[Bioperl-l] PDB Parser

neeti somaiya neetisomaiya at gmail.com
Fri Aug 17 06:42:09 EDT 2007


Hi,

I have done it currently as follows :

 while ( my $struc = $in->next_structure() )
                {
                        my $title;

                        my $pdb_id = $struc->id;
                        print "Structure ", $pdb_id,"\n";

                        my $ac = $struc->annotation();

                        foreach my $key ( $ac->get_all_annotation_keys() )
                        {
                                if($key eq "title")
                                {
                                        my @values =
$ac->get_Annotations($key);
                                        foreach my $value (@values)
                                        {
                                                $title = $value->as_text;
                                                chomp($title);
                                                if($title =~ /Value\: (.*)/)
                                                {
                                                        $title = $1;
                                                }
                                                $title =~ s/\s+/ /g;

                                                print "Title ",$title,"\n";
                                                last;
                                        }
                                        last;
                                }
                  }
}

Is this ok?

On 8/17/07, neeti somaiya <neetisomaiya at gmail.com> wrote:
>
> Hi,
>
> My main concern is just the pdb id and title. PDB id I am able to fetch
> easily, but is there a method which can give me the title of the PDB
> structure?
>
> Like for example from the following :-
>
> HEADER    DNA/RNA                                 05-DEC-94   100D
> TITLE     CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER
> TITLE    2 R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO
> TITLE    3 PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING
> COMPND    MOL_ID: 1;
> COMPND   2 MOLECULE: DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)-
> COMPND   3 R(*G)-3');
> COMPND   4 CHAIN: A, B;
> .
> .
> .
> .
>
> I just want "CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER
> R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND
> MINOR GROOVE TERTIARY BASE-PAIRING".
>
> Thanks,
> Neeti.
>
> On 8/16/07, Chris Fields <cjfields at uiuc.edu> wrote:
> >
> >
> > 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
> >
>
>
>
> --
> -Neeti
> Even my blood says, B positive
>



-- 
-Neeti
Even my blood says, B positive


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