Hello, i am new to Perl and i m trying to write a code that will accept a pdb file, it will extract all the informations (atom number, atom type,residue name, residue number, x, y, z, b factor) and it will rearrange the residue number and it shoud save the new pdb in a new archive, i can't find a way to use a loop with a string array, this is the code: 
 print "\nEnter the input file: ";
$inputFile = <STDIN>;
chomp $inputFile;

unless (open(INPUTFILE, $inputFile)) {
    print "Cannot read from '$inputFile'.\nProgram closing.\n";
    <STDIN>;
    exit;}      
chomp(@dataArray = <INPUTFILE>);
close(INPUTFILE);
for ($line = 0; $line <= scalar @dataArray; $line++) {
    if ($dataArray[$line] =~ m/ATOM\s+(\d+)\s+(\w+)\s+(\w{3})\s+(\w)+\
+s+(\d+)\s+(\S+\.\S+)\s+(\S+\.\S+)\s+(\S+\.\S+)\s+(.+\S)(.\d\d+\.\d\d.
++)/ig)  

                             {
$m1=$1;        
$m2=$2; 
$m3=$3;
$m5=$5;
$m6=$6;
$m7=$7; 
$m8=$8;
$m9=$9; 
$m10=$10;
push(@m3,$m3);
push(@m5,$m5);    
foreach $line (@m3,@m5)

    {if ($m3[$line] eq $m3[$line+1])
    {$m5[$line]=$m5[$line+1];}

    elsif ($m3[$line] ne $m3[$line+1]){$m5[$line+1]=$m5[$line]+1;}}

$~="PDBFORMAT";

format PDBFORMAT = 

ATOM @|||| @||| @|| @|||     @|||||| @|||||| @|||||| @>>>>> @>>>>> 

      $m1, $m2, $m3,$m5,     $m6,    $m7,    $m8,    $m9,   $m10 
.


open(PDBFORMAT,">>my2pdb.txt") or die "Can't open anything";
write PDBFORMAT;}}
close PDBFORMAT;

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In reply to Rearrange the residue number of a pdb file according to the residues names by nastaziales

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