Frank Noe

We just plotted contactmaps using a combination of mdtraj and pyemma. I think this is a useful feature and easy to implement, so why not offer a plotting function for...

Microstate label and connected set discussion

3

I've just received a comment from a PyEMMA user: ``` In this work, we assigned an additional label to each microstate in the unused digit position of the state labels,...

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 =...

Fast kmeans++

3

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...

Refers to: https://github.com/markovmodel/adaptivemd/blob/master/examples/tutorial/4_example_advanced_tasks.ipynb But addresses also general package/API issues along the way. I'll have a number of questions / comments about the details of this notebook, but first of all...

This refers to https://github.com/markovmodel/adaptivemd/blob/master/examples/tutorial/3_example_adaptive.ipynb While I'm working through the notebook, some of the questions / comments refer to the framework in general. Apologies if I am making comments or asking...

Complete API docs of all user-accessible objects and functions. Currently only a small fraction of these have docs.

This refers to the tutorial part 2: https://github.com/markovmodel/adaptivemd/blob/master/examples/tutorial/2_example_run.ipynb - General: - I think it would be important to make clear that this notebook (if I understand correctly) defines an execution...

These are comments / requests for tutorial part I: https://github.com/markovmodel/adaptivemd/blob/master/examples/tutorial/1_example_setup_project.ipynb Overall I really like the API. Here are a few minor issues and comments: General: The hardest part in learning...