Sure. If you supply this version:

#! perl -slw
use strict;
use List::Util qw[ sum ];

BEGIN{ @ARGV = map glob( $_ ), @ARGV }

my %stats;

while( <> ) {
    next unless m[^ATOM];
    my @fields = unpack 'a6 a5 a3 a3 a4 x2 a3 x4 a8 a8 a7 a7 a6 a12', 
+$_;
#    print join'|', @fields;
    push @{ $stats{ $fields[ 4 ] } }, $fields[ 10 ];
}

printf "%3s : %.3f%%\n", $_,
    sum( @{ $stats{ $_ } } ) / @{ $stats{ $_ } }
    for sort keys %stats;
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with a wildcard path/filename on the command line,

theScript.pl /path/to/*.pdb
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it will perform the stats across all the matching files.

Alternatively, if you want the stats on a file-by-file basis, then supply the filenames one at a time:

## For windows; something similar is possible on *nix
for %i in (\path\to\*.pdb) do @theScript.pl \path\to\%i
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