def test_init_from_trajectory(GS6_CO, NTL9_CO, GS6_CP, NTL9_CP):
trajs = [GS6_CO, NTL9_CO]
proteins = [GS6_CP, NTL9_CP]
for ct_traj, ct_protein in zip(trajs, proteins):
protein_from_md = ssprotein.SSProtein(ct_traj)
assert protein_from_md.n_frames > 0
assert protein_from_md.n_residues > 0
assert protein_from_md.length() == ct_protein.length()
protein_from_ct = ssprotein.SSProtein(ct_traj.traj)
assert protein_from_ct.n_frames > 0
assert protein_from_ct.n_residues > 0
assert protein_from_ct.length() == ct_protein.length()
def test_properties(GS6_CO, NTL9_CO, GS6_CP, NTL9_CP):
properties = 'resid_with_CA,ncap,ccap,n_frames,n_residues,residue_index_list'.split(
',')
trajs = [GS6_CO, NTL9_CO]
proteins = [GS6_CP, NTL9_CP]
for ct_traj, ct_protein in zip(trajs, proteins):
protein_from_ct = ssprotein.SSProtein(ct_traj)
for prop in properties:
assert getattr(protein_from_ct, prop) == getattr(ct_protein, prop)
def test_residue_atom_com_new_resid_atom_name_CA(GS6_CO, NTL9_CO):
trajs = [GS6_CO, NTL9_CO]
for traj in trajs:
# instantiate a new protein object since the previous reference is modified
# elsewhere - hence our residue count will be off.
protein = ssprotein.SSProtein(traj)
unavailable_residue_index = protein.n_residues + 1
protein.residue_atom_com(unavailable_residue_index, atom_name='CA')
assert len(
protein._SSProtein__residue_atom_table) == protein.n_residues + 1
def test_init_from_trajectory_invalid():
args = [1, 1.0, 'test', None]
for arg in args:
with pytest.raises(RuntimeError):
protein = ssprotein.SSProtein(arg)
def lengthen_protein_trajectory(protein_traj, num_copies):
trajectories = [protein_traj.traj for i in range(num_copies)]
traj = protein_traj.traj.join(trajectories)
protein = ssprotein.SSProtein(traj)
return protein