 , |
||
unsigned int | maxPath = 7 , |
||
unsigned int | fpSize = 2048 , |
||
std::vector< unsigned int > * | atomCounts = 0 , |
||
ExplicitBitVect * | setOnlyBits = 0 , |
||
bool | branchedPaths = true , |
||
const std::vector< boost::uint32_t > * | fromAtoms = 0 |
||
) |
Generates a topological (Daylight like) fingerprint for a molecule using a layer-based hashing algorithm.
Experimental: This function is experimental. The API or results may change from release to release.
mol | the molecule to be fingerprinted |
layerFlags | the layers to be included (see below) |
minPath | the minimum path length (in bonds) to be included |
maxPath | the minimum path length (in bonds) to be included |
fpSize | the size of the fingerprint |
atomCounts | if provided, this will be used to provide the count of the number of paths that set bits each atom is involved in. The vector should have at least as many entries as the molecule has atoms and is not zeroed out here. |
setOnlyBits | if provided, only bits that are set in this bit vector will be set in the result. This is essentially the same as doing: (*res) &= (*setOnlyBits); but also has an impact on the atomCounts (if being used) |
branchedPaths | toggles generation of branched subgraphs, not just linear paths |
Notes:
delete
ing the resultLayer definitions:
T* RDKit::makeAtomAliphaticQuery | ( | const std::string & | descr | ) |
returns a Query for matching aliphatic atoms
Definition at line 258 of file QueryOps.h.
References queryAtomAliphatic().
ATOM_EQUALS_QUERY* RDKit::makeAtomAliphaticQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomAromaticQuery | ( | const std::string & | descr | ) |
returns a Query for matching the isAromatic
flag
Definition at line 250 of file QueryOps.h.
References queryAtomAromatic().
ATOM_EQUALS_QUERY* RDKit::makeAtomAromaticQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomExplicitDegreeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching explicit degree
Definition at line 209 of file QueryOps.h.
References queryAtomExplicitDegree().
ATOM_EQUALS_QUERY* RDKit::makeAtomExplicitDegreeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomExplicitValenceQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching explicit valence
Definition at line 193 of file QueryOps.h.
References queryAtomExplicitValence().
ATOM_EQUALS_QUERY* RDKit::makeAtomExplicitValenceQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomFormalChargeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching formal charge
Definition at line 282 of file QueryOps.h.
References queryAtomFormalCharge().
ATOM_EQUALS_QUERY* RDKit::makeAtomFormalChargeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomHasImplicitHQuery | ( | const std::string & | descr | ) |
returns a Query for matching ring atoms
Definition at line 233 of file QueryOps.h.
References queryAtomHasImplicitH().
ATOM_EQUALS_QUERY* RDKit::makeAtomHasImplicitHQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomHasRingBondQuery | ( | const std::string & | descr | ) |
returns a Query for matching atoms with a particular number of ring bonds
Definition at line 342 of file QueryOps.h.
References makeAtomNullQuery(), makeBondDirEqualsQuery(), makeBondInNRingsQuery(), makeBondInRingOfSizeQuery(), makeBondIsInRingQuery(), makeBondMinRingSizeQuery(), makeBondNullQuery(), makeBondOrderEqualsQuery(), and queryAtomHasRingBond().
ATOM_EQUALS_QUERY* RDKit::makeAtomHasRingBondQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomHCountQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching hydrogen count
Definition at line 225 of file QueryOps.h.
References queryAtomHCount().
ATOM_EQUALS_QUERY* RDKit::makeAtomHCountQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomHybridizationQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching hybridization
Definition at line 290 of file QueryOps.h.
References queryAtomHybridization().
ATOM_EQUALS_QUERY* RDKit::makeAtomHybridizationQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomImplicitHCountQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching implicit hydrogen count
Definition at line 242 of file QueryOps.h.
References queryAtomImplicitHCount().
ATOM_EQUALS_QUERY* RDKit::makeAtomImplicitHCountQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomImplicitValenceQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching implicit valence
Definition at line 185 of file QueryOps.h.
References queryAtomImplicitValence().
ATOM_EQUALS_QUERY* RDKit::makeAtomImplicitValenceQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomInNRingsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms in a particular number of rings
Definition at line 315 of file QueryOps.h.
References makeAtomInRingOfSizeQuery(), and queryIsAtomInNRings().
