def test_mdtraj_equivalence():
traj, ref = _random_trajs()
feat = LigandRMSDFeaturizer(reference_frame=ref, align_by='custom',
calculate_for='custom', align_indices=range(ref.n_atoms),
calculate_indices=range(ref.n_atoms))
multi_chain = feat.transform([traj])
md_traj = md.rmsd(traj,ref,frame=0)
np.testing.assert_almost_equal(multi_chain[0][:, 0], md_traj, decimal=4)
def test_mdtraj_equivalence():
traj, ref = _random_trajs()
feat = LigandRMSDFeaturizer(reference_frame=ref, align_by='custom',
calculate_for='custom', align_indices=range(ref.n_atoms),
calculate_indices=range(ref.n_atoms))
multi_chain = feat.transform([traj])
md_traj = md.rmsd(traj,ref,frame=0)
np.testing.assert_almost_equal(multi_chain[0][:, 0], md_traj, decimal=4)
def test_single_index_rmsd():
traj, ref = _random_trajs()
feat = LigandRMSDFeaturizer(reference_frame=ref,
calculate_indices=[ref.n_atoms-1])
single_cindex = feat.transform([traj])
assert np.unique(single_cindex).shape[0] > 1
def test_single_index_rmsd():
traj, ref = _random_trajs()
feat = LigandRMSDFeaturizer(reference_frame=ref,
calculate_indices=[ref.n_atoms-1])
single_cindex = feat.transform([traj])
assert np.unique(single_cindex).shape[0] > 1