Hi Andrew and Greg,
thanks a lot for the quick replies.
I tested Greg's suggested solution, and it works ... but only with the
RDKit version 2016.03.1. With Version 2015.09.2, I still get the wrong
stereochemistry after fragmentation (maybe relevant for people working with
older versions).
Bests,
Christian
*Dr. Christian Kramer*
Computer-Aided Drug Design (CADD) Scientist
F. Hoffmann-La Roche Ltd
Pharma Research and Early Development
Bldg. 092/2.56
CH-4070 Basel
Phone +41 61 682 2471
mailto: christian.kra...@roche.com
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On Tue, Jun 21, 2016 at 5:54 PM, Andrew Dalke <da...@dalkescientific.com>
wrote:
> On Jun 21, 2016, at 5:26 PM, Greg Landrum wrote:
> > Because chirality is represented relative to the ordering of the bonds
> around an atom, it's pretty difficult to do this if you want to actually
> break and add bonds on your own. This would probably be somewhat easier if
> there were an RWMol.ReplaceBond() method analogous to the
> RWMol.ReplaceAtom() method, but that's not available at the moment.
> ...
> > p.s. this all reminds me that there's a long email from Andrew on this
> topic that I still haven't worked my way all the way through. <sigh>
>
> I pretty much had to give up with working in molecule space and switch to
> working in SMILES space.
>
> That is, I did a SMARTS match or whatever to get the atom to change,
> backtracked to the original SMILES, which I tokenized to find the
> corresponding term, then at the token level substituted in the new group.
>
> What made it relatively simple was that I wanted to fragment R-groups
> along non-ring single bonds. In that case, I find the pair of atoms (i, j),
> along the bond, find the token corresponding to atom j, insert "*.*" before
> that token, and reparse the modified SMILES.
>
> On Jun 21, 2016, at 4:50 PM, Kramer, Christian wrote:
> > Is there a simple way of preserving chirality during splits on chiral
> atoms?
>
> To preserve chirality, I had to map from the new molecule space back to
> the original molecule space, bearing in mind the newly added atom. Then
> figure out which chiralities were missing in the "*.*"-inserted molecule
> (since an asymmetric molecule with chirality in the core might have a
> symmetric core after fragmentation, causing chirality information to
> disappear), and determine which chirality terms to put back.
>
> It's very tricky.
>
> I was hoping to present this as the RDKit User's Group Meeting, but I
> won't be able to make it. :(
>
>
> Andrew
> da...@dalkescientific.com
>
>
>
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