#! /usr/bin/perl
use File::Copy;

################################################
#                                              #
# program to convert old pdb files to a usable #
# format.                                      #
#                                              #
################################################

foreach my $pdb (@ARGV) {
	if ($pdb =~ /(.+?).pdb$/ && -e $pdb) {
		$pdb = $1;
#		$pdb = substr($pdb, 0, -4);
		open(IN, "<$pdb.pdb");
		open(OUT, ">$pdb.tmp");
		while(<IN>) {
			if ($_ =~ /^\S+\s+\d+\s+(\D)/) {
				my $line = $_;
				chomp($line);
				print OUT "$line           $1\n";
			}
			else {
				print OUT $_;
			}
		}
		close(IN);
		close(OUT);
		move("$pdb.pdb", "$pdb.pdb.old");
		move("$pdb.tmp", "$pdb.pdb");
		print "converted $pdb.pdb. the old file has been saved as $pdb.pdb.old\n";
	}
	elsif (! -e $pdb) {
		print "file $pdb does not appear to exist\n";
	}
	else {
		print "file $pdb is not a .pdb file or there was an unknown error\n";
	}
}