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.
ATOM_EQUALS_QUERY* RDKit::makeAtomInRingOfSizeQuery | ( | int | tgt | ) |
returns a Query for matching atoms in rings of a particular size
Referenced by makeAtomInNRingsQuery().
T* RDKit::makeAtomInRingQuery | ( | const std::string & | descr | ) |
returns a Query for matching ring atoms
Definition at line 307 of file QueryOps.h.
References queryIsAtomInRing().
ATOM_EQUALS_QUERY* RDKit::makeAtomInRingQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomIsotopeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms with a particular isotope
Definition at line 274 of file QueryOps.h.
References queryAtomIsotope().
ATOM_EQUALS_QUERY* RDKit::makeAtomIsotopeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomMassQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms with a particular mass
Definition at line 266 of file QueryOps.h.
References queryAtomMass().
ATOM_EQUALS_QUERY* RDKit::makeAtomMassQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomMinRingSizeQuery | ( | int | tgt, |
const std::string & | descr | ||
) |
returns a Query for matching an atom's minimum ring size
Definition at line 326 of file QueryOps.h.
References queryAtomMinRingSize().
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.
ATOM_NULL_QUERY* RDKit::makeAtomNullQuery | ( | ) |
returns a Query for matching any atom
Referenced by makeAtomHasRingBondQuery().
T* RDKit::makeAtomNumQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atomic number
Definition at line 177 of file QueryOps.h.
References queryAtomNum().
ATOM_EQUALS_QUERY* RDKit::makeAtomNumQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomRingBondCountQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms with a particular number of ring bonds
Definition at line 334 of file QueryOps.h.
References queryAtomRingBondCount().
ATOM_EQUALS_QUERY* RDKit::makeAtomRingBondCountQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomSimpleQuery | ( | int | what, |
int | funcAtom const *, | ||
const std::string & | description = "Atom Simple" |
||
) |
Definition at line 166 of file QueryOps.h.
T* RDKit::makeAtomTotalDegreeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atomic degree
Definition at line 217 of file QueryOps.h.
References queryAtomTotalDegree().
ATOM_EQUALS_QUERY* RDKit::makeAtomTotalDegreeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomTotalValenceQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching total valence
Definition at line 201 of file QueryOps.h.
References queryAtomTotalValence().
ATOM_EQUALS_QUERY* RDKit::makeAtomTotalValenceQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomUnsaturatedQuery | ( | const std::string & | descr | ) |
returns a Query for matching atoms with unsaturation:
Definition at line 298 of file QueryOps.h.
References queryAtomUnsaturated().
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.
BOND_EQUALS_QUERY* RDKit::makeBondDirEqualsQuery | ( | Bond::BondDir | what | ) |
returns a Query for matching bond directions
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondInNRingsQuery | ( | int | tgt | ) |
returns a Query for matching bonds in a particular number of rings
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondInRingOfSizeQuery | ( | int | what | ) |
returns a Query for matching bonds in rings of a particular size
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondIsInRingQuery | ( | ) |
returns a Query for matching ring bonds
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondMinRingSizeQuery | ( | int | what | ) |
returns a Query for matching a bond's minimum ring size
Referenced by makeAtomHasRingBondQuery().
BOND_NULL_QUERY* RDKit::makeBondNullQuery | ( | ) |
returns a Query for matching any bond
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondOrderEqualsQuery | ( | Bond::BondType | what | ) |
returns a Query for matching bond orders
Referenced by makeAtomHasRingBondQuery().
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 535 of file QueryOps.h.
Queries::EqualityQuery<int, const Target *, true>* RDKit::makePropQuery | ( | const std::string & | propname, |
const T & | val, | ||
const T & | tolerance = T() |
||
) |
Definition at line 661 of file QueryOps.h.
