[BiO BB] Re: [BioPython] Automated ligand extraction from PDB

Shameer Khadar skhadar at gmail.com
Fri Oct 20 06:53:00 EDT 2006

I strongly beleive this can be done using a 'grep' and 'substitution'
commands in linux.
Since the ligand data starts with HETATM, they can  be easily grepable.

No need any 'parser' - a simple perl script can do this !
Shameer Khadar

On 10/20/06, Tomek Jarzynka <tomee at genesilico.pl> wrote:
> Hi,
> I would like to create a script that would take a PDB file as input,
> try and identify the ligand structures and delete them from the PDB
> file. I figured this would be possible with Biopython by looking at
> the atom id (whether it contains 'H_') and subclassing Select to
> not allow those items to be written to a file.
> Is there any more elegant way of doing this, perhaps another PDB parser
> framework, or maybe someone has already done similar work?
> Thanks in advance,
> --
> Tomasz K. Jarzynka  /  +48 601 706 601  /  tomee(a-t)genesilico(d-o-t)pl
> Laboratory of Bioinformatics and Protein Engineering | www.genesilico.pl
> International Institute of Molecular and Cell Biology | www.iimcb.gov.pl
> "You can have either freedom of speech or quality of communication.
>         -- Orson Scott Card"
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