def pyScorePair(at1, at2, dist, atomCodes=None):
""" Returns a score for an individual atom pair.
>>> 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
"""
if not atomCodes:
code1 = Utils.GetAtomCode(at1)
code2 = Utils.GetAtomCode(at2)
else:
code1, code2 = atomCodes
accum = int(dist) % _maxPathLen
accum |= min(code1, code2) << numPathBits
accum |= max(code1, code2) << (
rdMolDescriptors.AtomPairsParameters.codeSize + numPathBits)
return accum
def 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
"""
codes = [None] * size
for i in range(size):
if i == 0 or i == (size - 1):
sub = 1
else:
sub = 2
if not atomCodes:
codes[i] = Utils.GetAtomCode(mol.GetAtomWithIdx(path[i]), sub)
else:
base = atomCodes[path[i]]
codes[i] = base - sub
# "canonicalize" the code vector:
beg = 0
end = len(codes) - 1
while (beg < end):
if codes[beg] > codes[end]:
codes.reverse()
break
elif codes[beg] == codes[end]:
beg += 1
end -= 1
else:
break
accum = 0
for i in range(size):
accum |= codes[i] << (rdMolDescriptors.AtomPairsParameters.codeSize *
i)
return accum