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

function mega1(molecule)
{

transfer(3);

     var f_exchange=read(1,10000,1,2);

transfer_and_mod(1, f_exchange);

     var rmatrix=read(1,100,1,100);

     var grupper=new Array(0);
     var matrix1=new Array(0);
     var matrix2=new Array(0);
     var n=0;
     var limit=rmatrix[0][0];
     var aintervals=parseInt(rmatrix[2][0]);
     var dintervals=parseInt(rmatrix[aintervals+4][0]);
     var ng=parseInt(rmatrix[dintervals+aintervals+7][0]);
     var nf=parseInt(rmatrix[dintervals+aintervals+7][0]);

ng=12;

     var maxg=0;
     var startrow=dintervals+aintervals+8;
     var endrow=dintervals+aintervals+8+nf;
     var bitstrings_all=new Array(0);
     var featured_ligands_all=new Array(0);
     var molecule_counter=0;
     var frame_1="";
     var frame_2="";
     var frame_3="";

// In this loop, the vector in which many variables corresponds to features, get
// its highest index according to the number of the highest feature number. If
// the feature numbers are defined by the program from feature names, this is simple. 

  for(n=startrow;n<endrow;n++){
  maxg=Math.max(maxg,rmatrix[n][0]);
  }

grupper=new Array(maxg);
  for(n=startrow;n<endrow;n++) grupper[rmatrix[n][0]]="";

// A loop is reading in all groups in their feature variables, according to the
// list, where the first row with group-feature information is the row "startrow"
// and the last one is "endrow". So "45   9" makes 9 to b put in variable 45. NOT the
// other way around. Every feature will then end up with a list of groups, in which
// it can be sorted, exactly like one, single distance can be within two, defined
// distance ranges at the same time.

  for(n=startrow;n<endrow;n++){
  grupper[rmatrix[n][0]]=grupper[rmatrix[n][0]]+rmatrix[n][1]+" ";
  }

// The fallowing commands reads in the lower limits and the upper limits for
// distance1 and distance2 -> matrix1; & angles -> matrix2
// So matrix1[row][0] will be the lower limit for the angle defined on row=row,
// matrix1[row][1] the upper limit for the same angle. 

matrix1=read(4,3+aintervals,1,2);
matrix2=read(aintervals+6,5+aintervals+dintervals,1,2);

// The map must contain a file list named file_list.txt. With this list, the molecule
// files will be found and exhaustively performed. The list will be opened immedately
// with the base document.

transfer(2);
var listed_files = read(1,1000000,1,1);

bitstrings_all=new Array(listed_files.length);
featured_ligands_all=new Array(listed_files.length);
molecule_counter=0;

if(molecule) listed_files[0]=molecule;

frame_1="bitstrings/"+listed_files[0]+".txt";
frame_2="featurecollection/"+listed_files[0]+".txt";
frame_3="basic_molecules/"+listed_files[0]+".txt";

load_frames(frame_1,frame_2,frame_3);

var gear_commands = new Array(3);
gear_commands[0]=limit;
gear_commands[1]=ng;
gear_commands[2]=nf;
gear_commands[3]=molecule_counter;

// Some time must be given for loading of the frames. 100 milliseconds is enough.
// Here is much information copied for each loop, but it is just to keem every
// function 'isolated' and well defined.

if(!molecule) window.setTimeout(function(){mega2(bitstrings_all,featured_ligands_all,f_exchange,matrix1,matrix2,grupper,listed_files,gear_commands);},100);

if(molecule) window.setTimeout(function(){single_molecule_continue(featured_ligands_all,f_exchange,matrix1,matrix2,grupper,molecule,gear_commands,"");},100);

parent.right.hidden.location="empty.htm";
parent.right.hidden.location.reload();

}

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