def test_groups_1(self):
m = Molecule([
Atom('C', [ 0.00000000, 0.00000000, 0.00000000 ] ),
Atom('C', [ 0.00000000, 0.00000000, 4.76992933 ] ),
Atom('O', [ 0.00000000, -1.04316184, 0.61707065 ] ),
Atom('O', [ 0.01905095, 1.04298787, 4.15285868 ] ),
Atom('C', [ -0.11039651, 1.34908096, 0.68132447 ] ),
Atom('C', [ -0.13501595, -1.34683982, 4.08860486 ] ),
Atom('C', [ 0.10780157, 0.01502933, -1.51597276 ] ),
Atom('C', [ 0.10750912, -0.01699557, 6.28590209 ] ),
Atom('H', [ -0.08557151, 1.24276213, 1.76717696 ] ),
Atom('H', [ -0.10825342, -1.24099210, 3.00275237 ] ),
Atom('H', [ 0.69789248, 2.01081145, 0.34934100 ] ),
Atom('H', [ 0.66105324, -2.02322149, 4.42058833 ] ),
Atom('H', [ -1.04824273, 1.83250625, 0.38051647 ] ),
Atom('H', [ -1.08153441, -1.81305690, 4.38941286 ] ),
Atom('H', [ 0.11566492, -1.00528185, -1.90094854 ] ),
Atom('H', [ 0.13400478, 1.00300183, 6.67087787 ] ),
Atom('H', [ -0.72590461, 0.57377279, -1.95554705 ] ),
Atom('H', [ -0.73626218, -0.56042012, 6.72547638 ] ),
Atom('H', [ 1.02679855, 0.52908924, -1.82068069 ] ),
Atom('H', [ 1.01696471, -0.54775311, 6.59061002 ] )
], units=Angstroms
)
groups = m.geometric_subgroups()
self.assertEqual(len(groups), 2)
def assertAlmostEqualMolecules(self, act, exp, msg=None, places=7):
a_atoms = copy(exp.atoms)
b_atoms = copy(act.atoms)
for atom in a_atoms:
atom.position = Vector(
[round(num, places) for num in atom.position])
for atom in b_atoms:
atom.position = Vector(
[round(num, places) for num in atom.position])
round_a = Molecule(a_atoms)
round_b = Molecule(b_atoms)
if not round_a == round_b:
seq_a = []
for a in round_a:
seq_a.append((a.symbol, a.position))
seq_b = []
for b in round_b:
seq_b.append((b.symbol, b.position))
seq_msg = None
try:
self.assertSequenceEqual(seq_a, seq_b)
except AssertionError as err:
seq_msg = err.message
if not seq_msg:
raise RuntimeError(
"Molecule almost equal assertion inconclusive: Rounded sequences are equal but rounded molecules are not."
)
if msg is None:
msg = "\nExpected:\n{exp}\nGot:\n{act}\n\nAs sequences:\n".format(
exp=exp, act=act, ndigits=places) + seq_msg
raise unittest.TestCase.failureException(msg)
def test_groups_1(self):
m = Molecule([
Atom('C', [0.00000000, 0.00000000, 0.00000000]),
Atom('C', [0.00000000, 0.00000000, 4.76992933]),
Atom('O', [0.00000000, -1.04316184, 0.61707065]),
Atom('O', [0.01905095, 1.04298787, 4.15285868]),
Atom('C', [-0.11039651, 1.34908096, 0.68132447]),
Atom('C', [-0.13501595, -1.34683982, 4.08860486]),
Atom('C', [0.10780157, 0.01502933, -1.51597276]),
Atom('C', [0.10750912, -0.01699557, 6.28590209]),
Atom('H', [-0.08557151, 1.24276213, 1.76717696]),
Atom('H', [-0.10825342, -1.24099210, 3.00275237]),
Atom('H', [0.69789248, 2.01081145, 0.34934100]),
Atom('H', [0.66105324, -2.02322149, 4.42058833]),
Atom('H', [-1.04824273, 1.83250625, 0.38051647]),
Atom('H', [-1.08153441, -1.81305690, 4.38941286]),
Atom('H', [0.11566492, -1.00528185, -1.90094854]),
Atom('H', [0.13400478, 1.00300183, 6.67087787]),
Atom('H', [-0.72590461, 0.57377279, -1.95554705]),
Atom('H', [-0.73626218, -0.56042012, 6.72547638]),
Atom('H', [1.02679855, 0.52908924, -1.82068069]),
Atom('H', [1.01696471, -0.54775311, 6.59061002])
],
units=Angstroms)
groups = m.geometric_subgroups()
self.assertEqual(len(groups), 2)
def test_create_representation_bond(self):
