def test_ca_binaries(): traj, ref = _random_natural_trajs() feat = BinaryLigandContactFeaturizer(reference_frame=ref, cutoff=0.1, scheme='ca') binaries = feat.transform(traj) assert np.sum(binaries[:]) <= len(binaries)*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_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])