def test_bond_angle(self, molecule, control_filepath, delete_tmp_dir):
ms = MoleculeSystem(molecule)
ms.add_bond_angle(0, 1, 2, value=30, weights=[1.0])
assert ms.has_inconsistencies()
with temp_dir(delete_tmp_dir) as tmp_dir:
ms.to_file("coord", fmt="coord")
shutil.copy2(control_filepath, "control")
dr = DefineRunner(parameters=dr_parameters)
assert dr.run_update_internal_coords()
ms_new = MoleculeSystem.from_file("coord")
assert not ms_new.has_inconsistencies()
# check that intdef is present and that the value has been updated
assert len(ms_new.int_def) == 1
assert ms_new.int_def[0].value == pytest.approx(
ms.int_def[0].value, abs=1e-4)
# check that there are the same user-defined bonds
assert ms.user_defined_bonds == ms_new.user_defined_bonds
# check that in redundant the coordinate has been taken into account
dg = DataGroups.from_file("coord")
redundant = dg.sdg("redundant", strict=True)
assert re.search(r"\d+\s+f\s+1\.0+\s+bend\s+1\s+2\s+3\s+val=\s*30",
redundant)
assert str(ms_new.int_def[0])
def test_add_bond_angle(self, molecule):
ms = MoleculeSystem(molecule)
ms.add_bond_angle(1, 2, 3)
assert not ms.has_inconsistencies()
assert len(ms.user_defined_bonds) == 2
ms.add_bond_angle(0,
1,
2,
status="k",
add_user_def_bonds=False,
value=35.26438972)
assert not ms.has_inconsistencies()
assert len(ms.user_defined_bonds) == 2
ms.add_bond_angle(2, 3, 4, value=10, weights=1.0)
assert ms.has_inconsistencies()
ms.add_bond_angle([0, 1], [2, 3], [3, 4])
assert len(ms.int_def[-1].indices) == 2
with pytest.raises(ValueError):
ms.add_bond_angle([1, 2, 3], [1, 2], [2, 3])