[Bioperl-l] How to distinguish pdb Helix from Sheet?

[Jason Stajich]

I'm not entirely sure of the best way to do this - but here is something
to get you started.    If you work out a good strategy to the data I think
we'd appreciate any useable scripts back in Bioperl.  There seem to a
scant few doing structural stuff and using Bioperl so we don't have a lot
of good example applications written yet for the Structure objects.

use Bio::Structure::IO;
use strict;

my $in = new Bio::Structure::IO(-format => 'pdb',
				-file   => $filename);

                             # first 2 nums are from the rol definition
	                     # that Kris sets up in the pdb parser
	                     # the 3rd number is the index of the
                             # Chain ID for that type of feature
my %rol_length = ('sheet' => [8,70,5],
		  'helix' => [8,76,4]);
my $struc = $in->next_structure;

foreach my $type ( keys %rol_length ) {
    my $uct = uc($type);
    my @header = $struc->annotation->get_Annotations($type);
    my $h = shift @header;
    next unless defined $h;
    my ($rol_begin,$rol_end,$chain_index) = @{$rol_length{$type}};
    my $length = $rol_end - $rol_begin +1;
    my $k = $h->value;
    my $uct = uc($type);
    # change the whole concatenated string into \n delimited
    # string
    $k =~ s/(.{$length})/$uct$1\n/g;
    $k .= "\n";
#    print $k; # print if you want to see the whole $type record
    my @records = split(/\n/,$k);
    foreach my $r ( @records ) {
	# based on
        # http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
	my @line = split(/\s+/,$r);
	print "chain $line[$chain_index] contains $uct\n";
    }
}


--jason


On Fri, 21 Nov 2003, Jeff Donner wrote:

> Hi,
>
>    How can you tell which chains are HELIX and which SHEET
> after you've read a pdb file with Bio::Structure::IO?
>
> Is it possible even?
>
> Thanks,
>
> Jeff Donner
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu