def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
mdio.write_traj("test_1.pdb", traj[0], top=traj.top, overwrite=True)
mdio.write_traj("test_1.dcd", traj[0], top=traj.top, overwrite=True)
with TrajectoryWriter("./output/test_1", overwrite=True) as trajout:
trajout.write(traj[0])
def test_trajectory_writer():
traj = pt.iterload(tc5b_trajin, tc5b_top)
with tempfolder():
pt.write_traj("test_1.pdb", traj[0], top=traj.top, overwrite=True)
pt.write_traj("test_1.dcd", traj[0], top=traj.top, overwrite=True)
with TrajectoryWriter("test_1", overwrite=True) as trajout:
trajout.write(traj[0])
def test_write_pdb():
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = pt.iterload(tc5b_trajin, tc5b_top)[:]
TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `pt.write_traj`
with tempfolder():
basename = "test_pdb_files_pt_write_traj.pdb"
pt.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
with pytest.raises(IOError):
# write files again, raise if file exists
pt.write_traj(basename, traj, overwrite=False, options="multi")
# keepext
with tempfolder():
basename = 'test_pdb_files_pt_write_traj.pdb'
basename2 = 'test_pdb_files_pt_write_traj'
pt.write_traj(basename, traj, overwrite=True, options="multi keepext")
for i in range(10):
fname = "{}.{}.pdb".format(basename2, i + 1)
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
with pytest.raises(IOError):
pt.write_traj(basename,
traj,
overwrite=False,
options="multi keepext")
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = pt.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `model` keyword
# write to output so we can manually check
basename = "test_pdb_files_model.pdb"
with tempfolder():
traj.save(basename, overwrite=True, options='model')
traj3 = pt.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)
def test_write_force_from_scratch():
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
assert traj[0].force is None
def add_force(traj):
for frame in traj:
frame.force = np.zeros(traj.n_atoms * 3) + 1.
yield frame
with tempfolder():
out_fn = 'out.nc'
with TrajectoryWriter(out_fn, top=traj.top, crdinfo={'has_force': True}) as writer:
for frame in add_force(traj):
writer.write(frame)
traj2 = pt.iterload(out_fn, top=traj.top)
assert traj2.metadata['has_force']
assert not traj2.metadata['has_velocity']
def test_write_velocity_from_scratch():
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
assert traj[0].velocity is None
def add_velocity(traj):
for frame in traj:
frame.velocity = np.zeros(traj.n_atoms * 3) + 1.
yield frame
with tempfolder():
out_fn = 'out.nc'
with TrajectoryWriter(out_fn,
top=traj.top,
crdinfo={'has_velocity': True}) as writer:
for frame in add_velocity(traj):
writer.write(frame)
traj2 = pt.iterload(out_fn, top=traj.top)
assert traj2.metadata['has_velocity']
assert not traj2.metadata['has_force']
# make sure no segmentation fault
# issues/1486
assert traj2[:].n_frames == traj2.n_frames
def test_1(self):
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:]
trajout = TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `mdio.write_traj`
with tempfolder():
basename = "test_pdb_files_mdio_write_traj.pdb"
mdio.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `model` keyword
# write to output so we can manually check
basename = "./output/test_pdb_files_model.pdb"
traj.save(basename, overwrite=True, options='model')
traj3 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)