> What are you trying to accomplish? If it is getting a dependency graph, you > will have all sorts of problems with nonbonded lists and other sorts of > indirect relationships.
It is for generating the dependency graph. The idea is to generate the graph and then run inference on it. I am not really interested in all the restraints that build one logic restraint, but Frido and I have for example a restraint set of all the Y2H restraints. I would like to be able to go over it.
> How about requiring that Restraint::get_particles() always returns all the > particles that affect the Restraint? It would be horribly expensive in the > worst case, but.... Maybe we can specific the level of particles we are intersted in, for example if we are working on the protein level, I will not be intersted in getting all the atom particles but just the protein ones.
> We may need to introduce some lower level mechanism. For example, a method on > Object which returns a list of all pointers contained to other objects. I may > be able to implement that in a clean way with only the overhead of one extra > int per pointer. great :) - but we'll have to decide what the list should contain ... :) > > On Feb 23, 2008, at 5:19 PM, Keren Lasker wrote: > >> hi, >> >> I would like to iterate over all restraints. >> To my understating the way to do that today is using >> model.get_restraints(), although the restraints I get might also be >> of type RestraintSet. >> It seems that today one basically needs to know which restraint sets the >> model contains. >> I suggest to add a function Flat() in class Restraint that returns a flat >> list of all restraint in that instance ( will be called >> recursively with RestraintSet). >> >> thoughts? >> >> Keren. >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev