// ############################## START FUNC ############################################
function over_all1()
{
// #########################################
 
     var covalent_radii = new Array(0);  // N*4 matrix
covalent_radii = set_radii_matrix(1.3);

     var atom_sorts = new Array(0);
     var x = new Array(0);
     var y = new Array(0);
     var z = new Array(0);

var atom_sorts=read(1,1000000,1,1);
x=read(1,1000000,2,2);
y=read(1,1000000,3,3);
z=read(1,1000000,4,4);

     var sumstring = mass_point(atom_sorts,x,y,z);
     var helpv=new Array(0);
     helpv=sumstring.split("&&");
     sumstring=helpv[0];
     var MW=parseInt(helpv[1]);

     var dist_table = new Array(0);
dist_table= intra_molecular_distances(atom_sorts, x,y,z);

     var con_table = new Array(0);
con_table=intra_molecular_connections(atom_sorts, dist_table, covalent_radii);

     var connections = neighbours(con_table);
connections=sort_connections(connections, atom_sorts);

     var branch4 = new List(4, connections, atom_sorts);
     var branch3 = new List(3, connections, atom_sorts);
     var allcarbon = new List("carbon4", connections, atom_sorts);
     var branchlist = new List("branch", connections, atom_sorts);
     var pot_ring_atom = new List(2, connections, atom_sorts);
     var poschir = new List("chir", connections, atom_sorts);
     var double_bond_atoms = new List("double", connections, atom_sorts);
     var triple_bond_atoms = new List("triple", connections, atom_sorts);
     var carbonyle_atoms = new List("carbonyle", connections, atom_sorts);
     var fattyends = new List("ends", connections, atom_sorts);
     var conj_end = new List("cunjugate_end", connections, atom_sorts);
     var branchstop= new List("branch3", connections, atom_sorts);

     var n_two_bond_atoms = pot_ring_atom.Span();
// If there are no branches in the molecule one pot_ring_atom is added as start
// atom for ring calculations
     if(branchlist.Span()==0) branchlist.l[pot_ring_atom.First()]=true;
// ... branchlist.Add(pot_ring_atom.First());   does not work - unbelivible

// multibonds is a vector. Note that branch eyes MAY (unlikely) create duplicates on som atoms.
     var multibonds = d_t_bonds(conj_end, connections, atom_sorts, double_bond_atoms, triple_bond_atoms, branchstop);
     multibonds = determine_muliple_bonds(multibonds, atom_sorts, double_bond_atoms, triple_bond_atoms);

     var ringcollection = rings(x.length, branchlist, connections);
     var a_list="";
     var red_list="";
     var ringatoms="";
if(ringcollection!=""){
ringcollection=clear_rings(ringcollection);
ringatoms=ringcollection;
helpv=ringatoms.split("#");
ringatoms=" "+helpv.join(" ")+" ";
ringcollection = calculate_ring_centra(ringcollection, x, y, z, atom_sorts, double_bond_atoms, triple_bond_atoms, multibonds);
helpv=ringcollection.split("?");
     if(helpv.length>1) a_list=helpv[1];
     if(helpv.length>1) red_list=ar_red(a_list);
sumstring=sumstring+helpv[0]+"#";
// Suddenly it does not work to retrieve 2 values from one function and the ugly
// split above is necessary
}

     var chirmax=prepare_chir(atom_sorts, connections, poschir);
chirmax=chirmax+2;
// Necessary because
// 1) function "chirality" starts from the chiral atom, not its neighbour.
// 2) Because double bonds are marked after the development out to another neighbour.

// The +"#" undo the final action in the subroutines, but creates clean output.

     var chirstring= chirality(poschir, branch3, branch4, double_bond_atoms, triple_bond_atoms, connections, n_two_bond_atoms, atom_sorts, multibonds, chirmax);
if(chirstring!=""){
chirstring=substitute(chirstring, atom_sorts);
     // Here cis- trans- paths can be extracted
          multibonds,c_t_string = cis_trans(multibonds, chirstring, atom_sorts, connections, x, y, z,a_list);
     // multibonds must be first. JavaScript seems to fail with an vector last
      if(c_t_string!="") sumstring=sumstring+c_t_string+"#";
 chirstring = dim3mak(chirstring, poschir, atom_sorts, connections, x, y, z, allcarbon);
if(chirstring!="") sumstring=sumstring+chirstring+"#";  // (new chirstring)
}

// ******************** New List Object ************************
     var fatty = new List("fat", connections, atom_sorts, ringatoms);
// *************************************************************

     var features = groups(atom_sorts, carbonyle_atoms, connections, double_bond_atoms, fattyends, fatty, x,y,z, a_list, ringatoms, red_list);
if(features!=""){
features = recognize_features(features,MW);
sumstring=sumstring+features+"#";
}

// Does finally remove duplets and put some simple functional groups in
sumstring=complete(sumstring, atom_sorts, multibonds, x, y, z, a_list);
     var temparray=sumstring.split("#");
sumstring=temparray.join("\n");
document.form1.text1.value=sumstring;

return;

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