[Biopython-dev] Parsing "element" out of PDB file

Peter biopython at maubp.freeserve.co.uk
Wed Jun 23 09:11:06 UTC 2010

On Tue, Jun 22, 2010 at 8:25 PM, João Rodrigues <anaryin at gmail.com> wrote:
> Hello all,
> I've been using some non-standard pdb files outputted by some programs and
> they miss the chemical element column in each ATOM line. I was looking at
> the PDBParser code and element is dealt with like this:
>        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():
>            raise ValueError(element)
>        self.element=element
> In my case, the element line is not "None" but just an empty string - ' ' -
> which fails these tests and is then passed on.

That makes sense, since element=line[76:78].strip() will give an empty
string. A change as you suggest makes sense, but I think just using
"if element:" would be nicer.


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