CharmmRstFile

class openmm.app.charmmcrdfiles.CharmmRstFile(fname)

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

natom

Number of atoms in the system

Type

int

resname

Names of all residues

Type

list

positions

All cartesian coordinates [x1, y1, z1, x2, …]

Type

list

positionsold

Old cartesian coordinates

Type

list

velocities

List of all cartesian velocities

Type

list

Examples

>>> chm = CharmmRstFile('testfiles/sample-charmm.rst')
>>> print chm.header[0]
REST    37     1
>>> natom, nc, nco = chm.natom, len(chm.positions), len(chm.positionsold)
>>> nv = len(chm.velocities)
>>> print '%d atoms; %d crds; %d old crds; %d vels' % (natom, nc, nco, nv)
256 atoms; 256 crds; 256 old crds; 256 vels

__init__(fname)

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

Methods

__init__(fname)	Initialize self.
printcoords(crds)