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simtk.openmm.app.charmmcrdfiles Namespace Reference

Classes

class  CharmmCrdFile
 Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc. More...
 
class  CharmmRstFile
 Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name 'fname' into class attributes. More...
 

Variables

int CHARMMLEN = 22
 
float TIMESCALE = 4.888821E-14
 
int ONE_TIMESCALE = 1
 

Detailed Description

Provides a class for parsing CHARMM-style coordinate files, namely CHARMM .crd

(coordinate) files and CHARMM .rst (restart) file. Uses CharmmFile class in

_charmmfile.py for reading files 



This file is part of the OpenMM molecular simulation toolkit originating from

Simbios, the NIH National Center for Physics-Based Simulation of Biological

Structures at Stanford, funded under the NIH Roadmap for Medical Research,

grant U54 GM072970. See https://simtk.org.  This code was originally part of

the ParmEd program and was ported for use with OpenMM.



Copyright (c) 2014 the Authors



Author: Jason Deckman

Contributors: Jason M. Swails

Date: June 6, 2014



Permission is hereby granted, free of charge, to any person obtaining a

copy of this software and associated documentation files (the "Software"),

to deal in the Software without restriction, including without limitation

the rights to use, copy, modify, merge, publish, distribute, sublicense,

and/or sell copies of the Software, and to permit persons to whom the

Software is furnished to do so, subject to the following conditions:



The above copyright notice and this permission notice shall be included in

all copies or substantial portions of the Software.



THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,

DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR

OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE

USE OR OTHER DEALINGS IN THE SOFTWARE.

Variable Documentation

int CHARMMLEN = 22
int ONE_TIMESCALE = 1
float TIMESCALE = 4.888821E-14