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Gen pharms
New database format. The pharmacophores are loaded when the tool is installed by pip
Fixes:
- 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.
- Rename "Multiprofiling the molecules" to "Profiling of molecules using multiple pharmacophores". Do not use multiprofiling term, it is undefined. Fix the remaining text correspondingly.
- Top-end molecules, what are they? Rephrase text.
- 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.
- Avoid using arg names consisting of multiple characters with a single dash, e.g. -vs. This is very uncommon.
- Sort target names (columns) in the output file of the prediction script.
Improvements:
- Add progress tracking to screen_db (invoked by arg -v).