How to print only predefined sequence in perl - perl

Question

I am trying to print only predefined sequence (ATOM Name) but not getting expected output. I want to print input file as per following expected output. Chain ID may be A to H.
Code:
my $OutputDir = 'C:\test_result_file';
open my $dir, "Document1.txt" or die "Failed to open Document1.txt:$!";
chomp(my #files = <$dir>);
foreach my $file (#files) {
my $win_len = 4;
my #window = ();
my $prev_chain = "";
open my $input, $file or die "failed to open $file: $!\n";
open my $output, '>', "$OutputDir/$file" or die "failed to open $OutputDir/$file.pdb: $!\n";
while (<$input>) {
my ($atom_name, $chain) = (split)[2, 4];
next unless $atom_name =~ /\b(?:C4B|O4B|C1B|C2B|O4B|C1B|C2B|C3B|C1B|C2B|C3B|C4B|C2B|C3B|C4B|O4B|C3B|C4B|O4B|C1B)\b/;
if ($chain eq $prev_chain) {
if (#window == $win_len) {
print_window($output, #window);
shift #window;
}
push #window, $_;
} else {
print_window($output, #window) if #window;
#window = ($_);
$prev_chain = $chain;
}
}
print_window($output, #window) if #window;
}
sub print_window {
my $fh = shift;
print $fh $_ foreach #_;
print $fh "\n";
}
Input File:
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
Expected Output:
A chain:
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
B chain:
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10958 C2B NAD B 363 42.883 -56.336 140.942 1.00 38.13 C
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10956 C3B NAD B 363 42.061 -55.476 141.894 1.00 37.13 C
HETATM10954 C4B NAD B 363 41.496 -54.407 140.932 1.00 39.26 C
HETATM10955 O4B NAD B 363 41.936 -54.715 139.568 1.00 41.96 O
HETATM10960 C1B NAD B 363 42.233 -56.127 139.593 1.00 42.92 C
Description: I want to sort HETATM predefined ATOM name (e.g.: C4B, O4B, C1B, C2B etc.). I have above script so far. So please anyone help me to solve this problem. In my current script I am getting same format but not able to get expected result.
I don't want separate file for A chain and B chain or any chain id. I want to sort ATOM name as per my sequence (Predefined).
My sequence is:
C4B-O4B-C1B-C2B
O4B-C1B-C2B-C3B
C1B-C2B-C3B-C4B
C2B-C3B-C4B-O4B
C3B-C4B-O4B-C1B
e.g., first row: C4B
HETATM10910 C4B NAD A 363 60.856 -58.575 149.282 1.00 40.44 C
Second row: O4B
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
Third Row: C1B
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
Fourth Row: C2B
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
Fifth Row: O4B
HETATM10911 O4B NAD A 363 61.320 -59.488 148.275 1.00 43.48 O
Sixth Row: C1B
HETATM10916 C1B NAD A 363 61.394 -58.766 147.056 1.00 43.29 C
Seventh Row: C2B
HETATM10914 C2B NAD A 363 60.167 -57.970 147.054 1.00 40.90 C
Eighth Row: C3B
HETATM10912 C3B NAD A 363 60.243 -57.426 148.473 1.00 40.37 C
.
.
.
so on
same format for B and other chain also.
Its means I need each row multiple times. all off above atom name should be there in input file and chain wise. we need to copy all of above atom name file and then we need to paste as per above sequence.

Answer 1

It seems to me that your error comes from this line:
my ($atom_name, $chain) = (split)[2, 4];
This will put the 3rd column in $atom_name and the 5th one in $chain.
I guess you want:
my ($atom_name, $chain) = (split)[1, 3];
For the first line you'll get:
$atom_name = C4B and $chain = B