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 EM2. 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 <> 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 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 betweenthe modules. Ben -- http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle _______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev