Use RDKit to write sdf file for PDB CCD
- mol and the related sdf file formats are the standard way to pass molecules with chemical information between application
- Currently pdbechem provides 4 different molfile/sdf for each chemical component (with/without hydrogen atoms and ideal/model coordinates), see http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/readme.htm
- This feature request to get RDKit to be able to write each of the 4 different sdf files.
- It is possible to include atom names and other information in sdf files. This may be useful. For an example see rcsb:
- should be relatively easy method in pdb_chemical_components_rdkit.py
- Note that the adding/removing hydrogen atoms should not effect the main self.rdkit_mol object in the class
This is a big issue so lets separate out into checklist:
- write sdf ideal with hydrogen atoms and alias
- write different sdf model and ideal
- write sdf without hydrogen atoms
- turn on/off atom alias in the sdf.