[Biopython-dev] PDB occupancy behavior

[Lenna Peterson]

On Friday, 9 August 2013, Peter Cock wrote:

> On Fri, Aug 9, 2013 at 10:07 AM, Morten Kjeldgaard <mok at bioxray.dk<javascript:;>>
> wrote:
>
> > On 09/08/2013, at 10:47, Peter Cock <p.j.a.cock at googlemail.com<javascript:;>>
> wrote:
> >
> > > How about the special float values NaN or NA instead?
> > > Or the Python special value None?
> >
> > TBH I don't think there is any good reason to change the current
> defaults.
> > On the contrary, we should be careful when changing default values since
> > this might break users' programs.
> >
> > My point is, that Lenna wants to read files that does not follow the PDB
> > standard, and so she needs to make provisions for that in her own
> program,
> > not the toolkit.
> >
> >
> Do you think this should be something handled differently in strict and
> permissive mode? Should missing occupancy give a warning or error in strict
> mode?


(Resending to dev list)

None in permissive mode makes a lot of sense to me.

Missing occupancy is a fatal error in strict mode.

Lenna