#!/bin/bash 
set -x

rm *.dat

  #Run curves on generated trajectory
  #./curves.bash
  
  #Run canal on generated curves info for 12 base-pair 
 # ./canal-base_pairs.bash

  #Run canal on generated curves info for the overall structure
#  ./canal-overall.bash

  #Generate data file 
  for bp in {1..14}
  do
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_shear.ser 2 line >> shear.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_stretch.ser 2 line >> stretch.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_stagger.ser 2 line >> stagger.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_buckle.ser 2 line >> buckle.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_propel.ser 2 line >> propel.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_opening.ser 2 line >> opening.dat

       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_shift.ser 2 line >> shift.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_slide.ser 2 line >> slide.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_rise.ser 2 line >> rise.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_xdisp.ser 2 line >> xdisp.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_ydisp.ser 2 line >> ydisp.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_tilt.ser 2 line >> tilt.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_roll.ser 2 line >> roll.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_twist.ser 2 line >> twist.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_inclin.ser 2 line >> inclin.dat

       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_majw.ser 2 line >> majw.dat
       ~/scripts/avg.sh $bp.basepair/$bp.cn_out_minw.ser 2 line >> minw.dat

    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_tip.ser 2 line >> tip.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_ax-bend.ser 2 line >> ax-bend.dat

    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_alphaC.ser 2 line >> alphaC.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_alphaW.ser 2 line >> alphaW.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_betaC.ser 2 line >> betaC.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_betaW.ser 2 line >> betaW.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_gammaC.ser 2 line >> gammaC.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_gammaW.ser 2 line >> gammaW.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_deltaC.ser 2 line >> deltaC.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_deltaW.ser 2 line >> deltaW.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_epsilC.ser 2 line >> epsilC.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_epsilW.ser 2 line >> epsilW.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_zetaC.ser 2 line >> zetaC.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_zetaW.ser 2 line >> zetaW.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_chiC.ser 2 line >> chiC.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_chiW.ser 2 line >> chiW.dat

    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_phaseC.ser 2 line >> phaseC.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_phaseW.ser 2 line >> phaseW.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_ampC.ser 2 line >> ampC.dat
    ~/scripts/avg.sh $bp.basepair/$bp.cn_out_ampW.ser 2 line >> ampW.dat
  done

done