with self.assertRaisesRegexp(ValueError, r'atomics.*only representable as.*Cannot create'):
Molecule.from_z_matrix('O', create_representation=True)
mol = Molecule.from_z_matrix('H\nH 1 0.9', create_representation=True)
self.assertEqual(len(mol.internal_representations), 1)
self.assertEqual(len(mol.internal_representations[0]), 1)
def test_zmat(self):
self.assertEqual(
Molecule([Atom("O", [0.0, 0.0, 0.0])]),
Molecule.from_z_matrix("""
O
"""
)
)
self.assertEqual(
Molecule([
Atom("O", [0.0, 0.0, 0.0]),
Atom("O", [0.0, 0.0, 1.0])
]),
Molecule.from_z_matrix("""
O1
O2 O1 1.0
"""
)
)
self.assertEqual(
Molecule([
Atom("O", [0.0, 0.0, 0.0]),
Atom("H", [0.0, 0.0, 1.0]),
Atom("H", [0.0, -1.0, 0.0])
]),
Molecule.from_z_matrix("""
O
H1 O 1.0
H2 O 1.0 H1 90
"""
)
)
def test_errors_19(self):
with self.assertRaisesRegexp(InvalidZMatrixException, r'atom indices in z-matrix line'):
Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 2 1.35 1 89.5 1 84.3
''', create_representation=True)
def test_errors_18(self):
with self.assertRaisesRegexp(IndexError, r"z-matrix index '0' is out of range"):
Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 2 1.35 1 89.5 0 84.3
''', create_representation=True)
def test_future_errors(self):
with self.assertRaisesRegexp(ValueError,
r'Ambiguous atom identifier in z-matrix'):
Molecule.from_z_matrix("""
O
H O 1.0
H H 1.0 O 3.7
""")
def test_create_representation_bond(self):
with self.assertRaisesRegexp(
ValueError, r'atomics.*only representable as.*Cannot create'):
Molecule.from_z_matrix('O', create_representation=True)
mol = Molecule.from_z_matrix('H\nH 1 0.9', create_representation=True)
self.assertEqual(len(mol.internal_representations), 1)
self.assertEqual(len(mol.internal_representations[0]), 1)
def test_errors_11(self):
with self.assertRaisesRegexp(ValueError,
r'Ambiguous atom identifier in z-matrix'):
Molecule.from_z_matrix("""
O
H O 1.0
H O -1.0 H 37
O2 H 1.5 O 150 H 25
""")
def test_future_errors(self):
with self.assertRaisesRegexp(ValueError, r'Ambiguous atom identifier in z-matrix'):
Molecule.from_z_matrix(
"""
O
H O 1.0
H H 1.0 O 3.7
"""
)
def test_errors_18(self):
with self.assertRaisesRegexp(IndexError,
r"z-matrix index '0' is out of range"):
Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 2 1.35 1 89.5 0 84.3
''',
create_representation=True)
def test_errors_11(self):
with self.assertRaisesRegexp(ValueError, r'Ambiguous atom identifier in z-matrix'):
Molecule.from_z_matrix(
"""
O
H O 1.0
H O -1.0 H 37
O2 H 1.5 O 150 H 25
"""
)
def test_errors_19(self):
with self.assertRaisesRegexp(InvalidZMatrixException,
r'atom indices in z-matrix line'):
Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 2 1.35 1 89.5 1 84.3
''',
create_representation=True)
def test_misc(self):
# getitem
self.assertEqual(Molecule.from_z_matrix("O")[0].symbol, "O")
# contains
mol = Molecule.from_z_matrix("O")
self.assertIn(mol[0], mol)
self.assertNotIn(Atom("H", 0, 0, 0), mol)
# less than
self.assertLess(mol, Molecule("O 0.0 0.0 1.0"))
def test_misc(self):
# getitem
self.assertEqual(Molecule.from_z_matrix("O")[0].symbol, "O")
# contains
mol = Molecule.from_z_matrix("O")
self.assertIn(mol[0], mol)
self.assertNotIn(Atom("H", 0, 0, 0), mol)
# less than
self.assertLess(mol, Molecule("O 0.0 0.0 1.0"))
def test_displace(self):
mol = Molecule.from_z_matrix('H')
mol.displace(Vector(1., -1., 0.))
