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

João Rodrigues anaryin at gmail.com
Mon Aug 12 20:39:30 UTC 2013

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"



2013/8/12 Peter Cock <p.j.a.cock at googlemail.com>

> On Monday, August 12, 2013, João Rodrigues wrote:
>> Hi all,
>> Moving to a new thread because this is a very specific issue.
>> I think that, from a programming point of view (but I'm a biologist so
>> correct me if I'm wrong) having None values upon parsing is probably a
>> better idea. Then, when writing, these should be translated to whatever
>> default there is in the PDB documentation.
> Or throw an error to force the user to fix it?
> Or write a blank occupancy to allow preservation of the
> (flawed) input?
> (Thank you for raising the output question now, it is a logically
> consequence of putting None in the parsed structure)
> Peter

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