Hi,
> I want to ask about the position of the fonctional groups within the
> molecules.
> For example, i have the substance like C(C)CC=C.
> Can i use Pybel for determining the position of branch CH3 at the position 2
> in this molecule ?
You can get the idx of the atom bearing your CH3 group:
smarts = pybel.Smarts("[CX4H3]") # match only one atom, C([H])([H])[H]
will match 4 atoms
...
for neighbor in ob.OBAtomAtomIter(mol.atoms[num-1].OBAtom):
if neighbor.GetAtomicNum() != 1:
print neighbor.GetIdx()
Is the neighbor idx equivalent to the position you want?
Regards,
Pascal
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