bool RDKit::MCSAtomCompareAny | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
bool RDKit::MCSAtomCompareElements | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
bool RDKit::MCSAtomCompareIsotopes | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
bool RDKit::MCSBondCompareAny | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData | ||
) |
bool RDKit::MCSBondCompareOrder | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData | ||
) |
bool RDKit::MCSBondCompareOrderExact | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData | ||
) |
bool RDKit::MCSProgressCallbackTimeout | ( | const MCSProgressData & | stat, |
const MCSParameters & | params, | ||
void * | userData | ||
) |
RWMol* RDKit::Mol2BlockToMol | ( | const std::string & | molBlock, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA |
||
) |
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 |
RWMol* RDKit::Mol2DataStreamToMol | ( | std::istream * | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA |
||
) |
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 |
RWMol* RDKit::Mol2DataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA |
||
) |
RWMol* RDKit::Mol2FileToMol | ( | std::string | fName, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA |
||
) |
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 |
RWMol* RDKit::MolBlockToMol | ( | const std::string & | molBlock, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
molBlock | - string containing the mol block |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
strictParsing | - if set, the parser is more lax about correctness of the contents. |
RWMol* RDKit::MolDataStreamToMol | ( | std::istream * | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
inStream | - stream containing the data |
line | - current line number (used for error reporting) |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
line | - current line number (used for error reporting) |
strictParsing | - if not set, the parser is more lax about correctness of the contents. |
RWMol* RDKit::MolDataStreamToMol | ( | std::istream & | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
RWMol* RDKit::MolFileToMol | ( | std::string | fName, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
fName | - string containing the file name |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
strictParsing | - if set, the parser is more lax about correctness of the contents. |
std::string RDKit::MolFragmentToSmiles | ( | const ROMol & | mol, |
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = 0 , |
||
const std::vector< std::string > * | atomSymbols = 0 , |
||
const std::vector< std::string > * | bondSymbols = 0 , |
||
bool | doIsomericSmiles = false , |
||
bool | doKekule = false , |
||
int | rootedAtAtom = -1 , |
||
bool | canonical = true , |
||
bool | allBondsExplicit = false , |
||
bool | allHsExplicit = false |
||
) |
returns canonical SMILES for part of a molecule
mol | : the molecule in question. |
atomsToUse | : indices of the atoms in the fragment |
bondsToUse | : indices of the bonds in the fragment. If this is not provided, all bonds between the atoms in atomsToUse will be included |
atomSymbols | : symbols to use for the atoms in the output SMILES |
bondSymbols | : sybmols to use for the bonds in the output SMILES |
doIsomericSmiles | : include stereochemistry and isotope information in the SMILES |
doKekule | : do Kekule smiles (i.e. don't use aromatic bonds) |
rootedAtAtom | : make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical. |
canonical | : if false, no attempt will be made to canonicalize the SMILES |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
NOTE: the bondSymbols are not currently used in the canonicalization.
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) |
void RDKit::MolToMolFile | ( | const ROMol & | mol, |
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) |
std::string RDKit::MolToPDBBlock | ( | const ROMol & | mol, |
int | confId = -1 , |
||
unsigned int | flavor = 0 |
||
) |
mol | - the molecule in question |
confId | - selects the conformer to be used |
flavor | - controls what gets written: flavor & 1 : Write MODEL/ENDMDL lines around each record flavor & 2 : Don't write any CONECT records flavor & 4 : Write CONECT records in both directions flavor & 8 : Don't use multiple CONECTs to encode bond order flavor & 16 : Write MASTER record flavor & 32 : Write TER record |
void RDKit::MolToPDBFile | ( | const ROMol & | mol, |
const std::string & | fname, | ||
int | confId = -1 , |
||
unsigned int | flavor = 0 |
||
) |
mol | - the molecule in question |
fName | - the name of the file to use |
confId | - selects the conformer to be used |
flavor | - controls what gets written: flavor & 1 : Write MODEL/ENDMDL lines around each record flavor & 2 : Don't write any CONECT records flavor & 4 : Write CONECT records in both directions flavor & 8 : Don't use multiple CONECTs to encode bond order flavor & 16 : Write MASTER record flavor & 32 : Write TER record |
std::string RDKit::MolToSmarts | ( | ROMol & | mol, |
bool | doIsomericSmarts = false |
||
) |
returns the SMARTS for a molecule
std::string RDKit::MolToSmiles | ( | const ROMol & | mol, |
bool | doIsomericSmiles = false , |
||
bool | doKekule = false , |
||
int | rootedAtAtom = -1 , |
||
bool | canonical = true , |
||
bool | allBondsExplicit = false , |
||
bool | allHsExplicit = false |
||
) |
returns canonical SMILES for a molecule
mol | : the molecule in question. |
doIsomericSmiles | : include stereochemistry and isotope information in the SMILES |
doKekule | : do Kekule smiles (i.e. don't use aromatic bonds) |
rootedAtAtom | : make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical. |
canonical | : if false, no attempt will be made to canonicalize the SMILES |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
void RDKit::MolToTPLFile | ( | const ROMol & | mol, |
std::string | fName, | ||
std::string | partialChargeProp = "_GasteigerCharge" , |
||
bool | writeFirstConfTwice = false |
||
) |
std::string RDKit::MolToTPLText | ( | const ROMol & | mol, |
std::string | partialChargeProp = "_GasteigerCharge" , |
||
bool | writeFirstConfTwice = false |
||
) |
int RDKit::nextCombination | ( | INT_VECT & | comb, |
int | tot | ||
) |
given a current combination of numbers change it to the next possible combination
comb | the sorted vector to consider |
tot | the maximum number possible in the vector |
Referenced by RDKit::charptr_functor::operator()().
