parmed.charmm.CharmmRstFile

class parmed.charmm.CharmmRstFile(fname)

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

Parameters

fnamestr

Name of the restart file to parse

Attributes

natomint

Number of atoms in the system

resnamelist of str

Names of all residues in the system

coordinatesnp.ndarray shape(1, natom, 3)

List of all coordinates in the format [x1, y1, z1, x2, y2, z2, …]

coordinatesoldnp.ndarray shape(1, natom, 3)

List of all old coordinates in the format [x1, y1, z1, x2, y2, z2, …]

velocitiesnp.ndarray shape(1, natom, 3)

Atomic velocities in Angstroms/picoseconds

positionsnatom x 3 distance Quantity

Atomic positions with units

positionsoldnatom x 3 distance Quantity

Old atomic positions with units

Methods

id_format(filename)

Identifies the file type as a CHARMM restart file

scan

__init__(fname)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(fname)	Initialize self.
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