// ############################## START FUNC ############################################
// The connection table is made up separately for best possible overview
  // Integers:                  n,m, number_of_atoms, temp_int   
  // Floating number matrix:    distance_matrix, atom_radii_matrix
  // Integer matrix:            atom_sorts, connection_table_matrix

function intra_molecular_connections(atom_sorts, distance_matrix, atom_radii_matrix)
{

     var temp_int=0;
     var number_of_atoms = atom_sorts.length;

// This command creates a number_of_atoms*number_of_atoms matrix with bond markers
     var connection_table_matrix = def_matrix(number_of_atoms, number_of_atoms, 0, "undefined");

// Also, secondary connections can be introduced
// ************ START LOOP (n) BELOW *********************
       for(n=0;n<number_of_atoms;n++){
// ************ START LOOP (m) BELOW *********************
         for(m=0;m<number_of_atoms;m++){
         temp_int=0;
// It had been even faster to copy m,n=1 from n,m=1, but this looks clean and nice
// ************ If - START ********************
           if(distance_matrix[n][m]<(atom_radii_matrix[atom_sorts[n]][1]+atom_radii_matrix[atom_sorts[m]][1])){
           temp_int=1;
           }
// ************ If - END ********************
// Somewhat inefficient to calculate "n=m" first, but it renders a shorter expression
           if(n==m) temp_int=0;
         connection_table_matrix[n][m]=temp_int;
         }
// ************ END OF LOOP (m) ABOVE ********************
       }
// ************ END OF LOOP (n) ABOVE ********************

return connection_table_matrix;

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