def test_process_rb_torsions():
"""Test that the GROMACS driver reports Ryckaert-Bellemans torsions"""
import foyer
import mbuild as mb
oplsaa = foyer.Forcefield(name="oplsaa")
ethanol = Molecule.from_smiles("CCO")
ethanol.generate_conformers(n_conformers=1)
ethanol.generate_unique_atom_names()
# Run this OFFMol through MoSDeF infrastructure and OPLS-AA
from openff.interchange.components.mbuild import offmol_to_compound
my_compound = offmol_to_compound(ethanol)
my_compound.box = mb.Box(lengths=[4, 4, 4])
oplsaa = foyer.Forcefield(name="oplsaa")
struct = oplsaa.apply(my_compound)
struct.save("eth.top", overwrite=True)
struct.save("eth.gro", overwrite=True)
# Get single-point energies using GROMACS
oplsaa_energies = _run_gmx_energy(top_file="eth.top",
gro_file="eth.gro",
mdp_file=_get_mdp_file("default"))
assert oplsaa_energies.energies["Torsion"].m != 0.0
def test_mbuild_conversion_element_names(self):
"""Test that the generated Compound has particle names that can be
interpreted as elements"""
offmol = Molecule.from_smiles(
"CSC(CO[P]([O-])([O-])=O)c1cc(Br)c(F)c(Cl)n1",
allow_undefined_stereo=True,
)
comp = offmol_to_compound(offmol)
known_elements = {"C", "H", "O", "N", "Cl", "Br", "F", "S", "P"}
for particle in comp.particles():
assert particle.name in known_elements
def test_basic_mol_to_compound(self):
"""Test basic behavior of conversion to mBuild Compound"""
offmol = Molecule.from_smiles("CCO")
offmol.generate_conformers(n_conformers=1)
comp = offmol_to_compound(offmol)
assert comp.n_particles == offmol.n_atoms
assert comp.n_bonds == offmol.n_bonds
np.testing.assert_equal(
offmol.conformers[0].value_in_unit(simtk_unit.nanometer),
comp.xyz,
)
def test_mbuild_conversion_generate_conformers(self):
"""Test that a single conformer is automatically generated"""
offmol = Molecule.from_smiles("CCO")
comp = offmol_to_compound(offmol)
assert comp.n_particles == offmol.n_atoms
assert comp.n_bonds == offmol.n_bonds
offmol.generate_conformers(n_conformers=1)
expected_conf = offmol.conformers[0]
np.testing.assert_equal(
expected_conf.value_in_unit(simtk_unit.nanometer),
comp.xyz,
)
def test_mbuild_conversion_first_conformer_used(self):
"""Test that only the first conformer in an OFFMol is used"""
offmol = Molecule.from_smiles("C1=CC=C(C=C1)C2=CC=C(C=C2)C3=CC=CC=C3")
offmol.generate_conformers(n_conformers=3,
rms_cutoff=0.0 * simtk_unit.angstrom)
comp = offmol_to_compound(offmol)
np.testing.assert_equal(
offmol.conformers[0].value_in_unit(simtk_unit.nanometer),
comp.xyz,
)
with np.testing.assert_raises(AssertionError):
np.testing.assert_equal(
offmol.conformers[1].value_in_unit(simtk_unit.nanometer),
comp.xyz,
)
with np.testing.assert_raises(AssertionError):
np.testing.assert_equal(
offmol.conformers[2].value_in_unit(simtk_unit.nanometer),
comp.xyz,
)