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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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Fixed parsing bugs for input cif and added cif write functionality. #189

Closed danny305 closed 1 year ago

danny305 commented 3 years ago

I refactored parts of cif.py that were buggy. In my opinion, all of cif.py needs to be refactored. I just did the functions that were giving me consistent parsing errors (atom_site, source, and origx).

I added the capability of writing out cif file #175 when the input is a cif file. I added a category to the out cif file with pdb2pqr metadata (similar to pdb2pqr headers).

Currently, it outputs both the pqr file and a cif file. I don't know what y'all want to do? Keep outputting both? output just one? added a cli option to specify a cif output? Let me know how y'all would like to proceed.

I am more than happy to work with you guys to edit/clean up and get it merged so the rest of the community could read/write cif files.

danny305 commented 3 years ago

Let me know what else I need to do!

sobolevnrm commented 2 years ago

@intendo what do you think we should do with this PR? It doesn't appear to pass the tests.

intendo commented 2 years ago

The PR has some good code in it so I want to keep it. The main reason it is failing is that there is a merge conflict and some flake8 checks failed.

sobolevnrm commented 1 year ago

This PR has conflicts that haven't been resolved for some time. I'm going to close it and we can revist in the future, if needed. Thank you.