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  • pdbepdbe
  • ccdutilsccdutils
  • Issues
  • #17
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Issue created Jun 01, 2017 by Oliver Smart@oliver_smartMaintainer

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
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