pytraj.TrajectoryIterator¶

out-of-core TrajectoryIterator

class pytraj.trajectory_iterator.TrajectoryIterator(filename=None, top=None, *args, **kwd)¶

Bases: pytraj.c_traj.c_trajectory.TrajectoryCpptraj

out-of-core trajectory holder.

Notes

It’s a bit tricky to pickle this class. As default, new TrajectoryIterator will use original trj filename and top filename. If set _pickle_topology to True, its Topology will be pickled (slow but more accurate if you change the topology in the fly)

Examples

>>> import pytraj as pt
>>> from pytraj.testing import get_fn
>>> traj_name, top_name = get_fn('tz2')
>>> traj = pt.TrajectoryIterator(traj_name, top_name)

>>> # user should always use :method:`pytraj.iterload` to load TrajectoryIterator
>>> traj = pt.iterload(['remd.x.000', 'remd.x.001'], 'input.parm7') 

Attributes

filelist	return a list of input filenames. Order does matter
filename	return 1st filename in filelist. For testing only
metadata	return a dict of general information
n_atoms	used for frame_iter
n_frames
shape	(n_frames, n_atoms, 3)
temperatures
top
topology	traditional name for Topology file
unitcells	return unitcells (Box) with shape=(n_frames, 6)
xyz	return 3D array of coordinates

Methods

__call__	Call self as a function.
at(index)
copy()	return a deep copy. Use this method with care since the copied traj just reuse
iterchunk([chunksize, start, stop, ...])	iterate trajectory by chunk
iterframe([start, stop, step, mask, ...])	iterate trajectory with given frame_indices or given (start, stop, step)
save(self[, filename, overwrite])	convenient method to save Trajectory

at(index)¶

copy()¶

return a deep copy. Use this method with care since the copied traj just reuse the filenames

filelist¶

return a list of input filenames. Order does matter

filename¶

return 1st filename in filelist. For testing only

iterchunk(chunksize=2, start=0, stop=-1, autoimage=False, rmsfit=None)¶

iterate trajectory by chunk

Parameters:	chunk : int, default=2 size of each chunk. Notes: final chunk’s size might be changed start : int, default=0 (first frame) stop : int, default=-1 (last frame) autoimage : bool, default=False rmsfit : None | tuple/list of (reference frame, mask)

Notes

if using ‘autoimage` with reference frame for rms-fit, make sure to autoimage ref first

Examples

>>> import pytraj as pt
>>> traj = pt.load_sample_data('tz2')
>>> ref = traj[3]
>>> for chunk in traj.iterchunk(3, autoimage=True, rmsfit=(ref, '@CA')): pass

iterframe(start=0, stop=None, step=1, mask=None, autoimage=False, rmsfit=None, copy=False, frame_indices=None)¶

iterate trajectory with given frame_indices or given (start, stop, step)

Parameters:

start : int, default 0 stop : {None, int}, default None if None, iterate to final frame step : int, default 1 mask : {None, str}, default None if None, use all atoms. If not None, use given mask autoimage : bool, default False if True, perform autoimage for each frame rmsfit : {None, int, tuple}, default None if not None, perform superpose each Frame to to reference. frame_indices : {None, array-like} if not None, iterate trajectory for given indices. If frame_indices is given, (start, stop, step) will be ignored.

Examples

>>> import pytraj as pt
>>> traj = pt.load_sample_data('tz2')
>>> for frame in traj.iterframe(0, 8, 2): pass
>>> for frame in traj.iterframe(0, 8, 2, autoimage=True): pass
>>> # use negative index
>>> traj.n_frames
10
>>> fi = traj.iterframe(0, -1, 2, autoimage=True)
>>> fi.n_frames
5
>>> # mask is atom indices
>>> fi = traj.iterframe(0, -1, 2, mask=range(100), autoimage=True)
>>> fi.n_atoms
100

metadata¶

return a dict of general information

Examples

>>> traj.metadata
{'box_type': 'ortho',
 'has_box': True,
 'has_force': False,
 'has_replcica_dims': False,
 'has_temperature': False,
 'has_time': True,
 'has_velocity': False,
 'n_atoms': 5293,
 'n_frames': 10}

n_atoms¶

used for frame_iter

n_frames¶

save(self, filename='', overwrite=True, **kwd)¶

convenient method to save Trajectory

Examples

>>> # save to DCD file
>>> traj.save('traj.dcd')
>>> # save to AMBER netcdf file
>>> traj.save('traj.nc')

shape¶

(n_frames, n_atoms, 3)

>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()
>>> traj.shape
(10, 5293, 3)

temperatures¶

top¶

topology¶

traditional name for Topology file

Examples

>>> import pytraj as pt
>>> from pytraj.testing import get_fn
>>> fname, tname = get_fn('ala3')
>>> traj = pt.iterload(fname, tname)
>>> traj.topology
<Topology: 34 atoms, 3 residues, 1 mols, non-PBC>
>>> new_traj = pt.TrajectoryIterator()
>>> new_traj.topology = traj.topology
>>> new_traj._load(traj.filename)

unitcells¶

return unitcells (Box) with shape=(n_frames, 6)

xyz¶

return 3D array of coordinates