she=keren I guess so: Once we will resolve the set_transformation issue I intend to submit the rigid fitting procedure into the svn as follows: 1. rigid_fitting(RigidBody, DensityMap) - will be in EM 2. the code that takes the pdb file and makes an IMP rigid body out of it will be in helpers 3. the code that calls these two functions function and writes out the transformations and scores will be in application. sounds good ? On May 25, 2009, at 4:59 PM, Daniel Russel wrote:
> Helper is explicitly high level functionality built on top of other > modules, so it is likely to depend on everything ultimately. My > thought was that she wanted a function that took a bunch of pdbs and > a map and does rigid fitting. Assuming that is a common operation > that should be outside of an application, helper makes sense, IMHO. > > > > On May 22, 2009, at 11:10 PM, Ben Webb ben@salilab.org 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. >> 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. >> >> Ben >> -- >> ben@salilab.org http://salilab.org/~ben/ >> "It is a capital mistake to theorize before one has data." >> - Sir Arthur Conan Doyle >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev