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Re: [IMP-dev] Update SphericalRestraint

while the second is the excluded volume restraint, a loop over all nonbonded pairs. Part of the nonbonded pair generation mechanism excludes bonded particles.
Right, then the interesting question is how to do the non-bonded particle generation. From what I gather with modeller, the speedups compared to what I am describing come from using a proximity structure and caching the list rather than separating the bonded from the nonbonded computations. When generating the list you have to do a similar lookup to see if each pair is bonded? Or is there some more clever way of structuring things?