// ############################## START FUNC ############################################
// This function sorts the neighbour for each atom with heavy neighbours and neigbours
// with many connections first.

  // Integers:                  n,q
  // Strings:                   temp
  // Floating numbers:          thjalp
  // String matrix:             temp_int_array
  // Integer matrix:            atom_sorts, atom_connections

function sort_connections(atom_connections, atom_sorts)
{
     var number_of_atoms = atom_sorts.length;
     var n=0;
     var q=0;
     var temp="";
     var temp_int_array=new Array(0);
// ************ START LOOP (n) BELOW *********************
  for(n=0;n<number_of_atoms;n++){
  temp_int_array=new Array(atom_connections[n].length);
if(atom_connections[n]=="") alert("The atom "+n+" seems to have no connections. Please increase the covalent radii or the factor.");
      for(q=0;q<atom_connections[n].length;q++){
      thjalp=atom_sorts[atom_connections[n][q]]/100+atom_connections[[atom_connections[n][q]]].length/1000;
      // The substring part below should not be needed
      temp=thjalp+"";
      temp_int_array[q]=temp.substring(0,5)+" "+atom_connections[n][q];
      }
    temp_int_array=temp_int_array.sort();
    temp_int_array=temp_int_array.reverse();
    // ************ One row loop ***************
    for(q=0;q<temp_int_array.length;q++)     temp_int_array[q]=parseInt(temp_int_array[q].substring(6,temp_int_array[q].length));
    // ************ End one row loop ***********
    // ************ One row loop ***************
    for(q=0;q<temp_int_array.length;q++) atom_connections[n][q]=temp_int_array[q];
    // ************ End one row loop ***********
  }
// ************ END OF LOOP (n) ABOVE ********************

     return atom_connections;
}
// ############################### end func ############################################