Hello im new to programming i need help

what i am trying to do is to compare a set of coordinates from one file to another set of coordinates from many different files. i am having trouble doing this please can some 1 help me here is what i have done so far which compares 2 sets. i want to be able to change the first part to cycle through all files i have in a directory.

#!/usr/bin/perl -w

#$dir = "/net/klab2/u2/home/fmohammad/GFP2/run1";

#opendir (DIR, $dir) or die $!;
#@one = readdir (DIR);

#foreach $file (@one)
#{

$initialfile2 = "UM_802_R203E112_1GFL_clean_gfp_5.pdb";

open FILETWO, "$initialfile2" or die "cannot open $initialfile2 for read\n";
while ($line2 = <FILETWO>)
{
chomp $line2;

@one=split(/\s+/, $line2);

if ($one[0]=~m/^HETATM/)
{
if ($one[2]eq "C4")
{
$xC4=$one[6];
$yC4=$one[7];
$zC4=$one[8];
}

if ($one[2]eq "C1")
{
$xC1=$one[6];
$yC1=$one[7];
$zC1=$one[8];
}

if ($one[2]eq "C13")
{
$xC13=$one[6];
$yC13=$one[7];
$zC13=$one[8];
}
}
}
close FILETWO;

$initialfile = "1GFL.pdb";
open FILEONE, "$initialfile" or die "cannot open $initialfile for read\n";
while ($line = <FILEONE>)
{
chomp $line;

@two=split(/\s+/, $line);

if ($two[0]=~m/^ATOM/)
{
if ($two[1]eq "479")
{
$xS=$two[6];
$yS=$two[7];
$zS=$two[8];
}

if ($two[1]eq "484")
{
$xY=$two[6];
$yY=$two[7];
$zY=$two[8];
}

if ($two[1]eq "496")
{
$xG=$two[6];
$yG=$two[7];
$zG=$two[8];
}
}
}
close FILEONE;

$part1 = ((($xC1 - $xS)**2) + (($yC1 - $yS)**2) + (($zC1 - $zS)**2));
$part2 = ((($xC4 - $xY)**2) + (($yC4 - $yY)**2) + (($zC4 - $zY)**2));
$part3 = ((($xC13 - $xG)**2) + (($yC13 - $yG)**2) + (($zC13 - $zG)**2));
$sum = $part1 + $part2 + $part3;
$sum1 = $sum / 3;
$rmsd = sqrt ($sum1);
print"$rmsd\n";
#}

Unless I missed something, what you have commented out at the top of your program should happily iterate over each file in the directory, which I assume is what you want to do. Please tell us where you think you have a problem.

The only thing you might want to add is to discard entries starting with a dot or, better, to test with the -f file test operator that the entry you will use next is a plain file (not a directory or something else).

Also take a look at the glob function, which can make your iteration simpler, because it returns a list of files with their path (which readdir gives you only the filenames).