[Bioperl-l] Structure::IO

[Adam Kraut]

Hi bernd,

Can you better explain what it is you want to do with pdb files?  From your
example it looks like you want to do something with each chain, but it is
unclear what you want to do here:
my @chains = $struc->chain($chain);

With that said, I was never able to use Bio::Structure in the way that I
wanted.  I now use the MMTSB Perl libraries instead:
http://mmtsb.scripps.edu/cgi-bin/tooldoc?perlpackages

Specifically the Molecule module may be useful here.

Regards,
Adam

On 7/25/06, 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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-- 
Adam N. Kraut
National Resource for Biomedical Supercomputing
http://www.nrbsc.org/sb/