def test_specified_c_table_assert_first_three_nonlinear():
path = os.path.join(STRUCTURE_PATH, 'MIL53_beta.xyz')
molecule = cc.Cartesian.read_xyz(path, start_index=1)
fragment = molecule.get_fragment([(12, 2), (55, 2), (99, 2)])
connection = fragment.get_construction_table()
connection.loc[2] = [99, 12, 18]
connection.loc[8] = [2, 99, 12]
connection = connection.loc[[2, 8]]
c_table = molecule.get_construction_table(fragment_list=[(fragment,
connection)],
perform_checks=False)
with pytest.raises(UndefinedCoordinateSystem):
c_table = molecule.correct_dihedral(c_table)
new = c_table.iloc[:4].copy()
new.loc[99] = c_table.loc[17]
new.loc[17] = c_table.loc[99]
new = new.loc[[17, 12, 55, 99]]
new.loc[12, 'b'] = 17
new.loc[55, 'b'] = 17
new.loc[99, 'a'] = 17
c_table = molecule.get_construction_table(
fragment_list=[(molecule.get_without(fragment)[0],
new), (fragment, connection)])
c_table = molecule.correct_dihedral(c_table)
zmolecule = molecule.get_zmat(c_table)
assert allclose(molecule,
zmolecule.get_cartesian(),
align=False,
atol=1e-6)
def test_concat_with_zmats():
path = os.path.join(STRUCTURES, 'MIL53_small.xyz')
m = cc.Cartesian.read_xyz(path, start_index=1)
zm = m.get_zmat()
zm1 = zm.change_numbering(new_index=range(1, len(zm) + 1))
zm2 = zm.change_numbering(new_index=zm1.index + len(zm1))
new = cc.xyz_functions.concat(
[zm1.get_cartesian(),
zm2.get_cartesian() + [0, 0, 10]])
c_table = zm2.loc[:, ['b', 'a', 'd']]
c_table.loc[57, ['b', 'a', 'd']] = [4, 1, 2]
c_table.loc[58, ['a', 'd']] = [1, 2]
c_table.loc[59, 'd'] = 1
large_c_table = new.get_construction_table(
fragment_list=[(zm2.get_cartesian(), c_table)])
znew = new.get_zmat(large_c_table)
cc.xyz_functions.allclose(new, znew.get_cartesian())
znew.safe_loc[57, 'bond'] = 20. - 0.89
assert allclose(
zm1.get_cartesian().append(zm2.get_cartesian() + [0, 0, 20]),
znew.get_cartesian())
def test_concat():
path = os.path.join(STRUCTURES, 'MIL53_small.xyz')
molecule = cc.Cartesian.read_xyz(path)
cartesians = [molecule + i * 10 for i in range(5)]
with pytest.raises(ValueError):
cc.xyz_functions.concat(cartesians)
joined = cc.xyz_functions.concat(cartesians, ignore_index=True)
for i, molecule in enumerate(cartesians):
molecule2 = joined.iloc[(i * len(molecule)):(i + 1) * len(molecule)]
molecule2.index = molecule.index
assert allclose(molecule, molecule2)
key_joined = cc.xyz_functions.concat(cartesians, keys=['a', 'b'])
assert allclose(key_joined.loc['a'], (key_joined.loc['b'] - 10))
def test_write_and_read():
# Created because of https://github.com/mcocdawc/chemcoord/issues/58
water_1 = cc.Cartesian.read_xyz(
join(STRUCTURE_PATH, 'water.xyz'), start_index=1)
z_water_str = water_1.get_zmat().to_zmat(upper_triangle=True)
water_2 = cc.Zmat.read_zmat(StringIO(z_water_str)).get_cartesian()
assert allclose(water_1, water_2, atol=1e-6)
z_water_str = water_1.get_zmat().to_zmat(upper_triangle=False)
cc.Zmat.read_zmat(StringIO(z_water_str)).get_cartesian()
def back_and_forth(filepath):
molecule1 = cc.Cartesian.read_xyz(filepath)
zmolecule = molecule1.get_zmat()
molecule2 = zmolecule.get_cartesian()
assert allclose(molecule1, molecule2, align=False, atol=1e-7)
def test_overloaded_operators():
assert allclose(molecule + 1, molecule + [1, 1, 1])
assert allclose(1 + molecule, molecule + [1, 1, 1])
assert allclose(molecule + molecule, 2 * molecule)
index = molecule.index
assert allclose(molecule + molecule.loc[reversed(index)], 2 * molecule)
assert allclose(molecule + molecule.loc[:, ['x', 'y', 'z']].values,
2 * molecule)
assert allclose(1 * molecule, molecule)
assert allclose(molecule * 1, molecule)
assert allclose(1 * molecule, +molecule)
assert allclose(-1 * molecule, -molecule)
assert allclose(-molecule, 0 - molecule)
assert allclose(molecule, molecule - 0)
molecule2 = molecule[~(np.isclose(molecule['x'], 0)
| np.isclose(molecule['y'], 0)
| np.isclose(molecule['z'], 0))]
assert np.allclose(np.full(molecule2.loc[:, ['x', 'y', 'z']].shape, 1),
(molecule2 / molecule2).loc[:, ['x', 'y', 'z']])
assert np.allclose(np.full(molecule2.loc[:, ['x', 'y', 'z']].shape, 0),
(molecule2 - molecule2).loc[:, ['x', 'y', 'z']])