int RDKit::nullDataFun | ( | T | arg | ) |
Definition at line 482 of file QueryOps.h.
bool RDKit::nullQueryFun | ( | T | arg | ) |
Definition at line 484 of file QueryOps.h.
DiscreteValueVect RDKit::operator+ | ( | const DiscreteValueVect & | p1, |
const DiscreteValueVect & | p2 | ||
) |
Referenced by RDKit::DiscreteValueVect::getNumInts().
DiscreteValueVect RDKit::operator- | ( | const DiscreteValueVect & | p1, |
const DiscreteValueVect & | p2 | ||
) |
Referenced by RDKit::DiscreteValueVect::getNumInts().
int RDKit::parseFeatureData | ( | const std::string & | defnText, |
MolChemicalFeatureDef::CollectionType & | featDefs | ||
) |
int RDKit::parseFeatureData | ( | std::istream & | istream, |
MolChemicalFeatureDef::CollectionType & | featDefs | ||
) |
int RDKit::parseFeatureFile | ( | const std::string & | fileName, |
MolChemicalFeatureDef::CollectionType & | featDefs | ||
) |
void RDKit::parseMCSParametersJSON | ( | const char * | json, |
MCSParameters * | params | ||
) |
Referenced by RDKit::MCSResult::isCompleted().
void RDKit::parseQueryDefFile | ( | std::string | filename, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true , |
||
std::string | delimiter = "\t" , |
||
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 |
void RDKit::parseQueryDefFile | ( | std::istream * | inStream, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true , |
||
std::string | delimiter = "\t" , |
||
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.
void RDKit::parseQueryDefText | ( | const std::string & | queryDefText, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true , |
||
std::string | delimiter = "\t" , |
||
std::string | comment = "//" , |
||
unsigned int | nameColumn = 0 , |
||
unsigned int | smartsColumn = 1 |
||
) |
equivalent to parseQueryDefFile() but the query definitions are explicitly passed in
ExplicitBitVect* RDKit::PatternFingerprintMol | ( | const ROMol & | mol, |
unsigned int | fpSize = 2048 , |
||
std::vector< unsigned int > * | atomCounts = 0 , |
||
ExplicitBitVect * | setOnlyBits = 0 |
||
) |
Generates a topological fingerprint for a molecule using a series of pre-defined structural patterns.
Experimental: This function is experimental. The API or results may change from release to release.
mol | the molecule to be fingerprinted |
fpSize | the size of the fingerprint |
atomCounts | if provided, this will be used to provide the count of the number of paths that set bits each atom is involved in. The vector should have at least as many entries as the molecule has atoms and is not zeroed out here. |
setOnlyBits | if provided, only bits that are set in this bit vector will be set in the result. This is essentially the same as doing: (*res) &= (*setOnlyBits); but also has an impact on the atomCounts (if being used) |
Notes:
delete
ing the result RWMol* RDKit::PDBBlockToMol | ( | const char * | str, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
RWMol* RDKit::PDBBlockToMol | ( | const std::string & | str, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
RWMol* RDKit::PDBDataStreamToMol | ( | std::istream * | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
RWMol* RDKit::PDBDataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
RWMol* RDKit::PDBFileToMol | ( | const std::string & | fname, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
INT_MAP_INT RDKit::pickBondsToWedge | ( | const ROMol & | mol | ) |
ROMol* RDKit::prepareMol | ( | const ROMol & | mol, |
const FragCatParams * | fparams, | ||
MatchVectType & | aToFmap | ||
) |
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Reads an integer from a char * in packed format and returns the result. The argument is advanced
Definition at line 187 of file StreamOps.h.
