[OpenBabel-Devel] Stereochemistry check using InChIKey

[Naruki Y. <nar...@gm...>]

Hi all,

I've been developing a new distance geometry method these days.
https://github.com/openbabel/openbabel/pull/1875

I generated SMILES from experimental structures and predict a 3D
structure from the SMILES.
I compare InChIKey of experimental structure and predicted structure
to evaluate stereochemistry correctness.
The distance geometry function uses
OBDistanceGeometry::CheckStereoConstraints() to check stereo
constraints are satisfied.
https://github.com/openbabel/openbabel/blob/528f73fe64376ce8922897748e2879a6d599e7ed/src/distgeom.cpp#L953
Even though stereo constraints are satisfied judging from this
function, InChIKey did not match in some molecules.

I prepared test cases here:
https://gist.github.com/n-yoshikawa/00dc043694b539fb5f9340f48fb5d2b0#file-checkstereo-cpp
This gist includes SDFs predicted from SMILES and they have the above
problem as shown in result.txt.

Could you suggest possible cause of this problem?

Naruki