[Bioperl-l] Structure::IO

[Brian Osborne]

Bernd,

I'm not following your question. The POD in the latest Bio::Structure::Entry
shows:

=head2 chain()

 Title   : chain
 Usage   : @chains  = $structure->chain($chain);
 Function: Connects a Chain or a list of Chain objects to a
             Bio::Structure::Entry.
 Returns : List of Bio::Structure::Chain objects
 Args    : A Chain or a reference to an array of Chain objects

=cut

Which is not what you've copied and pasted. What version of Bioperl do you
use?

Brian O.



On 7/25/06 6:47 AM, "Bernd Web" <bernd.web at gmail.com> wrote:

> Hi,
> 
> Does someone have experience with Bio::Structure::IO?
> The example III.9.1 from the bptutorial.pl covers most, but what is e.g. the
> chain() method of Bio::Structure::Entry doing? The POD states:
> 
>  Title   : chain
>  Usage   : @chains  = $structure->chain($chain);
>  Function: Connects a (or a list of) Chain objects to a Bio::Structure::Entry.
>  Returns : list of Bio::Structure::Residue objects
>  Args    : One Residue or a reference to an array of Residue objects
> 
> But in e.g
> my $stream = Bio::Structure::IO->new(-file => $filename,
> -format => 'pdb');
> while ( my $struc = $stream->next_structure() ) {
>     for my $chain ($struc->get_chains) {
> my $chainid = $chain->id;
> my @chains = $struc->chain($chain);
>    }
> }
> 
> I get Bio::Structure::Chain=HASH(0x9f1ab50).
> 
> What is the function of the chain method and how to use it?
> 
> Best regards,
> bernd
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