1         2   3   4  5  6   
ATOM      1  CA  PRO A 889      84.370  72.820  26.830  1.00  0.00            
ATOM      2  CA  THR A 890      87.370  73.900  28.080  1.00  0.00            
ATOM      3  CA  VAL A 891      90.920  72.490  27.750  1.00  0.00            
ATOM      4  CA  PHE A 892      93.640  74.890  28.970  1.00  0.00            
ATOM      5  CA  HIS B 893      97.060  74.200  27.360  1.00  0.00            
ATOM      6  CA  LYS B 894      99.880  73.920  29.990  1.00  0.00 
##</code><code>##

1         2  3    4  5  6 
     
ATOM      1  N   PRO A 889      16.220  12.185   1.804  1.00 71.54           N  
ATOM      2  CA  PRO A 889      16.101  12.990   3.034  1.00 70.89           C  
ATOM      3  C   PRO A 889      15.432  14.346   2.803  1.00 72.31           C  
ATOM      4  O   PRO A 889      14.743  14.852   3.703  1.00 72.20           O  
ATOM      5  CB  PRO A 889      17.553  13.151   3.502  1.00 72.96           C  
ATOM      6  CG  PRO A 889      18.315  12.067   2.782  1.00 78.00           C  
ATOM      7  CD  PRO A 889      17.626  11.907   1.465  1.00 73.35           C  
##</code><code>##

print "\nEnter the network pdb file file: ";
$inputFile = <STDIN>;
chomp $inputFile;

unless (open(INPUTFILE, $inputFile)) {
    print "Cannot read from '$inputFile'";
    <STDIN>;
    exit;
}
# load the file into an array
chomp(@networkpdb = <INPUTFILE>);

# close the file
close(INPUTFILE);

print "\nEnter the pdb output file: ";
$inputFile2 = <STDIN>;
chomp $inputFile2;

unless (open(INPUTFILE, $inputFile2)) {
    print "Cannot read from '$inputFile2'";
    <STDIN>;
    exit;
}

chomp(@pdb = <INPUTFILE>);


close(INPUTFILE);


            
for ($line1 = 0; $line1 < scalar @networkpdb; $line1++) {
    if ($networkpdb[$line1] =~ m/ATOM\s+\d+\s+\w+\s+\w{3}\s*(\w+)\s*(\d*)\s+\S+\.\S+\s+\S+\.\S+\s+\S+\.\S+\s+.+\..+\..*/ig) {
               my  $resnum=$2;
               my  $chain=$1;
for ($line = 0; $line < scalar @pdb; $line++) {
     if ($pdb[$line]=~ m/(ATOM\s+\d+\s+\w+\s+\w{3}\s*)(\w+)\s*(\d*)(\s+\S+\.\S+\s+\S+\.\S+\s+\S+\.\S+\s+.+\..+\..*)/ig) {
                my $begining=$1;
                my  $resnum1=$3;
                my  $chain1=$2;
                my $end=$4;
 if ($resnum1=$resnum)
                 {$chain1=$chain;
 $parsedData{$line} = $begining.$chain1."\s".$resnum1.$end;
        
    
}}}}}

# create the output file name
$outputFile = "WithNetwork_".$inputFile;

# open the output file
open (OUTFILE, ">$outputFile");
# print the data lines
foreach $line (sort {$a <=> $b} keys %parsedData) {
    print OUTFILE $parsedData{$line}."\n";
}

# close the output file
close (OUTFILE);