[Biopython-dev] Bio.PDB - Missing values (was Moratorium on commits?)

Lenna Peterson arklenna at gmail.com
Thu Aug 15 13:18:35 UTC 2013

On Monday, 12 August 2013, João Rodrigues wrote:

> Throwing an error might not be a good idea because when dealing with models
> they sometimes have missing fields... then we'd have to fix them all
> somehow before parsing them.
> The None value seems a good indicator that something is amiss, while not
> putting any value there. There should also be a warning upon writing that
> the value is being replaced by a default value. Blank is also good
> actually, maybe we could add an option to the writer/parser to "preserve"
> values?
I don't think writing string "None" into a fixed width field would be a
good idea. So it's probably best to change occupancy (and any other missing
values set to None) to blank, correct width fields for writing.

I've never tangled with the writer and I have incoming PhD students this
week but I can attempt to add this functionality early next week.


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