[Biopython] PDBParser Class --> Output

[Edvin Fuglebakk]

On 13. feb. 2011, at 18.54, Peter Cock wrote:

> On Sun, Feb 13, 2011 at 5:39 PM, Willis, Jordan R
> <jordan.r.willis at vanderbilt.edu> wrote:
>> 1.56,
>> 
>> As it turns out, our molecular modeling suite does not output an
>> element field.
> 
> Could you ask the authors to populate this field?

I would just like to comment on this remark that prior to pdb 2.0 there were no slots for element symbols in the ATOM / HETATM records. So it is probably not uncommon for old software to not populate this field. I have encountered missing elements myself from time to time.

cheers
-Edvin

> 
>> I went into Bio/PDB/Atom.py and commented out:
>> 
>>  if element is None :
>>            import warnings
>>            from PDBExceptions import PDBConstructionWarning
>>            warnings.warn("Atom object (name=%s) without element" % name,
>>                          PDBConstructionWarning)
>>            element = "?"
>>            print name, "--> ?"
>>        elif len(element)>2 or element != element.upper() or element != element.strip():
>> 
>> But it is still taking the time on checking the error even though its
>> not printing it. I wonder if you can just turn it off the error checking
>> completely.
> 
> Commenting it out for now should be harmless - but as I said,
> this bit of code has changed a bit since Biopython 1.56, so I'd
> be interested to hear how the current code in github works for
> you.
> 
> Peter
> 
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