Ok cool! I did actually just run into an issue while doing some tests:
https://github.com/rdkit/rdkit/issues/2183. This issue brings up a question
for me about where the smiles writer actually looks for stereochem info when it
decides what to write.
Also, I ran into the same snag earlier too Dan!
- Kovas
From: Dan Nealschneider <dan.nealschnei...@schrodinger.com>
Date: Tuesday, December 4, 2018 at 10:05 AM
To: "col...@gmail.com" <col...@gmail.com>
Cc: Kovas Palunas <kovas.palu...@arzeda.com>, rdkit discuss
<rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Double Bond Stereochemistry in the RDKit
I've done some in-memory translation of molecules to ROMols, and have used #2
without major problems. I do remember needing to make sure that the stereoatoms
are in the correct order - that is, that the first stereoatom is bonded to the
beginAtom of the bond. In Python, this is something like:
bond = mol.GetBondBetweenAtoms(begin, end)
if bond.GetBeginAtomIdx() != begin:
assert bond.GetBeginAtomIdx() == end
stereoatom1, stereoatom2 = stereoatom2, stereoatom1
bond.SetStereoAtoms(stereoatom1, stereoatom2)
bond.SetStereo(stereo)
- dan nealschneider
(né wandschneider)
Senior Developer
Schrödinger, Inc
Portland, OR
On Tue, Dec 4, 2018 at 7:02 AM Brian Cole
<col...@gmail.com<mailto:col...@gmail.com>> wrote:
Hi Kovas,
For your use-case #2 should suffice, "set STEREOCIS/STEREOTRANS tags + manually
set stereo atoms". This is what the EnumerateStereoisomers code does:
https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/EnumerateStereoisomers.py#L38
As to what is the 'ground truth', that is a more difficult question that I fear
the answer may be 'none of them'. STEREOCIS/STEREOTRANS are rather recent
additions to the RDKit API, while we strived to make sure STEREOCIS/STEREOTRANS
across the RDKit, there are probably looming bugs in untested parts of the
RDKit that don't handle them properly. However, I think those other APIs should
be fixed to handle them properly, so please do report any problems you spot
into the github issue tracker.
Cheers,
Brian
On Mon, Dec 3, 2018 at 7:00 PM Kovas Palunas
<kovas.palu...@arzeda.com<mailto:kovas.palu...@arzeda.com>> wrote:
Hi All,
I’m looking for a bit more clarity regarding double bond stereochem in RDKit.
Currently, my understanding is that there are 3 ways to currently store this
information:
1. STEREOE/STEREOZ tags + stereo atoms on either side of bond set by CIP
ranks, as computed when calling MolFromSmiles to make a new molecule or
AssignStereochemistry on an existing molecule
2. Manually set STEREOCIS/STEREOTRANS tags + manually set stereo atoms
3. ENDUPRIGHT/etc. single bond directionality tags, which are set when
reading a molecule from smiles/inchi/mol file
Is one of these methods the “ground truth” that is looked for by RDKit
functions that care about this info, like the substructure matching code or the
SMILES writing code?
I am currently working on code that mutates molecules using a predetermined
list of changes to be made to the molecule. I’d like to be able to include
bond stereochemistry changing/creation/destruction here, and was thinking of
doing so using the STEREOCIS/STEREOTRANS tags (and also providing the reference
stereo atoms). Before I do this I want to make sure that molecules with these
tags will be handled correctly by other RDKit functions downstream. Would
these tags be a good choice here? Are there any caveats I should keep in mind
as I work with this information?
Thanks!
- Kovas
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