mdtraj.formats.XYZTrajectoryFile¶

class mdtraj.formats.XYZTrajectoryFile(filename, mode='r', force_overwrite=True)¶

Interface for reading and writing to xyz files.

This is a file-like object, that both reading or writing depending on the mode flag. It implements the context manager protocol, so you can also use it with the python ‘with’ statement.

Parameters:	filename : str The filename to open. A path to a file on disk. mode : {‘r’, ‘w’} The mode in which to open the file, either ‘r’ for read or ‘w’ for write. force_overwrite : bool If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?

Methods

close()	Close the xyz file.
read([n_frames, stride, atom_indices])	Read data from a xyz file.
read_as_traj(topology[, n_frames, stride, ...])	Read a trajectory from a XYZ file
seek(offset[, whence])	Move to a new file position.
tell()	Current file position.
write(xyz[, types])	Write one or more frames of data to a xyz file.

__init__(filename, mode='r', force_overwrite=True)¶

Open a xyz file for reading/writing.

Methods

__init__(filename[, mode, force_overwrite])	Open a xyz file for reading/writing.
close()	Close the xyz file.
read([n_frames, stride, atom_indices])	Read data from a xyz file.
read_as_traj(topology[, n_frames, stride, ...])	Read a trajectory from a XYZ file
seek(offset[, whence])	Move to a new file position.
tell()	Current file position.
write(xyz[, types])	Write one or more frames of data to a xyz file.

Attributes

distance_unit

close()¶

Close the xyz file.

read(n_frames=None, stride=None, atom_indices=None)¶

Read data from a xyz file.

Parameters:	n_frames : int, None The number of frames you would like to read from the file. If None, all of the remaining frames will be loaded. stride : np.ndarray, optional Read only every stride-th frame. atom_indices : array_like, optional If not none, then read only a subset of the atoms coordinates from the file.
Returns:	xyz : np.ndarray, shape=(n_frames, n_atoms, 3), dtype=np.float32

read_as_traj(topology, n_frames=None, stride=None, atom_indices=None)¶

Read a trajectory from a XYZ file

Parameters:

topology : Topology The system topology n_frames : int, optional If positive, then read only the next n_frames frames. Otherwise read all of the frames in the file. stride : np.ndarray, optional Read only every stride-th frame. atom_indices : array_like, optional If not none, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it required an extra copy, but will save memory.

Returns:

trajectory : Trajectory A trajectory object containing the loaded portion of the file.

seek(offset, whence=0)¶

Move to a new file position.

Parameters:	offset : int A number of frames. whence : {0, 1, 2} 0: offset from start of file, offset should be >=0. 1: move relative to the current position, positive or negative 2: move relative to the end of file, offset should be <= 0. Seeking beyond the end of a file is not supported

tell()¶

Current file position.

Returns:	offset : int The current frame in the file.

write(xyz, types=None)¶

Write one or more frames of data to a xyz file.

Parameters:	xyz : np.ndarray, shape=(n_frames, n_atoms, 3) The cartesian coordinates of the atoms to write. By convention for this trajectory format, the lengths should be in units of angstroms. types : np.ndarray, shape(3, ) The type of each particle.