AMBER Archive (2002)

Subject: RE: Antibody residue numbering

From: Mark Hsieh (hsieh_at_abmaxis.com)
Date: Tue Aug 20 2002 - 11:52:24 CDT

Here's the residue renumbering perl script some people have
asked me for (provided as is, i.e., no guarantee, no support,
etc.):

MH
------------------------------cut-----------------------------------
#!/usr/bin/perl

############################################################################
####
# pdbresrenum3.pl
#
# Author:
# Mark Hsieh
# 8/19/02
#
# Description:
# This script renumbers the residue numbers in a pdb file so that there
# are no discontinuities in the numbering within each chain.
# Any numbering that involves letters in column 26 such as 100A, 100B,
100C,
# get renumbered sequentially as well (101, 102, 103,...)
# Atom numbers are not renumbered.
#
# Usage:
# pdbresrenum3.pl <input_pdbfile>
# pdbresrenum3.pl <input_pdbfile> [ > output_pdbfile ]
#
############################################################################
####

use strict;

my $res_count=0;
my $old_resname;
my $old_chain;
my $old_resnum;
my $new_resnum;
my $head;
my $tail;
my $resname;
my $chain;
my $resnum;

if (! $ARGV[0]) {
  print "Usage:\n";
  print "\tpdbresrenum3.pl <input_pdbfile>\n";
  print "\tpdbresrenum3.pl <input_pdbfile> [ > output_pdbfile ]\n";
  exit;
}
my $infile=$ARGV[0];
open(INFILE,"<$infile");
while (<INFILE>) {

  if (/^ATOM|^HETATM|^TER/) {
    chomp;
    if (/^ATOM|^HETATM/) {
      $head = substr($_,0,17);
      $tail = substr($_,27,);
      $resname = substr($_,17,4);
      $chain = substr($_,21,1);
      $resnum = substr($_,22,5);
    }

    if (($resname eq $old_resname) && ($chain eq $old_chain) && ($resnum eq
$old_resnum)) {
      if (/^TER/) {
        # Use and modify data from previous record.
        my $atom=substr($head,12,5);
        my $atomnum=substr($head,7,4);
        my $new_atomnum=$atomnum+1;
        my $new_atomnum=sprintf "%4i",$new_atomnum;
        $head=~s/$atom/ /;
        $head=~s/$atomnum/$new_atomnum/;
        $head=~s/ATOM/TER /;
        print $head.$resname.$chain.$new_resnum,"\n";
      }
      else {
        print $head.$resname.$chain.$new_resnum.$tail,"\n";
      }
      next;
    }
    else {
      if ($chain ne $old_chain) {
        $res_count=0;
      }
      $res_count++;
      $new_resnum=sprintf "%4s ",$res_count;
      print $head.$resname.$chain.$new_resnum.$tail,"\n";
      $old_resnum = $resnum;
      $old_chain = $chain;
      $old_resname = $resname;
    }
  }
}