[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:

You'll probably want to look at the docs for the other Structure modules 
as well:

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.

More information about the Bioperl-l mailing list