Adding pKa-ANI as an option to assign titratable states #391
Conversation
…moleculeContainer file stream
|
@sastrys1 can you please check the Python 3.11 build fail? |
|
It seems like it doesnt have some of the necessary modules. I added these modules to the install_requires list in setup.py - is this the right place to add dependency modules? I mentioned in the original PR message that pKa-ANI has its own dependencies and I wasnt sure where to add those in to the existing requirements. |
|
@sobolevnrm I need your help with this dependency thing. I don't understand how to properly loop in the extra dependencies that pKa-ANI requires with what is already there. If you explain to me clearly what to do with that I can implement it but right now I have no idea how to integrate these extra dependencies which is why these jobs are failing. |
|
Also, could you set it so that each push triggers an auto CI build test? That way I could test stuff and see if it breaks much quicker |
|
@sobolevnrm @orbeckst Could one of you re-test this to see if it works now? I added all of the pKa-ANI dependencies to setup.py |
Did some work to get #389 90% accomplished. I ended up copying over and making a lot of tweaks to the repo files, because they don't export a package that you can import in python, only a command line tool installable with conda. I've credited their repo on all their file headers and printed a header statement that asks the user cite them with a citation printed to the console.
I had a couple things that I wasn't sure how to do:
One is that pKa-ANI contains its own dependencies, and I wasn't sure how you wanted the dependencies to be added into the setuptools setup.py. The dependencies are python=3.8, numpy, scipy, pytorch, torchani=2.2.0, scikit-learn=1.0.2, ase, joblib, ambertools, setuptools=58.2.0. Other possible requirements are os, math, sys, io, csv, getopt, shutil, urllib.request, and warnings. I think some of those are already requirements for PDB2PQR.
I couldn't get the propka test code to work (issues with SSL certificate when sending requests to the RCSB website), and I don't know much about pytest framework so I just wrote a manual test case of my own using barstar (PDB: 1brs). I generated a pqr file at pH 1.1 and made sure the residues were protonated appropriately in the PQR using cat/grep commands. I can expand this to more pHs and more PDB files as well.