Hello everyone, I’m working on a few iperl notebooks for a publication that I’m trying to push through. I want to show an analysis of protein fluctuations and correlated motion using a gaussian network model (GNM). GNM is easy to implement, you just need to calculate a Kirchoff matrix and then compute the pseudo inverse (first eigenvalue is zero). See the following:
https://github.com/demianriccardi/HackaMol/blob/master/examples/Notebooks/HackaMol-GNM.ipynb <https://github.com/demianriccardi/HackaMol/blob/master/examples/Notebooks/HackaMol-GNM.ipynb> I use PDL::LinearAlgebra to calculate the pseudo inverse, but I felt a little squeamish when I downloaded it and looked around at the test suite. Is PDL::LinearAlgebra my best option, or are there other recommended ways of going. Thanks! Demian p.s. Zaki’s iperl notebook has changed my life almost as much as moose has.
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