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Definition at line 67 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAliphaticQuery().
unsigned int RDKit::queryAtomAllBondProduct | ( | Atom const * | at | ) |
Referenced by queryAtomHybridization().
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Definition at line 66 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAromaticQuery().
unsigned int RDKit::queryAtomBondProduct | ( | Atom const * | at | ) |
Referenced by queryAtomHybridization().
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Definition at line 68 of file QueryOps.h.
References RDKit::Atom::getDegree().
Referenced by makeAtomExplicitDegreeQuery().
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Definition at line 75 of file QueryOps.h.
References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getNumExplicitHs().
Referenced by makeAtomExplicitValenceQuery().
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Definition at line 86 of file QueryOps.h.
References RDKit::Atom::getFormalCharge().
Referenced by makeAtomFormalChargeQuery().
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Definition at line 73 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHasImplicitHQuery().
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Definition at line 112 of file QueryOps.h.
References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), and RDKit::RingInfo::numBondRings().
Referenced by makeAtomHasRingBondQuery().
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Definition at line 71 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHCountQuery().
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Definition at line 70 of file QueryOps.h.
References RDKit::Atom::getTotalDegree(), and RDKit::Atom::getTotalNumHs().
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Definition at line 89 of file QueryOps.h.
References RDKit::Atom::getHybridization(), queryAtomAllBondProduct(), and queryAtomBondProduct().
Referenced by makeAtomHybridizationQuery().
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Definition at line 72 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomImplicitHCountQuery().
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Definition at line 74 of file QueryOps.h.
References RDKit::Atom::getImplicitValence().
Referenced by makeAtomImplicitValenceQuery().
int RDKit::queryAtomIsInRingOfSize | ( | Atom const * | at | ) |
Definition at line 148 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isAtomInRingOfSize().
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Definition at line 83 of file QueryOps.h.
References RDKit::Atom::getIsotope().
Referenced by makeAtomIsotopeQuery().
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Definition at line 80 of file QueryOps.h.
References RDKit::Atom::getMass(), and round().
Referenced by makeAtomMassQuery().
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Definition at line 126 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minAtomRingSize().
Referenced by makeAtomMinRingSizeQuery().
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Definition at line 78 of file QueryOps.h.
References RDKit::Atom::getAtomicNum().
Referenced by makeAtomNumQuery().
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Definition at line 133 of file QueryOps.h.
References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), and RDKit::RingInfo::numBondRings().
Referenced by makeAtomRingBondCountQuery().
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Definition at line 366 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by RDKit::AtomRingQuery::AtomRingQuery().
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Definition at line 69 of file QueryOps.h.
References RDKit::Atom::getTotalDegree().
Referenced by makeAtomTotalDegreeQuery().
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Definition at line 76 of file QueryOps.h.
References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getImplicitValence().
Referenced by makeAtomTotalValenceQuery().
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Definition at line 77 of file QueryOps.h.
References RDKit::Atom::getDegree(), and RDKit::Atom::getExplicitValence().
Referenced by makeAtomUnsaturatedQuery().
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Definition at line 98 of file QueryOps.h.
References RDKit::Bond::getBondDir().
int RDKit::queryBondIsInRingOfSize | ( | Bond const * | bond | ) |
Definition at line 156 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isBondInRingOfSize().
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Definition at line 129 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minBondRingSize().
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Definition at line 97 of file QueryOps.h.
References RDKit::Bond::getBondType().
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Definition at line 106 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by makeAtomInNRingsQuery().
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Definition at line 109 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by makeAtomInRingQuery().
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Definition at line 99 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().
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Definition at line 123 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().
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< boost::uint32_t > * | atomInvariants = 0 , |
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const std::vector< boost::uint32_t > * | fromAtoms = 0 , |
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std::vector< std::vector< boost::uint32_t > > * | atomBits = 0 |
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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 MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::string | fileName | ) |
MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::istream & | inStream, |
int | nToRead = -1 |
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) |
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Reads an integer from a stream in packed format and returns the result.
