def test_similarity():
filename_a = os.path.join("data", "276.pdb")
filename_b = os.path.join("data", "4629.pdb")
activesite_a = io.read_active_site(filename_a)
activesite_b = io.read_active_site(filename_b)
assert cluster.compute_similarity(activesite_a, activesite_a) == 0.0
assert cluster.compute_similarity(
activesite_a,
activesite_b) == cluster.compute_similarity(activesite_b, activesite_a)
def test_residues(filename, names, numbers):
filepath = os.path.join("data", filename)
activesite = io.read_active_site(filepath)
assert [residue.type for residue in activesite.residues] == names
assert [residue.number for residue in activesite.residues] == numbers
def test_atoms(filename, residue_number, atoms, xs, ys, zs):
filepath = os.path.join("data", filename)
activesite = io.read_active_site(filepath)
residue = activesite.residues[residue_number]
assert [atom.type for atom in residue.atoms] == atoms
assert [atom.coords for atom in residue.atoms] == list(zip(xs, ys, zs))
def test_partition_clustering():
# tractable subset
pdb_ids = [276, 4629, 10701]
active_sites = []
for id in pdb_ids:
filepath = os.path.join("data", "%i.pdb" % id)
active_sites.append(io.read_active_site(filepath))
sim_matrix = cluster.get_sim_matrix(active_sites)
assert cluster.cluster_by_partitioning([], {}) == []
assert cluster.cluster_by_partitioning([active_sites[0]],
{}) == [[active_sites[0]]]
clustering = cluster.cluster_by_partitioning(active_sites, sim_matrix)
assert len(clustering) == 1
s = set(active_sites)
assert set(clustering[0]) == s
def test_hierarchical_clustering():
# tractable subset
pdb_ids = [276, 4629, 10701]
active_sites = []
for id in pdb_ids:
filepath = os.path.join("data", "%i.pdb" % id)
active_sites.append(io.read_active_site(filepath))
sim_matrix = cluster.get_sim_matrix(active_sites)
# update this assertion
assert cluster.cluster_hierarchically([], {}) == []
assert cluster.cluster_hierarchically([active_sites[0]],
{}) == [[active_sites[0]]]
clustering = cluster.cluster_hierarchically(active_sites, sim_matrix)
assert len(clustering) == 2
assert clustering[0] == [active_sites[2]]
assert set(clustering[1]) == set([active_sites[0], active_sites[1]])