You probably are aware of this, but OBfit can probably start you if you can
manipulate the smarts pattern to include what you want as the scaffold in a
more generalized SMARTS pattern? Maybe you could generate a list of
possible substitutions for a functional group in the pattern, and then it
would try to align those?
Just a suggestion.
On Thu, Apr 12, 2012 at 1:39 PM, Adam Tenderholt <atenderh...@gmail.com>wrote:
> > You could probably code something like this using the OBBuilder code,
> but it would take some work (i.e, it sounds like you'd need to remove or
> mutate some atoms, adjust bond lengths, grow new fragments).
> >
> > I assume the idea is to do this in an automated fashion, or I'd suggest
> doing it manually using Avogadro. :-)
> >
> > If you'd like to code it, I think we can probably point you in the right
> directions.
>
> Yes, I'd like to be able to do this in an automated fashion. I'm
> currently making these changes using Avogadro, but it's rather
> time-consuming for more than a couple of molecules.
>
> I'd be willing to code it, but my C++ skills are a bit rusty so I'd
> prototype it in Python first. Any pointers or methods already
> implemented in OpenBabel? Is it possible to compare two SMILES
> strings, and get a list that maps atoms in functional groups between
> the two? I could start by placing atoms in the same positions for
> common groups, and build from there.
>
> Adam
>
>
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