def test_pipe(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
# from TrajectoryIterator
fi = pt.pipe(traj, ['autoimage', 'rms'])
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = traj[:].autoimage().superpose()
aa_eq(xyz, t0.xyz)
# from FrameIterator
fi = pt.pipe(traj(), ['autoimage', 'rms'])
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = traj[:].autoimage().superpose()
aa_eq(xyz, t0.xyz)
# from FrameIterator with indices
fi = pt.pipe(traj(0, 8, 2), ['autoimage', 'rms'])
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = traj[:8:2].autoimage().superpose()
aa_eq(xyz, t0.xyz)
# from TrajectoryIterator, cpptraj's command style
fi = pt.pipe(traj, '''
autoimage
rms''')
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = traj[:].autoimage().superpose()
aa_eq(xyz, t0.xyz)
def test_pipe(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
# from TrajectoryIterator
fi = pt.pipe(traj, ['autoimage', 'rms'])
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = traj[:].autoimage().superpose()
aa_eq(xyz, t0.xyz)
# from FrameIterator
fi = pt.pipe(traj(), ['autoimage', 'rms'])
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = traj[:].autoimage().superpose()
aa_eq(xyz, t0.xyz)
# from FrameIterator with indices
fi = pt.pipe(traj(0, 8, 2), ['autoimage', 'rms'])
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = traj[:8:2].autoimage().superpose()
aa_eq(xyz, t0.xyz)
# from TrajectoryIterator, cpptraj's command style
fi = pt.pipe(traj, '''
autoimage
rms''')
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = traj[:].autoimage().superpose()
aa_eq(xyz, t0.xyz)
def test_pieline(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
fi = pt.pipe(traj, ['autoimage', ])
aa_eq(pt.get_coordinates(fi), traj[:].autoimage().xyz)
fi = pt.pipe(traj, ['autoimage', ], frame_indices=[3, 5])
aa_eq(pt.get_coordinates(fi), traj[[3, 5]].autoimage().xyz)
def test_pieline(self):
traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
fi = pt.pipe(traj, ['autoimage', ])
aa_eq(pt.get_coordinates(fi), traj[:].autoimage().xyz)
fi = pt.pipe(traj, ['autoimage', ], frame_indices=[3, 5])
aa_eq(pt.get_coordinates(fi), traj[[3, 5]].autoimage().xyz)
def test_from_iterables(self):
'''test_from_iterables, tests are ind its doc. Test raise here
'''
traj = pt.datafiles.load_tz2_ortho()
fi = pt.pipe(traj, ['autoimage'])
# does not have Topology info
self.assertRaises(ValueError, lambda: pt.Trajectory.from_iterable(fi))
def test_from_iterables(self):
'''test_from_iterables, tests are ind its doc. Test raise here
'''
traj = pt.datafiles.load_tz2_ortho()
fi = pt.pipe(traj, ['autoimage'])
# does not have Topology info
self.assertRaises(ValueError, lambda: pt.Trajectory.from_iterable(fi))
def test_save_traj_from_file(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:5]
pt.write_traj(filename="./output/test_0.binpos",
traj=traj,
top="./data/Tc5b.top",
overwrite=True)
savedtraj = pt.iterload("./output/test_0.binpos", traj.top)
assert savedtraj.n_frames == traj.n_frames
# write_xyz
pt.write_traj("./output/test_0.nc",
traj.xyz,
top="./data/Tc5b.top",
overwrite=True)
aa_eq(pt.iterload('output/test_0.nc', traj.top).xyz, traj.xyz)
