PyEMMA

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The `plot_cktest()` function in the current (pyemma-2.5.4) release is not flexible enough as we have seen in markovmodel/pyemma_tutorials#142. For instance, I would like to have an auxiliary function for individual...

cwehmeyer

Order of coarse grained states in coarse grained flux unclear

5

The order (indices) of the coarse grained states obtained by fluxAB = msm.tpt(M, A, B) fluxAB.coarse_grain(my_coarse_sets) is unclear. A is always at index 0 and and B is always at...

nsplattner

Improper LaTeX rendering in tutorial notebooks

1

Hi, Some tutorial notebooks have this LaTeX rendering issue: These are the notebooks that I see the problem: - http://www.emma-project.org/v2.5.5/generated/05-pcca-tpt.html - http://www.emma-project.org/v2.5.5/generated/07-hidden-markov-state-models.html There might be more though: You can try...

p16i

Koopman ignores dim setting

6

koopman ignores the number of dimensions requested, and later gives fatal error. Here koopman method of tica generates 3 dimensions, but I have set dim=5 for the tica. tica_obj calculation...

euhruska

relative entropy between two MSM matrices

2

feature request: calculation of the relative entropy between two MSM matrices of the same protein, like in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637129/

euhruska

Following the example of `pyemma.msm.api`, it would be nice to have a `show_progress` parameter in the API functions of - [ ] `pyemma.coordinates` - [ ] `pyemma.thermo`

cwehmeyer

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...

franknoe

Provide n_atoms and other useful selection stuff in featurizer

2

franknoe

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,...

franknoe

ITS/MSM: allow to extend nsamples for error='bayes' a posteriori?

4

It would be great to be able to keep adding samples to an object without having to re-compute from scratch. E.g., after having called msm.its with `nsamples=10`, if I want...

gph82