Skip to content

GitLab

Open
Created by Oliver Smart@oliver_smartMaintainer

Develop utility command line script to read single cif and write coordinate files/images etc.

What

  • Want a command line script so a user can read in any ccd cif and
    • write a sdf if they want to - with options for ideal/model coordinates, hydrogen, alias on off
    • write a pdb file with options ...
    • write an image with options ....
  • Display properties about the molecule - lipinski things - num rings, rotable bonds etc. etc.

How

  • The command line arguments and the help text for each must be proposed as a comment on this page. The proposal must be agreed to before any coding is done!
  • Script is to use argparse
  • All points except 2 in https://ajminich.com/2013/08/01/10-things-i-wish-every-python-script-did/ must be followed.
  • Can you unit test a command line script?
  • If there are exceptions (file does not exist etc.) catch them produce a sensible error message to the user and call sys.exit(1) to indicate to the calling process there was problem.
Edited by Oliver Smart