# VERSION 1.0 - 01-10-2012

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# ".OOO .....OOO...OO.....OO..OOO...,OO..7OO....OO.OO....ZOO.....?OO .......7OO...."
# "~OO:.......OO=.ZOO.....OO..OOO...ZOO..OOO....OOOO....OOOI+??0..OOO?...O..OOO...."
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# "........................by...Juan.Bustamante..Victoria.Dumas..&..Marcelo.Marti.."
# "..........................................................................2012.."

set pasos 600;

puts "Enter the initial coordinates separated by 'q'";
set j [gets stdin];
set fields [split $j "q"];
set crd_ini(0) [lindex $fields 0];
set crd_ini(1) [lindex $fields 1];
set crd_ini(2) [lindex $fields 2];

puts "Enter the final coordinates separated by 'q'";
set j [gets stdin];

set fields [split $j "q"];
set crd_fin(0) [lindex $fields 0];
set crd_fin(1) [lindex $fields 1];
set crd_fin(2) [lindex $fields 2];


puts "Enter the references coordinates to the X axis for the energetic curve graphic separated by 'q'";
set j [gets stdin];

set fields [split $j "q"];
set xref [lindex $fields 0];
set yref [lindex $fields 1];
set zref [lindex $fields 2];


puts "\nDo you want to enter a threshold? (Y or N)";
puts "this value set a weight based on distance between initial and final minima to the possible pathway that connects them. 
By this way, if you set a value of '1.3', you are allowing to calculating pathway go in some steps acquiring a distance at least 30% more than the initial distance between minima";
puts "Default threshold: 1.3";
set decision [gets stdin];
puts "\n";

if {[string compare $decision "Y"] == 0 || [string compare $decision "y"] == 0} \
{
  puts "Enter the thershold:";
  set threshold [gets stdin];
} else { set threshold 1.3; }


puts "\nYou can set other threshold.. (Y or N)";
puts "If you think or if you know that the barrier is big, sets this value up to 1. Try with differents thersholds to reach the desired pathway.";
puts "Default threshold: 1.0";
set decision2 [gets stdin];
puts "\n";

if {[string compare $decision2 "Y"] == 0 || [string compare $decision2 "y"] == 0} \
{
  puts "Enter the threshold:";
  set thresholdBarrier [gets stdin];
} else { set thresholdBarrier 1.0; }



set ini_pos(0) [expr int([expr (($crd_ini(0) - $xOrigen) / $xdelta)])];
set ini_pos(1) [expr int([expr (($crd_ini(1) - $yOrigen) / $ydelta)])];
set ini_pos(2) [expr int([expr (($crd_ini(2) - $zOrigen) / $zdelta)])];

set fin_pos(0) [expr int([expr (($crd_fin(0) - $xOrigen) / $xdelta)])];
set fin_pos(1) [expr int([expr (($crd_fin(1) - $yOrigen) / $ydelta)])];
set fin_pos(2) [expr int([expr (($crd_fin(2) - $zOrigen) / $zdelta)])];


set posic(0) $ini_pos(0);
set posic(1) $ini_pos(1);
set posic(2) $ini_pos(2);

set camino 0;
set iter 0;
set minimo 0;

puts "\nComputing...";


#-------------------------------------------------------------------------------
#------------------------------- PATHWAY MAPPING -------------------------------
#-------------------------------------------------------------------------------

set semaforo 0;

set dirx [expr $fin_pos(0) - $ini_pos(0)];
set diry [expr $fin_pos(1) - $ini_pos(1)];
set dirz [expr $fin_pos(2) - $ini_pos(2)];

set disprev [expr sqrt( pow($dirx, 2) + pow($diry, 2) + pow($dirz, 2) )];

while {($posic(0) != $fin_pos(0) || $posic(1) != $fin_pos(1) || $posic(2) != $fin_pos(2)) && $semaforo < $pasos} \
{
  set best 1000;
  set bestx 0;
  set besty 0;
  set bestz 0;

  for {set i -1} {$i <= 1} {incr i} \
  {
    for {set j -1} {$j <= 1} {incr j} \
    {
      for {set k -1} {$k <= 1} {incr k} \
      {
	set dirfx [expr $fin_pos(0) - [expr $posic(0)+$i]];
	set dirfy [expr $fin_pos(1) - [expr $posic(1)+$j]];
	set dirfz [expr $fin_pos(2) - [expr $posic(2)+$k]];

