Exemplo n.º 1
0
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
Exemplo n.º 2
0
 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)
Exemplo n.º 3
0
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
Exemplo n.º 4
0
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