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Gen pharms

Open meddwl opened this issue 3 years ago • 1 comments

New database format. The pharmacophores are loaded when the tool is installed by pip

meddwl avatar Nov 03 '21 14:11 meddwl

Fixes:

  1. Reduce the chunk size in gen_db to 1. This will not result in much overhead but will distribute calculations better, especially small data sets on multi-cpu machines.
  2. Rename "Multiprofiling the molecules" to "Profiling of molecules using multiple pharmacophores". Do not use multiprofiling term, it is undefined. Fix the remaining text correspondingly.
  3. Top-end molecules, what are they? Rephrase text.
  4. Fix the issue with the help message "screen_db -h". I suggest to use None as a default value and if the arg is None then assign paths to all ChEMBL models to it.
  5. Avoid using arg names consisting of multiple characters with a single dash, e.g. -vs. This is very uncommon.
  6. Sort target names (columns) in the output file of the prediction script.

Improvements:

  1. Add progress tracking to screen_db (invoked by arg -v).

DrrDom avatar Nov 04 '21 16:11 DrrDom