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* **done** and it works
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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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* summary - ATP and the sugars GLC and MAN now give consistent inchikeys only CMO, HEM, and NAD still have issues.
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## Supply the formal charges from the CCD to RDKit
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* CCD includes a formal (integer) charge on each atom. Setting this charge should sort the issue for carbon monoxide (hopefully)
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* get charges from ccd for this, done in [Commit 00435dee](https://gitlab.com/pdbe/ccd_utils/commit/00435deef5bc07053b08679fe64999a3a24109a7)
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* Then supply these to rdkit:
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* [Commit 1df92212](https://gitlab.com/pdbe/ccd_utils/commit/1df92212d35ce7a41389900296261d5a3ebb6cdf)
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* commit message shows the encouraging result all the test cases other than HEM now work (so CMO and NAD are fixed).
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* Can now use the Greg Landrum recommendation of Chem.Sanitize to avoid problems down stream [Commit 360eca41](https://gitlab.com/pdbe/ccd_utils/commit/360eca41aa95b89616ea9a8a135afec215aa0497)
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## Conclusion
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*28 May 2017*
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* First version of pdb_chemical_components_rdkit.py written and tested.
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* deals with basic setup of the rdkit molecule.
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* Tested by comparison of the inchikey from rdkit with that from the PDB CCD cif - this works for the limited number of test cases used so far, with the exception of HEM.
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* Next stage is to extend the class to do something - in the first instance write a sdf file [:pen_fountain: link to be added!]() |
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