Hi Markus,
On Thu, Feb 23, 2017 at 1:41 AM, Markus Metz <metm...@gmail.com> wrote:
>
> According to the example it is possible to use the option
> labelByIndex=True in ReplaceCore.
> Converting the sidechains from mol to smiles with isomericSmiles=True
> labels the sidechains with 1 and 5.
> Where do these numbers come from?
>
They are the indices of the atoms in the core.
> I included the atom indices in the mol drawing but the core atoms are 1
> and 8. (please see attached jupyter file). What am I missing?
>
The code where you assign the atom map numbers so that you can see the
indices:
matches = m1.GetSubstructMatch(core)
print(matches)
for i, atom_idx in enumerate(matches, 1):
m1.GetAtomWithIdx(atom_idx).SetProp('molAtomMapNumber', str(atom_idx))
is using the indices in m1. You want the indices in the core:
for i, atom_idx in enumerate(matches, 1):
m1.GetAtomWithIdx(atom_idx).SetProp('molAtomMapNumber', str(i))
(Note: you can also do SetIntProp() and skip the conversion of i to a
string).
Best,
-greg
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