Handle changes in anecdotal names of PDB files #10
Description
Bug:
As of writing the code filter_scripts doesn't handle any alternative nomenclature at all. This means that if an isoalloxazine is labelled as "C4a" (C4-alpha) instead of "C4x" that an error will be logged and the atom will be ignored by the script altogether.
Effect:
While this results in incorrect data (since correct data is missing), I suspect that there may be cases where a collision with alternate nomenclature occurs and the van Der Waals' forces are incorrectly looked up and the calculation may be altogether wrong; however, given a tolerance of 0.2 angstroms I don't think this case is causing any inaccuracies in the data).
Solution:
makeshift patch: extend filter_scripts/physical_constants.py to detect or use this alternative nomenclature so that we aren't currently missing any data
higher quality patch: scan the PDB file before doing any computation, look for alternate naming in the residues and attempt to map them to known ones names.