[Bioperl-l] PDB Parser

neeti somaiya neetisomaiya at gmail.com
Mon Aug 20 00:33:17 EDT 2007


Hi,

Thanks for the responses.
Another question I had was, I am interested only in pdb id and title, and
for this I am downloading and unzipping each of the full pdb structure
files, parsing to get just id and title. Is there any other data source
which can give me just id and title of pdb structures, without me having to
download the full file of each structre?

Thanks,
Neeti.

On 8/17/07, Sendu Bala <bix at sendu.me.uk> wrote:
>
> neeti somaiya wrote:
> > Hi,
> >
> > I have done it currently as follows :
> [snip]
> > Is this ok?
>
> If it works, of course. There seems to be some redundant code there,
> however. I'm guessing this would be better (assuming your code worked in
> the first place):
>
> while (my $struc = $in->next_structure()) {
>      my $pdb_id = $struc->id;
>      print "Structure ", $pdb_id,"\n";
>
>      my $ac = $struc->annotation();
>      my ($title) = $ac->get_Annotations('title');
>      $title = $title->as_text;
>      chomp($title);
>      if ($title =~ /Value\: (.*)/) {
>          $title = $1;
>      }
>      $title =~ s/\s+/ /g;
>
>      print "Title ",$title,"\n";
> }
>



-- 
-Neeti
Even my blood says, B positive


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