sobolevnrm
commented
4 years ago @intendo - per our conversation today, here's a list of files ready for refactoring:
- pdb2pqr.cif -- really needs test coverage first
- pdb2pqr.cli
- pdb2pqr.definitions
- pdb2pqr.errors -- however, I'd prefer to nuke this module for now and handle errors using standard exception classes
- pdb2pqr.forcefield
- pdb2pqr.hydrogens
- pdb2pqr.inputgen
- pdb2pqr.na
- pdb2pqr.pdb
Some of the worst problems with hydrogens.py and related modules have been cleaned up but there is still several problems with the length and complexity of the code. Many of these could be broken up into subdirectories (and simpler) functions to increase robustness of the code.