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869 discussions

Broken tests
by Daniel Russel 08 Nov '10

08 Nov '10

I'm having some technical difficulties and so have not gotten around to fixing the problem breaking the tests. The problem is caused by not providing has_x=False for missing dependencies. I'll fix it when I get back Tuesday unless it gets in someones way before.

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tutorials module in IMP?
by Keren Lasker 05 Nov '10

05 Nov '10

hi - We have few sets of tutorial scripts that are currently scattered in various modules within imp and outside of imp. I think it would make sense to have a module named tutorials and then subdirectories for the different tutorials. For example, our recent book chapter on assembly modeling by comparative modeling and em can go there. thoughts? keren.

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domino
by Daniel Russel 05 Nov '10

05 Nov '10

Keren proposes renaming domino2 to domino (and domino to domino_old or something similar that doesn't break various scripts). In general, changing external source code to use then renamed module would just be a matter of running sed (I'll provide the sed command details if we move it). Any opposition?

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recently in IMP
by Daniel Russel 05 Nov '10

05 Nov '10

Some recent changes of note: - the IMP.statistics module can now be used in other modules as it no longer depends on IMP.em - IMP graphs in python now have a method show_dotty() which displays the graph in an X-window. Welcome to the 1980s. - IMP.domino is now officially deprecated. If you want to build it, add "localmodules='True'" to your config - the typemaps have been fixed so that now passing Objects by things other than pointers and values not be value (or const ref) is likely to produce visible compilation errors. - IMP::atom::Hierarchy requires radii on its leaves - IMP::atom::read_pdb adds radii to the atoms - IMP::helper was merged into IMP::restrainer as all the functionality there was primarily to provide support for restrainer - IMP::domino2::SubsetEvaluatorTable was removed. Pass the model and IMP::domino2::ParticleStatesTable to the IMP::domino2::RestraintScoreSubsetFilterTable instead. - IMP::atom::Selection was added to allow specification of parts of IMP::atom::Hierarchy using biological sorts of names. A few functions to create restraints from them were added too.

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header field for Restraint
by Keren Lasker 03 Nov '10

03 Nov '10

hi - How about adding a std::string variable to Restraint class named header. It can serve as a place holder for useful data about the restraint (papers it was described at etc). Useful when dealing with restraints such as proteomics. Keren.

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radii and read pdbs
by Daniel Russel 01 Nov '10

01 Nov '10

Given that - doing almost anything useful requires adding radii to atoms - we currently have only one way to do that - it generally doesn't matter what radii we use for atoms for most of what we do - one can always overwrite the radii with other values if one wants other values I propose the read_pdb function add radii to the atoms it creates. Comments?

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thoughts on merging IMP.helpers into IMP.restrainer
by Daniel Russel 26 Oct '10

26 Oct '10

Currently, IMP.helpers is only one .h and one .cpp used primarily by restrainer and has now interesting external dependencies. If they are not used much outside of restrainer and there are no plans to add significantly more functionality, I think it might make more sense to move them into the restrainer module. Adapting existing code would be trivial (simply replace IMP.helper by IMP.restrainer), so the cost is small. And reducing the number of modules is always nice.

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Correction: Keren is talking thursday at 3
by Daniel Russel 25 Oct '10

25 Oct '10

Sorry.

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Recently in IMP
by Daniel Russel 25 Oct '10

25 Oct '10

Recent changes: • IMP::atom::Selection was added to allow specification of parts of IMP::atom::Hierarchy using biological sorts of names. A few functions to create restraints from them were added too. • a new example was added in the kernel to show IMP used on a biological system • IMP::display::PymolWriter now supports adding labels to things • IMP::display::PairRestraintGeometry and IMP::display::ConnectivityRestraintGeometry were added to aid in visualizing those restraints. • IMP::bullet was added with an optimizer to use hard body physics to resolve local collisions. • IMP::atom::setup_as_rigid_body() has been deprecated and replaced by IMP::atom::create_rigid_body(). The latter creates the rigid body as a separtate particle so that the molecular hierarchy doesn't have to worry about having its bounding sphere large enough to enclose all the members. • IMP::core::KClosePairsPairScore was added to have count based cutoffs for close pair scoring. • IMP::algebra::get_surface_area_and_volume() was added to compute the two numbers for a set of balls • Two examples were added to the kernel, Nup84 CG and Nup84 RB which illustrate the usage of many aspects of IMP. As a reminder, Keren is discussing the RNAPII example tomorrow at 1.

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next meeting: modeling the RNAPii complex
by Keren Lasker 22 Oct '10

22 Oct '10

based on homology modeling, em and proteomics The meeting will take place on Thursday 3pm.

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