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