currently, a user would run molpal like so: $ python PATH/TO/MOLPAL/DIR/run.py [...] even after installing the package. Moreover, when using MolPAL for docking, it is not straightforward for analyzing the output docking results (even though they are all saved to the output directory.)
New workflow
This PR introduces two changes:
MolPAL can now be run (after installing the package) like so:
molpal run [...].
You no longer need to have the run.py script explicitly located on your filesystem
A new extract mode is introduced to the CLI to extract the output poses from the tarballs saved in a molpal run:
molpal extract OUTPUT_DIR -k K --name POSE_FOLDER_NAME
Questions
If there are open questions about implementation strategy or scope of the PR, include them here
Relevant issues
If appropriate, please tag them here and include a quick summary
Checklist
[x] linted with flake8?
[x] (if appropriate) unit tests added? (no new logic was added)
Description
this PR refactors the CLI interface
Current workflow
currently, a user would run molpal like so:
$ python PATH/TO/MOLPAL/DIR/run.py [...]even after installing the package. Moreover, when using MolPAL for docking, it is not straightforward for analyzing the output docking results (even though they are all saved to the output directory.)New workflow
This PR introduces two changes:
MolPAL can now be run (after installing the package) like so:
molpal run [...].You no longer need to have the
run.pyscript explicitly located on your filesystemA new
extractmode is introduced to the CLI to extract the output poses from the tarballs saved in a molpal run:molpal extract OUTPUT_DIR -k K --name POSE_FOLDER_NAMEQuestions
If there are open questions about implementation strategy or scope of the PR, include them here
Relevant issues
If appropriate, please tag them here and include a quick summary
Checklist