I have two file of given structure
File 1 structure :

    SER A     
    ARG A    
    GLU A    
    LYS A    
    ASN A    
    GLN A    
    PRO A    
    LYS A    
    PRO A    
    SER A    
    PRO A    
    LYS A    
    ARG A
[download]

File 2 structures (PDB file):

ATOM      2  CA  PRO A   6       2.437   5.295 -23.029  1.00  0.00    
+       C  
ATOM      3  C    PRO A   6       2.307   5.113 -21.515  1.00  0.00   
+        C  
ATOM      4  O   PRO A   6       3.276   4.869 -20.823  1.00  0.00    
+       O  
ATOM     15  N  TRP A   7       1.114   5.225 -20.998  1.00  0.00     
+      N  
ATOM     16  CA  TRP A   7       0.916   5.054 -19.531  1.00  0.00    
+       C  
ATOM     17  C   TRP A   7       0.772   3.567 -19.197  1.00  0.00    
+       C  <>
[download]

the above given two file I have to match file one value with third column value(PRO A) of second which is repeated but I have to consider this only one and pick the column fourth value(6). i have created I subroutine for that for first time it matching correctly but for second file it has missing some value.these both file value will change after completion of first time.

MY code

sub parse_pdb() {
    
    my $file = shift;

    my %hash_pdb = ();

    # Opening of PDB file after dowloading    
    open(FH, $file);
    @atomrecord = <FH>;
    
    foreach my $record (@atomrecord) 
    {   
        chomp($record);
        if($record =~/^ATOM/) {       
            @temp      = split(/\s+/, $record);
            $con_key   = "";
            $con_key   = "$temp[3]"." "."$temp[4]";
            $count = 0;
            
            if( $hash_pdb{$con_key} ) {
                if($val_seen{$temp[5]}) { }
                else {
                    $hash_pdb{$con_key} = $hash_pdb{$con_key}."\t"."$t
+emp[5]"; 
                }
            }
            else {
                $hash_pdb{$con_key} = $temp[5];
            }
            $val_seen{$temp[5]} = 1; 
         }
        if($record =~ /^ENDMDL/){
            print "i am going out of loop\n";
            last;
        }
        
    }
    return \%hash_pdb;
}
[download]

thanks in advance

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