def test_similarity():
filename_a = os.path.join("data", "97612.pdb") #276
filename_b = os.path.join("data", "47023.pdb") #4629
activesite_a = io.read_active_site(filename_a)
activesite_b = io.read_active_site(filename_b)
assert cluster.compute_similarity(activesite_a,
activesite_b) == 0.5421899871113518
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_hierarchical_clustering():
# tractable subset
#pdb_ids = [276, 4629, 10701]
pdb_ids = [46495, 23812, 41729] #pick first 3
active_sites = []
for id in pdb_ids:
filepath = os.path.join("data", "%i.pdb" % id)
active_sites.append(io.read_active_site(filepath))
result = [[active_sites[2]], [active_sites[0], active_sites[1]]]
assert cluster.cluster_hierarchically(active_sites, k=2)[0] == result