// ############################## START FUNC ############################################
// This function remove missed ring duplicates and fat_group multiplicates dependent of
// several end points. Halogens are also set. It would be a pity to have the feature routine 
// handling that. Double- or triplebonds which are not cis- or trans- are set here.

function complete(sumstring, atom_sorts, d_conn, x, y, z, arom_atoms)
{

   var number_of_atoms=atom_sorts.length;
   var au=sumstring.split("#");
   var saml="";
   var prefix="";
   var sx=0;
   var sy=0;
   var sz=0;
   var n=0;
   var m=0;
   var r_matrix=new Array(0);   // Later 2 dimension
   var xl=0;
   var yl=0;
   var zl=0;
   var dist=0;

// Remove duplicates

       for(n=0;n<au.length;n++){
        if(saml.indexOf(au[n])==-1) saml=saml+au[n]+"#";
       }

// This removes most of it. In case of small decimal deviations and "complex" groups
// one last routine is necessary It is done last, although it put some extra work on
// the program.

// It must be the user who with his choise of further group settings determine who similar these
// atoms are
for(n=0;n<number_of_atoms;n++){
if(atom_sorts[n]==9) saml=saml+" fluorine  "+x[n]+" "+y[n]+" "+z[n]+"#";
if(atom_sorts[n]==17) saml=saml+" chlorine  "+x[n]+" "+y[n]+" "+z[n]+"#";
if(atom_sorts[n]==35) saml=saml+" bromine  "+x[n]+" "+y[n]+" "+z[n]+"#";
if(atom_sorts[n]==53) saml=saml+" iodide  "+x[n]+" "+y[n]+" "+z[n]+"#";

if(d_conn[n]!=""){
opp=parseInt(d_conn[n].substring(2,d_conn[n].length));
if(atom_sorts[n]!=6 || atom_sorts[opp]!=6) continue;
// Double bonds in functional groups counts not separate.
   if(d_conn[n].indexOf("s")>-1) prefix=" =C=  ";
   if(d_conn[n].indexOf("d")>-1) prefix=" double_bond  ";
   if(d_conn[n].indexOf("t")>-1) prefix=" triple_bond  ";

 if(prefix!=" =C=  "){
  if(d_conn[opp].indexOf("s")>-1) continue;   // =C= are set at the central carbon
  if(n<opp) continue;                         // count every double- or triplebond only once
  if(arom_atoms.indexOf(" "+n+" ")!=-1) continue;  // In aromatic rings with amines, db should not be set
  sx=(parseFloat(x[n]+x[opp])+parseFloat(x[n]+x[opp]))/2;
  sy=(parseFloat(y[n]+y[opp])+parseFloat(y[n]+y[opp]))/2;
  sz=(parseFloat(z[n]+z[opp])+parseFloat(z[n]+z[opp]))/2;
  saml=saml+prefix+sx+" "+sy+" "+sz+"#";
 }
 else{
 saml=saml+prefix+x[n]+" "+y[n]+" "+z[n]+"#";
// Chirality according to =C= structures are so rare that such features are not revealed or treated
// The solution would be to fallow the =C= paths like it has been done for multiple bonds and count
// priority for connected branches in the chirality function.
 }
}

}

   saml=saml.substring(0,saml.length-1);

// The last removance of duplicates

     au=saml.split("#");
     saml="";
             r_matrix=new Array(au.length);
             for(n=0;n<au.length;n++) r_matrix[n]=au[n].split(" ");

// Because the format is name__x_y_z r_matrix[n][1] will be empty for the _-pair

     for(n=0;n<au.length;n++){
      if(au[n]=="") continue;
     for(m=0;m<n;m++){
        if(au[m]=="") continue;
       xl=r_matrix[n][2]-r_matrix[m][2];
       yl=r_matrix[n][3]-r_matrix[m][3];
       zl=r_matrix[n][4]-r_matrix[m][4];
       dist=Math.sqrt(xl*xl+yl*yl+zl*zl);
        if(dist<0.5){
         if(r_matrix[n][0]==r_matrix[m][0]) au[m]="";   // Remove "almost exact" duplicate
         if(r_matrix[n][0].indexOf("Compl_")!=-1) au[m]=="";  // Remove ring/electroneg complex against Complex
         if(r_matrix[m][0].indexOf("Compl_")!=-1) au[n]=="";  // Remove ring/electroneg complex against Complex
        }
     }       // m-loop ends
     }       // n-loop ends

saml=au.join("#");
saml=saml.replace(/#+/g,"#");    // Erases multiple "#" in the middle of the string
if(saml.charAt(0)=="#") saml=saml.substring(1,saml.length);
if(saml.charAt(saml.length-1)=="#") saml=saml.substring(0,saml.length-1);

return saml;

}

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