__author__ = "Magdalena A. Jonikas"
__version__ = "1.0"
__doc__ = """Script to run second part of c2a calcs (assemble molecules)."""


import sys, time
import simtk.c2a.c2a_assembleOptions as ao

t0 = time.time()
ao.assemble(fragIn = '6TNA-FD.txt',
            coarseIn = '6TNA-A-1.pdb',
            centerAtoms = ["C3'"],
            pieceLib = open('6TNA-A-1-1N32-0-lib.pkl'),
            outName = 'test-6TNA-A-1',
            n = 1,
            cutoff = 0.5
           )

sys.stdout.write("Total run time: %.1f Sec\n" % (time.time()-t0))