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import numpy as np
import pytest
from ase.geometry.analysis import Analysis
from ase.build import molecule
@pytest.mark.filterwarnings('ignore:the matrix subclass')
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
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