[cctbxbb] sgtbx.space_group and sgtbx.space_group_info query

Mon Oct 14 03:46:23 PDT 2019

sgtbx.space_group is a pure C++ object (well, almost, there are a few auxilliary Python methods injected). Its constructor expects a hall symbol as input:

https://github.com/cctbx/cctbx_project/blob/54344b84c0b4fd00c5ca8438b98a501eca503fae/cctbx/sgtbx/space_group.h#L73-L85

In contrast, sgtbx.space_group_info is a pure Python object that contains utility methods related to handling space groups. Its constructor is much more flexible and can interpret various "conventional" space group strings or from a space group number:

https://github.com/cctbx/cctbx_project/blob/54344b84c0b4fd00c5ca8438b98a501eca503fae/cctbx/sgtbx/__init__.py#L81-L114

I haven't delved into exactly what is happening when you construct an sgtbx.space_group() with the input "C2", but I'm not sure it's a valid hall symbol:

http://cci.lbl.gov/sginfo/hall_symbols.html

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
________________________________
From: cctbxbb-bounces at phenix-online.org <cctbxbb-bounces at phenix-online.org> on behalf of Winter, Graeme (DLSLtd,RAL,LSCI) <Graeme.Winter at diamond.ac.uk>
Sent: 14 October 2019 11:33
To: cctbx mailing list <cctbxbb at phenix-online.org>
Subject: Re: [cctbxbb] sgtbx.space_group and sgtbx.space_group_info query

HI Luc

Thanks for this - it’s a helpful description of the difference which would make a good addition to the documentation

Does not explain why the output is different (or whether the output _should_ be different) though

All the best Graeme

> On 14 Oct 2019, at 11:03, Luc Bourhis <luc_j_bourhis at mac.com> wrote:
>
> Hi,
>
> For the particular operation you showed, space_group_info is more efficient because it caches the result of determining space group type. The computation is delegated to an underlying sgtbx.space_group object. Asking such an object for the type results in a significant bunch of computations being done every time you ask. That’s because essentially a sgtbx.space_group object is just a list of rotation matrices and translation vectors. A space_group_info is more clever!
>
> Moreover, space_group_info provides an easy entry point for many operations which would otherwise be more obscure to write. For example, if you want to change the hand, without space_group_info, you would need to do, starting from a space_group object sg
>
> sgt = sg.type()
> op = sgt.change_of_hand_op()
> sg_other_hand = sg.change_basis(op)
>
> With a space_group_info sgi, you can just do
>
> sgi_other_hand = sgi.change_hand()
>
> to you get a new space_group_info with the opposite hand.
>
> Best wishes,
>
> Luc
>
>
>
>> On 9 Oct 2019, at 18:08, Ben Williams <ben.williams at diamond.ac.uk> wrote:
>>
>> Dear CCTBX devs,
>>
>>  What is a sgtbx.space_group_info object, and why does it do something subtly different to sgtbx.space_group?
>>
>>>>> from cctbx import sgtbx
>>>>> print(sgtbx.space_group('C2').type().universal_hermann_mauguin_symbol())
>>    P 1 2 1 (c,2*a+c,b)
>>>>> print(sgtbx.space_group_info('C2').group().type().universal_hermann_mauguin_symbol())
>>    C 1 2 1
>>
>> sgtbx.space_group_info is notably lacking in docstring (or indeed comments in the code). sgtbx.space_group isn't too hot on the documentation either...
>>
>>  Cheers,
>>   Ben
>>
>> --
>> Ben Williams
>> Post-doctoral research associate
>> Scientific Software
>> Diamond Light Source
>>
>>
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