#!/usr/bin/env python

__author__ = "Randall J. Radmer"
__version__ = "1.0"
__doc__ = """Example script to run a Nast simulation for tRNA."""

pdbInFilename		= "SCL_MFE.seq"
pdbOutFilename		= "SCL_MFE.pdb"
#helixFilename		= "SCL_MFE-helix.txt"
helixFilename		= ""
contactsFilename	= ""
numSteps		    = 500
stepsPerReport		= 10
defaultTemperature	= 300
randomSeed		    = None
verbose			    = True

import simtk.nast.molecule as molecule
molecule.run(pdbInFilename=pdbInFilename,
             pdbOutFilename=pdbOutFilename,
             helixFilename=helixFilename,
             contactsFilename=contactsFilename,
             numSteps=numSteps,
             stepsPerReport=stepsPerReport,
             defaultTemperature=defaultTemperature,
             randomSeed=randomSeed,
             verbose=verbose)