another text parser 2

#!/usr/bin/perl
#
# nuskaityti bindingdb sdf failus
# H-Se/DB26984_50278320.sdf kaip testas imtas
#
# VR
#

#use warnings;
use Data::Dumper;


#nuskaityti failus i @molekules
die "usage VR_bindingdb_parse.pl file.sdf 'TARGET Biomolecule'" if (@ARGV != 2);
$FILE = $ARGV[0];
$target = $ARGV[1];
open FILE, "<", $FILE or die $!;
$x=0;
$key='str';
while(<FILE>) {
 chop($_);
 next if ($_ =~ /^$/);   #jei eilute tuscia praleidziam
 if ($_ =~ /\$\$\$\$/) { #jei eiluteje yra: $$$$
  $x++;
  $key = 'str';
  next;
 }
 #print $x, $_;
 if ($_ =~ /^\>/) {      #jei eilute prasideda: >
  chop();
  $_ =~ s/>  <//;
  $key = $_;
 } else {
  #$molekules[molekules nr.]{irasas}
  push @{ $molekules[$x]{$key} }, $_;
 }
}
close FILE;
#print STDERR Dumper \@molekules;
print STDERR $FILE, " ", $target, "\n";


#rasti nuo kur prasideda kitokia molekule
#pirmoji kita yra $ta_pati+1
kita();
sub kita {
$y=0;
$ta_pati=0;
while($molekules[$y]{'str'}) {
 #print STDERR Dumper $molekules[$y]{'str'}, "\n";
 $z=0;
 while($molekules[$y]{'str'}[$z]) {
  #jei z eilute nesutampa y ir y+1 nors karta tai kita molekule
  if ($molekules[$y]{'str'}[$z] ne $molekules[$y+1]{'str'}[$z]) {
   $ta_pati=$y;
   #print STDERR $y, " :", $molekules[$y]{'str'}[$z], " ir ", $molekules[$y+1]{'str'}[$z], "\n";
   last;
  }
  $z++;
 }
 last if ($ta_pati);
 $y++;
}
}
#print STDERR Dumper $molekules[0], "\n";


#eiti per molekules iki pirmos tos pacios ir
#nuo pirmos tos pacios eiti per visas ir rasti vienoda 'TARGET Biomolecule'
$x=0;
$skaitiklis=0;
while($x <= $ta_pati) {
$y=$ta_pati+1;
 while($molekules[$y]{'str'}[0]) {
  if (($target eq $molekules[$x]{'TARGET Biomolecule'}[0]) && ($target eq $molekules[$y]{'TARGET Biomolecule'}[0])) {
  #print STDERR "Target: ", $molekules[$x]{'TARGET Biomolecule'}[0], "\n";
  print STDERR "Ki ", $molekules[$x]{'BindingDB Display Name'}[0], " molekulei: ", $molekules[$x]{'Enzymologic: Ki nM'}[0], " nM\n";
  print STDERR "Ki ", $molekules[$y]{'BindingDB Display Name'}[0], " molekulei: ", $molekules[$y]{'Enzymologic: Ki nM'}[0], " nM\n";
  #kiek x molekule geresne uz y nM skaitiklis
  $skaitiklis=$skaitiklis+($molekules[$x]{'Enzymologic: Ki nM'}[0]-$molekules[$y]{'Enzymologic: Ki nM'}[0]);
  }
 $y++;
 }
$x++;
}
print $molekules[0]{'BindingDB Display Name'}[0], " geriau uz ", $molekules[$ta_pati+1]{'BindingDB Display Name'}[0],
" vidutiniskai\t", $skaitiklis/$x, "\tnM\n";
#print STDERR "Ki ", $molekules[0]{'BindingDB Display Name'}[0], " molekulei:\n";
#print STDERR Dumper @pirma;
#print STDERR "Ki ", $molekules[$ta_pati+1]{'BindingDB Display Name'}[0], " molekulei:\n";
#print STDERR Dumper @antra;