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#!/usr/bin/perl
# This program renumbers an input pdb file with sequential integers, starting at a user-specified integer. Gaps in numbering disappear, and inserted regions are renumbered as integers.
# Usage: ./renumber.pl [input file name] [new first residue number] > [output file name]
print "REMARK Usage: ./renumber.pl [input file name] [new first residue number] > [output file name]\n";
#open FILE, "input.pdb" or die $!;
open FILE, $ARGV[0] or die $!;
$oldResNum = "ZZZZ";
$currentResNum = "XXXX";
$renumberedResNum = $ARGV[1]-1;
#print "REMARK renumberedResNum =$renumberedResNum \n";
while (<FILE>) {
if ((substr($_,0,4) eq "ATOM") || (substr($_,0,6) eq "HETATM")) {
#print substr($_,0,4),"\n";
#print $_;
$currentResNum = substr($_,22,5);
#print "currentResNum = >",$currentResNum,"<\n";
#print "oldResNum = >",$oldResNum,"<\n";
if ($currentResNum ne $oldResNum) {
$renumberedResNum++;
}
#print "renumberedResNum = >",$renumberedResNum,"<\n";
$paddedRenumberedResNum= sprintf("%04d", $renumberedResNum);
#print "paddedRenumberedResNum = >",$paddedRenumberedResNum,"<\n";
substr($_,22,4) = $paddedRenumberedResNum;
substr($_,26,1) = " ";
print $_;
$oldResNum = $currentResNum;
}
}
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