[Biopython] PDBparser question

[Hongbo Zhu 朱宏博]

Hi, Bingding,

try this:

from Bio.PDB.PDBParser import PDBParser

p = PDBParser()
s = p.get_structure('pdbid', YOURPDBFILE)
for m in s:            # iterate over each model
    for c in m:        # iterate over each chain
        for r in c:    # iterate over each residue
            if r.id[0] != ' ' and r.id[0] != 'W':  # non-water HETATM record
                print m.id, c.id, r.resname
                for a in r:
                    print a.name, a.coord

cheers,
Hongbo

On Wed, Sep 17, 2014 at 2:07 PM, Bingding Huang <bdhuang at gmail.com> wrote:

> Dear All,
>    Is that a way to get getting all the ligands residue name and their
> corresponding coordinates from a PDB File using  Bio.PDB.PDBParser ?
> For example, for PDB ID 1F86, the ligand name is T44.
>
> Many thanks
> Bingding
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>



-- 
Hongbo
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20140919/844bb7e6/attachment.html>