[Biopython-dev] PDB occupancy behavior

[Peter Cock]

On Fri, Aug 9, 2013 at 2:07 PM, Lenna Peterson <arklenna at gmail.com> wrote:
> 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

Good (error in strict mode).

Do you think a warning in permissive mode for missing occupancy
is also worth adding, or would using None as the value indicate
that nicely?

Peter