Definition at line 146 of file StreamOps.h.
void RDKit::removeDuplicates | ( | std::vector< MatchVectType > & | v, |
unsigned int | nAtoms | ||
) |
ROMol* RDKit::replaceCore | ( | const ROMol & | mol, |
const ROMol & | coreQuery, | ||
bool | replaceDummies = true , |
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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 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). |
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. 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
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. 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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) |
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 occurances of the substructure replaced, will be returned. |
replacementConnectionPoint | index of the atom in the replacement that the bond should made to |
mol
with the matching atoms and bonds (if any) replaced double RDKit::round | ( | double | v | ) |
rounds a value to the closest int
Referenced by RDKit::charptr_functor::operator()(), and queryAtomMass().
std::vector<MOL_SPTR_VECT> RDKit::run_Reactants | ( | const ChemicalReaction & | rxn, |
const MOL_SPTR_VECT & | reactants | ||
) |
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! |
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.
ChemicalReaction* RDKit::RxnBlockToChemicalReaction | ( | const std::string & | rxnBlock | ) |
Parse a text block in MDL rxn format into a ChemicalReaction.
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ChemicalReaction* RDKit::RxnDataStreamToChemicalReaction | ( | std::istream & | rxnStream, |
unsigned int & | line | ||
) |
Parse a text stream in MDL rxn format into a ChemicalReaction.
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ChemicalReaction* RDKit::RxnFileToChemicalReaction | ( | const std::string & | fileName | ) |
Parse a file in MDL rxn format into a ChemicalReaction.
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ChemicalReaction* RDKit::RxnMolToChemicalReaction | ( | const ROMol & | mol | ) |
Parse a ROMol into a ChemicalReaction, RXN role must be set before.
Alternative to build a reaction from a molecule (fragments) which have RXN roles set as atom properties: common_properties::molRxnRole (1=reactant, 2=product, 3=agent)
mol | ROMol with RXN roles set |
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ChemicalReaction* RDKit::RxnSmartsToChemicalReaction | ( | const std::string & | text, |
std::map< std::string, std::string > * | replacements = 0 , |
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bool | useSmiles = false |
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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 |
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RWMol* RDKit::SLNQueryToMol | ( | std::string | smi, |
bool | mergeHs = true , |
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int | debugParse = 0 |
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) |
RWMol* RDKit::SLNToMol | ( | std::string | smi, |
bool | sanitize = true , |
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int | debugParse = 0 |
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) |
RWMol* RDKit::SmartsToMol | ( | std::string | sma, |
int | debugParse = 0 , |
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bool | mergeHs = false , |
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std::map< std::string, std::string > * | replacements = 0 |
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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. |
RWMol* RDKit::SmilesToMol | ( | std::string | smi, |
int | debugParse = 0 , |
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bool | sanitize = 1 , |
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std::map< std::string, std::string > * | replacements = 0 |
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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 responsiblity of the caller to make sure that substitutions results in legal and sensible SMILES.
Examples of substitutions:
void RDKit::StandardPDBResidueBondOrders | ( | RWMol * | mol | ) |
void RDKit::streamRead | ( | std::istream & | ss, |
T & | loc | ||
) |
does a binary read of an object from a stream
Definition at line 241 of file StreamOps.h.
Referenced by RDKit::SparseIntVect< IndexType >::fromString(), and RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream().
void RDKit::streamWrite | ( | std::ostream & | ss, |
const T & | val | ||
) |
does a binary write of an object to a stream
Definition at line 235 of file StreamOps.h.
Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream(), and RDKit::SparseIntVect< IndexType >::toString().
std::string RDKit::strip | ( | const std::string & | orig | ) |
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 bool RDKit::SubstructMatch | ( | const ROMol & | mol, |
const ROMol & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
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bool | useChirality = false , |
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bool | useQueryQueryMatches = false |
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) |
Find a substructure match for a query in a molecule.
mol | The ROMol to be searched |
query | The query ROMol |
matchVect | Used to return the match (pre-existing contents will be deleted) |
recursionPossible | flags whether or not recursive matches are allowed |
useChirality | use atomic CIP codes as part of the comparison |
useQueryQueryMatches | if set, the contents of atom and bond queries will be used as part of the matching |
unsigned int RDKit::SubstructMatch | ( | const ROMol & | mol, |
const ROMol & | 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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) |
Find all substructure matches for a query in a molecule.
mol | The ROMol to be searched |
query | The query ROMol |
matchVect | Used to return the matches (pre-existing contents will be deleted) |
uniquify | Toggles uniquification (by atom index) of the results |
recursionPossible | flags whether or not recursive matches are allowed |
useChirality | use atomic CIP codes as part of the comparison |
useQueryQueryMatches | if set, the contents of atom and bond queries will be used as part of the matching |
maxMatches | The maximum number of matches that will be returned. In high-symmetry cases with medium-sized molecules, it is very easy to end up with a combinatorial explosion in the number of possible matches. This argument prevents that from having unintended consequences |
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inline |
Definition at line 40 of file StreamOps.h.
double RDKit::TanimotoSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
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double | bounds = 0.0 |
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) |
Definition at line 545 of file SparseIntVect.h.
