def testDuplicateSystemNames(self): """ Tests that Gromacs topologies never have duplicate moleculetypes """ parm = load_file(get_fn('phenol.prmtop')) parm = parm * 20 + load_file(get_fn('biphenyl.prmtop')) * 20 top = GromacsTopologyFile.from_structure(parm) self.assertEqual(top.combining_rule, 'lorentz') top.write(get_fn('phenol_biphenyl.top', written=True)) top2 = GromacsTopologyFile(get_fn('phenol_biphenyl.top', written=True)) self.assertEqual(len(top.residues), 40)
def _amber_to_gromacs(self): # Load prmtop and inpcrd as a Structure parmstruct = load_file(self.outprefix + ".prmtop", xyz=self.outprefix + ".inpcrd", structure=True) # Save .gro coordinate file GromacsGroFile.write(struct=parmstruct, dest=self.outprefix + ".gro") # Save .top topology and parameter file grotop = GromacsTopologyFile.from_structure(parmstruct, copy=False) grotop.write(dest=self.outprefix + ".top", parameters="inline")
def to_parmed_GromacsTopologyFile(item, atom_indices='all', check=True): if check: digest_item(item, 'parmed.Structure') atom_indices = digest_atom_indices(atom_indices) from . import extract from parmed.gromacs import GromacsTopologyFile as GromacsTopologyFile tmp_item = extract(item, atom_indices=atom_indices, copy_if_all=False, check=False) tmp_item = GromacsTopologyFile.from_structure(tmp_item) return tmp_item