#!/usr/bin/perl

$basepairs = $ARGV[0];
$out_lol = $ARGV[1];

open(IN, "<$basepairs") or die "Reqd args: file.in out.lol";
open(OUT_LOL, ">$out_lol") or die "Reqd args: file.in out.lol";

while (<IN>) {
   ($base1, $res1, $base2, $res2) = split; 
    if (($base1 eq "RGUA") and ($base2 eq "RCYT")) {
      printf OUT_LOL "
$res1 $base1  C4    $res2 $base2 C6      8.30  10.00E+00
$res1 $base1  N9    $res2 $base2 H6     10.75  10.00E+00
";

    } elsif (($base1 eq "RCYT") and ($base2 eq "RGUA")) {
           printf OUT_LOL "
$res1 $base1  C6    $res2 $base2 C4      8.30  10.00E+00
$res1 $base1  H6    $res2 $base2 N9     10.75  10.00E+00
";

    } elsif (($base1 eq "RADE") and ($base2 eq "URA")) {
           printf OUT_LOL "
$res1 $base1  C4    $res2 $base2  C6      8.30  10.00E+00
$res1 $base1  N9    $res2 $base2  H6     10.75  10.00E+00
";

    } elsif (($base1 eq "URA") and ($base2 eq "RADE")) {
           printf OUT_LOL "
$res1  $base1  C6    $res2 $base2 C4      8.30  10.00E+00
$res1  $base1  H6    $res2 $base2 N9     10.75  10.00E+00
";
    }
}
close(IN);
close(OUT_LOL);