msmbuilder

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Link examples <--> api reference

1

Each api reference page in the docs (e.g. featurization) should have one or many examples to go with it, and they should be linked. Each example should link to the...

mpharrigan

Added DSSPFeaturizer

2

- [x] Implement feature / fix bug - [ ] Add tests - [ ] Update changelog

HWaymentSteele

Multisequence support

9

I think having ability to juggle multiple sequences within msmbuilder would be awesome. I have been writing some code to that effect in one of my [repos](https://github.com/msultan/kinase_msm) though it would...

msultan

Errors from timescales calculations

1

Hi, I am trying to calculate the implied timescales on my systems, however, it pops up these errors that I had never seen before. Could you help me to interpret...

juanmit

As seen in - https://en.wikipedia.org/wiki/Hidden_Markov_model#Examples - http://emma-project.org/latest/api/generated/pyemma.msm.bayesian_hidden_markov_model.html#pyemma.msm.bayesian_hidden_markov_model

cxhernandez

Would be nice to have more consistency between the MSM and HMM classes.

cxhernandez

try to implement some sort of convergence tests

1

a la pymc: https://pymc-devs.github.io/pymc/modelchecking.html It's not perfect but at least it's a start. We should also consult the stats dept. at some point.

cxhernandez

fs-peptide folding gif from tutorial

1

I received this email > I have a brief question about using MSM Builder, specifically on creating a trajectory of the 1st tICA coordinate. In the the online tutorial, a...

mpharrigan

A lot of defaults are not stated....

cxhernandez

revisit commute mapping NaNs?

1

Commute mapping generates NaNs when the timescale of the process is shorter than the tICA lag time. See #954. I mapped the NaNs to zeros in my original fix (lower...

brookehus