69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101,
102, 103)
new_mol = Chem.RWMol(new_mol)
for atom in new_mol.GetAtoms():
// HACK: termini oxygens get matched twice due to removal from templates
// Terminus treatment
if atom.GetPDBResidueInfo().GetName().strip() == "OXT":
After Change
if removeHs and atomicnum == 1:
removal_queue.append(aix)
// Remove waters
elif removeHOHs and atomicnum in [1,8] and atom.GetPDBResidueInfo().GetResidueName() == "HOH":
removal_queue.append(aix)
// Break bonds with metals
elif disconnect_metals and atomicnum in METALS:
