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RDKit
Open-source cheminformatics and machine learning.
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33 #ifndef __RD_ATOMPAIRS_H__
34 #define __RD_ATOMPAIRS_H__
81 const ROMol &mol,
unsigned int minLength,
unsigned int maxLength,
82 const std::vector<std::uint32_t> *fromAtoms = 0,
83 const std::vector<std::uint32_t> *ignoreAtoms = 0,
84 const std::vector<std::uint32_t> *atomInvariants = 0,
85 bool includeChirality =
false,
bool use2D =
true,
int confId = -1);
88 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms = 0,
89 const std::vector<std::uint32_t> *ignoreAtoms = 0,
90 const std::vector<std::uint32_t> *atomInvariants = 0,
91 bool includeChirality =
false,
bool use2D =
true,
int confId = -1);
122 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int minLength = 1,
124 const std::vector<std::uint32_t> *fromAtoms = 0,
125 const std::vector<std::uint32_t> *ignoreAtoms = 0,
126 const std::vector<std::uint32_t> *atomInvariants = 0,
127 bool includeChirality =
false,
bool use2D =
true,
int confId = -1);
159 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int minLength = 1,
161 const std::vector<std::uint32_t> *fromAtoms = 0,
162 const std::vector<std::uint32_t> *ignoreAtoms = 0,
163 const std::vector<std::uint32_t> *atomInvariants = 0,
164 unsigned int nBitsPerEntry = 4,
bool includeChirality =
false,
165 bool use2D =
true,
int confId = -1);
195 const ROMol &mol,
unsigned int targetSize = 4,
196 const std::vector<std::uint32_t> *fromAtoms = 0,
197 const std::vector<std::uint32_t> *ignoreAtoms = 0,
198 const std::vector<std::uint32_t> *atomInvariants = 0,
199 bool includeChirality =
false);
229 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int targetSize = 4,
230 const std::vector<std::uint32_t> *fromAtoms = 0,
231 const std::vector<std::uint32_t> *ignoreAtoms = 0,
232 const std::vector<std::uint32_t> *atomInvariants = 0,
233 bool includeChirality =
false);
260 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int targetSize = 4,
261 const std::vector<std::uint32_t> *fromAtoms = 0,
262 const std::vector<std::uint32_t> *ignoreAtoms = 0,
263 const std::vector<std::uint32_t> *atomInvariants = 0,
264 unsigned int nBitsPerEntry = 4,
bool includeChirality =
false);
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::int32_t > * getHashedAtomPairFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< std::uint32_t > *fromAtoms=0, const std::vector< std::uint32_t > *ignoreAtoms=0, const std::vector< std::uint32_t > *atomInvariants=0, bool includeChirality=false, bool use2D=true, int confId=-1)
returns the hashed atom-pair fingerprint for a molecule
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< boost::int64_t > * getHashedTopologicalTorsionFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int targetSize=4, const std::vector< std::uint32_t > *fromAtoms=0, const std::vector< std::uint32_t > *ignoreAtoms=0, const std::vector< std::uint32_t > *atomInvariants=0, bool includeChirality=false)
returns a hashed topological-torsion fingerprint for a molecule
const std::string atomPairsVersion
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * getHashedTopologicalTorsionFingerprintAsBitVect(const ROMol &mol, unsigned int nBits=2048, unsigned int targetSize=4, const std::vector< std::uint32_t > *fromAtoms=0, const std::vector< std::uint32_t > *ignoreAtoms=0, const std::vector< std::uint32_t > *atomInvariants=0, unsigned int nBitsPerEntry=4, bool includeChirality=false)
returns a hashed topological-torsion fingerprint for a molecule as a bit
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::int32_t > * getAtomPairFingerprint(const ROMol &mol, unsigned int minLength, unsigned int maxLength, const std::vector< std::uint32_t > *fromAtoms=0, const std::vector< std::uint32_t > *ignoreAtoms=0, const std::vector< std::uint32_t > *atomInvariants=0, bool includeChirality=false, bool use2D=true, int confId=-1)
returns the atom-pair fingerprint for a molecule
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * getHashedAtomPairFingerprintAsBitVect(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< std::uint32_t > *fromAtoms=0, const std::vector< std::uint32_t > *ignoreAtoms=0, const std::vector< std::uint32_t > *atomInvariants=0, unsigned int nBitsPerEntry=4, bool includeChirality=false, bool use2D=true, int confId=-1)
returns the hashed atom-pair fingerprint for a molecule as a bit vector
Pulls in all the BitVect classes.
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< boost::int64_t > * getTopologicalTorsionFingerprint(const ROMol &mol, unsigned int targetSize=4, const std::vector< std::uint32_t > *fromAtoms=0, const std::vector< std::uint32_t > *ignoreAtoms=0, const std::vector< std::uint32_t > *atomInvariants=0, bool includeChirality=false)
returns the topological-torsion fingerprint for a molecule
#define RDKIT_FINGERPRINTS_EXPORT
const unsigned int maxPathLen
a class for efficiently storing sparse vectors of ints
a class for bit vectors that are densely occupied