#!/usr/bin/env python

__author__ = "Randall J. Radmer"
__version__ = "1.0"
__doc__ = """Example script to test Nast."""


pdbInFilename		= "6TNA_C3.pdb"
pdbOutFilename		= "6TNA_C3-md.pdb"
helixFilename		= "6TNA_helix.txt"
contactsFilename	= "6TNA_contacts.txt"
numSteps		    = 10000
stepsPerReport		= 100
defaultTemperature	= 300.0
randomSeed		    = None
explosionDetection  = 10 # Numer of previous steps that explosion detection
                         # is based on. Set to False for no detection.
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,
             explosionDetection=explosionDetection,
             verbose=verbose)
print explosion_detected

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