33#ifndef __RD_ATOMPAIRS_H__
34#define __RD_ATOMPAIRS_H__
80[[deprecated(
"please use AtomPairGenerator")]]
82 const ROMol &mol,
unsigned int minLength,
unsigned int maxLength,
83 const std::vector<std::uint32_t> *fromAtoms =
nullptr,
84 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
85 const std::vector<std::uint32_t> *atomInvariants =
nullptr,
86 bool includeChirality =
false,
bool use2D =
true,
int confId = -1);
88[[deprecated(
"please use AtomPairGenerator")]]
90 const ROMol &mol,
const std::vector<std::uint32_t> *fromAtoms =
nullptr,
91 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
92 const std::vector<std::uint32_t> *atomInvariants =
nullptr,
93 bool includeChirality =
false,
bool use2D =
true,
int confId = -1);
122[[deprecated(
"please use AtomPairGenerator")]]
125 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int minLength = 1,
127 const std::vector<std::uint32_t> *fromAtoms =
nullptr,
128 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
129 const std::vector<std::uint32_t> *atomInvariants =
nullptr,
130 bool includeChirality =
false,
bool use2D =
true,
int confId = -1);
160[[deprecated(
"please use AtomPairGenerator")]]
163 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int minLength = 1,
165 const std::vector<std::uint32_t> *fromAtoms =
nullptr,
166 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
167 const std::vector<std::uint32_t> *atomInvariants =
nullptr,
168 unsigned int nBitsPerEntry = 4,
bool includeChirality =
false,
169 bool use2D =
true,
int confId = -1);
197[[deprecated(
"please use TopologicalTorsionGenerator")]]
200 const ROMol &mol,
unsigned int targetSize = 4,
201 const std::vector<std::uint32_t> *fromAtoms =
nullptr,
202 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
203 const std::vector<std::uint32_t> *atomInvariants =
nullptr,
204 bool includeChirality =
false);
232[[deprecated(
"please use TopologicalTorsionGenerator")]]
235 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int targetSize = 4,
236 const std::vector<std::uint32_t> *fromAtoms =
nullptr,
237 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
238 const std::vector<std::uint32_t> *atomInvariants =
nullptr,
239 bool includeChirality =
false);
264[[deprecated(
"please use TopologicalTorsionGenerator")]]
267 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int targetSize = 4,
268 const std::vector<std::uint32_t> *fromAtoms =
nullptr,
269 const std::vector<std::uint32_t> *ignoreAtoms =
nullptr,
270 const std::vector<std::uint32_t> *atomInvariants =
nullptr,
271 unsigned int nBitsPerEntry = 4,
bool includeChirality =
false);
Pulls in all the BitVect classes.
a class for bit vectors that are densely occupied
a class for efficiently storing sparse vectors of ints
#define RDKIT_FINGERPRINTS_EXPORT
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< boost::int64_t > * getTopologicalTorsionFingerprint(const ROMol &mol, unsigned int targetSize=4, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, bool includeChirality=false)
returns the topological-torsion fingerprint for a molecule
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=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, 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=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, bool includeChirality=false)
returns a hashed topological-torsion fingerprint for a molecule
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect * getHashedTopologicalTorsionFingerprintAsBitVect(const ROMol &mol, unsigned int nBits=2048, unsigned int targetSize=4, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, unsigned int nBitsPerEntry=4, bool includeChirality=false)
const std::string atomPairsVersion
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=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, 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
RDKIT_FINGERPRINTS_EXPORT SparseIntVect< std::int32_t > * getAtomPairFingerprint(const ROMol &mol, unsigned int minLength, unsigned int maxLength, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, bool includeChirality=false, bool use2D=true, int confId=-1)
returns the atom-pair fingerprint for a molecule
const unsigned int maxPathLen