[Biopython-dev] Atom.py - _assign_element function (small bug)
p.j.a.cock at googlemail.com
Tue Jan 25 15:38:03 UTC 2011
On Tue, Jan 25, 2011 at 3:00 PM, João Rodrigues <anaryin at gmail.com> wrote:
> Hey all,
> I stumbled upon a little bug today in this function. There's a formatting
> argument missing in line 92:
> msg = "Could not assign element %r for Atom (name=%s) with
> given element %r" \
> % (*putative_element,* self.name, element)
> Apart from this "typo", there's a problem with hydrogens.
> For example with
> Glutamine, the hydrogens HE21 and HE22 (if present) fail to be assigned
> decently with the current setting. I'm adding an additional condition to the
> if-clause in line 77 to correct this. This correction now parses correctly
> these hydrogens (and everyone else). The tests run fine too and I don't
> think I should add anything to them either.
> GLN 205
> HE22 [ 8.46199989 -1.04999995 -15.40400028] 4368
> Final Assignment: H
> I'm pushing this fix to my github atom-element branch, I guess that's easy
> to cherry-pick?
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