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?
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