[Biopython] Xpdb error
Markus
Markus.Piotrowski at ruhr-uni-bochum.de
Mon May 23 21:08:52 UTC 2016
Dries Van Rompaey <dries.vanrompaey <at> gmail.com> writes:
>
> Hi everyone,
>
> I'm using biopython to parse some MD files for further processing. I'm
> using the SloppyStructureBuilder from xpdb.py (as described in
> http://biopython.org/wiki/Reading_large_PDB_files), as I have quite a lot
> of residues and the standard class doesn't support that very well.
> Unfortunately, I get the following error:
>
> File "/Users/dvr/Dropbox/Work/xpdb.py", line 76, in init_residue
> residue = Residue(res_id, resname, self.segid)
> NameError: global name 'Residue' is not defined
>
> Does anyone know what's going on here?
>
> Thanks,
> Kind regards,
>
> Dries
>
As Peter has written, add this import in the xpdb file:
from Bio.PDB import Residue
Then in the class
SloppyStructureBuilder(...)
in
def init_residue(...)
replace
residue = Residue(...)
with:
residue = Residue.Residue(...)
Hope this helps.
-Markus
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