def test_2_atoms(self):
smi = 'CCC'
mol = Molecule().from_smiles(smi)
atom_indices = [1, 2]
distances = compute_atom_distance(atom_indices, mol)
expected = {(1, 2): 1}
self.assertEquals(distances, expected)
def _compute_agglomerate_distance(agglomerates, mol):
"""
Iterates over a list of lists containing atom indices.
For each list the distances between the atoms is computed.
A list of distances is returned.
"""
cython.declare(
distances=list,
agglomerate=list,
dist=dict,
)
distances = []
for agglomerate in agglomerates:
dist = pathfinder.compute_atom_distance(agglomerate, mol)
distances.append(dist)
return distances
def _compute_agglomerate_distance(agglomerates, mol):
"""
Iterates over a list of lists containing atom indices.
For each list the distances between the atoms is computed.
A list of distances is returned.
"""
cython.declare(
distances=list,
agglomerate=list,
dist=dict,
)
distances = []
for agglomerate in agglomerates:
dist = pathfinder.compute_atom_distance(agglomerate, mol)
distances.append(dist)
return distances