I have a little bit problem in my code which I am unable to sort out. My input file is

536 ENERGY = -176.2 pro
1 G 0 2 0 1
2 G 1 3 533 2
3 G 2 4 532 3
536 ENERGY = -175.9 pro
1 G 0 2 0 1
2 G 1 3 533 2
3 G 2 4 532 3

My code is 

$data_file="HIVgag.ct";

open(MYFILE, $data_file) || die("Could not open file!");
$b=$between=$energy=0;
while (<MYFILE>) {
    if (/energy/i) {
        $energy++;
        $between=$b;
    }
    elsif ($energy) {$b++}
}

print "$energy / $between\n";
close(MYFILE);

open(MYFILE, $data_file) || die("Could not open file!");
open(WRITE, ">final.net");
print WRITE "*vertices $between\n";

 while(<MYFILE>)
 {
 foreach $row (<MYFILE>)
 {
 @row = $row;
(@row[0],@row[1],@row[2], @row[3], @row[4], @row[5], @row[6])=split(/\
+s+/,$row);
if (@row[2] ne ENERGY)
{
 print  WRITE "@row[1]  $row[2]\n";
 print"@row[1]  $row[2]\n";
 }
    }
 }
 close(MYFILE);
 
 open(MYFILE, $data_file) || die("Could not open file!");
 {
print WRITE "*edges\n";
my $energy;
while ( <MYFILE> ) {
    if ( /\bENERGY\b/ ) {
        ++$energy;
        next;
       }
       
    my ( $key, @fields ) = grep $_, split;
    for my $field ( @fields ) {
    if ( $field ne 'G' && $field ne 'A' && $field ne 'C' && $field ne 
+'G' )
    {
        print WRITE "$key $field $energy\n";
        }
    }
    }
    }
close(WRITE);

[download]

My code rearranges the input file in a way such that the first two columns of the file is written in *vertices portion. And in the *edges portion the 1st column of the input file makes a pair with the 3rd, 4th , 5th and 6th column omitting the pairs containing zero in 3rd, 4th, 5th and 6th column. The 3rd column of *edges consists of the number of “energy block” in which the pair exists. Thus the output file is

*vertices 3
1 G
2 G
3 G
1 G
2 G
3 G
*edges
1 2 1
1 1 1
2 1 1
2 3 1
2 533 1
2 2 1
3 2 1
3 4 1
3 532 1
3 3 1
1 2 2
1 1 2
2 1 2
2 3 2
2 533 2
2 2 2
3 2 2
3 4 2
3 532 2
3 3 2

What I want is in the *vertices portion it should only read the first two columns of the first “energy block” and then it should jump to *edges portion which implies that in this case it should only print 1 G, 2 G and 3 G and then jump to *edges portion. And in *edges portion the first column of input file should not make pair with 6th (last) column. So the output should be like

*vertices 3
1 G
2 G
3 G
*edges
1 2 1
2 1 1
2 3 1
2 533 1
3 2 1
3 4 1
3 532 1
1 2 2
2 1 2
2 3 2
2 533 2
3 2 2
3 4 2
3 532 2

I shall be very thankful for help.

In reply to Spliting file + removing column by AG87

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