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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

velocities

Referenced by AmberInpcrdFile.getVelocities().

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

- charmmcrdfiles.py