[Biopython-dev] PDB occupancy behavior

Morten Kjeldgaard mok at bioxray.dk
Fri Aug 9 09:07:13 UTC 2013

On 09/08/2013, at 10:47, Peter Cock <p.j.a.cock at googlemail.com> 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. 

Putting None in the value of a field that isn't there, but should be according the format specification is more reasonable, since it alerts the user to the fact that something is fishy. However, it should only be done this way if that is a philosophy used throughout the Biopython toolkit. Is it?

I would warn against using NaN since it is non-pythonic and a nightmare to deal with in practice.


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