Development documentation: use RDKit to write sdf file for PDB CCD
28 May 2017
- previous work RDKit molecule from PDB CCD definition now extend to write sdf files.
- start with a stub implementation and unit tests Commit 5773ff0e
- initial implementation Commit 7eb159fe
- writes sdf files with the "ideal" coordinates successfully
- these sdf files can be read by Mogul and the atoms are labelled with their PDB atom name. For instance reading
tests_out/ATP.ideal_withH.sdfand selecting atom labels on results in:
- note that atoms are labelled according to the atom order in sdf - I thought that Mogul read alias. But it does not really matter.
- pymol can also load although it does not get atom order or alias
- obabel is confused by the alias but never mind.
- many things left to to do
- is this a sdf or a mol file?
- set sensible title for the molecule in the file
- what about the method line
- need option not to write hydrogen atoms
- need option to write exptl coords rather than ideal