February 2008 - IMP-dev

A few more patches
by Daniel Russel 19 Feb '08

19 Feb '08

I modified the log states to have a function to force writing of a file whether or not you are skipping files. Seems useful to have (and used in the next patch) and I wrote an example. Perhaps should have more documentation, but it is a start. finally, the BondDecoratorList now checks to make sure that both particles are contained in the list of particles. And really finally the SConscript files for the headers weren't all updated after the last move (the restraints one, for example).

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sundry patches
by Daniel Russel 19 Feb '08

19 Feb '08

smallest first: bonddecoratorlistscorestate returns and prints the number of bonds define types for pairs in base_types (a later patch exports them to python) I forgot to have the spheres list update the bonded lists Finally, a pairlist restraint and minor tweaks to list restraint since I was mimicking it

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DistanceRestraint
by Daniel Russel 19 Feb '08

19 Feb '08

It seems to me it should be PairRestraint and take a PairScore. Right? Currently I have issues if I want to apply it to two spheres.

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NULL model pointer in opt
by Daniel Russel 19 Feb '08

19 Feb '08

Optimizer was not initializing its member model_ pointer. The patch also has a few checks I added while trying to track the problem down.

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Re: [IMP-dev] cleanup of cruft
by Ben Webb 19 Feb '08

19 Feb '08

Jeremy Phillips wrote: > Frank's restrainer, yes, but nothing Bret did, which is what I assume > Ben meant. I think the consensus was to scrap that.... Yes, exactly - I meant Bret's web interface thingy: https://svn.salilab.org/impmod/trunk/restrainer/ Frank's Restrainer is, of course, its own little world, so nothing we do with IMP will break it. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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cleanup of cruft
by Daniel Russel 19 Feb '08

19 Feb '08

Can we just delete everything in kernel/doc/examples? The code I looked at doesn't work any more. Andrej pointed Marc at IMP and he was, quite reasonably, trying to figure things out based on code there. In addition, I Ben sets it up so that scons test runs the code in examples, I'll submit a few more reasonable instances. If the code doesn't get run, it will just rot again. Thanks. Finally, can we delete all the restraint IO stuff from the XML loader? It uses restraints we don't really want people to use, is quite inflexible etc. And I would not want someone to be tempted to use it.

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Nonbonded list for spheres
by Daniel Russel 18 Feb '08

18 Feb '08

Here is a non-bonded list for spheres. It works by binning the spheres based on radius and creating a grid for each bin. To build the nbl it searches between the grids as needed. It can be made a lot more efficient, but at least it seems to work and is straight forward. Somewhere this patch making printing of particles more useful got lost.

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Various minor patches
by Daniel Russel 18 Feb '08

18 Feb '08

In brief, NonbondedListScoreState is now an abstract class and the corresponding class is AllNonbondedListScoreScoreState. I don't like the name, so if you have a better one, please suggest it. I needed to have a base class for the lists so that I can implemented one which handles particles with varying radii nicely. In more depth: 1) Better string handling in the exception base class 2) added bounds check on vector access 3) Refactored the non-bonded list code. There is a new internal class which implements a voxel grid for particles. There is also a base class for non-bonded lists which AllNonbondedList and BipartiteNonbondedList both inherit from. I also got rid of the subdir for the bonded lists and fixed various documentation. SConscipt files and IMP.h changes are not submitted.

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Exception cleanup and mover cleanup
by Daniel Russel 16 Feb '08

16 Feb '08

The first patch - moves the exception definitions to a new header (IMP/exception). log.h includes this so no other headers have to change directly. As a side effect, exceptions are no longer exported to python. We can revert this easily enough - adds a IMP::Exception base class for all exceptions which stores a string and implements what() so the the string is passed to python - all exceptions (except ErrorException) now require a string (or const char*) in their constructor so that python gets the message - adds a ValueException to thrown when you have out of range values. I was throwing other more awkward ones before the second patch cleans up comments in the movers and adds methods to set the radius/standard deviation. As a side note, don't we want IMPDLLEXPORT on Linear? As it is, you end up with two separate copies of the class, on in libimp and one in _IMP. Not catastrophic, but probably not what we want. Such a problem appears to be catastrophic with exceptions :-)

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Montecarlo doc tweaks
by Daniel Russel 15 Feb '08

15 Feb '08

Added montecarlo to the optimizers group and created a subgroup for the movers. Also removed duplicate restraint documentation which snuck in there somehow.

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