DOMINO does not know what type of restraints is given. You can potentially give a NonBondedList - but then the optimization will not be efficient. The optimization workflow ( which calls DOMINO) excludes the restraint.
On Aug 18, 2008, at 11:29 PM, Daniel Russel wrote:
> 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 > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev