def featurize(self, x):
if self.input_type == 'smiles':
x_ = x
x = Chem.MolFromSmiles(x)
if x is None:
raise ValueError('cannot convert Mol from SMILES %s' % x_)
if self.input_type == 'any':
if not isinstance(x, Chem.rdchem.Mol):
x_ = x
x = Chem.MolFromSmiles(x)
if x is None:
raise ValueError('cannot convert Mol from SMILES %s' % x_)
if self.counting:
return count_fp(rdMol.GetHashedTopologicalTorsionFingerprint(x, nBits=self.n_bits), dim=self.n_bits)
else:
return list(rdMol.GetHashedTopologicalTorsionFingerprintAsBitVect(x, nBits=self.n_bits,
nBitsPerEntry=self.bit_per_entry))
def testHashedTopologicalTorsions(self):
mol = Chem.MolFromSmiles("c1ncccc1")
fp1 = rdMD.GetHashedTopologicalTorsionFingerprint(mol)
mol = Chem.MolFromSmiles("n1ccccc1")
fp2 = rdMD.GetHashedTopologicalTorsionFingerprint(mol)
self.assertEqual(DataStructs.DiceSimilarity(fp1, fp2), 1.0)
fpType -- the type of AP fingerprint ('normal', 'hashed', 'bv')
nBits -- the size of the bit vector (only for fpType='bv')
minLength -- the minimum path length for an atom pair
maxLength -- the maxmimum path length for an atom pair
nBitsPerEntry -- the number of bits available for each pair
"""
if fpType not in ['normal', 'hashed', 'bv']: raise ValueError("Unknown Atom pairs fingerprint type")
if atomId < 0:
return apDict[fpType](mol, nBits, minLength, maxLength, nBitsPerEntry, 0)
if atomId >= mol.GetNumAtoms(): raise ValueError("atom index greater than number of atoms")
return apDict[fpType](mol, nBits, minLength, maxLength, nBitsPerEntry, [atomId])
ttDict = {}
ttDict['normal'] = lambda m, bits, ts, bpe, ia: rdMD.GetTopologicalTorsionFingerprint(m, targetSize=ts, ignoreAtoms=ia)
ttDict['hashed'] = lambda m, bits, ts, bpe, ia: rdMD.GetHashedTopologicalTorsionFingerprint(m, nBits=bits, targetSize=ts, ignoreAtoms=ia)
ttDict['bv'] = lambda m, bits, ts, bpe, ia: rdMD.GetHashedTopologicalTorsionFingerprintAsBitVect(m, nBits=bits, targetSize=ts, nBitsPerEntry=bpe, ignoreAtoms=ia)
# usage: lambda m,i: GetTTFingerprint(m, i, fpType, nBits, targetSize)
def GetTTFingerprint(mol, atomId=-1, fpType='normal', nBits=2048, targetSize=4, nBitsPerEntry=4):
"""
Calculates the topological torsion fingerprint with the pairs of atomId removed.
Parameters:
mol -- the molecule of interest
atomId -- the atom to remove the torsions for (if -1, no torsion is removed)
fpType -- the type of TT fingerprint ('normal', 'hashed', 'bv')
nBits -- the size of the bit vector (only for fpType='bv')
minLength -- the minimum path length for an atom pair
maxLength -- the maxmimum path length for an atom pair
nBitsPerEntry -- the number of bits available for each torsion
