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# Developer documentation: RDKit molecule from PDB CCD definition
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* 25 May 2017: got initial version working in commit [26111ee5 First version of PdbChemicalComponentsRDKit that works (a bit!)](https://gitlab.com/pdbe/ccd_utils/commit/26111ee59f745bea16cdf37013d84540b752bf01) testing that the inchikey from the RDKit molecule matches that from stored in the cif file for 14 example ccd cif files in [/data/cif/](/data/cif/) directory |
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\ No newline at end of file |
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* *25 May 2017*: got initial version working in commit [26111ee5 First version of PdbChemicalComponentsRDKit that works (a bit!)](https://gitlab.com/pdbe/ccd_utils/commit/26111ee59f745bea16cdf37013d84540b752bf01) testing that the inchikey from the RDKit molecule matches that from stored in the cif file for 14 example ccd cif files in [/data/cif/](https://gitlab.com/pdbe/ccd_utils/tree/master/data/cif) directory. Test results (can be found in the commit message), show that that:
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* in inchikeys match for 007, FES, V55 and EOH
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* in other cases get `WARNING: Omitted undefined stereo` from RDKit. So most other problems with chirality - would expect the first 14 characters of the inchikeys to match. This is true to 009 ATP GLC GLU MAN SAC SEH
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* CMO, NAD and HEM has complete mismatch
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* for CMO (carbon monoxide) the likely problem is that do not process the charges smiles is `[C-]#[O+]`
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* HEM (heme) I think the CCD definition is wrong and pubchem defined it correctly
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* NAD: not sure what the problem is.
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* Sameer's prototype code [](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*: |