my $file = get_file('pdb244l.ent'); #execute get_file subroutine for a
+ given input file
...
my %record_types = parse_pdb_file($file);
...
sub get_file { #to read from a file
  my ($input_file) = @_;
  open (IN, $input_file) || die "Cannot open $input_file for reading: 
+$OS_ERROR\n"; #open a filehandle or die  
  my $sequence = '';
  foreach my $line (<IN>) { #for each line in the filehandle IN
    $sequence .= $line # add (concatenate) to a string sequence
  }
  return $sequence; #return the string sequence
  close (IN);
}
...
sub parse_pdb_file { #to return a hash with keys that are record type 
+names and
                     #values that are scalar containing lines for that
+ record type
  my @file = @_;
  my %record_types = ();
  foreach my $line (@file) {
    my ($record_type) = ($line =~ /^(\S+)/); #the pattern (\S+) is ret
+urned and saved in $recordtype
    if (defined $record_types{$record_type} ) {
      $record_types{$record_type} .= $line;
    } else {
      $record_types{$record_type} = $line; #.= fails if a key is undef
+ined
    }
  }
  return %record_types;
}
[download]

You are reading in the file as a single block of data but then you are parsing the file as if it were separated into lines which means that you are only populating %record_types from the first line of the file.

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