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RDKit
Open-source cheminformatics and machine learning.
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12 #ifndef RD_FINGERPRINTUTIL_H_2018_07
13 #define RD_FINGERPRINTUTIL_H_2018_07
30 5, 6, 7, 8, 9, 14, 15, 16, 17, 33, 34, 35, 51, 52, 43};
55 const Atom *atom,
unsigned int branchSubtract = 0,
56 bool includeChirality =
false);
69 std::uint32_t codeI, std::uint32_t codeJ,
unsigned int dist,
70 bool includeChirality =
false);
78 const std::vector<std::uint32_t> &atomCodes,
bool includeChirality =
false);
81 const std::vector<std::uint32_t> &pathCodes);
84 namespace MorganFingerprints {
98 typedef boost::tuple<boost::dynamic_bitset<>, uint32_t,
unsigned int>
112 const ROMol &mol, std::vector<std::uint32_t> &invars,
113 bool includeRingMembership =
true);
130 const ROMol &mol, std::vector<std::uint32_t> &invars,
131 std::vector<const ROMol *> *patterns = 0);
136 namespace RDKitFPUtils {
139 const ROMol &mol, std::vector<std::uint32_t> &lAtomInvariants);
142 const ROMol &mol, std::map<
int, std::list<std::vector<int>>> &allPaths,
143 const std::vector<std::uint32_t> *fromAtoms,
bool branchedPaths,
bool useHs,
144 unsigned int minPath,
unsigned int maxPath);
147 const ROMol &mol, std::vector<const Bond *> &bondCache,
148 std::vector<short> &isQueryBond);
151 const ROMol &mol, boost::dynamic_bitset<> &atomsInPath,
152 const std::vector<const Bond *> &bondCache,
153 const std::vector<short> &isQueryBond,
const std::vector<int> &path,
154 bool useBondOrder,
const std::vector<std::uint32_t> *atomInvariants);
boost::tuple< boost::dynamic_bitset<>, uint32_t, unsigned int > AccumTuple
RDKIT_FINGERPRINTS_EXPORT std::uint32_t getAtomCode(const Atom *atom, unsigned int branchSubtract=0, bool includeChirality=false)
const unsigned int atomNumberTypes[1<< numTypeBits]
RDKIT_FINGERPRINTS_EXPORT void getConnectivityInvariants(const ROMol &mol, std::vector< std::uint32_t > &invars, bool includeRingMembership=true)
returns the connectivity invariants for a molecule
RDKIT_FINGERPRINTS_EXPORT std::vector< std::string > defaultFeatureSmarts
The class for representing atoms.
RDKIT_FINGERPRINTS_EXPORT void getFeatureInvariants(const ROMol &mol, std::vector< std::uint32_t > &invars, std::vector< const ROMol * > *patterns=0)
returns the feature invariants for a molecule
const unsigned int numTypeBits
RDKIT_FINGERPRINTS_EXPORT void buildDefaultRDKitFingerprintAtomInvariants(const ROMol &mol, std::vector< std::uint32_t > &lAtomInvariants)
RDKIT_FINGERPRINTS_EXPORT void enumerateAllPaths(const ROMol &mol, std::map< int, std::list< std::vector< int >>> &allPaths, const std::vector< std::uint32_t > *fromAtoms, bool branchedPaths, bool useHs, unsigned int minPath, unsigned int maxPath)
const unsigned int numAtomPairFingerprintBits
const unsigned int numBranchBits
pulls in the core RDKit functionality
RDKIT_FINGERPRINTS_EXPORT std::uint64_t getTopologicalTorsionCode(const std::vector< std::uint32_t > &atomCodes, bool includeChirality=false)
RDKIT_FINGERPRINTS_EXPORT std::vector< unsigned int > generateBondHashes(const ROMol &mol, boost::dynamic_bitset<> &atomsInPath, const std::vector< const Bond * > &bondCache, const std::vector< short > &isQueryBond, const std::vector< int > &path, bool useBondOrder, const std::vector< std::uint32_t > *atomInvariants)
const std::string morganFeatureInvariantVersion
const unsigned int codeSize
RDKIT_FINGERPRINTS_EXPORT std::uint32_t getTopologicalTorsionHash(const std::vector< std::uint32_t > &pathCodes)
const unsigned int maxNumPi
const unsigned int numChiralBits
RDKIT_FINGERPRINTS_EXPORT void identifyQueryBonds(const ROMol &mol, std::vector< const Bond * > &bondCache, std::vector< short > &isQueryBond)
RDKIT_FINGERPRINTS_EXPORT std::uint32_t getAtomPairCode(std::uint32_t codeI, std::uint32_t codeJ, unsigned int dist, bool includeChirality=false)
const std::string morganConnectivityInvariantVersion
Pulls in all the BitVect classes.
#define RDKIT_FINGERPRINTS_EXPORT
const unsigned int maxPathLen
const unsigned int numPiBits
const unsigned int maxNumBranches
functionality for finding subgraphs and paths in molecules
const unsigned int numPathBits
boost::shared_ptr< ROMol > ROMOL_SPTR