Hello Greg:
Duh! I guess I sat too long in front of the screen.
As always, thank you very much for your help!
Markus
On Wed, Feb 22, 2017 at 7:50 PM, Greg Landrum
wrote:
> Hi Markus,
>
>
> On Thu, Feb 23, 2017 at 1:41 AM, Markus Metz 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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