CharmmRstFile

class simtk.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

int – Number of atoms in the system

resname

list – Names of all residues

positions

list – All cartesian coordinates [x1, y1, z1, x2, ...]

positionsold

list – Old cartesian coordinates

velocities

list – List of all cartesian velocities

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)

Methods

__init__(fname)
printcoords(crds)
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__
__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__