rdkit.Chem.AtomPairs.Torsions module

Contains an implementation of Topological-torsion fingerprints, as described in:

R. Nilakantan, N. Bauman, J. S. Dixon, R. Venkataraghavan; “Topological Torsion: A New Molecular Descriptor for SAR Applications. Comparison with Other Descriptors” JCICS 27, 82-85 (1987).

The fingerprints can be accessed through the following functions: - GetTopologicalTorsionFingerprint - GetHashedTopologicalTorsionFingerprint - GetTopologicalTorsionFingerprintAsIntVect (identical to GetTopologicalTorsionFingerprint) - GetTopologicalTorsionFingerprintAsIds

rdkit.Chem.AtomPairs.Torsions.ExplainPathScore(score, size=4)

>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('C=CC')
>>> score=pyScorePath(m, (0, 1, 2), 3)
>>> ExplainPathScore(score, 3)
(('C', 1, 0), ('C', 2, 1), ('C', 1, 1))

Again, it’s order independent:

>>> score = pyScorePath(m, (2, 1, 0), 3)
>>> ExplainPathScore(score, 3)
(('C', 1, 0), ('C', 2, 1), ('C', 1, 1))

>>> m = Chem.MolFromSmiles('C=CO')
>>> score=pyScorePath(m, (0, 1, 2), 3)
>>> ExplainPathScore(score, 3)
(('C', 1, 1), ('C', 2, 1), ('O', 1, 0))

>>> m = Chem.MolFromSmiles('OC=CO')
>>> score=pyScorePath(m, (0, 1, 2, 3), 4)
>>> ExplainPathScore(score, 4)
(('O', 1, 0), ('C', 2, 1), ('C', 2, 1), ('O', 1, 0))

>>> m = Chem.MolFromSmiles('CC=CO')
>>> score=pyScorePath(m, (0, 1, 2, 3), 4)
>>> ExplainPathScore(score, 4)
(('C', 1, 0), ('C', 2, 1), ('C', 2, 1), ('O', 1, 0))

>>> m = Chem.MolFromSmiles('C=CC(=O)O')
>>> score=pyScorePath(m, (0, 1, 2, 3), 4)
>>> ExplainPathScore(score, 4)
(('C', 1, 1), ('C', 2, 1), ('C', 3, 1), ('O', 1, 1))
>>> score=pyScorePath(m, (0, 1, 2, 4), 4)
>>> ExplainPathScore(score, 4)
(('C', 1, 1), ('C', 2, 1), ('C', 3, 1), ('O', 1, 0))

>>> m = Chem.MolFromSmiles('OOOO')
>>> score=pyScorePath(m, (0, 1, 2), 3)
>>> ExplainPathScore(score, 3)
(('O', 1, 0), ('O', 2, 0), ('O', 2, 0))
>>> score=pyScorePath(m, (0, 1, 2, 3), 4)
>>> ExplainPathScore(score, 4)
(('O', 1, 0), ('O', 2, 0), ('O', 2, 0), ('O', 1, 0))

rdkit.Chem.AtomPairs.Torsions.GetTopologicalTorsionFingerprintAsIds(mol, targetSize=4)

rdkit.Chem.AtomPairs.Torsions.pyScorePath(mol, path, size, atomCodes=None)

Returns a score for an individual path.

>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('CCCCC')
>>> c1 = Utils.GetAtomCode(m.GetAtomWithIdx(0), 1)
>>> c2 = Utils.GetAtomCode(m.GetAtomWithIdx(1), 2)
>>> c3 = Utils.GetAtomCode(m.GetAtomWithIdx(2), 2)
>>> c4 = Utils.GetAtomCode(m.GetAtomWithIdx(3), 1)
>>> t = c1 | (c2 << rdMolDescriptors.AtomPairsParameters.codeSize) | (c3 << (rdMolDescriptors.AtomPairsParameters.codeSize * 2)) | (c4 << (rdMolDescriptors.AtomPairsParameters.codeSize * 3))
>>> pyScorePath(m, (0, 1, 2, 3), 4) == t
1

The scores are path direction independent:

>>> pyScorePath(m, (3, 2, 1, 0), 4) == t
1

>>> m = Chem.MolFromSmiles('C=CC(=O)O')
>>> c1 = Utils.GetAtomCode(m.GetAtomWithIdx(0), 1)
>>> c2 = Utils.GetAtomCode(m.GetAtomWithIdx(1), 2)
>>> c3 = Utils.GetAtomCode(m.GetAtomWithIdx(2), 2)
>>> c4 = Utils.GetAtomCode(m.GetAtomWithIdx(4), 1)
>>> t = c1 | (c2 << rdMolDescriptors.AtomPairsParameters.codeSize) | (c3 << (rdMolDescriptors.AtomPairsParameters.codeSize * 2)) | (c4 << (rdMolDescriptors.AtomPairsParameters.codeSize * 3))
>>> pyScorePath(m, (0, 1, 2, 4), 4) == t
1