>
> If what you are looking for is information about what type of atom
> [*:1] is in the original molecule, I think you can probably figure
> it out based on the additional info that's present in the output
> from Jameed's code.
>
> For example, here's one of the output lines from an indexing.py run
> that I did for an RDKit blog post I'm working on (hopefully going up
today):
> Cc1c(CCN2CCNCC2)ccc3cc(F)ccc13,Fc1ccc2cc(CCN3CCNCC3)ccc2c1,521767,
> 521766,[*:1]C>>[*:1][H],[*:1]c1c(CCN2CCNCC2)ccc2cc(F)ccc21
> The last entry in that line is the "core", which shows where the [*:
> 1] is attached.
>
> Using these cores, you can get information about where points are
> attached to them like this:
> In [2]: m = Chem.MolFromSmiles('[*:1]c1c(CCN2CCNCC2)ccc2cc(F)ccc21')
> In [3]: attaches = [x for x in m.GetAtoms() if x.GetAtomicNum()==0]
> In [7]: for at in attaches:
> if at.HasProp("molAtomMapNumber"):
> nbr = at.GetNeighbors()[0]
> print at.GetProp("molAtomMapNumber"),nbr.GetSymbol
> (),nbr.GetIsAromatic()
> ...:
> 1 C True
>
> This says that attachment point 1 is connected to a carbon which is
aromatic.
>
> Does that help?
Absolutely, this saves my day!
Thank you very much for this snippet!
Paul
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