[cctbxbb] Documentation .... again

[Claudia Millán Nebot]

What about some wiki format? :)

Claudia Millán (cmncri at ibmb.csic.es)

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain



2012/12/7 Pavel Afonine <pafonine at lbl.gov>

>  These are basic parameters for FFT based Fcalc calculation.
>
> algorithm = fft or direct summation
> wing_cutoff - is how far away from atomic center you sample density around
> atom;
> u_base (or b_base) - is additional smearing B-factor if input atom has too
> small B so it falls between the grid nodes;
> quality_factor - determines accuracy of sampled density.
>
> For s review, see:
>
> Acta Cryst. (2004). A60, 19-32
> On a fast calculation of structure factors at a subatomic resolution
> P. V. Afonine and A. Urzhumtsev
>
> and references therein.
>
> Pavel
>
>
>
> On 12/7/12 12:35 PM, Richard Gildea wrote:
>
> Hi Graeme,
>
>  I agree that the documentation of much of the cctbx code is somewhat
> lacking, although I am not sure what is the best solution (especially for
> the huge volumes of code that is already written). Perhaps some combination
> of people adding documentation when asking or answering questions on here
> about specifics would go some way to helping future users of the code.
>
>  As to your specific question:
>
>  Setting cos_sin_table=True uses interpolation of values from
> a pre-calculated lookup table for trigonometric function calls in the
> structure factor calculations in preference to calling the system
> libraries. Ralf makes some comment on the speed (and variation in speed) of
> the trigonometric functions in system math libraries in his FABLE paper:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448510/
>
>  However, without digging into the source, I am not sure of the meaning
> of some of the other keywords to that function (e.g. wing_cutoff), which
> makes it hard for me to write comprehensive documentation for this class.
>
>  Cheers,
>
>  Richard
>
>
> On 7 December 2012 01:59, <Graeme.Winter at diamond.ac.uk> wrote:
>
>>  Hi Folks,
>>
>>
>>
>> Been thinking some more about the old chestnut of documentation. The lack
>> thereof is a well understood issue, and to be honest one which is not going
>> to change any time soon as no one has the time to maintain a manual – this
>> is fine and well understood.
>>
>>
>>
>> As a kind of “patch” for this I was wondering if it would be possible to
>> have a forum where someone could ask for e.g. documentation for a currently
>> undocumented function, which could then be added to the subversion in the
>> code itself. For example:
>>
>>
>>
>> cctbx_project/cctbx/xray/structure.py
>>
>>
>>
>> …
>>
>>
>>
>>   def structure_factors(self, anomalous_flag=None, d_min=None,
>>
>>                               algorithm=None,
>>
>>                               cos_sin_table=False,
>>
>>                               quality_factor=None,
>>
>>                               u_base=None,
>>
>>                               b_base=None,
>>
>>                               wing_cutoff=None):
>>
>>
>>
>> what is cos_sin_table for? with things like this there is the attitude
>> that it is safe to ignore, however if we’re writing code to guide people’s
>> experiments it would be good to be sure of this. Some simple documentation
>> explaining this would be very useful.
>>
>>
>>
>> I’m definitely not suggesting (i) that anyone writes a manual or (ii)
>> that all undocumented functions are suddenly documented, only that there is
>> a mechanism set up that someone could ask about this and that someone who
>> knows the answer could commit the changes to cctbx and then reply with the
>> diffs – perhaps the way that stackoverflow works, or an email, or something
>> really lightweight. Even this mailing list could be used I guess?
>>
>>
>>
>> I would be happy to help with this, though the above example is not one
>> where I know the answer!
>>
>>
>>
>> Thoughts?
>>
>>
>>
>> Best wishes,
>>
>>
>>
>> Graeme
>>
>>
>>
>> Dr. Graeme Winter
>>
>> Senior Software Scientist
>>
>> Diamond Light Source
>>
>>
>>
>> +44 1235 778091 <%2B44%201235%20778091> (work)
>>
>> +44 7786 662784 <%2B44%207786%20662784> (work mobile)
>>
>>
>>
>>
>>
>>
>>
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>
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