Module Pairs

Returns a score for an individual atom pair.

>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('CCCCC')
>>> c1 = Utils.GetAtomCode(m.GetAtomWithIdx(0))
>>> c2 = Utils.GetAtomCode(m.GetAtomWithIdx(1))
>>> c3 = Utils.GetAtomCode(m.GetAtomWithIdx(2))
>>> t = 1 | min(c1,c2)<<numPathBits | max(c1,c2)<<(rdMolDescriptors.AtomPairsParameters.codeSize+numPathBits)
>>> pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1)==t
1
>>> pyScorePair(m.GetAtomWithIdx(1),m.GetAtomWithIdx(0),1)==t
1
>>> t = 2 | min(c1,c3)<<numPathBits | max(c1,c3)<<(rdMolDescriptors.AtomPairsParameters.codeSize+numPathBits)
>>> pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(2),2)==t
1
>>> pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(2),2,
...  atomCodes=(Utils.GetAtomCode(m.GetAtomWithIdx(0)),Utils.GetAtomCode(m.GetAtomWithIdx(2))))==t
1

>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('C=CC')
>>> score = pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1)
>>> ExplainPairScore(score)
(('C', 1, 1), 1, ('C', 2, 1))
>>> score = pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(2),2)
>>> ExplainPairScore(score)
(('C', 1, 0), 2, ('C', 1, 1))
>>> score = pyScorePair(m.GetAtomWithIdx(1),m.GetAtomWithIdx(2),1)
>>> ExplainPairScore(score)
(('C', 1, 0), 1, ('C', 2, 1))
>>> score = pyScorePair(m.GetAtomWithIdx(2),m.GetAtomWithIdx(1),1)
>>> ExplainPairScore(score)
(('C', 1, 0), 1, ('C', 2, 1))

We can optionally deal with chirality too
>>> m = Chem.MolFromSmiles('C[C@H](F)Cl')
>>> score = pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1)
>>> ExplainPairScore(score)
(('C', 1, 0), 1, ('C', 3, 0))
>>> score = pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1,includeChirality=True)
>>> ExplainPairScore(score,includeChirality=True)
(('C', 1, 0, ''), 1, ('C', 3, 0, 'R'))
>>> m = Chem.MolFromSmiles('F[C@@H](Cl)[C@H](F)Cl')
>>> score = pyScorePair(m.GetAtomWithIdx(1),m.GetAtomWithIdx(3),1,includeChirality=True)
>>> ExplainPairScore(score,includeChirality=True)
(('C', 3, 0, 'R'), 1, ('C', 3, 0, 'S'))

Returns the Atom-pair fingerprint for a molecule as
a SparseBitVect. Note that this doesn't match the standard
definition of atom pairs, which uses counts of the
pairs, not just their presence.

**Arguments**:

  - mol: a molecule

**Returns**: a SparseBitVect

>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('CCC')
>>> v = [ pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1),
...       pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(2),2),
...     ]
>>> v.sort()
>>> fp = GetAtomPairFingerprintAsBitVect(m)
>>> list(fp.GetOnBits())==v
True