Python Analysis.get_dihedrals Examples

Example #1

File: test_analysis.py Project: maurergroup/ase_local

def test_analysis():
    #test the geometry.analysis module

    mol = molecule('CH3CH2OH')
    ana = Analysis(mol)
    assert np.shape(ana.adjacency_matrix[0].todense()) == (9, 9)
    for imI in range(len(ana.all_bonds)):
        l1 = sum([len(x) for x in ana.all_bonds[imI]])
        l2 = sum([len(x) for x in ana.unique_bonds[imI]])
        assert l1 == l2 * 2

    for imi in range(len(ana.all_angles)):
        l1 = sum([len(x) for x in ana.all_angles[imi]])
        l2 = sum([len(x) for x in ana.unique_angles[imi]])
        assert l1 == l2 * 2

    for imi in range(len(ana.all_dihedrals)):
        l1 = sum([len(x) for x in ana.all_dihedrals[imi]])
        l2 = sum([len(x) for x in ana.unique_dihedrals[imi]])
        assert l1 == l2 * 2

    assert len(ana.get_angles('C', 'C', 'H', unique=False)[0]) == len(
        ana.get_angles('C', 'C', 'H', unique=True)[0]) * 2

    csixty = molecule('C60')
    mol = molecule('C7NH5')

    ana = Analysis(csixty)
    ana2 = Analysis(mol)
    for imI in range(len(ana.all_bonds)):
        l1 = sum([len(x) for x in ana.all_bonds[imI]])
        l2 = sum([len(x) for x in ana.unique_bonds[imI]])
        assert l1 == l2 * 2
    for imI in range(len(ana.all_angles)):
        l1 = sum([len(x) for x in ana.all_angles[imI]])
        l2 = sum([len(x) for x in ana.unique_angles[imI]])
        assert l1 == l2 * 2
    for imI in range(len(ana.all_dihedrals)):
        l1 = sum([len(x) for x in ana.all_dihedrals[imI]])
        l2 = sum([len(x) for x in ana.unique_dihedrals[imI]])
        assert l1 == l2 * 2

    assert len(ana2.get_angles('C', 'C', 'H', unique=False)[0]) == len(
        ana2.get_angles('C', 'C', 'H', unique=True)[0]) * 2
    assert len(ana2.get_dihedrals('H', 'C', 'C', 'H', unique=False)[0]) == len(
        ana2.get_dihedrals('H', 'C', 'C', 'H', unique=True)[0]) * 2

Example #2

File: analysis.py Project: martin-stoehr/ase-devel

for imi in range(len(ana.all_dihedrals)):
    l1 = sum([len(x) for x in ana.all_dihedrals[imi]])
    l2 = sum([len(x) for x in ana.unique_dihedrals[imi]])
    assert l1 == l2 * 2

assert len(ana.get_angles('C','C','H', unique=False)[0]) == len(ana.get_angles('C','C','H', unique=True)[0])*2


csixty = molecule('C60')
mol = molecule('C7NH5')

ana = Analysis(csixty)
ana2 = Analysis(mol)
for imI in range(len(ana.all_bonds)):
    l1 = sum([len(x) for x in ana.all_bonds[imI]])
    l2 = sum([len(x) for x in ana.unique_bonds[imI]])
    assert l1 == l2 * 2
for imI in range(len(ana.all_angles)):
    l1 = sum([len(x) for x in ana.all_angles[imI]])
    l2 = sum([len(x) for x in ana.unique_angles[imI]])
    assert l1 == l2 * 2
for imI in range(len(ana.all_dihedrals)):
    l1 = sum([len(x) for x in ana.all_dihedrals[imI]])
    l2 = sum([len(x) for x in ana.unique_dihedrals[imI]])
    assert l1 == l2 * 2

assert len(ana2.get_angles('C','C','H', unique=False)[0]) == len(ana2.get_angles('C','C','H', unique=True)[0]) * 2
assert len(ana2.get_dihedrals('H','C','C','H',unique=False)[0]) == len(ana2.get_dihedrals('H','C','C','H',unique=True)[0]) * 2