References TverskySimilarity().
double RDKit::toPrime | ( | const MatchVectType & | v | ) |
RWMol* RDKit::TPLDataStreamToMol | ( | std::istream * | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
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. |
RWMol* RDKit::TPLFileToMol | ( | std::string | fName, |
bool | sanitize = true , |
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bool | skipFirstConf = false |
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) |
construct a multi-conf molecule from a TPL (BioCad format) file
fName | the name of the file from which to read |
sanitize | toggles sanitization and stereochemistry perception of the molecule |
skipFirstConf | according to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set. |
double RDKit::TverskySimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
double | a, | ||
double | b, | ||
bool | returnDistance = false , |
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double | bounds = 0.0 |
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) |
Definition at line 517 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getLength().
Referenced by TanimotoSimilarity().
calculate the union of two INT_VECTs and put the results in a third vector
void RDKit::Union | ( | const VECT_INT_VECT & | rings, |
INT_VECT & | res, | ||
const INT_VECT * | exclude = NULL |
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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. |
Referenced by RDKit::charptr_functor::operator()().
void RDKit::updateFromSequence | ( | SparseIntVect< IndexType > & | vect, |
const SequenceType & | seq | ||
) |
Definition at line 405 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getLength(), RDKit::SparseIntVect< IndexType >::getNonzeroElements(), RDKit::SparseIntVect< IndexType >::getVal(), and RDKit::SparseIntVect< IndexType >::setVal().
void RDKit::updateProductsStereochem | ( | ChemicalReaction * | rxn | ) |
std::string RDKit::additionalParamData |
const unsigned int RDKit::BITS_PER_INT =32 |
Definition at line 20 of file DiscreteValueVect.h.
const char* RDKit::boostVersion ="1_60" |
Definition at line 13 of file versions.h.
const int RDKit::ci_ATOM_HOLDER |
const int RDKit::ci_LEADING_BOND |
const int RDKit::ci_RIGHTMOST_ATOM |
const double RDKit::DAMP = 0.5 |
Definition at line 27 of file GasteigerParams.h.
const double RDKit::DAMP_SCALE = 0.5 |
Definition at line 26 of file GasteigerParams.h.
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Definition at line 22 of file MolWriters.h.
const double RDKit::EPS_DOUBLE = std::numeric_limits<double>::epsilon() |
const int RDKit::FILE_MAXLINE =256 |
const double RDKit::IONXH = 20.02 |
Definition at line 24 of file GasteigerParams.h.
const std::string RDKit::isotopesAtomData[] |
const std::string RDKit::LayeredFingerprintMolVersion ="0.7.0" |
Definition at line 109 of file Fingerprints.h.
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Definition at line 79 of file QueryOps.h.
const double RDKit::MAX_DOUBLE = std::numeric_limits<double>::max() |
Definition at line 136 of file types.h.
Referenced by RDPickers::MaxMinPicker::lazyPick().
const double RDKit::MAX_INT = static_cast<double>(std::numeric_limits<int>::max()) |
const double RDKit::MAX_LONGINT = static_cast<double>(std::numeric_limits<LONGINT>::max()) |
const unsigned int RDKit::maxFingerprintLayers =10 |
Definition at line 108 of file Fingerprints.h.
const int RDKit::MOLFILE_MAXLINE =256 |
Definition at line 24 of file FileParsers.h.
const int RDKit::NUM_PRIMES_AVAIL = 1000 |
std::string RDKit::paramData |
const std::string RDKit::periodicTableAtomData |
const std::string RDKit::RDKFingerprintMolVersion ="2.0.0" |
Definition at line 61 of file Fingerprints.h.
const char* RDKit::rdkitVersion ="2015.03.1" |
Definition at line 8 of file versions.h.
const unsigned int RDKit::substructLayers =0x07 |
Definition at line 110 of file Fingerprints.h.