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Re: [IMP-dev] IMP's first application


On May 22, 2009, at 11:10 PM, Ben Webb wrote:


Keren Lasker wrote:

It is just not fully clear to me if em_fit should be part of helper
or em ?


Well, it was a hypothetical application, but... neither.
it is not a hypothetical one - because I am actually trying to wrap it up these days .... ;) 


Calculation of
an EM fit should go in the IMP.em module, of course. But if you wanted
to write a little command line application that took a PDB and a density 
map from the user and reported the CCF, for example, that would go in
the 'applications' directory, not in the IMP.em module. (The important
point is that the bulk of the functionality - i.e. reading a PDB file,
reading an EM map, calculating the CCF - should stay in IMP.atom and
IMP.em where it currently is, so that other applications or modules can 
use it.) I don't think anything EM-related should go in IMP.helper,
since we don't want to end up with too many interdependencies between
the modules.
yes - I just was not sure where we draw the line between stuff that should be helper vs. in modules. I think that Daniel meant for the modules to have just a very basic functionality, although I agree that rigid fitting should go in EM. I guess that the decision would be on a case-to-case basis, for example flexible fitting should probably go directly to application and not to em. 


	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle
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