Electrostatics
Fixed parsing bugs for input cif and added cif write functionality.
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.
@intendo what do you think we should do with this PR? It doesn't appear to pass the tests.
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.
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.