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

Edited Sep 21, 2017 by Oliver Smart