32 #ifndef __RD_ATOMPAIRS_H__ 33 #define __RD_ATOMPAIRS_H__ 37 #include <boost/cstdint.hpp> 45 5, 6, 7, 8, 9, 14, 15, 16, 17, 33, 34, 35, 51, 52, 43};
69 boost::uint32_t
getAtomCode(
const Atom *atom,
unsigned int branchSubtract = 0,
70 bool includeChirality =
false);
82 boost::uint32_t
getAtomPairCode(boost::uint32_t codeI, boost::uint32_t codeJ,
84 bool includeChirality =
false);
121 const ROMol &mol,
unsigned int minLength,
unsigned int maxLength,
122 const std::vector<boost::uint32_t> *fromAtoms = 0,
123 const std::vector<boost::uint32_t> *ignoreAtoms = 0,
124 const std::vector<boost::uint32_t> *atomInvariants = 0,
125 bool includeChirality =
false,
bool use2D =
true,
int confId = -1);
128 const ROMol &mol,
const std::vector<boost::uint32_t> *fromAtoms = 0,
129 const std::vector<boost::uint32_t> *ignoreAtoms = 0,
130 const std::vector<boost::uint32_t> *atomInvariants = 0,
131 bool includeChirality =
false,
bool use2D =
true,
int confId = -1);
161 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int minLength = 1,
162 unsigned int maxLength = maxPathLen - 1,
163 const std::vector<boost::uint32_t> *fromAtoms = 0,
164 const std::vector<boost::uint32_t> *ignoreAtoms = 0,
165 const std::vector<boost::uint32_t> *atomInvariants = 0,
166 bool includeChirality =
false,
bool use2D =
true,
int confId = -1);
197 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int minLength = 1,
198 unsigned int maxLength = maxPathLen - 1,
199 const std::vector<boost::uint32_t> *fromAtoms = 0,
200 const std::vector<boost::uint32_t> *ignoreAtoms = 0,
201 const std::vector<boost::uint32_t> *atomInvariants = 0,
202 unsigned int nBitsPerEntry = 4,
bool includeChirality =
false,
203 bool use2D =
true,
int confId = -1);
211 const std::vector<boost::uint32_t> &atomCodes,
212 bool includeChirality =
false);
241 const ROMol &mol,
unsigned int targetSize = 4,
242 const std::vector<boost::uint32_t> *fromAtoms = 0,
243 const std::vector<boost::uint32_t> *ignoreAtoms = 0,
244 const std::vector<boost::uint32_t> *atomInvariants = 0,
245 bool includeChirality =
false);
274 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int targetSize = 4,
275 const std::vector<boost::uint32_t> *fromAtoms = 0,
276 const std::vector<boost::uint32_t> *ignoreAtoms = 0,
277 const std::vector<boost::uint32_t> *atomInvariants = 0,
278 bool includeChirality =
false);
304 const ROMol &mol,
unsigned int nBits = 2048,
unsigned int targetSize = 4,
305 const std::vector<boost::uint32_t> *fromAtoms = 0,
306 const std::vector<boost::uint32_t> *ignoreAtoms = 0,
307 const std::vector<boost::uint32_t> *atomInvariants = 0,
308 unsigned int nBitsPerEntry = 4,
bool includeChirality =
false);
const std::string atomPairsVersion
Pulls in all the BitVect classes.
const unsigned int maxPathLen
const unsigned int numPathBits
SparseIntVect< boost::int32_t > * getHashedAtomPairFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< boost::uint32_t > *fromAtoms=0, const std::vector< boost::uint32_t > *ignoreAtoms=0, const std::vector< boost::uint32_t > *atomInvariants=0, bool includeChirality=false, bool use2D=true, int confId=-1)
returns the hashed atom-pair fingerprint for a molecule
const unsigned int maxNumPi
ROMol is a molecule class that is intended to have a fixed topology.
boost::uint32_t getAtomCode(const Atom *atom, unsigned int branchSubtract=0, bool includeChirality=false)
ExplicitBitVect * getHashedAtomPairFingerprintAsBitVect(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< boost::uint32_t > *fromAtoms=0, const std::vector< boost::uint32_t > *ignoreAtoms=0, const std::vector< boost::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
const unsigned int numPiBits
Includes a bunch of functionality for handling Atom and Bond queries.
const unsigned int maxNumBranches
SparseIntVect< boost::int64_t > * getTopologicalTorsionFingerprint(const ROMol &mol, unsigned int targetSize=4, const std::vector< boost::uint32_t > *fromAtoms=0, const std::vector< boost::uint32_t > *ignoreAtoms=0, const std::vector< boost::uint32_t > *atomInvariants=0, bool includeChirality=false)
returns the topological-torsion fingerprint for a molecule
const unsigned int numBranchBits
boost::uint64_t getTopologicalTorsionCode(const std::vector< boost::uint32_t > &atomCodes, bool includeChirality=false)
ExplicitBitVect * getHashedTopologicalTorsionFingerprintAsBitVect(const ROMol &mol, unsigned int nBits=2048, unsigned int targetSize=4, const std::vector< boost::uint32_t > *fromAtoms=0, const std::vector< boost::uint32_t > *ignoreAtoms=0, const std::vector< boost::uint32_t > *atomInvariants=0, unsigned int nBitsPerEntry=4, bool includeChirality=false)
returns a hashed topological-torsion fingerprint for a molecule as a bit
const unsigned int numAtomPairFingerprintBits
SparseIntVect< boost::int64_t > * getHashedTopologicalTorsionFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int targetSize=4, const std::vector< boost::uint32_t > *fromAtoms=0, const std::vector< boost::uint32_t > *ignoreAtoms=0, const std::vector< boost::uint32_t > *atomInvariants=0, bool includeChirality=false)
returns a hashed topological-torsion fingerprint for a molecule
a class for efficiently storing sparse vectors of ints
a class for bit vectors that are densely occupied
boost::uint32_t getAtomPairCode(boost::uint32_t codeI, boost::uint32_t codeJ, unsigned int dist, bool includeChirality=false)
const unsigned int codeSize
const unsigned int atomNumberTypes[1<< numTypeBits]
The class for representing atoms.
SparseIntVect< boost::int32_t > * getAtomPairFingerprint(const ROMol &mol, unsigned int minLength, unsigned int maxLength, const std::vector< boost::uint32_t > *fromAtoms=0, const std::vector< boost::uint32_t > *ignoreAtoms=0, const std::vector< boost::uint32_t > *atomInvariants=0, bool includeChirality=false, bool use2D=true, int confId=-1)
returns the atom-pair fingerprint for a molecule
const unsigned int numChiralBits
const unsigned int numTypeBits