November 2013 - IMP-dev

changes to RMF format
by Barak Raveh 25 Nov '13

25 Nov '13

Hi Daniel, can you give a quick informal description of the main updates in the format of the new RMF and the major interface changes (or point me to a doc where those exist). I would like to try to hack things to work for the npc with cimera, but will need help with getting started :) Cheers! Barak

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randon number generation on GPUs
by Barak Raveh 18 Nov '13

18 Nov '13

Hi, has anyone experimented with using the GPU to accelerate random number generation in IMP simulations - something along the lines of: http://arxiv.org/abs/1204.6193 http://www.sciencedirect.com/science/article/pii/S0021999111003329 Thanks! Barak

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adding periodic boundary conditions?
by Barak Raveh 15 Nov '13

15 Nov '13

I am considering the addition of periodic boundary conditions support to the BD simulation. I guess it would apply to any optimizer in IMP - what would be the technical complications? I guess naively,what is needed is mainly to reformulate the restraints in a periodic way, but I wonder if it affects any sort of score evaluator optimizations (ClosePairs, etc. - the latter is probably easy to handle as it mainly affects particles at the boundary). In the future it will also allow periodically optimized restraints (such as ones using FFT). Barak p.s. in my particular case, I thought of PBC over the x,y plane only, if that matter for anything, which I believe it doesn't

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MD and WLC functions
by Davide Baù 14 Nov '13

14 Nov '13

Hi, I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. Are they safe to use? Thanks, Davide

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clang-format and autopep8
by Daniel Russel 08 Nov '13

08 Nov '13

My recent favorite coding tools are clang-format and autopep8 that do auto-formatting of C++ and python code respectively. They are pretty easy to set up on a mac given homebrew and access to easy_install. Using them results in nicely formatted python and C++ code with little effort. I put some instructions at < https://github.com/salilab/imp/wiki/Code-formatting>.

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