self.assertEqual(mol, Molecule("H 1 -1 0"))
mol = Molecule.from_z_matrix('H\nH 1 0.9')
mol.displace(Vector(1., 0., 0., 1., 0., 0.))
self.assertEqual(mol, Molecule("H 1 0 0.0\nH 1 0 0.9 "))
with self.assertRaisesRegexp(ValueError, 'dimension mismatch'):
mol.displace(Vector(1., 0., 0.))
with self.assertRaises(TypeError):
mol.displace(Matrix(1., 0., 0.))
def test_displace(self):
mol = Molecule.from_z_matrix('H')
mol.displace(Vector(1., -1., 0.))
self.assertEqual(mol, Molecule("H 1 -1 0"))
mol = Molecule.from_z_matrix('H\nH 1 0.9')
mol.displace(Vector(1., 0., 0., 1., 0., 0.))
self.assertEqual(mol, Molecule("H 1 0 0.0\nH 1 0 0.9 "))
with self.assertRaisesRegexp(ValueError, 'dimension mismatch'):
mol.displace(Vector(1., 0., 0.))
with self.assertRaises(TypeError):
mol.displace(Matrix(1., 0., 0.))
def test_errors_14(self):
with self.assertRaises(InvalidXYZFormatError):
Molecule("""
H 1.00 1.00 7.5
C 3.2a 1.0 1.0
O 2.2 2.2 2.2
""")
def test_bond_length_2(self):
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
# 'randomize' the position in xyz space to avoid miniscule displacement amounts
mol.rotate(Vector(1, 2, 1), 32. * Degrees)
coord = mol.internal_representation[0]
assert_has_valid_b_tensor(coord, 2)
def test_2_torsions_4_dry_run(self):
mol = Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 3 1.35 2 89.5 1 83.2
O 4 1.25 3 89.5 2 -23.2
''',
create_representation=True)
mol.recenter()
order = 4
coord = mol.internal_representation[5]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3 * natoms, ) * order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(
c.index for c in cartcoords)] = btens[(coord, ) + cartcoords]
coord = mol.internal_representation[8]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3 * natoms, ) * order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(
c.index for c in cartcoords)] = btens[(coord, ) + cartcoords]
def _parse_stream(self, f):
if self.inner_regex.groups < 4:
raise ValueError("Not enough capturing groups in inner regex.")
#----------------------------------------#
data = f.read()
matches = list(self.outer_regex.finditer(data))
if len(matches) == 0:
raise ValueError("No molecule section found in file {}".format(self.file_path))
elif len(matches) > 1:
raise ValueError("More than one molecule section in file {} (total of {} matches found)".format(
self.file_path,
len(matches)
))
else:
xyz_lines = []
natoms = 0
mol_section = matches[0].group(1)
for m in self.inner_regex.finditer(mol_section):
xyz_lines.append("{0} {1} {2} {3}".format(*m.groups()))
natoms += 1
if natoms == 0:
raise ValueError("No atoms found in geometry section of {}".format(self.file_path))
return Molecule(
xyz_string="\n".join(xyz_lines)
)
def phi(i, j, k):
mol = Molecule([
Atom('H', args[i - 1]),
Atom('H', args[j - 1]),
Atom('H', args[k - 1])
])
return BondAngle(mol[0], mol[1], mol[2])
def test_bond_length_2(self):
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
# 'randomize' the position in xyz space to avoid miniscule displacement amounts
mol.rotate(Vector(1,2,1), 32.*Degrees)
coord = mol.internal_representation[0]
assert_has_valid_b_tensor(coord, 2)
def _convert_obmol(self, obmol):
symbols = []
positions = []
for atom in openbabel.OBMolAtomIter(obmol):
symbols.append(ElementData.get(atomic_number=atom.GetAtomicNum()).symbol)
positions.append((atom.x(), atom.y(), atom.z()))
charge = self._get_charge(obmol)
multiplicity = self._get_multiplicity(obmol)
description = self._get_description(obmol)
rv = Molecule(
atom_names=symbols,
cart_mat=positions,
charge=charge,
multiplicity=multiplicity,
description=description
)
rv.obmol = obmol
return rv
def test_create_representation_tors_2(self):
mol = Molecule.from_z_matrix("""
H
O 1 1.0
O 2 1.0 1 90
H 3 1.0 2 90 1 -90
""", create_representation=True
)
self.assertEqual(mol.internal_representations[0].coords[5].value_with_units.in_units(AngularUnit.default),
(-90.*Degrees).in_units(AngularUnit.default))
def test_bond_length_7_dry_run(self):
self.setUp()
order = 7
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
coord = mol.internal_representation[0]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3*natoms,)*order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(c.index for c in cartcoords)] = btens[(coord,) + cartcoords]
def test_bond_length_7_dry_run(self):
self.setUp()
order = 7
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
coord = mol.internal_representation[0]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3 * natoms, ) * order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(
c.index for c in cartcoords)] = btens[(coord, ) + cartcoords]
def test_create_representation_tors_2(self):
mol = Molecule.from_z_matrix("""
H
O 1 1.0
O 2 1.0 1 90
H 3 1.0 2 90 1 -90
""",
create_representation=True)
self.assertEqual(
mol.internal_representations[0].coords[5].value_with_units.
