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_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_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 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 test_init(self):
self.assertEqual(Molecule("H 1 -1 0"),
Molecule([Atom('H', [1, -1, 0])]))
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_errors_15(self):
# Stupid things to do to _init_atom_list
self.assertRaises(TypeError, Molecule,
[Atom("O", 1.0, 1.0, 1.0), [7.5, 5.0, 3.5]])