[Biopython] Xpdb error

[Dries Van Rompaey]

Thanks for the help everyone, works like a charm now.
I made a pull request featuring the updated imports.

On 23 May 2016 at 23:53, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Well spotted Markus,
>
> Sorry, I forgot about the confusing import - something
> PEP8 guidelines would prevent with new modules.
> You can probably do this as a one line change:
>
> from Bio.PDB.Residue import Residue
>
> Peter
>
>
> On Mon, May 23, 2016 at 10:08 PM, Markus <
> Markus.Piotrowski at ruhr-uni-bochum.de> wrote:
>
>> 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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>
>
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