IMP-dev June 2008

imp-dev@salilab.org

4 participants
13 discussions

ParticleRefiner
by Daniel Russel 06 Jun '08

06 Jun '08

I think we should have a new class of object, which I am, for the time being calling a ParticleRefiner to handle hierarchical collision detection and generation of particles on the fly. I am currently using it to generate particles to cover the edges of my unstructured chains in order to better preserve excluded volume. The interface looks more or less like: ParticleRefiner { // return a bunch of particles which refines p Particles refine(Particle p) // clean up the particles which refined p if needed cleanup(Particle p, Particles); }; And the methods must be called as a pair with the result of the first method passed as the second argument to the second method. To use this I currently have a PairScore which I apply to the nonbonded pairs and a ParticleRefine which covers each bond with a set of particles chosen to conserve volume. The PairScore then applies another pair score to all pairs of refined particles. For that particle refined, "refine" creates new particles and "cleanup" destroys them (it probably makes sense to cache particles later). ParticleRefines could also simply move down in a hierarchy, allowing hierarchical collision detection and such. Then cleanup wouldn't do anything at all. Do other people have related use cases they are interested in?

2 2

Bug in GDB 6.6
by Daniel Russel 03 Jun '08

03 Jun '08

The version of GDB installed on the fedora 8 machines has a bug dealing with infinity when running on 64 bit machines. Floats with the value infinity are printed as 0 in the debugger and any functions which take the float by value all called with 0 instead of infinity if you call then the debugger. It can be very confusing :-) It is fixed in gdb 6.8 but there aren't rpms for fedora 8 that I could find. Just so people are aware.

2 2

ParticleRefiner 2
by Daniel Russel 03 Jun '08

03 Jun '08

And cleanup can propagate derivatives to the correct particles.

1 0

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IMP-dev June 2008