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* Sameer's prototype code [sameer_prototype_chem.py](https://gitlab.com/pdbe/ccd_utils/blob/master/sameer_prototype_chem.py) has procedure for setting chirality from the chem_comp_atom.pdbx_stereo_config value
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* *27 May 2017*:
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* Try the procedure from [sameer_prototype_chem.py](https://gitlab.com/pdbe/ccd_utils/blob/master/sameer_prototype_chem.py)
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* Try the procedure from [sameer_prototype_chem.py](https://gitlab.com/pdbe/ccd_utils/blob/master/sameer_prototype_chem.py) results:
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* commit [d4cd4046](https://gitlab.com/pdbe/ccd_utils/commit/d4cd40468c2fc999be8a92bd4fc095f5b27491bb) "Adapt procedure from sameer_prototype_chem.py to set the chirality of the rdkit atoms."
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* failure [commit message](https://gitlab.com/pdbe/ccd_utils/commit/d4cd40468c2fc999be8a92bd4fc095f5b27491bb) includes details.
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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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* 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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* assignChiralTypesFrom3D(mol);
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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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