def test_optimize_geometry(lines):
"""
Tests if the geometry optimizer performs correct optimization
of simple geometries. This guards against changes in scipy
optimize that might effect optimization.
"""
lines = textwrap.dedent(lines).splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
polyply.src.polyply_parser.read_polyply(lines, force_field)
block = force_field.blocks['test']
init_coords = _expand_inital_coords(block)
status, coords = optimize_geometry(block, init_coords)
assert status
for bond in itertools.chain(block.interactions["bonds"],
block.interactions["constraints"]):
ref = float(bond.parameters[1])
dist = np.linalg.norm(coords[bond.atoms[0]] - coords[bond.atoms[1]])
assert np.isclose(dist, ref, atol=0.05)
for inter in block.interactions["angles"]:
ref = float(inter.parameters[1])
ang = angle(coords[inter.atoms[0]], coords[inter.atoms[1]],
coords[inter.atoms[2]])
assert np.isclose(ang, ref, atol=2)
for virtual_site in block.interactions["virtual_sitesn"]:
ref_coord = construct_vs("virtual_sitesn", virtual_site, coords)
vs_coords = coords[virtual_site.atoms[0]]
assert np.allclose(ref_coord, vs_coords)
def test_expand_inital_coords():
lines = """
[ moleculetype ]
GLY 1
[ atoms ]
1 P4 1 ALA BB 1
2 P3 1 ALA SC1 2
3 P2 1 ALA SC2 3
4 VS 1 ALA SC3 3
[ bonds ]
1 2 1 0.2 100
2 3 1 0.6 700
[ virtual_sitesn ]
4 2 3 1
"""
lines = textwrap.dedent(lines).splitlines()
ff = vermouth.forcefield.ForceField(name='test_ff')
polyply.src.polyply_parser.read_polyply(lines, ff)
block = ff.blocks['GLY']
coords = _expand_inital_coords(block)
assert len(coords) == 4
for pos in coords.values():
assert len(pos) == 3
def test_compute_volume():
lines = """
[ moleculetype ]
GLY 1
[ atoms ]
1 P1 1 ALA BB 1
2 P1 1 ALA SC1 2
3 P1 1 ALA SC2 3
4 P1 1 ALA SC3 3
[ bonds ]
1 2 1 0.2 100
2 3 1 0.6 700
3 4 1 0.2 700
"""
meta_mol = polyply.MetaMolecule()
nonbond_params = {frozenset(["P1", "P1"]): {"nb1": 0.47, "nb2":0.5}}
lines = textwrap.dedent(lines).splitlines()
ff = vermouth.forcefield.ForceField(name='test_ff')
polyply.src.polyply_parser.read_polyply(lines, ff)
block = ff.blocks['GLY']
coords = _expand_inital_coords(block)
vol = compute_volume(meta_mol, block, coords, nonbond_params)
assert vol > 0.
def test_optimize_geometry(lines):
"""
Tests if the geometry optimizer performs correct optimization
of simple geometries. This guards against changes in scipy
optimize that might effect optimization.
"""
lines = textwrap.dedent(lines).splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
polyply.src.polyply_parser.read_polyply(lines, force_field)
block = force_field.blocks['test']
for _iteration in range(0, 10):
init_coords = _expand_inital_coords(block)
success, coords = optimize_geometry(block, init_coords,
["bonds", "constraints", "angles"])
success, coords = optimize_geometry(
block, coords, ["bonds", "constraints", "angles", "dihedrals"])
if success:
break
else:
print(_iteration)
# sanity check
assert success
# this part checks that the tolarances are actually obayed in the minimizer
for bond in itertools.chain(block.interactions["bonds"],
block.interactions["constraints"]):
ref = float(bond.parameters[1])
dist = np.linalg.norm(coords[bond.atoms[0]] - coords[bond.atoms[1]])
assert np.isclose(dist, ref, atol=0.05)
for inter in block.interactions["angles"]:
ref = float(inter.parameters[1])
ang = angle(coords[inter.atoms[0]], coords[inter.atoms[1]],
coords[inter.atoms[2]])
assert np.isclose(ang, ref, atol=5)
# only improper dihedrals
for inter in block.interactions["dihedrals"]:
if inter.parameters[0] == "2":
ref = float(inter.parameters[1])
ang = dih(coords[inter.atoms[0]], coords[inter.atoms[1]],
coords[inter.atoms[2]], coords[inter.atoms[3]])
assert np.isclose(ang, ref, atol=5)
for virtual_site in block.interactions["virtual_sitesn"]:
ref_coord = construct_vs("virtual_sitesn", virtual_site, coords)
vs_coords = coords[virtual_site.atoms[0]]
assert np.allclose(ref_coord, vs_coords)
def test_map_from_CoG():
lines = """
[ moleculetype ]
GLY 1
[ atoms ]
1 P4 1 ALA BB 1
2 P3 1 ALA SC1 2
3 P2 1 ALA SC2 3
4 P2 1 ALA SC3 3
[ bonds ]
1 2 1 0.2 100
2 3 1 0.6 700
3 4 1 0.2 700
"""
lines = textwrap.dedent(lines).splitlines()
ff = vermouth.forcefield.ForceField(name='test_ff')
polyply.src.polyply_parser.read_polyply(lines, ff)
block = ff.blocks['GLY']
coords = _expand_inital_coords(block)
points = np.array(list(coords.values()))
CoG = center_of_geometry(points)
new_coords = map_from_CoG(coords)
for coord in coords:
coords[coord] == new_coords[coord] + CoG