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# Developer documentation: RDKit molecule from PDB CCD definition
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# Development 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/](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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* 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 from ccd for this, done in [Commit da94277f](https://gitlab.com/pdbe/ccd_utils/commit/da94277fb9900b4d878ed9985edd160601ecde8f)
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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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* found that the python method is AssignAtomChiralTagsFromStructure rather than assignChiralTypesFrom3D
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* [commit 70e50a91](https://gitlab.com/pdbe/ccd_utils/commit/70e50a914d9549e8739b753dbfce182250129389#970d1f070e53958f9808344f5522ca910295c71f_16_16) - message includes 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.11 |
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