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).

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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