mdtraj.formats.MDCRDTrajectoryFile

class mdtraj.formats.MDCRDTrajectoryFile(filename, n_atoms=None, mode='r', has_box='detect', force_overwrite=True)

Interface for reading and writing to an AMBER mdcrd 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.

The conventional units in the mdcrd file are angstroms. The format only supports storing the cartesian coordinates and box lengths.

Parameters
filenamestr

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

n_atomsint

The number of atoms in the system. This is _required_ when mode == ‘r’ and irrelevant when mode == ‘w’.

mode{‘r’, ‘w’}

The mode in which to open the file, either ‘r’ for read or ‘w’ for write.

has_box = ‘detect’

Does the mdcrd file contain box length information? This is optional when mode == ‘r’ (and irrelevant when mode == ‘w’). The presence or absence of box information can generally be inferred from the file, but there might be corner cases in which this is not possible, because of limitations in the mdcrd format.

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 mdcrd file

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

Read data from a mdcrd file

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

Read a trajectory from a mdcrd file

seek(self, offset[, whence])

Move to a new file position

tell(self)

Current file position

write(self, xyz[, cell_lengths])

Write one or more frames of data to a mdcrd file

__init__(self, filename, n_atoms=None, mode='r', has_box='detect', force_overwrite=True)

Open an AMBER mdcrd file for reading/writing.

Methods

__init__(self, filename[, n_atoms, mode, …])

Open an AMBER mdcrd file for reading/writing.

close(self)

Close the mdcrd file

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

Read data from a mdcrd file

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

Read a trajectory from a mdcrd file

seek(self, offset[, whence])

Move to a new file position

tell(self)

Current file position

write(self, xyz[, cell_lengths])

Write one or more frames of data to a mdcrd file

Attributes

distance_unit