CharmmRstFile Class Reference

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

Inheritance diagram for CharmmRstFile:

Public Member Functions
def	__init__
def	printcoords

Public Attributes
	header
	title
	enrgstat
	positionsold
	positions
	velocities
	ff_version
	natom
	npriv
	nstep
	nsavc
	nsavv
	jhstrt

Detailed Description

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

Main 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

Example:

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

Constructor & Destructor Documentation

def __init__	(		self,
			fname
	)

Member Function Documentation

def printcoords	(		self,
			crds
	)

Member Data Documentation

enrgstat

ff_version

header

jhstrt

natom

npriv

nsavc

nsavv

nstep

positions

Referenced by Modeller.add(), Modeller.addExtraParticles(), Modeller.addHydrogens(), Modeller.addSolvent(), Modeller.convertWater(), Modeller.delete(), Modeller.getPositions(), AmberInpcrdFile.getPositions(), and DesmondDMSFile.getPositions().

positionsold

title

Referenced by CharmmPsfFile.writePsf().

velocities

Referenced by AmberInpcrdFile.getVelocities().

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The documentation for this class was generated from the following file:

• charmmcrdfiles.py