IMP-dev November 2011

imp-dev@salilab.org

5 participants
5 discussions

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Maximum number of restraints
by Davide Baù 29 Nov '11

29 Nov '11

Hi, is it possible to set a maximum number of restraints to a particle? Thanks, Davide

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algebra::get_unit_bounding_box_d()
by Daniel Russel 23 Nov '11

23 Nov '11

algebra::get_unit_bounding_box_d() currently returns a bounding box with diameter 1 (that is, one reaching from 0 to 1 in each coordinate). This isn't documented and is kind of inconsistent with algebra::get_unit_sphere_d() which returns a sphere with radius 1. I'd like to change the former to be consistent (so get_bounding_box(get_unit_sphere_d()) == get_unit_bounding_box_d()). It doesn't look like anything in IMP depends on the old behavior, but it is used in various tests and examples (at least some of which seem to assume the behavior I'd like to change it to). Thoughts? Objections?

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Documentation pages
by Davide Baù 21 Nov '11

21 Nov '11

Hi, is there a problem with the online documentation? It seems I can access only the example pages. Thanks! Davide

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breaking changes to RMF
by Daniel Russel 09 Nov '11

09 Nov '11

I'm making some breaking changes to RMF files as part of a cleanup. I think they are all in obscure areas that no one is using yet, but I just want to make sure that no one is surprised: - bonds will be stored using a different scheme. As a result, existing bonds in the file will be ignored. Adding backward compatibility support for this would be pretty easy. - the API for storing/extracting bonds has changed (the old API is still there, just no longer documented and now deprecated). There is now a general purpose API for storing data related to tuples. - the way triangulated surfaces are store is changing (and triangulated surfaces from IMP aren't supported at the moment as I have not gotten around to updating it). It now uses the variable length entries rather than external hdf5 data sets - the way segments and cylinders are stored has changed On the plus side: - you can now associate arbitrary data with any tuple of hierarchy nodes (at the moment, the tuple must have size <= 4). So you can store information about bonds, torsion angles, angles etc. - mesh surfaces that vary from frame to frame are now supported - external HDF5 data sets are not used - polylines and poly-cylinders are now supported

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IMP.atom.Chain.set_id()
by Keren Lasker 31 Oct '11

31 Oct '11

hi: IMP.atom.Chain(mh).set_id('A') does not result in: IMP.atom.get_chain(IMP.atom.get_leaves(mh)[0]) == 'A' what am i doing wrong? thanks, keren.

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IMP-dev November 2011