[Biopython-dev] Parsing "element" out of PDB file
João Rodrigues
anaryin at gmail.com
Wed Jun 23 16:52:47 UTC 2010
Ok, I've changed it in my local branch to if not element since that covers
both None and empty strings.
Best,
João [...] Rodrigues
@ http://doeidoei.wordpress.org
On Wed, Jun 23, 2010 at 4:11 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:
> 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.
>
> Peter
>
More information about the Biopython-dev
mailing list