def test_run_0(self):
# load traj
farray = pt.load(filename="./data/tz2.truncoct.nc",
top="./data/tz2.truncoct.parm7")[:2]
fold = farray.copy()
act = allactions.Action_Image()
ptrajin = """
center :2-11
image center familiar com :6
"""
# create 'strip' action
stripact = allactions.Action_Strip()
# creat datasetlist to hold distance data
dsetlist = CpptrajDatasetList()
dflist = DataFileList()
# creat ActionList to hold actions
alist = ActionList()
top = farray.top
# add two actions: Action_Strip and Action_Distance
alist.add(allactions.Action_Center(), ArgList(":2-11"), top=top)
alist.add(allactions.Action_Image(),
ArgList("center familiar com :6"),
top=top)
# do checking
alist.check_topology(top)
farray2 = Trajectory()
frame0 = Frame()
# testing how fast to do the actions
# loop all frames
# use iterator to make faster loop
# don't use "for i in range(farray.n_frames)"
for frame in farray:
# perform actions for each frame
# we make a copy since we want to keep orginal Frame
frame0 = frame.copy()
alist.compute(frame0)
# we need to keep the modified frame in farray2
farray2.append(frame0)
# make sure that Action_Strip does its job in stripping
assert farray2.n_frames == farray.n_frames
fsaved = pt.iterload(cpptraj_test_dir + "/Test_Image/image4.crd.save",
"data/tz2.truncoct.parm7")
assert fsaved.n_frames == 2
def test_run_0(self):
# load traj
farray = pt.load(filename="./data/tz2.truncoct.nc",
top="./data/tz2.truncoct.parm7")[:2]
fold = farray.copy()
act = allactions.Action_Image()
ptrajin = """
center :2-11
image center familiar com :6
"""
# create 'strip' action
stripact = allactions.Action_Strip()
# creat datasetlist to hold distance data
dsetlist = CpptrajDatasetList()
dflist = DataFileList()
# creat ActionList to hold actions
alist = ActionList()
top = farray.top
# add two actions: Action_Strip and Action_Distance
alist.add(allactions.Action_Center(), ArgList(":2-11"), top=top)
alist.add(allactions.Action_Image(),
ArgList("center familiar com :6"),
top=top)
# do checking
alist.check_topology(top)
farray2 = Trajectory()
frame0 = Frame()
# testing how fast to do the actions
# loop all frames
# use iterator to make faster loop
# don't use "for i in range(farray.n_frames)"
for frame in farray:
# perform actions for each frame
# we make a copy since we want to keep orginal Frame
frame0 = frame.copy()
alist.compute(frame0)
# we need to keep the modified frame in farray2
farray2.append(frame0)
# make sure that Action_Strip does its job in stripping
assert farray2.n_frames == farray.n_frames
fsaved = pt.iterload(cpptraj_test_dir + "/Test_Image/image4.crd.save",
"data/tz2.truncoct.parm7")
assert fsaved.n_frames == 2
def load_MDAnalysis(universe, top=None):
"""load MDAnalysis' Universe object to pytra's traj object
Notes
-----
All coords will be loaded
See Also
--------
load_MDAnalysisIterator
"""
from MDAnalysis import Universe
from pytraj.Trajectory import Trajectory
from ..Frame import Frame
# don't import here since we import load_pseudo_parm in
# TrajectoryMDAnalysisIterator
# MDAnalysis needs numpy. So we always have numpy when using this
if not isinstance(universe, Universe):
raise ValueError("must be a Universe")
# creat pseudotop
if top is None:
raise ValueError("need a Topology or pdb/mol2/...")
else:
pseudotop = top
# creat atom group
ag = universe.atoms
farray = Trajectory()
farray.top = pseudotop
for _ in universe.trajectory:
frame = Frame(farray.top.n_atoms)
# set box for each Frame
frame.boxview[:] = farray.top.box[:]
# load xyz coords, let numpy do automatically casting
frame.xyz[:] = ag.positions
# we don't need to make copy=True since we already created
# frame and `farray` can 'keep' it
farray.append(frame, copy=False)
return farray
def load_MDAnalysis(its_obj, top=None):
"""load MDAnalysis' Universe object to pytra's traj object
Notes
-----
All coords will be loaded
See Also
--------
load_MDAnalysisIterator
"""
from MDAnalysis import Universe
from pytraj.Trajectory import Trajectory
from ..Frame import Frame
# don't import here since we import load_pseudo_parm in
# TrajectoryMDAnalysisIterator
# MDAnalysis needs numpy. So we always have numpy when using this
if not isinstance(its_obj, Universe):
raise ValueError("must be a Universe")
# creat pseudotop
if top is None:
raise ValueError("need a Topology or pdb/mol2/...")
else:
pseudotop = top
# creat atom group
ag = its_obj.atoms
farray = Trajectory()
farray.top = pseudotop
for _ in its_obj.trajectory:
frame = Frame(farray.top.n_atoms)
# set box for each Frame
frame.boxview[:] = farray.top.box[:]
# load xyz coords, let numpy do automatically casting
frame.xyz[:] = ag.positions
# we don't need to make copy=True since we already created
# frame and `farray` can 'keep' it
farray.append(frame, copy=False)
return farray