def test_load_trajectory(get_fn):
# Compare a TNG file to the PDB file it was created from.
pdbtraj = md.load_pdb(get_fn('frame0.pdb'))
tngtraj = md.load_tng(get_fn('frame0.tng'), top=pdbtraj.topology)
eq(pdbtraj.n_frames, tngtraj.n_frames)
eq(pdbtraj.unitcell_vectors, tngtraj.unitcell_vectors)
eq(pdbtraj.xyz, tngtraj.xyz)
def test_load_trajectory():
"""Compare a TNG file to the PDB file it was created from."""
pdbtraj = md.load_pdb(get_fn('frame0.pdb'))
tngtraj = md.load_tng(get_fn('frame0.tng'), top=pdbtraj.topology)
eq(pdbtraj.n_frames, tngtraj.n_frames)
eq(pdbtraj.unitcell_vectors, tngtraj.unitcell_vectors)
eq(pdbtraj.xyz, tngtraj.xyz)
def test_load_topology(get_fn):
# Test loading a Topology from a TNG file.
traj = md.load_tng(get_fn('tng_example.tng'))
top = traj.topology
eq(5, top.n_residues)
eq(10, top.n_bonds)
bonds = [(a, b) for a, b in top.bonds]
for res in top.residues:
eq('HOH', res.name)
eq(3, res.n_atoms)
eq(md.element.oxygen, res.atom(0).element)
eq(md.element.hydrogen, res.atom(1).element)
eq(md.element.hydrogen, res.atom(2).element)
assert (res.atom(0), res.atom(1)) in bonds
assert (res.atom(0), res.atom(2)) in bonds
def test_load_topology():
"""Test loading a Topology from a TNG file."""
traj = md.load_tng(get_fn("tng_example.tng"))
top = traj.topology
eq(5, top.n_residues)
eq(10, top.n_bonds)
bonds = list(top.bonds)
for res in top.residues:
eq("HOH", res.name)
eq(3, res.n_atoms)
eq(md.element.oxygen, res.atom(0).element)
eq(md.element.hydrogen, res.atom(1).element)
eq(md.element.hydrogen, res.atom(2).element)
assert (res.atom(0), res.atom(1)) in bonds
assert (res.atom(0), res.atom(2)) in bonds
def test_load_topology():
"""Test loading a Topology from a TNG file."""
traj = md.load_tng(get_fn('tng_example.tng'))
top = traj.topology
eq(5, top.n_residues)
eq(10, top.n_bonds)
bonds = list(top.bonds)
for res in top.residues:
eq('HOH', res.name)
eq(3, res.n_atoms)
eq(md.element.oxygen, res.atom(0).element)
eq(md.element.hydrogen, res.atom(1).element)
eq(md.element.hydrogen, res.atom(2).element)
assert((res.atom(0), res.atom(1)) in bonds)
assert((res.atom(0), res.atom(2)) in bonds)