[Bioperl-l] PDB Parser

Sendu Bala bix at sendu.me.uk
Thu Aug 16 05:59:08 EDT 2007


neeti somaiya wrote:
> I tried using Bio::Structure::IO::pdb with some code like :-
> use Bio::Structure::IO;
> 
>     $in  = Bio::Structure::IO->new(-file => "pdb100d.ent",
>                                    -format => 'pdb');
> 
>     while ( my $struc = $in->next_structure() ) {
>        print "Structure ", $struc->id,"\n";
>     }
> 
> It works well. But I am not able to find documentation of other methods
> which will give me various specific details available in a pdb file, right
> from title, keywords, references to structure details, atoms, coordinates
> etc. There must be different methods to fetch and parse each of this data
> from a pdb file, right? Where can I find the details?

$struct is a Bio::Structure::Entry, so look at the docs for that:
http://doc.bioperl.org/bioperl-live/Bio/Structure/Entry.html

You'll probably want to look at the docs for the other Structure modules 
as well:
http://doc.bioperl.org/bioperl-live/Bio/Structure/modules.html


I agree, the documentation in this area could be improved. 
Bio::Structure::StructureI could actually contain something, and 
Bio::Structure should actually exist or not be referenced in the docs.


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