March 2009 - IMP-dev - salilab.org

This week in IMP
by Daniel Russel 06 Mar '09

06 Mar '09

- Helper functions for creating centroid and cover particles have been added since it is kind of painful and obscure to do on your own. The examples now use these helper functions. - a FixedParticleRefiner has been added for setting up ad-hoc refinement. It just returns a fixed list of particles and so means you can skip creating a hierarchy if you just have one particle you want to refine. - the atom module as been created and all atom and molecule related functionality has been … [View More]

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breaking change with move to IMP.atom
by Daniel Russel 05 Mar '09

05 Mar '09

Molecule-related classes such as ResidueDecorator and AtomDecorator are now in IMP.atom. The IMP.core versions of most things have been left for the time being (but marked as deprecated). Unfortunately, technical difficulties with SWIG prevent that being done easily for ResidueDecorator and AtomDecorator and anything which uses them. The fix is just to replace core.AtomDecorator with atom.AtomDecorator (etc.) (a good excuse to learn sed if you don't already know it :-)

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how do you call VectorD<X> from python ?
by Keren Lasker 04 Mar '09

04 Mar '09

thanks, keren.

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is there a fast way to copy attributes from one particle to another ?
by Keren Lasker 04 Mar '09

04 Mar '09

thanks, keren.

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Other optimizers and salilab only modules
by Daniel Russel 03 Mar '09

03 Mar '09

When trying to figure out why some of my optimizations were failing, I wrapped a number of optimizers available in GSL so they can be used in IMP. These include another implementation of CG, a quasi-newton optimizer and simplex (I mostly wanted CG, but the other came for free). We can't ship the wrappers (unless we want to ship a GPL-ed special edition of IMP along with the LGPL one), but they might be useful to people to experiment with. If others are interested, I'll add a … [View More]

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IMP_LOG and show
by Keren Lasker 01 Mar '09

01 Mar '09

hi, Sometimes it is useful to use X.show() in logging ( for example transformation.show()) is there a way to do that? thanks, keren.

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