I implemented a 1 particle analog of the new Nonbonded restraint. It stores a list of particles and applies a SingletonScore to each particle in the list. One SingletonScore is provided which applies a unary function to the distance to a fixed point. Other ones we might want are ones which restraint based on a single coordinate or pairs of coordinates.
On a separate note, I would move that we remove SphericalRestraint immediately and DistanceRestraint eventually as both roles are better served by bulk restraints.
Daniel Russel wrote: > I implemented a 1 particle analog of the new Nonbonded restraint. It > stores a list of particles and applies a SingletonScore to each particle > in the list. One SingletonScore is provided which applies a unary > function to the distance to a fixed point. Other ones we might want are > ones which restraint based on a single coordinate or pairs of coordinates.
Sounds reasonable. But the patch doesn't apply: $ patch -p0 < ~/list patching file kernel/include/IMP/restraints/ListRestraint.h patching file kernel/include/IMP/SingletonScore.h patching file kernel/include/IMP/singleton_scores/DistanceToSingletonScore.h patching file kernel/include/IMP/singleton_scores/SConscript patching file kernel/src/singleton_scores/SConscript patching file kernel/src/singleton_scores/DistanceToSingletonScore.cpp patching file kernel/src/restraints/ListRestraint.cpp patching file kernel/test/restraints/test_list.py patching file kernel/pyext/IMP.i patch: **** malformed patch at line 400: @@ -82,6 +91,7 @@
> On a separate note, I would move that we remove SphericalRestraint > immediately and DistanceRestraint eventually as both roles are better > served by bulk restraints.
There are plenty of applications for individual distance restraints. But SphericalRestraint should certainly be handled with a ListRestraint and SingletonScore, agreed.
Ben
> There are plenty of applications for individual distance restraints. Are there? I have trouble thinking of examples where you wouldn't have more than one pair and then we are better off with a trivial PairListRestraint (which I think we probably need anyway).
Daniel Russel wrote: >> There are plenty of applications for individual distance restraints. > Are there? I have trouble thinking of examples where you wouldn't have > more than one pair and then we are better off with a trivial > PairListRestraint (which I think we probably need anyway).
In the Modeller world, people want to add individual distance restraints to their systems all the time. Of course, we should have a PairListRestraint as well, but we shouldn't force people to use it just for a single distance.
Ben
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Ben Webb -
Daniel Russel