[Biopython-dev] PDB occupancy behavior

Peter Cock p.j.a.cock at googlemail.com
Fri Aug 9 08:47:15 UTC 2013

On Fri, Aug 9, 2013 at 9:39 AM, Morten Kjeldgaard <mok at bioxray.dk> wrote:

> Lenna wrote:
> >  In summary, I am using software-produced PDB files that simply stop
> after
> >  the coordinate data, so occupancy data is missing. Currently, the
> Biopython
> >  PDBParser sets missing or blank occupancy to 0.0. I am suggesting
> changing
> >  this to 1.0.
> I think it is an incorrect default behaviour to set the occupancy

to 1 if it's not present in the file. If the occupancy is not there,

you can't say anything about it, and it should be set to 0, so the

current defaults are correct IMO.
> If, for some reason, you NEED the occupancy to be 1, and it

is not, it is very simple to write a loop modifying it. I.e. special

needs should be taken care of in the users program, not Bio.PDB.
> Cheers,
> Morten
How about the special float values NaN or NA instead?
Or the Python special value None?


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