#!/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;

##</code><code>##

ATOM    310 1HH2 ARG A 607     -31.278  29.882  25.723  1.00 99.99
ATOM    311 2HH2 ARG A 607     -32.344  30.932  24.851  1.00 99.99
ATOM    312  N   LEU A 608     -36.327  31.914  18.187  1.00 65.62
ATOM    313  CA  LEU A 608     -37.435  32.634  17.559  1.00 67.47
ATOM    314  C   LEU A 608     -38.434  33.052  18.624  1.00 74.29
ATOM    315  O   LEU A 608     -38.982  32.201  19.331  1.00 71.12
ATOM    316  CB  LEU A 608     -38.110  31.803  16.459  1.00 64.64
ATOM    317  CG  LEU A 608     -39.261  32.481  15.719  1.00 71.07
ATOM    318  CD1 LEU A 608     -38.782  33.704  14.929  1.00 73.68
ATOM    319  CD2 LEU A 608     -39.981  31.498  14.829  1.00 69.63
ATOM    320  H   LEU A 608     -36.638  31.041  18.563  1.00 99.99
ATOM    321  N   ARG A 565     -38.634  34.587  18.911  1.00 22.27
ATOM    322  CA  ARG A 565     -39.655  35.200  19.766  1.00 23.04
ATOM    323  C   ARG A 565     -40.963  35.104  19.007  1.00 22.72
ATOM    324  O   ARG A 565     -41.046  35.500  17.847  1.00 24.21
ATOM    325  CB  ARG A 565     -39.275  36.643  20.105  1.00 99.99
ATOM    326  CG  ARG A 565     -38.044  36.770  20.986  1.00 99.99

##</code><code>##

ATOM   310 1HH2 ARG A    1     -31.278  29.882  25.723   1.00  99.99
ATOM   311 2HH2 ARG A    1     -32.344  30.932  24.851   1.00  99.99
ATOM   312    N LEU A    2     -36.327  31.914  18.187   1.00  65.62
ATOM   313   CA LEU A    2     -37.435  32.634  17.559   1.00  67.47
ATOM   314    C LEU A    2     -38.434  33.052  18.624   1.00  74.29
ATOM   315    O LEU A    2     -38.982  32.201  19.331   1.00  71.12
ATOM   316   CB LEU A    2     -38.110  31.803  16.459   1.00  64.64
ATOM   317   CG LEU A    2     -39.261  32.481  15.719   1.00  71.07
ATOM   318  CD1 LEU A    2     -38.782  33.704  14.929   1.00  73.68
ATOM   319  CD2 LEU A    2     -39.981  31.498  14.829   1.00  69.63
ATOM   320    H LEU A    2     -36.638  31.041  18.563   1.00  99.99
ATOM   321    N ARG A    3     -38.634  34.587  18.911   1.00  22.27
ATOM   322   CA ARG A    3     -39.655  35.200  19.766   1.00  23.04
ATOM   323    C ARG A    3     -40.963  35.104  19.007   1.00  22.72
ATOM   324    O ARG A    3     -41.046  35.500  17.847   1.00  24.21
ATOM   325   CB ARG A    3     -39.275  36.643  20.105   1.00  99.99
ATOM   326   CG ARG A    3     -38.044  36.770  20.986   1.00  99.99