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docking-org / pydock3

Python package wrapping the DOCK Fortran program and providing several tools built on top of it.
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top_poses.py not executing code #34

Open baltruke opened 1 year ago

baltruke commented 1 year ago

Hi @ianscottknight !

I was running top_poses.py script on the generated by DOCK3.8 test.mol2.gz file, in the following way: python3 ///pydock3-1.0.0/pydock3/top_poses.py dirlist but the code seems to be not executed, it doesn't produce any errors with different input and doesn't produce help message, as described in wiki (https://wiki.docking.org/index.php?title=Docking_Analysis_in_DOCK3.8#top_poses.py). Is there any special packages needed to run top_poses.py, or what could be the reason of this issue?

Another question that I would like to ask is regarding executing: "pydock3 topposes" command, which is not described in the wiki, but seems to work for retrieving poses. Is there a way to set the number of poses/output prefix/etc using that command?

Thank you a lot in advance for the help!

ianscottknight commented 1 year ago

@hannabalt Thanks for your question. I'll take a look later tonight.

baltruke commented 1 year ago

@ianscottknight thank you very much in advance :)

ianscottknight commented 1 year ago

I apologize for the confusion. To be clear, the file top_poses.py included in whatever version of pydock3 that came with your distribution of DOCK 3 is not a script meant to be run directly. For example, note that it does not have a main function or if __name__ == '__main__': conditional expression. Rather, it is meant to be run through the pydock3 topposes script exposed to the user by installing pydock3.

Unfortunately, it appears that the documentation for how to use the TopPoses script never got created and the documentation you found refers to an older version of the script before it was incorporated into pydock3. That is our bad and we will resolve this ASAP.

Note that the most recent version of pydock3 on the develop branch does not expose the pydock3 topposes script for the time being due to the need for further vetting & documentation.

btingle commented 1 year ago

@hannabalt The top_poses.py in this repository is a little bit different from the one described in the wiki page you reference. There is a standalone version of top_poses.py located @ this repository which is the one referenced by the wiki.