- IMP-dev - salilab.org

Nonbonded list
by Daniel Russel 05 Feb '08

05 Feb '08

The nonbonded list reports pairs of particles based on the distance between their centers. This is fine as long as all spheres have roughly the same radius. However, if some spheres are much larger than others, then we have problems as the sphere distance may be small when the center distance is large. Offhand, I don't have a simple solution to this problem.

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Rewrite of connectivityrestraint
by Daniel Russel 05 Feb '08

05 Feb '08

I have a rewritten connectivity restraint. The key differences are that - it now looks like the other new restraints (it uses a PairScore and Particles) - the equivalence sets are described purely through the structure of the restraint, rather than, as before, through an attribute. This makes the code simpler and does not remove any documented functionality. - it is actually documented what it does - the test code is simpler I wanted to get people's comments on the new interface and all.

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VRML tweaks
by Daniel Russel 05 Feb '08

05 Feb '08

The VRML log is added to the log documentation module and cosmetic code tweaks.

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patches to utility.h
by Daniel Russel 05 Feb '08

05 Feb '08

I forgot to include the patches to utility.h with my Grid patch. The patch adds comparison operations based on three member variables. It also checks for uniqueness in the imp containers since by and large bad things will happen if you add an object more than once.

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Missing virtual functions
by Daniel Russel 29 Jan '08

29 Jan '08

On my machines the test suite complains that a couple of the restraints defined in python are missing the virtual functions for version and last_modified_by. This patch adds those. On a separate note, it is not clear to me that anyone will ever bother to actually update these fields. Especially since they are defined primarily in the headers and code changes are most likely to occur in the .cpp files. Is it possible to use a SVN hook to update them automatically?

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Re: [IMP-dev] Various small patches
by Ben Webb 25 Jan '08

25 Jan '08

Daniel Russel wrote: > My thought for an improved implementation was to throw the points into a > voxel grid and then have an iterator which traverses the voxel grid and > generates pairs on the fly (rather than generating and storing them). Well, that sounds essentially like a cell-based nonbonded list, which is the most common good way of implementing a nonbonded list (and is what Modeller does) except for the bit about generating pairs on the fly. > How far the iterator … [View More]

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Various small patches
by Daniel Russel 25 Jan '08

25 Jan '08

Here are a bunch of conceptually separate patches. They are unlikely to work entirely separately in practice due to external things like IMP.{ih} and SConscript files and test cases tying them together. The first cleans up the BondedListScoreState by deleted some commented out code adding a comment and adding a set_particles method to go along with the corresponding method in nonbonded list. The next updates the nonbonded list in two ways. First it is refactored so that the … [View More]

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Harmonic oddities
by Daniel Russel 22 Jan '08

22 Jan '08

Now that I actually tried to use it, I find the Harmonic class a bit odd. For one thing the parameter is called "standard deviation" or something, which doesn't mean anything for a harmonic. Secondly, once you figure out what it is, it is multiplied by a many significant figure constant before it is used (the documentation says this is for modeller compatibility). This multiplier makes it very hard to use the Harmonic as part of a scoring function (since it is hard to make the … [View More]

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documentation suggestion
by Daniel Russel 18 Jan '08

18 Jan '08

The IMP doxygen documentation currently throws a lot of class and function names in your face in no particular order (well, alphabetical, but no conceptual order). We can use doxygen modules to give it a nicer structure. This patch adds a module for logging and another for error checking. I think they help a lot. We probably want ones for - Restraints - Optimizers - States - The kernel - Decorators - random helpers - internal stuff To create a module put a \defgroup id Pretty name … [View More]

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Bonded restraint
by Daniel Russel 17 Jan '08

17 Jan '08

This patch adds a restraint for bonded particles using information created by the bond decorators. Currently you must use the decorator to set the length for each bond.

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