// ############################## START FUNC ############################################
// 

function single_molecule()
{

var molecule=document.form1.mName.value;

parent.right.ute1.location="intervalspec.txt";
parent.right.ute2.location="file_list.txt";
parent.right.ute3.location="feature_list.txt";

window.setTimeout(function(){mega1(molecule);},300);

// The thread will be passed to mega1 for parameters and then to single_molecule_continue.

}

// ############################### end func ############################################


// ############################## START FUNC ############################################
// 

function single_molecule_continue(f_ligands,f_ex,angle_intervals,dist_intervals,groups,molecule,g_commands)
{

var feature_rep="";
var bit_string="";
var convert=document.form1.cb.checked;
var tupp=new Array(0);

   if(verify_frame_content(2)){
   transfer_and_mod(2, f_ex);
   over_all2(f_ex,angle_intervals,dist_intervals,groups, g_commands);
   bit_string=read(1,1000000,1,1);
   }
   else{

     if(verify_frame_content(3)){
     transfer(3);
     over_all1();
       feature_rep = document.form1.text1.value
     transfer_and_mod(100, f_ex);
     over_all2(f_ex,angle_intervals,dist_intervals,groups, g_commands);
       bit_string=read(1,1000000,1,1);
     }
     else{
     alert("No basic or feature files on: "+files[g_commands[3]]);  
     }
   }


  if(convert){
    for(n=0;n<f_ex.length;n++){
    tupp=feature_rep.split(" "+f_ex[n][1]+"  ");
    saved=tupp.join(" "+f_ex[n][0]+"  ");
    }
  }

  feature_rep="<html><pre>"+feature_rep+"\n\n\n</pre></html>";
  parent.right.document.write(feature_rep);

}

// ############################### end func ############################################