parmed.charmm.CharmmRstFile

class parmed.charmm.CharmmRstFile(fname)[source]

Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name ‘fname’ into class attributes

Parameters:

fname : str

Name of the restart file to parse

Attributes

velocities Atomic velocities in Angstroms/picoseconds
positions Atomic positions with units
positionsold Old atomic positions with units
natom (int) Number of atoms in the system
resname (list of str) Names of all residues in the system
coordinates (np.ndarray shape(1, natom, 3)) List of all coordinates in the format [x1, y1, z1, x2, y2, z2, ...]
coordinatesold (np.ndarray shape(1, natom, 3)) List of all old coordinates in the format [x1, y1, z1, x2, y2, z2, ...]

Methods

id_format(filename) Identifies the file type as a CHARMM restart file
scan(handle, str[, r])
__init__(fname)[source]

Methods

__init__(fname)
id_format(filename) Identifies the file type as a CHARMM restart file
scan(handle, str[, r])

Attributes

box
coordinates
coordinatesold
positions Atomic positions with units
positionsold Old atomic positions with units
velocities Atomic velocities in Angstroms/picoseconds
static id_format(filename)[source]

Identifies the file type as a CHARMM restart file

Parameters:

filename : str

Name of the file to check format for

Returns:

is_fmt : bool

True if it is a CHARMM restart file

positions

Atomic positions with units

positionsold

Old atomic positions with units

velocities

Atomic velocities in Angstroms/picoseconds