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🚂 Python API for Emma's Markov Model Algorithms 🚂
Hi, Is it possible to generate continuous time MSM with pyEMMA. Mamta
Models that can provide coarse-grained views of the kinetics (MSMs, HMMs) should provide a hidden or viterbi path. In an MSM, we can roughly do this: ``` python mem =...
In pyemma/msm/estimators/bayesian_hmsm.py, the class BayesianHMS allows a prior to be input for the transmission matrix but not for the emission matrix. This limits the ways that other information can be...
If a class in a hierarchy misses a call to super, eg. the most basic interface does not call super on object (which is pretty common in our code base),...
This would be nice to have for estimating core MSMs. One can find an impl for R here: https://github.com/thomasp85/densityClust @giopina Frank told me, that you are working on this or...
This paper suggests a k-means seeding method that is much faster than kmeans++ and nearly as good. The algorithm constructs a Markov chain on the data points, and in practice...
maybe we can simply change the plot_timescales function to accept a list of TICA or a list of timescale arrays.
Thanks for submitting an issue! Here's a quick checklist in what to include: 1. I created a conda env 2. activated conda env 3. using conda installed pyemma, mdshare, nglview,...
When using the pyemma.plots.plot_contour function, adjusting the vmax and vmin does not change the labels on the associated color bar. I believe that I should be able to create my...
What is the difference between a working directory and a path? I am at a loss. I am trying to fetch the file pH10-amber-R1-dry.xtc via the command files = fetch(...
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🚂 Python API for Emma's Markov Model Algorithms 🚂