On May 25, 2009, at 5:04 PM, Keren Lasker wrote:
> she=keren I guess so: Indeed, was writing from my phone :-)
> 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 > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev