def test_distance(self, molecule, control_filepath, delete_tmp_dir):
ms = MoleculeSystem(molecule, frozen_indices={2, 3})
ms.add_distance(0, 1, weights=1.0, value=2.5)
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+stre\s+1\s+2\s+val=\s*2.5",
redundant)
# check the presence of the same frozen atoms
assert ms.frozen_indices == ms_new.frozen_indices
assert str(ms_new.int_def[0])
assert_MSONable(ms_new)
def test_linp(self, molecule, control_filepath, delete_tmp_dir):
ms = MoleculeSystem(molecule)
ms.int_def.append(
PerpendicularBendingAngle(indices=[[0, 1, 2, 3]],
value=20,
status="f"))
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+linp\s+1\s+2\s+3\s+4\s+val=\s*20",
redundant)
assert str(ms_new.int_def[0])
def test_distance_linear_combination(self, molecule, control_filepath,
delete_tmp_dir):
ms = MoleculeSystem(molecule)
ms.add_distance([0, 1], [1, 2], weights=[1.0, 1.0], value=None)
assert not 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(2.70995, abs=1e-4)
# 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+stre\s+1\s+2\s+val=\s*2\.70\d+\s+1\.0+\s+stre\s+2\s+3\s*$",
redundant, re.DOTALL | re.MULTILINE)
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])
def test_add_dihedral(self, molecule):
ms = MoleculeSystem(molecule)
ms.add_dihedral(1, 2, 3, 4)
assert not ms.has_inconsistencies()
assert len(ms.user_defined_bonds) == 3
ms.add_dihedral(0,
1,
2,
3,
status="k",
add_user_def_bonds=False,
value=35.26438972)
assert not ms.has_inconsistencies()
assert len(ms.user_defined_bonds) == 3
ms.add_dihedral(2, 3, 4, 1, value=10)
assert ms.has_inconsistencies()
ms.add_dihedral([0, 1], [2, 3], [3, 4], [1, 0])
assert len(ms.int_def[-1].indices) == 2
with pytest.raises(ValueError):
ms.add_dihedral([1, 2, 3], [1, 2], [2, 3], [3, 4])
def test_add_distance(self, molecule):
ms = MoleculeSystem(molecule)
ms.add_distance(1, 2)
assert not ms.has_inconsistencies()
assert len(ms.user_defined_bonds) == 1
ms.add_distance(0,
1,
status="k",
add_user_def_bonds=False,
value=2.058455873547)
assert not ms.has_inconsistencies()
assert len(ms.user_defined_bonds) == 1
ms.add_distance(2, 3, value=10, weights=1.0)
assert ms.has_inconsistencies()
ms.add_distance([0, 1], [2, 3])
assert len(ms.int_def[-1].indices) == 2
with pytest.raises(ValueError):
ms.add_distance([1, 2, 3], [1, 2])
assert_MSONable(ms)