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
[email protected]
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