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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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Find dat folder. #605

Closed kozlac closed 4 years ago

kozlac commented 4 years ago

Made changes to be able to find the dat folder when running from out of source folder. This resolves issue #604

intendo commented 4 years ago

@sobolevnrm I approve the changes made to find the .DAT files (e.g. PARSE.DAT). Do you want to review the changes and approve the pull request?

sobolevnrm commented 4 years ago

@intendo - I reviewed when it showed up in my queue and posted some follow-on questions for the underlying issue #604. I'm not trying to be difficult but I want to make sure we're "fixing" the right problem. It's not obvious that this patch is preferable to developing a different method for managing paths in PDB2PQR -- I'd like to make sure we're considering larger changes that will make the code more useful/sustainable in the long run.

kozlac commented 4 years ago

Added some new changes so that we can find the /dat folder regardless of where pdb2pqr is being run. Also, I added the setup.py script so that we can run pdb2pqr as a module. I'm excluding pdb2pka from the installation for now. And now that I remember I may be missing some dependencies in the setup script.

The building and installation are the same as propka: $ cd pdb2qqr $ python3 -m pip install --upgrade . $ python3 -m pdb2pqr [flags|options] <file_name>.pdb <file_name>.pqr

sobolevnrm commented 4 years ago

I will try to review this weekend; sorry for the delay.

sobolevnrm commented 4 years ago

@kozlac and @intendo -- do we have test coverage for this PR?

sobolevnrm commented 4 years ago

Added some new changes so that we can find the /dat folder regardless of where pdb2pqr is being run. Also, I added the setup.py script so that we can run pdb2pqr as a module. I'm excluding pdb2pka from the installation for now. And now that I remember I may be missing some dependencies in the setup script.

The building and installation are the same as propka: $ cd pdb2qqr $ python3 -m pip install --upgrade . $ python3 -m pdb2pqr [flags|options] <file_name>.pdb <file_name>.pqr

Is this documented anywhere? If not, can we add the documentation?

Note that for development, we probably want to suggest pip install -e ..