IMP-dev January 2010

imp-dev@salilab.org

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no imp-dev meeting tomorrow
by Daniel Russel 18 Jan '10

18 Jan '10

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The last while in IMP
by Daniel Russel 15 Jan '10

15 Jan '10

It has been a while, so the list is long: - IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves. This means that incremental evaluation of restraints in restraint sets now works and that restraints in restraint sets can be individually evaluated. Existing working usage should not have changed (so \c sed should manage updates just fine), but the internal implementation is completely new, so pay attention. - The IMP.examples module now documents how to use the needed aspects of scons and SWIG. - \imp now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are convertible to C++ streams and implicitly constructable from both streams and file paths. As a result, functions that take them will work when called with a string for a file path, a Python file or a C++ stream. - a new base class IMP::Constraint has been added for constraints. Various other classes have been renamed to be consistent. - The IMP::Model now uses dependency information from IMP::ScoreStates to automatically reorder the IMP::ScoreStates so that they are evaluated in the right order. Also, IMP::Model::evaluate() on a subset of the restraints now only updates the needed score states, not all of them. - Functions on rigid bodies no longer provide the IMP::core::RigidMemberRefiner as a default as it is, pretty much always, the wrong thing to use. That class may go away without notice in the future and is no longer documented. - IMP::UsageException and IMP::InternalException are now reserved for their respective checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API exceptions (which are thrown in any build mode and should be documented and tested) and helper exceptions which are only thrown when debug checks are turned on (and hence should not be documented or tested) clearer. - The IMP.examples module is used as the basis for new modules created by the make-module script, so those include more documentation and are tested. - Module overview pages are now generated from the information passed in the SConscript file, rather than from the (now removed) modulename.dox file. See the examples file for an example of the things you can do there. - boost program options is now a checked for dependency. - the IMP::helper::create_simple_connectivity_on_rigid_bodies() and IMP::helper::create_simple_excluded_volume_on_rigid_bodies() now both take an IMP::Refiner as an (optional) final argument. This makes it so they can be used with the rigid bodies created from molecular hierarchies. This code still needs to be updated and the docs don't reflect what the code was or is doing, so use with caution (see notes in the header file).

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IMP_LOG in fast mode ?
by Keren Lasker 09 Jan '10

09 Jan '10

is there a way to print messages using IMP_LOG using build=fast ? or should i just use std::cout ? thanks , keren.

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Samplers concept
by Daniel Russel 06 Jan '10

06 Jan '10

We count use a sampler-level concept. The idea is to provide something higher level that takes a Model and produces a set of good scoring models for analysis. Examples would include: - Domino - a MC/CG scheme for optimizing sets of spheres (a premature version is in helpers) Currently we have StructureSet which has the needed functionality and Domino which has some of it too. I propose I add a base class to kernel which provides a sample method which returns a structure set and provides support for the types of filtering that is currently in StructureSet (eg only keep solutions with low scores and where restraint r is < 10). This would also require moving StructureSet to the kernel. Something like: class Sampler { Sampler(Model *m); // find structures to fill virtual StructureSet* sample(); // filtering methods moved from structure set protected: // adds the model to the set if it satisfies the filters void add_model(); }; Adding the base class provides a place to put documentation for this level of interaction. It also would mean that Domino and the MC/CG protocols would automatically benefit from improvements in filtering and things as well as have more robust storage management (since handling changes to things other than optimized attributes can be tricky). Thoughts/Comments?

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imp-dev meeting today at 1pm
by Daniel Russel 05 Jan '10

05 Jan '10

The email from before the holidays: Since we are trying to clean everything up for the release, I thought it might be good to have a meeting to get people's thoughts on - the IMP documentation: what needs improvement - coming up with a checklist set of standards for documentation to provide some a better starting point than "write some examples and fill in the doxygen docs" - what is a good balance between what I'll call "reference" documentation such as doxygen docs and general examples of using some component and "cookbook" examples which provide a solution to a scenario which is hopefully close to what the user wants (but, on the down side, tends to provide little information about how to solve other problems). Please think about how you use the IMP documentation and documentation of other libraries. What other libraries provide particularly good docs and what guidelines can we draw from those? What are cookbook examples that IMP should include? See you tomorrow.

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quick Q about atom/data/top.lib
by Keren Lasker 02 Jan '10

02 Jan '10

hi, running IMP on a mac. trying to use add_radius , which requires reading force field parameters. however, IMP keeps compiling that it can not file top.lib. can someone please help ( guessing it has to do something with paths / install ) ? thanks, keren,

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IMP-dev January 2010