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_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 save(self, filename='', overwrite=False, options='', *args, **kwd):
'''save to different file format.
Notes
-----
FrameIterator will be exhausted since this is an iterator.
Examples
--------
>>> import pytraj as pt
>>> traj = pt.load_sample_data('tz2')
>>> fi = traj(2, 8, 2, mask='@CA')
>>> fi.save('output/test.nc', overwrite=True)
>>> # short version
>>> traj(2, 8, 2, mask='@CA').save('output/test.nc', overwrite=True)
'''
from pytraj.io import write_traj
write_traj(filename=filename,
traj=self,
top=self.top,
frame_indices=None,
overwrite=overwrite,
options=options,
*args,
**kwd)
def test_load_and_save_0(self):
traj = mdio.iterload(filename="./data/Tc5b.x",
top="./data/Tc5b.top")[:10]
indices = list(range(2, 3, 5)) + [3, 8, 9, 8]
mdio.write_traj(filename="./output/test_io_saved_.x",
traj=traj,
top="./data/Tc5b.top",
frame_indices=indices,
overwrite=True)
# check frames
traj2 = mdio.iterload(filename="./output/test_io_saved_.x",
top="./data/Tc5b.top")
assert traj2.n_frames == len(indices)
def test_load_and_save_0(self):
traj = mdio.iterload(filename="./data/Tc5b.x",
top="./data/Tc5b.top")[:10]
indices = list(range(2, 3, 5)) + [3, 8, 9, 8]
mdio.write_traj(filename="./output/test_io_saved_.x",
traj=traj,
top="./data/Tc5b.top",
frame_indices=indices,
overwrite=True)
# check frames
traj2 = mdio.iterload(filename="./output/test_io_saved_.x",
top="./data/Tc5b.top")
assert traj2.n_frames == len(indices)
def test_0(self):
trajlist = []
N = 4
for i in range(N):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
trajlist.append(traj)
traj0 = trajlist[0]
mdio.write_traj("./output/test_savedtrajlist.x",
traj=trajlist,
top=traj.top,
overwrite=True)
# test loading
traj2 = mdio.iterload("./output/test_savedtrajlist.x", traj.top)
Nsize = int(traj2.n_frames / 4)
traj0_new = traj2[:Nsize]
for frame0, frame0_new in zip(traj0, traj0_new):
assert (frame0.rmsd(frame0_new) < 1E-3)
def test_0(self):
trajlist = []
N = 4
for i in range(N):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
trajlist.append(traj)
traj0 = trajlist[0]
mdio.write_traj("./output/test_savedtrajlist.x",
traj=trajlist,
top=traj.top,
overwrite=True)
# test loading
traj2 = mdio.iterload("./output/test_savedtrajlist.x", traj.top)
Nsize = int(traj2.n_frames / 4)
traj0_new = traj2[:Nsize]
for frame0, frame0_new in zip(traj0, traj0_new):
assert (frame0.rmsd(frame0_new) < 1E-3)
def test_trajlist(self):
trajlist = []
N = 4
for i in range(N):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
trajlist.append(traj)
traj0 = trajlist[0]
with tempfolder():
pt.write_traj("test_savedtrajlist.x",
traj=trajlist,
top=traj.top,
overwrite=True)
# test loading
traj2 = pt.iterload("test_savedtrajlist.x", traj.top)
Nsize = int(traj2.n_frames / 4)
traj0_new = traj2[:Nsize]
for frame0, frame0_new in zip(traj0, traj0_new):
assert (frame0.rmsd(frame0_new) < 1E-3)
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)
def test_1(self):
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = mdio.iterload("../tests/data/Tc5b.x",
"../tests/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 = mdio.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 `optionsl` 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)