Subject: [IMP-dev] optimizing restraints for speed
From: Daniel Russel <>
Date: Tue, 28 Sep 2010 07:16:58 -0700
Reply-to: List for IMP development <>
prompted by work I did breaking up restraints in domino2 in order to improve filtering and restraint evaluation and work special casing restraints in order to handle spring natively in Bullet and openmm, I thought it could be cool to add functionality to IMP to automatically modify the set of restraints used in order to make them faster. The idea would be to have a static list in the kernel of known optimizations. Restraints, or anything else, could add optimizations to the list, and then optimizers would apply the optimizations before performing its optimization steps (and clean up the changes upon exit from the optimizer).
optimizations could include things like:
- automatically replacing DistancePairScores which use Harmonics with HarmonicDistancePairScore
- replacing BondSingletonScores with HarmonicDistancePairScores when appropopriate (the makeup of the bonds can't change) etc
- use the C++-only generic restraints in some common cases
These can provide a factor of two reduction in evaluation time in certain cases.
- calling optimize with only one iteration would be kind of slow, but why would you do that
- work needs to be done by me :-)
This would be different from the restraint/container optimization in Domino2--the name of that should probably change to decomposition or something less generic.
So, how much do people want more speed when evaluating lots of simple restraints?