#!/usr/bin/env python3
from mdjoy import top
itp = top.read("protein-chain.itp")
atoms = [inst for inst in itp if isinstance(inst, top.GmxTopAtom)]
for atom in atoms:
atom.comment = ""
top.write(itp, "test.itp")
itp = top.read("protein-chain.itp")
atoms = [inst for inst in itp if isinstance(inst, top.GmxTopAtom)]
for atom in atoms:
if atom.resnr == 21:
if atom.atom == "HD22":
HD22 = atom
elif atom.atom == "ND2":
ND2 = atom
deleted_nr = HD22.nr
ND2.charge += HD22.charge
new_itp = []
for inst in itp:
atom_nrs = inst.get_atom_nrs()
if deleted_nr in atom_nrs:
pass
else:
new_atom_nrs = []
for nr in atom_nrs:
if nr < deleted_nr:
new_atom_nrs.append(nr)
else:
new_atom_nrs.append(nr - 1)
inst.set_atom_nrs(new_atom_nrs)
new_itp.append(inst)
top.write(new_itp, "test.itp")