# write single Frame
pt.write_traj("./output/test_0.nc",
traj[0],
top=traj.top,
overwrite=True)
aa_eq(pt.iterload('output/test_0.nc', traj.top).xyz, traj[0].xyz)
# raise if traj is None
self.assertRaises(
ValueError,
lambda: pt.write_traj("./output/test_0.nc", None, overwrite=True))
# raise if _top is None
fi = pt.pipe(traj, [
'autoimage',
])
self.assertRaises(
ValueError, lambda: pt.write_traj(
"./output/test_0.nc", traj=fi, overwrite=True))
# raise if Frame with frame_indices
self.assertRaises(
ValueError, lambda: pt.write_traj("./output/test_0.nc",
traj[0],
top="./data/Tc5b.top",
frame_indices=[3, 2],
overwrite=True))
# raise if Frame with no Topology
self.assertRaises(
ValueError, lambda: pt.write_traj(
"./output/test_0.nc", traj[0], overwrite=True))
# test if xyz is not c-contiguous
# pytraj will autoconvert to c-contiguous
xyz = np.asfortranarray(traj.xyz)
# make sure no ValueError or TypeError is raised
pt.write_traj('output/xyz.nc', xyz, top=traj.top, overwrite=True)
def worker_by_actlist(rank,
n_cores=2,
traj=None,
lines=None,
dtype='dict',
ref=None,
kwd=None):
'''worker for cpptraj commands (string)
'''
# need to make a copy if lines since python's list is dangerous
# it's easy to mess up with mutable list
# do not use lines.copy() since this is not available in py2.7
# Note: dtype is a dummy argument, it is always 'dict'
if lines is None:
lines = []
frame_indices = kwd.pop('frame_indices', None)
new_lines, need_ref = check_valid_command(lines)
if frame_indices is None:
my_iter = traj._split_iterators(n_cores, rank=rank)
else:
my_iter = traj.iterframe(
frame_indices=np.array_split(frame_indices, n_cores)[rank])
if ref is not None:
if isinstance(ref, Frame):
reflist = [
ref,
]
else:
# list/tuplex
reflist = ref
else:
reflist = [
traj[0],
] if need_ref else []
dslist = CpptrajDatasetList()
if reflist:
for ref_ in reflist:
ref_dset = dslist.add('reference')
ref_dset.top = traj.top
ref_dset.add_frame(ref_)
# create Frame generator
fi = pipe(my_iter, commands=new_lines, dslist=dslist)
# just iterate Frame to trigger calculation.
for _ in fi:
pass
# remove ref
return (rank, dslist[len(reflist):].to_dict())
def worker_by_actlist(rank,
n_cores=2,
traj=None,
lines=None,
dtype='dict',
ref=None,
kwd=None):
'''worker for cpptraj commands (string)
'''
# need to make a copy if lines since python's list is dangerous
# it's easy to mess up with mutable list
# do not use lines.copy() since this is not available in py2.7
# Note: dtype is a dummy argument, it is always 'dict'
if lines is None:
lines = []
frame_indices = kwd.pop('frame_indices', None)
new_lines, need_ref = check_valid_command(lines)
if frame_indices is None:
my_iter = traj._split_iterators(n_cores, rank=rank)
else:
my_iter = traj.iterframe(
frame_indices=np.array_split(frame_indices, n_cores)[rank])
if ref is not None:
if isinstance(ref, Frame):
reflist = [ref, ]
else:
# list/tuplex
reflist = ref
else:
reflist = [traj[0],] if need_ref else []
dslist = CpptrajDatasetList()
if reflist:
for ref_ in reflist:
ref_dset = dslist.add('reference')
ref_dset.top = traj.top
ref_dset.add_frame(ref_)
# create Frame generator
fi = pipe(my_iter, commands=new_lines, dslist=dslist)
