November 2010 - IMP-dev

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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