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reading gromacs topologies with insertion codes fixed #1220

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Feb 7, 2022
Merged

reading gromacs topologies with insertion codes fixed #1220

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12 changes: 10 additions & 2 deletions parmed/gromacs/gromacstop.py
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Original file line number Diff line number Diff line change
Expand Up @@ -308,7 +308,8 @@ def read(self, fname, defines=None, parametrize=True):
dihedral_types = dict()
exc_types = dict()
elif current_section == 'atoms':
molecule.add_atom(*self._parse_atoms(line, params))
atom, resname, resnum, icode = self._parse_atoms(line, params)
molecule.add_atom(atom, resname, resnum, inscode=icode)
elif current_section == 'bonds':
bond, bond_type = self._parse_bonds(line, bond_types, molecule.atoms)
molecule.bonds.append(bond)
Expand Down Expand Up @@ -489,7 +490,14 @@ def _parse_atoms(self, line, params):
else:
atom = Atom(atomic_number=atomic_number, name=words[4],
type=words[1], charge=charge, mass=mass)
return atom, words[3], int(words[2])
# check for insertion code
if words[2].isnumeric():
icode = ''
resnum = int(words[2])
else:
icode = words[2][-1]
resnum = int(words[2][:-1])
return atom, words[3], resnum, icode

def _parse_bonds(self, line, bond_types, atoms):
""" Parses a bond line. Returns a Bond, BondType/None """
Expand Down