# just iterate Frame to trigger calculation.
for _ in fi:
pass
# remove ref
return (rank, dslist[len(reflist):].to_dict())
def test_reference(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
# store reference
dslist = CpptrajDatasetList()
ref = dslist.add('reference')
ref.top = traj.top
ref.append(traj[3])
fi = pt.pipe(traj, ['autoimage', 'rms refindex 0 @CA'], dslist=dslist)
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = (traj[:].autoimage().superpose(ref=traj[3], mask='@CA'))
aa_eq(xyz, t0.xyz)
t1 = traj[:].autoimage()
aa_eq(pt.rmsd(t1, ref=traj[3], mask='@CA'), dslist[-1].values)
def test_save_traj_from_file():
traj = pt.iterload(tc5b_trajin, tc5b_top)[:5]
with tempfolder():
pt.write_traj(filename="test_0.binpos",
traj=traj,
top=tc5b_top,
overwrite=True)
savedtraj = pt.iterload("test_0.binpos", traj.top)
assert savedtraj.n_frames == traj.n_frames
# write_xyz
pt.write_traj("test_0.nc", traj.xyz, top=tc5b_top, overwrite=True)
aa_eq(pt.iterload('test_0.nc', traj.top).xyz, traj.xyz)
# write single Frame
pt.write_traj("test_0.nc", traj[0], top=traj.top, overwrite=True)
aa_eq(pt.iterload('test_0.nc', traj.top).xyz, traj[0].xyz)
# raise if traj is None
with pytest.raises(ValueError):
pt.write_traj("test_0.nc", None, overwrite=True)
# raise if _top is None
fi = pt.pipe(traj, [
'autoimage',
])
with pytest.raises(ValueError):
pt.write_traj("test_0.nc", traj=fi, overwrite=True)
# raise if Frame with frame_indices:
with pytest.raises(ValueError):
pt.write_traj("test_0.nc",
traj[0],
top=tc5b_top,
frame_indices=[3, 2],
overwrite=True)
# raise if Frame with no Topology
with pytest.raises(ValueError):
pt.write_traj("test_0.nc", traj[0], overwrite=True)
# test if xyz is not c-contiguous
# pytraj will autoconvert to c-contiguous
xyz = np.asfortranarray(traj.xyz)
# make sure no ValueError or TypeError is raised
pt.write_traj('xyz.nc', xyz, top=traj.top, overwrite=True)
def test_get_coordinates_trajecotoryiterator(self):
'''immutable pytraj.TrajectoryIterator
'''
traj = self.traj_tz2_ortho.copy()
# all coordinates
xyz = pt.get_coordinates(traj)
aa_eq(traj.xyz, xyz)
# given frames
xyz = pt.get_coordinates(traj, frame_indices=[0, 5])
aa_eq(traj[[0, 5]].xyz, xyz)
# given frames, autoimage=True
xyz = pt.get_coordinates(traj, frame_indices=[0, 5], autoimage=True)
aa_eq(traj[[0, 5]].autoimage().xyz, xyz)
# given frames, autoimage=True, rmsfit=ref
ref = traj[-3]
pt.autoimage(ref, top=traj.top)
xyz = pt.get_coordinates(traj,
frame_indices=[0, 5],
autoimage=True,
rmsfit=ref)
aa_eq(traj[[0, 5]].autoimage().superpose(ref=ref).xyz, xyz)
xyz = pt.get_coordinates(traj,
frame_indices=range(3),
autoimage=True,
rmsfit=ref)
# with mask
xyz = pt.get_coordinates(traj, mask='@CA')
aa_eq(xyz, traj['@CA'].xyz)
# slow
fi = pt.pipe(traj, ['autoimage'])
aa_eq(pt.get_coordinates(fi), traj[:].autoimage().xyz)
# raise
self.assertRaises(
ValueError,
lambda: pt.get_coordinates(traj(), frame_indices=[0, 2]))
def test_reference(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
# store reference
dslist = CpptrajDatasetList()
ref = dslist.add_new('reference')
ref.top = traj.top
ref.append(traj[3])
fi = pt.pipe(traj,
['autoimage', 'rms refindex 0 @CA'],
dslist=dslist)
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = (traj[:]
.autoimage()
.superpose(ref=traj[3], mask='@CA'))
print('ok')
aa_eq(xyz, t0.xyz)
t1 = traj[:].autoimage()
aa_eq(pt.rmsd(t1, ref=traj[3], mask='@CA'), dslist[-1].values)