in_units(AngularUnit.default),
(-90. * Degrees).in_units(AngularUnit.default))
def test_create_rep_hooh(self):
mol = Molecule.from_z_matrix("""
H
O 1 0.963242
O 2 1.449863 1 100.120071
H 3 0.963242 2 100.120071 1 -67.344079
""",
create_representation=True)
rep = mol.internal_representation
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(
rep[5].value_with_units.in_units(AngularUnit.default),
-67.344079 * deg_to_def)
def test_create_representation_ang(self):
mol = Molecule.from_z_matrix("""
O
H1 O 1.0
H2 O 1.0 H1 90
""",
create_representation=True)
self.assertEqual(len(mol.internal_representations), 1)
self.assertEqual(len(mol.internal_representations[0]), 3)
self.assertEqual(
mol.internal_representations[0].coords[2].value_with_units.
in_units(AngularUnit.default),
(90. * Degrees).in_units(AngularUnit.default))
def test_create_representation_ang(self):
mol = Molecule.from_z_matrix("""
O
H1 O 1.0
H2 O 1.0 H1 90
""", create_representation=True
)
self.assertEqual(len(mol.internal_representations), 1)
self.assertEqual(len(mol.internal_representations[0]), 3)
self.assertEqual(
mol.internal_representations[0].coords[2].value_with_units.in_units(AngularUnit.default),
(90.*Degrees).in_units(AngularUnit.default)
)
def test_create_rep_hooh(self):
mol = Molecule.from_z_matrix("""
H
O 1 0.963242
O 2 1.449863 1 100.120071
H 3 0.963242 2 100.120071 1 -67.344079
""", create_representation=True
)
rep = mol.internal_representation
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(
rep[5].value_with_units.in_units(AngularUnit.default),
-67.344079 * deg_to_def)
def setUpForValue(self, val, randomize_cartesian_space=True):
self.mol = Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 3 1.35 2 89.5 1 ''' + str(val), create_representation=True)
self.mol.recenter()
if randomize_cartesian_space:
# 'randomize' the position in xyz space to avoid miniscule displacement amounts
self.mol.rotate(Vector(0,0,1), 32 * Degrees.to(Radians))
self.mol.rotate(Vector(0,1,0), 32 * Degrees.to(Radians))
self.mol.rotate(Vector(1,0,0), 32 * Degrees.to(Radians))
self.coord = self.mol.internal_representation[5]
def setUpForValue(self, val, randomize_cartesian_space=True):
self.mol = Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 3 1.35 2 89.5 1 ''' + str(val),
create_representation=True)
self.mol.recenter()
if randomize_cartesian_space:
# 'randomize' the position in xyz space to avoid miniscule displacement amounts
self.mol.rotate(Vector(0, 0, 1), 32 * Degrees.to(Radians))
self.mol.rotate(Vector(0, 1, 0), 32 * Degrees.to(Radians))
self.mol.rotate(Vector(1, 0, 0), 32 * Degrees.to(Radians))
self.coord = self.mol.internal_representation[5]
def _parse_stream(self, f):
data = f.read()
matches = list(self.regex.finditer(data))
if len(matches) == 0:
raise ValueError("No geometry found in file {}".format(self.file_path))
elif len(matches) > 1:
raise ValueError("More than 1 geometry found in file {} (total of {} matches found)".format(
self.file_path,
len(matches)
))
else:
return Molecule(
xyz_string=matches[0].group(1)
)
def setUp(self):
self.mol = Molecule("""
4
H2O2
H -1.21670000 -0.75630000 0.00000000
O -0.73020000 0.07940000 -0.00000000
O 0.73020000 -0.07940000 -0.00000000
H 1.21670000 0.75630000 0.00000000
""")
