[Biopython] PDBParser Class --> Output

[Peter Cock]

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 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