Adding non-standard residues manually

[OscarDS]

Add the 3 letter code, 1 letter code and atom count in aminoAcids.py, and the 3 letter code to protein_res_names in protein.py. Non-standard residues will not be recognized by MODELLER, so the input pdb file must not have chain breaks or missing sidechains. Topology must be present or provided to GROMACS.

Example:
in aminoAcids.py

class AminoAcids():
    def __init__(self):
        self.codes321 = {
            # [...]
            'NH2': 'Z'
        }
       self.codes123 = {
            # [...]
            'Z': 'NH2'
        }
        self.sideChains = {
            # [...]
            'NH2': Counter(
                N = 1
            ),
        }

in protein.py

class System(object):
    def __init__(self, **kwargs):
        protein_res_names = ["ALA", "ARG", "ASN", "ASP", "ASH", "CYS", "CYX", "GLN", "GLU", "GLY", "HIS",
                             "HIE", "HID", "HIP", "HISE", "HISD", "HISH", "ILE", "LEU", "LYS",
                             "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL", "NH2",]