#!/usr/bin/env python

__author__ = "Magdalena A. Jonikas"
__version__ = "2.0"
__doc__ = """Example script to run a Nast simulation for tRNA."""

pdbInFilename		= "6TNA_C3.pdb" # Change to 6TNA.seq to start 
                                    # from unfolded circle
pdbOutFilename		= "6TNA-MD.pdb"
helixFilename		= "6TNA_helix.txt"
contactsFilename	= "6TNA_contacts.txt"
numSteps		    = 200000
stepsPerReport		= 1000
defaultTemperature	= 300.0
randomSeed		    = None
verbose			    = True

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

lastPdbOut = open('%s-last.pdb' % pdbOutFilename[:-4], 'w')
lastPdbOut.writelines(lastPdb)