[cctbxbb] Documentation .... again
Pavel Afonine
pafonine at lbl.gov
Fri Dec 7 12:41:28 PST 2012
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
> <mailto: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 <tel:%2B44%201235%20778091> (work)
>
> +44 7786 662784 <tel:%2B44%207786%20662784> (work mobile)
>
>
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