self.rep = InternalRepresentation(self.mol, [
BondLength(1, 2, self.mol),
BondLength(1, 3, self.mol),
BondAngle(2, 1, 3, self.mol),
InternalCartesianX(1, 2, 3, 4, self.mol),
InternalCartesianY(1, 2, 3, 4, self.mol),
InternalCartesianZ(1, 2, 3, 4, self.mol)
])
def test_2_torsions_4_dry_run(self):
mol = Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 3 1.35 2 89.5 1 83.2
O 4 1.25 3 89.5 2 -23.2
''', create_representation=True)
mol.recenter()
order = 4
coord = mol.internal_representation[5]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3*natoms,)*order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(c.index for c in cartcoords)] = btens[(coord,) + cartcoords]
coord = mol.internal_representation[8]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3*natoms,)*order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(c.index for c in cartcoords)] = btens[(coord,) + cartcoords]
def test_zmat(self):
self.assertEqual(
Molecule([Atom("O", [0.0, 0.0, 0.0])]),
Molecule.from_z_matrix("""
O
"""))
self.assertEqual(
Molecule([Atom("O", [0.0, 0.0, 0.0]),
Atom("O", [0.0, 0.0, 1.0])]),
Molecule.from_z_matrix("""
O1
O2 O1 1.0
"""))
self.assertEqual(
Molecule([
Atom("O", [0.0, 0.0, 0.0]),
Atom("H", [0.0, 0.0, 1.0]),
Atom("H", [0.0, -1.0, 0.0])
]),
Molecule.from_z_matrix("""
O
H1 O 1.0
H2 O 1.0 H1 90
"""))
def _generated(self, aval):
mol = Molecule.from_z_matrix('H\nO 1 1.0\nH 2 1.0 1 ' + str(aval), create_representation=True)
coord = mol.internal_representation[2]
self.assertHasValidBVector(coord)
def test_bond_angle(self):
mol = Molecule.from_z_matrix('H\nO 1 1.0\nH 2 1.0 1 90', create_representation=True)
coord = mol.internal_representation[2]
self.assertHasValidBVector(coord)
def test_bond_length(self):
mol = Molecule.from_z_matrix('H\nO 1 1.0', create_representation=True)
coord = mol.internal_representation[0]
self.assertHasValidBVector(coord)
def test_reorient_2(self):
m = Molecule('H 0 0 0\nH 0 1 0')
self.assertEqual(m.reoriented('II'), Molecule('H 0 -0.5 0\nH 0 0.5 0'))
def test_bond_length_6(self):
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
coord = mol.internal_representation[0]
assert_has_valid_b_tensor(coord, 6)
def test_reorient_2(self):
m = Molecule('H 0 0 0\nH 0 1 0')
self.assertEqual(m.reoriented('II'), Molecule('H 0 -0.5 0\nH 0 0.5 0'))
def test_init(self):
self.assertEqual(Molecule("H 1 -1 0"),
Molecule([Atom('H', [1, -1, 0])]))
def R(i, j):
# This is ugly...
# TODO figure out a better way to do this
mol = Molecule([Atom('H', args[i - 1]), Atom('H', args[j - 1])])
return BondLength(mol[0], mol[1])
def _generated(self, aval):
mol = Molecule.from_z_matrix('H\nO 1 1.0\nH 2 1.0 1 ' + str(aval),
create_representation=True)
coord = mol.internal_representation[2]
self.assertHasValidBVector(coord)
def test_bond_angle(self):
mol = Molecule.from_z_matrix('H\nO 1 1.0\nH 2 1.0 1 90',
create_representation=True)
coord = mol.internal_representation[2]
self.assertHasValidBVector(coord)
def test_bond_length(self):
mol = Molecule.from_z_matrix('H\nO 1 1.0', create_representation=True)
coord = mol.internal_representation[0]
self.assertHasValidBVector(coord)
def test_bond_length_6(self):
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
coord = mol.internal_representation[0]
assert_has_valid_b_tensor(coord, 6)