my $dir = '/path/to/dir';

# read only pd files:

opendir DIR, $dir or die "read dir $dir - $!";

my @pdb_files = grep /\.pdb/, readdir DIR;


closedir DIR;

foreach my $file (@pdb_files)

{

open( FH,"$dir\\$file")

while(<FH>) 

{

$output_from_my_precompiled_tool = `/path/to/my/tool $file`;

}
close(FH);

}