#!/usr/bin/env perl

# Read a PDB file and change the residue numbers to be continuous.

use strict;
use warnings;

print "\nEnter the PDB input file: ";
my $inputFile = <STDIN>;
chomp $inputFile;

unless (open(INPUTFILE, "<", $inputFile)) {
    die "Cannot read from <$inputFile>, $!";
}

my $output_file = "my2pdb.txt";
open(PDBOUT,">>my2pdb.txt")
    or die "Cannot open <$output_file> for writing, $!";

my $last_residue_name = '';
my $last_residue_number = 0;

while (<INPUTFILE>) {
    if (m/^ATOM/) {
        my @m = split;

        # Increment the residue number if the residue name changes
        if ($m[3] eq $last_residue_name) {
            $m[5] = $last_residue_number;
        } else {
            $m[5] = ++$last_residue_number;
            $last_residue_name = $m[3];
        }
        printf PDBOUT "%4s %5s %4s %3s %1s %4s     %7s %7s %7s %6s %6s\n", @m;
    }
}

exit;