mdtraj.formats.AmberRestartFile¶

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

Interface for reading and writing AMBER ASCII restart files. This is a file-like object, that supports both reading and writing depending on the mode flag. It implements the context manager protocol, so you can also use it with the python ‘with’ statement.

Parameters:	filename : str The name of the file to open mode : {‘r’, ‘w’}, default=’r’ The mode in which to open the file. Valid options are ‘r’ or ‘w’ for ‘read’ or ‘write’ force_overwrite : bool, default=False In write mode, if a file named filename already exists, clobber it and overwrite it

See also

md.AmberNetCDFRestartFile

Low level interface to AMBER NetCDF-format

restart

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

Methods

__init__(filename[, mode, force_overwrite])
close()
read([atom_indices])	Read data from an AMBER ASCII restart file
read_as_traj(topology[, atom_indices])	Read an AMBER ASCII restart file as a trajectory.
write(coordinates[, time, cell_lengths, ...])	Write one frame of a MD trajectory to disk in the AMBER ASCII restart file format.

Attributes

distance_unit
n_atoms
n_frames

read_as_traj(topology, atom_indices=None)¶

Read an AMBER ASCII restart file as a trajectory.

Parameters:	topology : Topology The system topology 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 with 1 frame created from the file.

read(atom_indices=None)¶

Read data from an AMBER ASCII restart file

Parameters:

atom_indices : np.ndarray, dtype=int, optional The specific indices of the atoms you’d like to retrieve. If not supplied, all of the atoms will be retrieved.

Returns:

coordinates : np.ndarray, shape=(1, n_atoms, 3) The cartesian coordinates of the atoms, in units of angstroms. These files only ever contain 1 frame time : np.ndarray, None The time corresponding to the frame, in units of picoseconds, or None if no time information is present cell_lengths : np.ndarray, None The lengths (a, b, c) of the unit cell for the frame in angstroms, or None if the information is not present in the file cell_angles : np.ndarray, None The angles (lpha, eta, gamma) defining the unit cell for each frame, or None if the information is not present in the file.

write(coordinates, time=None, cell_lengths=None, cell_angles=None)¶

Write one frame of a MD trajectory to disk in the AMBER ASCII restart file format.

Parameters:

coordinates : np.ndarray, dtype=np.float32, shape=([1,] n_atoms, 3) The cartesian coordinates of each atom, in units of angstroms. Must be only a single frame (shape can be (1,N,3) or (N,3) where N is the number of atoms) time : array-like with 1 element or float, optional The time corresponding to this frame. If not specified, a place holder of 0 will be written cell_lengths : np.ndarray, dtype=np.double, shape=([1,] 3) The lengths (a,b,c) of the unit cell for the frame in Angstroms cell_angles : np.ndarray, dtype=np.double, shape=([1,] 3) The angles between the unit cell vectors for the frame in Degrees