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* the change sorts the inchikey match for GLU and SAC but GLC MAN remain problematic with end of inchikey not matching. GLU and SAC are simple with one chiral centre.
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* likely reason is that the pdbx_stereo_config is based on a different atom order from rdkit.
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* Could try to understand pdbx_chirality or randomly iterate through chiral centres flipping until chiral centres match but neither is a good idea! Instead:
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## Try using assignChiralTypesFrom3D
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## Try using ~~assignChiralTypesFrom3D~~ AssignAtomChiralTagsFromStructure
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* https://sourceforge.net/p/rdkit/mailman/message/35774134/ has Greg Landrum's suggestion:
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* sanitizeMol
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* Kekulize(mol);
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... | ... | @@ -23,4 +23,8 @@ |
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* assignStereochemistry(mol,true,true)
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* ~~compute2DCoords(mol)~~
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* this should also get rid of `WARNING: Omitted undefined stereo` message as RDKit would do its own stereo centre assignment.
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* will need ideal coordinates for this. |
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\ No newline at end of file |
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* will need ideal coordinates from ccd for this
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* **done** and it works
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* the python method is AssignAtomChiralTagsFromStructure rather than assignChiralTypesFrom3D
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* commit :pen_fountain: including test results.
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* summary - ATP and the sugars GLC and MAN now give consistent inchikeys only CMO, HEM, and NAD still have issues. |
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