def test_load_topology(self):
""" Tests loading an OpenMM Topology and System instance """
ommparm = app.AmberPrmtopFile(get_fn('complex.prmtop'))
parm = load_file(get_fn('complex.prmtop'))
system = ommparm.createSystem(implicitSolvent=app.OBC1)
structure = openmm.load_topology(ommparm.topology, system)
self.assertEqual(len(parm.atoms), len(structure.atoms))
self.assertEqual(len(parm.residues), len(structure.residues))
self.assertEqual(len(parm.bonds), len(structure.bonds))
def test_load_topology_uncondensed_atom_types(self):
""" Tests condense_atom_types arg """
ommparm = app.AmberPrmtopFile(get_fn('complex.prmtop'))
parm = load_file(get_fn('complex.prmtop'))
system = ommparm.createSystem(implicitSolvent=app.OBC1)
structure_condensed = openmm.load_topology(ommparm.topology, system, condense_atom_types=True)
structure_uncondensed = openmm.load_topology(ommparm.topology, system, condense_atom_types=False)
num_unique_atom_types_condensed = len(set([a.atom_type for a in structure_condensed]))
num_unique_atom_types_uncondensed = len(set([a.atom_type for a in structure_uncondensed]))
assert num_unique_atom_types_uncondensed > num_unique_atom_types_condensed
# This may change if this or a similar flag does a partial condensing, see PR #1087
assert num_unique_atom_types_uncondensed == len(structure_uncondensed.atoms)
