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869 discussions

Finer control of monte carlo moves
by Daniel Russel 07 May '08

07 May '08

Added a parameter to the montecarlo optimizer to limit the number of individual moves which are made. You can set the move probabiity and then each particle is moved with that probability. Also added some methods to track and get statistics about the number of accepted and rejected moves.

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Gravity center cleanup
by Daniel Russel 07 May '08

07 May '08

Remove an unused member variable, check that the particles have the needed attributes on addition, and then don't check later.

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Patches for boost 1.35
by Daniel Russel 07 May '08

07 May '08

Frank installed boost 1.35 (since nobody told him not to). The changes to support it are quite minor, just replacing some incomplete definitions with complete ones for objects used in ObjectPointers. The patch is against the current head, so is independent of the other changes.

2 1

Summary with regards to external libraries
by Daniel Russel 06 May '08

06 May '08

After a discussion with Ben it seem like the real holdups are 1) ease of commercially licensing of IMP as a whole. It is better to license something with a fast non-bonded list than without (and CGAL wants money from commercial users). The license of the package itself wouldn't be affected meaningfully by linking with QPL or LGPL or similar dependencies as it is easy enough to isolate contaminated code in particular .cpp files. Personally, I don't think we should put much effort towards the future until it arrives. As long as we abstract from the external libraries well, reimplementing the algorithms later won't be more work than writing it now (and in fact, should be easier since we have a good implementation to compare against). And wrapping it typically quite cheap to write an maintain. 2) Other people probably don't want to install another external library. Fine, as long as other people want to help develop the functionality :-) I would only propose only using libraries that are really easy to install (rpms on redhat, packages on ubuntu, and some sort of installer for mac os and windows and no more effort than "install- command --prefix=path" on the rest). My estimate is that installing a decent library isn't generally more work than than writing and maintaining a couple of lines of code. But maybe others have different weights. We also should not depend on libraries that are evolving too fast since those require the user to update frequently. 3) It is faster to test two separate runtime code paths rather than two separate compile time code paths (since the unchanged tests don't run more than once and the compilation doesn't have to be repeated). I think this is most substantial concern. The best solution I have to this so far is that we should make sure optional dependencies are independent so that simply testing with all of them and without all of them is enough. Strictly speaking, we already need tests without the dependencies (such as boost) to make sure that the installer fails properly. Any other thoughts? A couple less related ones: - We should adopt the policy of building as many things as possible at once-- e.g. impem should be built/installed along with everything else when embed is found (same way modeller support is done now). - I personally don't plan to put much effort into the grid-based nonbonded list and will use the CGAL one. With the yet-to-be-check-in cleanup, much of the code is the same and so many of the parameter tweaks will benefit both. - we need a cleaner way of adding search paths to scons. I had to go figure out what paths IMP already uses to search for boost and find one that wasn't owned by some software in order to tell Frank were to install boost (since mac ports choked while trying to build it on his machine). This is a bit silly.

1 0

More minor patches
by Daniel Russel 06 May '08

06 May '08

Since we are doing the patch game, here are some trivial ones: Add addition and multiplication by a scalar to vector3D (python support needs to be added separately). Just throw an exception on a bad cast (no error message) in the decorator. Currently catching an exception is the only way to check if a particle has the required fields or not. We may want to add a cleaner mechanism. Make sure that bonds connect two different particles.

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IMP todo list
by Daniel Russel 30 Apr '08

30 Apr '08

I added a link to a todo page on the IMP wiki to keep track of the things which should get done eventually.

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PairChainRestraint
by Daniel Russel 15 Apr '08

15 Apr '08

Added an analog of TripletChainRestraint which acts on pairs in the chain.

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decorators
by Daniel Russel 13 Apr '08

13 Apr '08

Another source of excess checks in the IMP code is the decorators. There are three reasons to create them - you have a new particle and need to add fields to it - you have a particle which may or may not have the needed fields - you have a particle which has the needed fields (you know already) We currently support the first two and have no way of expressing the third. In addition, the current syntax is kind of annoying. I propose adding constructors to the decorators from Particle* to express the third. The constructors would have an assertion that they particles have the correct attributes (but this assertion would go away in non debugged code). Thoughts?

2 2

Nightly builds failed
by Ben Webb 12 Apr '08

12 Apr '08

See https://salilab.org/internal/imp/tests.html Or more specifically, https://salilab.org/internal/imp/logs/imp/bin.i386-w32.log (since I've already addressed the other failures). Looks like MSVC doesn't like some part of Daniel's latest patch. I'm not super-familiar with the Boost traits stuff (which looks like the culprit). Anybody have any idea what may be wrong? Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

2 2

pyext sconscript
by Daniel Russel 10 Apr '08

10 Apr '08

make the libs change use a list so that it plays nicely with other changes to the lib path. Before if the LIBS var was non-empty, the last entry and ../src became one argument.

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