#  Run genearate_grid_edm2 program for all the proteins
#      which is listed in ../thinParam/proteinGridList
#      Also generate the thinParam file by calling the generate_thinParam script
# Input list file format:  PDBname  MinX(xOffset)  MaxX  MinY(yOffset)  MaxY  MinZ(zOffset)  MaxZ

set resIdx = "1"         #resolution index, resIdx/10 is the real resolution if resdIdx>3
                         #For undefined resolution/density, go down to modify directly
set denIdx = "07"      #For thinParam only. threshold density index denIdx/10 is the real density threshold

set proteinSuffix =   "."$resIdx".grid"   #suffix for output grid protein file
set thinParamSuffix = "."$resIdx"."$denIdx   #suffix for thinParam file
set grid = "/cis/msa1/hongzhi/thinParam/proteinGridList"   #proteinGridList file
set outDir = "/cis/msa1/hongzhi/grid/"  #output dir
set thinDir = "/cis/msa1/hongzhi/thinParam/"  #thinParam output dir

set resolution = $resIdx     #calculate resolution from $resIdx
if ($resIdx > 3) then
  set resolution = "0."$resIdx
endif

echo Generate $resolution resolution grid of proteins listed 
echo in $grid

set counter = 0   #counter each line of input
set list = ( 1 2 3 4 5 6 7 ) 
foreach x  (`cat $grid`)
  @ counter = $counter + 1
  set list[$counter] = $x 
  #echo $list[$counter]
  if ($counter == 7 ) then
    set pro = "/cis/msa2/ableson/index/"$list[1]"p.pro"   #index file
    set out = $outDir$list[1]$proteinSuffix  #output file
    set thinout = $thinDir$list[1]$thinParamSuffix  #out of thinParam
    echo  ~~~~~~~~~~~~~~~~Start of $list[1]$proteinSuffix ~~~~~~~~~~~~~~~~~
      /cis/msa2/ableson/msa/src/generate_grid_edm2 $pro $list[2] $list[3] $list[4] $list[5] $list[6] $list[7] $resolution $out 

      if (-e $thinout) then
        rm $thinout
      endif
      echo ThinParam file saved to $thinout
      generate_thinParam $list[1] $resIdx $denIdx $list[2] $list[4] $list[6] > $thinout

    echo  ~~~~~~~~~~~~~~~~End of $list[1]$proteinSuffix ~~~~~~~~~~~~~~~~~~~
    echo
    echo
  endif   
  @ counter = $counter % 7
end