#!/usr/bin/env python

__author__ = "Magdalena A. Jonikas"
__version__ = "1.0"
__date__ = "2010-05-22"
__doc__ = """Example script to test Nast random unfold algorithm."""

import sys
if len(sys.argv)>1: name = '-%s' % sys.argv[1]
else: name = ''

seqInName  		    = "6TNA.seq"
pdbOutName          = "6TNA-RU%s" % name
helixFilename		= "6TNA_helix.txt"
numSteps		    = 20000 
stepsPerReport		= 1000
defaultTemperature	= 300.0
randomSeed		    = None
verbose			    = True
movieOut            = "6TNA-RU%s" % name # Set to None for no movie trace
autoStepBack        = True # Set to False to quit when error is encountered
preferredPlatformName='Reference'
#preferredPlatformName=None

import simtk.nast.molecule as molecule
molecule.runRandomUnfold(seqInName=seqInName,
             pdbOutName=pdbOutName,
             helixFilename=helixFilename,
             numSteps=numSteps,
             stepsPerReport=stepsPerReport,
             defaultTemperature=defaultTemperature,
             randomSeed=randomSeed,
             verbose=verbose,
             autoStepBack=autoStepBack,
             preferredPlatformName=preferredPlatformName,
             movieOut=movieOut)