[Biopython-dev] Moratorium on commits?

Morten Kjeldgaard mok at bioxray.dk
Mon Aug 12 18:33:26 UTC 2013

On 11/08/2013, at 22:50, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> I still feel this was a minor change (although of
> course important to some, including you). This is
> parsing of malformed PDF files where the user
> ALREADY gets a warning (or error in strict mode,
> where there would be no functional change) that
> there is a problem with the occupancy data.
> One reason why I specifically talked about small
> commits (in the sense of a simple diff) above is
> they are trivial to revert if the need arises, or as
> in this case, modify:
> https://github.com/biopython/biopython/commit/500c3c2ea900fd8c8f5123f571d4d9a244ee898e
> This change was suggested and supported by
> people who've been actively contributing to the
> Biopython structural module for some time, so I
> had reason to trust their good judgement, and as
> I wrote at the time there was a clear consensus
> with three people in all happy with the idea:
> http://lists.open-bio.org/pipermail/biopython-dev/2013-August/010773.html

I respect that you listen more to developers that have been contributing for a long time. That is quite understandable, but I hope that does not prevent me from contributing my opinions.

What prompted my response was the suggestion that the occupancy should be set to 1.0 if it is abscent from the file, i.e. if the PDB file is malformed. I think that is an incorrect behavior, and I say that not as a core developer, but as a crystallographer. If invalid data is present in the file, you do not want the toolkit transforming it to valid data.

After thinking about it, the suggestion to set values to None when they are not defined in a malformed file now appears quite reasonable, but if it is done this way with occupancies, it should also done this way with B-factors, chain identifiers and other values that are mandatory in the file according to the format specs. From the users perspective, if the values returned are None, you are alerted to the fact that something is wrong, and you should make an appropriate choice, whatever that may be.


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