	set vecdis [expr sqrt( pow($dirfx, 2) + pow($dirfy, 2) + pow($dirfz, 2) )];

	set pase 0;

	for {set a 0} {$a < $semaforo} {incr a} \
	{
	  if {$caminox($a) == [expr $posic(0)+$i] && $caminoy($a) == [expr $posic(1)+$j] && $caminoz($a) == [expr $posic(2)+$k]} \
	  {
	    set pase 1;
	  }
	}

	if {$best >= [expr $grilla([expr $posic(0)+$i],[expr $posic(1)+$j],[expr $posic(2)+$k]) * $thresholdBarrier] &&  ($i!=0 || $j!=0 || $k!=0) &&  $vecdis < [expr $disprev* $threshold] && $pase == 0}\
	{
	  set best $grilla([expr $posic(0)+$i],[expr $posic(1)+$j],[expr $posic(2)+$k]);
	  set bestx $i;
	  set besty $j;
	  set bestz $k;
	} 
      }
    }
  }
  
  set caminot($semaforo) $best;
  set caminox($semaforo) [expr $posic(0)+$bestx];
  set caminoy($semaforo) [expr $posic(1)+$besty];
  set caminoz($semaforo) [expr $posic(2)+$bestz];
  
  set posic(0) [expr $posic(0)+$bestx];
  set posic(1) [expr $posic(1)+$besty];
  set posic(2) [expr $posic(2)+$bestz];

  incr semaforo;
  
}

puts "Pathway traced..."
puts "Saving pathway..."

set guardar [open pathway.pdb w]

for {set g 0} {$g < $semaforo} {incr g} \
{ 
  set pos_x [expr $xOrigen + ($caminox($g)) * $xdelta];
  set pos_y [expr $yOrigen + ($caminoy($g)) * $ydelta];
  set pos_z [expr $zOrigen + ($caminoz($g)) * $zdelta];

  if {$g < 10} \
  {
  puts $guardar "ATOM      $g  WAY WAY     $g      $pos_x   $pos_y  $pos_z  $caminot($g)  0.00";
  } elseif {$g >= 10 || $g < 100 } { puts $guardar "ATOM     $g  WAY WAY     $g     $pos_x   $pos_y  $pos_z  $caminot($g)  0.00";
  } else {  puts $guardar "ATOM    $g  WAY WAY     $g      $pos_x   $pos_y  $pos_z  $caminot($g)  0.00";}
}
close $guardar;
unset guardar;

for {set g 0} {$g < $semaforo} {incr g} \
{ 
  set posicion [ expr sqrt( pow( ($xOrigen + $caminox($g) * $xdelta) - $xref,2) + pow( ($yOrigen + $caminoy($g) * $ydelta) - $yref,2) + pow( ($zOrigen + $caminoz($g) * $zdelta) - $zref,2) )];

  set barrera1($g) $posicion;
  set barrera2($g) $caminot($g);
}

array set barrera1b {};
array set barrera1bX {};

set guardardat_ord [open pathway.dat w]

foreach {k v} [array get barrera1] {
  if {$v < 10} \
  {
    lappend barrera1bX($v) $k;
  } else {lappend barrera1b($v) $k;}
}

foreach va [lsort -decreasing [array names barrera1b]] {
  foreach ka $barrera1b($va) {
    puts $guardardat_ord "$va $barrera2($ka)";
  }
}

foreach vab [lsort -decreasing [array names barrera1bX]] {
  foreach kab $barrera1bX($vab) {
    puts $guardardat_ord "$vab $barrera2($kab)";
  }
}

close $guardardat_ord;

puts "\n\nDone. Enjoy it!"

mol new {pathway.pdb} type {pdb} first 0 last -1 step 1 waitfor 1

unset guardardat_ord;
unset pasos fields j crd_ini crd_fin xref yref zref decision threshold thresholdBarrier ini_pos fin_pos posic camino iter minimo best bestx besty bestz i k disprev dirfx dirfy dirfz vecdis pase a caminot caminox caminoy caminoz semaforo g posicion barrera1 barrera2 barrera1b v barrera1bX;