mdtraj.formats.BINPOSTrajectoryFile¶

class mdtraj.formats.BINPOSTrajectoryFile(filename, mode='r', force_overwrite=True, **kwargs)¶

Interface for reading and writing to an AMBER BINPOS file. 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 BINPOS file are angstroms. The format only supports storing the cartesian coordinates.

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?

Other Parameters:

min_chunk_size : int, default=100

BINPOS, In read mode, we need to allocate a buffer in which to store the data without knowing how many frames are in the file. This parameter is the minimum size of the buffer to allocate.

chunk_size_multiplier : int, default=1.5

In read mode, we need to allocate a buffer in which to store the data without knowing how many frames are in the file. We can guess this information based on the size of the file on disk, but it’s not perfect. This parameter inflates the guess by a multiplicative factor.

See also

mdtraj.load_binpos: High-level wrapper that returns a md.Trajectory

Examples

>>> # copy data from one file to another
>>> with BINPOSTrajectoryFile('traj.binpos') as f:
>>>     xyz = f.read()
>>> with BINPOSTrajectoryFile('out.binpos') as f:
>>>    f.write(xyz)

Attributes

distance_unit

Methods

`close`	Close the BINPOS file
`read`([n_frames, stride, atom_indices])	Read data from a BINPOS file
`read_as_traj`(topology[, n_frames, stride, ...])	Read a trajectory from a BINPOS file
`seek`(offset[, whence])	Move to a new file position
`tell`	Current file position
`write`(xyz)	Write cartesian coordinates to a binpos file

__init__()¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`close`	Close the BINPOS file
`read`([n_frames, stride, atom_indices])	Read data from a BINPOS file
`read_as_traj`(topology[, n_frames, stride, ...])	Read a trajectory from a BINPOS file
`seek`(offset[, whence])	Move to a new file position
`tell`	Current file position
`write`(xyz)	Write cartesian coordinates to a binpos file

Attributes

distance_unit

close()¶: Close the BINPOS file

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

Read data from a BINPOS 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. This may be slightly slower than the standard read because it required an extra copy, but will save memory.

Returns:

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

The cartesian coordinates, in angstroms

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

Read a trajectory from a BINPOS file

Parameters:

topology : Topology

The system topology

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 : int, 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.