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

close(self)¶: Close the .arc file

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

Read data from a TINKER .arc file.

Note that only the Cartesian coordinates are read in. The .arc file also contains TINKER-specific numeric atom types and some bonding information, which we do not read in.

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: The cartesian coordinates, in angstroms

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

Read a trajectory from a ARC file

Parameters

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.