[Bioperl-l] PDB Parser

Chris Fields cjfields at uiuc.edu
Thu Aug 16 10:12:30 EDT 2007


On Aug 16, 2007, at 4:59 AM, Sendu Bala wrote:

> 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.

There was a discussion a while back on refactoring the code within  
Bio::Structure to better deal with HETATM and other stuff.  As far as  
I'm concerned it's open for anyone wanted to tinker with it.

chris


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