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

filenamestr

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_overwritebool

If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?

Methods

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

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

Open a xyz file for reading/writing.

Methods

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

Attributes

distance_unit

close(self)

Close the xyz file.

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

Read data from a xyz file.

Parameters

n_framesint, None

The number of frames you would like to read from the file. If None, all of the remaining frames will be loaded.

stridenp.ndarray, optional

Read only every stride-th frame.

atom_indicesarray_like, optional

If not none, then read only a subset of the atoms coordinates from the file.

Returns

xyznp.ndarray, shape=(n_frames, n_atoms, 3), dtype=np.float32

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

Read a trajectory from a XYZ file

Parameters

topologyTopology

The system topology

n_framesint, optional

If positive, then read only the next n_frames frames. Otherwise read all of the frames in the file.

stridenp.ndarray, optional

Read only every stride-th frame.

atom_indicesarray_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

trajectoryTrajectory

A trajectory object containing the loaded portion of the file.

seek(self, offset, whence=0)

Move to a new file position.

Parameters

offsetint

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(self)

Current file position.

Returns

offsetint

The current frame in the file.

write(self, xyz, types=None)

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

Parameters

xyznp.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.

typesnp.ndarray, shape(3, )

The type of each particle.