[Bioperl-l] how to download PDB files using Bioperl script

[chirag matkar]

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;



Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data



On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu at gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
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-- 
Regards,
Chirag Matkar