So what is the protocol for dealing with NonBondedList-like restraints? Do you feed domino a list of restraints which exclude them? That is probably better than having it try to detect and skip such restraints.
On Aug 18, 2008, at 2:15 PM, Keren Lasker wrote:
> > On Aug 18, 2008, at 11:06 PM, Daniel Russel wrote: > >>>> Keren, what is your use case? If it's not "get a list of >>>> interacting >>>> pairs" then we'll need to do something different. >>> Ben - as I wrote in my last reply - it is not all_pairs, since the >>> optimization tries to find that. We get MSMS data which says >>> a,b,c,d,e >>> create a complex - but we do not know which interacts with which. so >>> what DOMINO needs out of the restraint is a-e . >> >> It seems there are four different classes of restraints: >> 1) simple restraints where all particles in the restraint do >> interaction (for example DistanceRestraint) >> >> 2) compound restraints where there are a number of different sets of >> particles where the particles interactions within the set but there >> are no interactions between sets within the restraint: >> PairListRestraint or BondedListRestraint or SingletonListRestraint or >> most of the other restraints >> >> 3) combinatorial restraits where ultimately there will be several >> interacting subsets of particles, but the makeup of the subsets are >> not known until the end of the optimization (ConnectivityRestraint or >> LowestNRestraint) >> >> 4) and a group without a good name where all of the particles >> interact >> in some sense, but only a few of the interactions directly affect the >> final solution (such as NonBondedRestraint). >> >> As far as I can tell, you want: >> 1) the set of all the particles >> 2) a list of sets of particles >> 3) the set of all the particles >> 4) I don't know what you want for this or perhaps just disallow it >> with Domino? >> >> So a get_interacting_sets method which returns a vector of >> Particles's >> (the two s's are intentional :-) would be what you want. >> ___________ > > thanks Daniel ! > DOMINO ignores NonBondedRestraint since otherwise the restraint graph > is a clique. > so yes - get_interacting_sets would be sufficient ! :) > For example, for the MSMS restraint we use ConnectivityRestraint. > > is your solution ok with everyone? > > > > > >> ____________________________________ >> 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