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
filenamestr

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(self)

Close the .arc file

read(self[, n_frames, stride, atom_indices])

Read data from a TINKER .arc file.

read_as_traj(self[, n_frames, stride, …])

Read a trajectory from a ARC file

seek(self, offset[, whence])

Move to a new file position

tell(self)

Current file position

write(self, 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__(self, filename, mode='r', force_overwrite=True)

Open an TINKER.arc file for reading/writing.

Methods

__init__(self, filename[, mode, force_overwrite])

Open an TINKER.arc file for reading/writing.

close(self)

Close the .arc file

read(self[, n_frames, stride, atom_indices])

Read data from a TINKER .arc file.

read_as_traj(self[, n_frames, stride, …])

Read a trajectory from a ARC file

seek(self, offset[, whence])

Move to a new file position

tell(self)

Current file position

write(self, 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