def test_chain_guessing():
traj, ref = _random_trajs()
feat = LigandContactFeaturizer(reference_frame=ref)
contacts = feat.transform(traj)
assert feat.protein_chain == 0
assert feat.ligand_chain == 1
assert len(contacts) == 100
assert contacts[0].shape[1] == 3
def test_chain_guessing():
traj, ref = _random_trajs()
feat = LigandContactFeaturizer(reference_frame=ref)
contacts = feat.transform(traj)
assert feat.protein_chain == 0
assert feat.ligand_chain == 1
assert len(contacts) == 100
assert contacts[0].shape[1] == 3
def test_binding_pocket():
traj, ref = _random_trajs()
feat = LigandContactFeaturizer(reference_frame=ref)
pocket_ref = feat.transform([ref])
limit = (max(pocket_ref[0][0]) + min(pocket_ref[0][0]))/2.0
number_included = sum(pocket_ref[0][0] < limit)
pocket_feat = LigandContactFeaturizer(reference_frame=ref,
binding_pocket=limit)
pocket_contacts = pocket_feat.transform(traj)
assert len(pocket_contacts[0][0]) == number_included
def test_binaries_binding_pocket():
traj, ref = _random_trajs()
feat = LigandContactFeaturizer(reference_frame=ref)
pocket_ref = feat.transform([ref])
limit = (max(pocket_ref[0][0]) + min(pocket_ref[0][0]))/2.0
cutoff = limit*0.8
number_included = sum(pocket_ref[0][0] < limit)
pocket_feat = BinaryLigandContactFeaturizer(reference_frame=ref,
cutoff=cutoff,
binding_pocket=limit)
pocket_binaries = pocket_feat.transform(traj)
assert len(pocket_binaries[0][0]) == number_included
assert (np.sum(pocket_binaries[:]) <=
len(pocket_binaries)*pocket_binaries[0].shape[1])
def test_binaries_binding_pocket():
traj, ref = _random_trajs()
feat = LigandContactFeaturizer(reference_frame=ref)
pocket_ref = feat.transform([ref])
limit = (max(pocket_ref[0][0]) + min(pocket_ref[0][0]))/2.0
cutoff = limit*0.8
number_included = sum(pocket_ref[0][0] < limit)
pocket_feat = BinaryLigandContactFeaturizer(reference_frame=ref,
cutoff=cutoff,
binding_pocket=limit)
pocket_binaries = pocket_feat.transform(traj)
assert len(pocket_binaries[0][0]) == number_included
assert (np.sum(pocket_binaries[:]) <=
len(pocket_binaries)*pocket_binaries[0].shape[1])
def test_binding_pocket():
traj, ref = _random_trajs()
feat = LigandContactFeaturizer(reference_frame=ref)
pocket_ref = feat.transform([ref])
limit = (max(pocket_ref[0][0]) + min(pocket_ref[0][0])) / 2.0
number_included = sum(pocket_ref[0][0] < limit)
pocket_feat = LigandContactFeaturizer(reference_frame=ref,
binding_pocket=limit)
pocket_contacts = pocket_feat.transform(traj)
assert len(pocket_contacts[0][0]) == number_included