def test_dihedral_ethene():
mol = Molecule.from_file("input/ethene.xyz")
c = mol.coordinates.copy()
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] - 1.0) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0]) < 1e-5
for i in xrange(1000):
angle = np.random.uniform(-np.pi, np.pi)
radius = np.random.uniform(0, 5*angstrom)
offset = np.random.uniform(0, 5*angstrom)
c[5] = [
offset,
-radius*np.cos(angle),
-radius*np.sin(angle),
]
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] - np.cos(angle)) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0] - angle) < 1e-5
def test_dihedral_ethene(self):
mol = XYZFile("input/ethene.xyz").get_molecule()
c = mol.coordinates.copy()
self.assertAlmostEqual(ic.dihed_cos(c[2], c[0], c[3], c[5])[0], 1.0)
self.assertAlmostEqual(ic.dihed_angle(c[2], c[0], c[3], c[5])[0], 0.0)
for i in xrange(1000):
angle = numpy.random.uniform(-numpy.pi, numpy.pi)
radius = numpy.random.uniform(0, 5*angstrom)
offset = numpy.random.uniform(0, 5*angstrom)
c[5] = [
offset,
-radius*numpy.cos(angle),
radius*numpy.sin(angle),
]
self.assertAlmostEqual(ic.dihed_cos(c[2], c[0], c[3], c[5])[0], numpy.cos(angle))
self.assertAlmostEqual(ic.dihed_angle(c[2], c[0], c[3], c[5])[0], angle)
def test_dihedral_ethene():
mol = Molecule.from_file(context.get_fn("test/ethene.xyz"))
c = mol.coordinates.copy()
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] - 1.0) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0]) < 1e-5
for i in xrange(1000):
angle = np.random.uniform(-np.pi, np.pi)
radius = np.random.uniform(0, 5 * angstrom)
offset = np.random.uniform(0, 5 * angstrom)
c[5] = [
offset,
-radius * np.cos(angle),
-radius * np.sin(angle),
]
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] -
np.cos(angle)) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0] - angle) < 1e-5
def test_dihedral_ethene():
mol = Molecule.from_file(
pkg_resources.resource_filename(__name__, "../data/test/ethene.xyz"))
c = mol.coordinates.copy()
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] - 1.0) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0]) < 1e-5
for i in range(1000):
angle = np.random.uniform(-np.pi, np.pi)
radius = np.random.uniform(0, 5 * angstrom)
offset = np.random.uniform(0, 5 * angstrom)
c[5] = [
offset,
-radius * np.cos(angle),
-radius * np.sin(angle),
]
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] -
np.cos(angle)) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0] - angle) < 1e-5