mdtraj.formats.ArcTrajectoryFile

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

Interface for reading and writing to an TINKER archive files. (Note that the TINKER .xyz format is identical to this.) 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.

The conventional units in the arc file is angstrom. The format only supports storing the cartesian coordinates and box lengths.

Parameters

filenamepath-like

The filename to open. A path to a file on disk.

mode{‘r’}

The mode in which to open the file, only ‘r’ for read is supported.

force_overwritebool

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

Attributes

topologyTopology

A single-chain, single-residue topology generated from the atom and bond information found in the TINKER archive/xyz file. It is only generated from the first member of the archive

Methods

close()	Close the .arc file
read([n_frames, stride, atom_indices])	Read data from a TINKER .arc file.
read_as_traj([n_frames, stride, atom_indices])	Read a trajectory from a ARC file
seek(offset[, whence])	Move to a new file position
tell()	Current file position
write(xyz)	The ArcTrajectoryFile does not have a write method, because TINKER .arc files have special numerical atom types which are not shared by any other trajectory file format.

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

Open an TINKER.arc file for reading/writing.

Methods

__init__(filename[, mode, force_overwrite])	Open an TINKER.arc file for reading/writing.
close()	Close the .arc file
read([n_frames, stride, atom_indices])	Read data from a TINKER .arc file.
read_as_traj([n_frames, stride, atom_indices])	Read a trajectory from a ARC file
seek(offset[, whence])	Move to a new file position
tell()	Current file position
write(xyz)	The ArcTrajectoryFile does not have a write method, because TINKER .arc files have special numerical atom types which are not shared by any other trajectory file format.

Attributes

distance_unit