process_components_cif script to read complete components.cif and produce PDBeChem ftp area
Issue #13 (closed) have got the basic functioning of process_components_cif_cli.py with a simple test with 4 chemical components.
Now exercise script on the real thing. We have not worried about edge cases so far - what happens if there are no ideal coordinates. Do so now:
- make sure script does not fall over on problems but log's error and continues
- for each problem deal with it (adding unit test were possible).
12 September 2017
Summary of progress and outstanding issues.
- Have got script that produces required output in a reasonable way.
- needs some clean up and further work of:
- need to look into inchi mismatch observation.
- improve command line options.
- logging output - would be good to list number of unsuccessful sdf, pdb, images etc.
- how gif images are produced (avoid svg conversion)
- need to look into RDKit Invariant Violation