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 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
