remarks file geomanal/distance_plot.inp -- Makes a matrix of all
remarks residue centroid to residue centroid distances.  The
remarks matrix can be interpreted by Mathematica. 

{===>}                                               {*Read structure file.*}
structure @../generate/generate.psf end 
 
{===>}                                                  {*Read coordinates.*}
coordinates @../xtalrefine/slowcool.pdb    

{===>} 
vector ident (store9) ( tag )              {*This selects all residues to  *}
                                           {*be analyzed.   Change it      *}
                                           {*to analyze portions,          *}
                                           {*e.g.,  ( tag and segid "A" ). *}
                                           {*"tag" assigns one unique atom *}
                                           {*per residue (see <selection>).*}
                 
parameter
{===>}  
   @TOPPAR:parhcsdx.pro                 {*Read empirical energy parameters.*}
end

set message off echo off end                     {*This reduces the output.*}
set abort off end


{====>}
set display distance_plot.matrix end              {*Filename of the matrix.*}

display  matrix={


evaluate ($count1=0)
for $id1 in id ( tag ) loop id1
   if ($count1=0) then
      display  {
   else
      display ,{
   end if
   evaluate ($count1=$count1+1)

   evaluate ($count2=0)
   for $id2 in id ( tag ) loop id2

  {*The following statement computes the distance between the mass-weighted*}
  {*centroids of the two residues.                                         *}
      pick bond 
        (byresidue ( id $id1)) (byresidue ( id $id2)) geometry

      evaluate ($distance=$result) 

      if ($count2=0) then
         display  $distance 
      else
         display , $distance
      end if
      evaluate ($count2=$count2+1)

   end loop id2
   display } 
end loop id1

display };


stop