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 .... ;)
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.Calculation of an EM fit should go in the IMP.em module, of course. But if you wantedto write a little command line application that took a PDB and a densitymap 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 andIMP.em where it currently is, so that other applications or modules canuse 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