def test_distance_under_threshold(multi_molecules,
assymetric_pair_selected):
distances = []
found_distances = []
for ((mol_a, key_a), (mol_b, key_b), dist) in assymetric_pair_selected:
node_a = multi_molecules[mol_a].nodes[key_a]
node_b = multi_molecules[mol_b].nodes[key_b]
distances.append(distance(node_a['coords'], node_b['coords']))
found_distances.append(dist)
assert all(d <= 2.0 for d in distances)
assert np.allclose(found_distances, distances)
def test_add_cystein_bridges_threshold(cys_protein):
"""
Test that :class:`vermouth.AddCysteinBridgesThreshold` detects a cystein
bridge in a PDB file.
"""
processor = vermouth.AddCysteinBridgesThreshold(threshold=0.22)
system = processor.run_system(cys_protein)
for edge in system.molecules[0].edges:
node_a = system.molecules[0].nodes[edge[0]]
node_b = system.molecules[0].nodes[edge[1]]
print('*', node_a, '--', node_b)
print(distance(node_a['position'], node_b['position']))
assert len(system.molecules[0].edges) == 1
assert (1285, 3508) in system.molecules[0].edges
def test_add_cystein_bridges_threshold(cys_protein):
"""
Test that :class:`vermouth.AddCysteinBridgesThreshold` detects a cystein
bridge in a PDB file.
"""
processor = vermouth.AddCysteinBridgesThreshold(threshold=0.22)
system = processor.run_system(cys_protein)
for edge in system.molecules[0].edges:
node_a = system.molecules[0].nodes[edge[0]]
node_b = system.molecules[0].nodes[edge[1]]
print('*', node_a, '--', node_b)
print(distance(node_a['position'], node_b['position']))
assert len(system.molecules[0].edges) == 1
# According to SSBOND record, cysbond should be between resid 171 and 876.
# Let's find the associated atoms.
atoms = tuple(system.molecules[0].find_atoms(resname='CYS',
atomname='SG',
resid=Choice([171, 876])))
assert atoms in system.molecules[0].edges
def test_distance(vec_and_dist):
"""
Test the results of :func:`utils.distance`.
"""
point1, point2, distance = vec_and_dist
assert_allclose(utils.distance(point1, point2), distance)