def nonbond_matrix():
toppath = TEST_DATA + "/struc_build/system.top"
topology = Topology.from_gmx_topfile(name="test", path=toppath)
topology.preprocess()
topology.volumes = {"PEO": 0.43}
return NonBondEngine.from_topology(topology.molecules,
topology,
box=np.array([10., 10., 10.]))
def test_add_positions_from_pdb():
top = Topology.from_gmx_topfile(TEST_DATA + "/topology_test/pdb.top",
"test")
top.add_positions_from_file(TEST_DATA + "/topology_test/test.pdb")
for meta_mol in top.molecules:
for node in meta_mol.molecule.nodes:
assert "position" in meta_mol.molecule.nodes[node].keys()
for meta_mol in top.molecules:
for node in meta_mol.nodes:
assert "position" in meta_mol.nodes[node].keys()
assert meta_mol.nodes[node]["build"] == False
def test_add_positions_from_gro():
top = Topology.from_gmx_topfile(
TEST_DATA + "/topology_test/system.top", "test")
top.add_positions_from_file(TEST_DATA + "/topology_test/test.gro")
for node in top.molecules[0].molecule.nodes:
if node < 14:
assert "position" in top.molecules[0].molecule.nodes[
node].keys()
for node in top.molecules[0].nodes:
if node != 2:
assert "position" in top.molecules[0].nodes[node].keys()
assert top.molecules[0].nodes[node]["build"] == False
else:
assert top.molecules[0].nodes[node]["build"] == True
def test_convert_to_vermouth_system():
top = Topology.from_gmx_topfile(
TEST_DATA + "/topology_test/system.top", "test")
system = top.convert_to_vermouth_system()
assert isinstance(system, vermouth.system.System)
assert len(system.molecules) == 1
def test_from_gmx_topfile():
top = Topology.from_gmx_topfile(
TEST_DATA + "/topology_test/system.top", "test")
assert len(top.molecules) == 1
def molecule():
toppath = TEST_DATA + "/struc_build/system.top"
topology = Topology.from_gmx_topfile(name="test", path=toppath)
return topology.molecules[0]