Christopher Ing

Shape Mismatch Error on MFPT(Errors=True)

4

Might be an easy fix. Here's an example of failing code (modified from the existing mfpt tests). ``` import numpy as np from msmbuilder import tpt from msmbuilder.msm import MarkovStateModel...

Mutual Information with Grassberger/Shuffle Not Matching KNN

1

There appears to be some discrepancy when using the standard CLI mutual information calculation with the grassberger estimator in the latest dev version of mdentropy. When you do >0 shuffle,...

Argument for time units in visualizations

4

There's a few mentions about keeping track of the "frame -> time" conversions in the msmbuilder code, but I didn't see any issue about it there or here. Seems like...

Adding 2D tIC trajectory visualization

3

Taken from [here](http://www.cell.com/biophysj/fulltext/S0006-3495(17)30806-8), but probably in many papers. Should have the 2D free energy underneath? Pretty useful for exploratory analysis, especially when you look at a big grid of them....

Dihedral Backbone Does Not Account for Gaps, Returns Incorrect Values

3

I didn't see anything in the docs that says `biotite.structure.dihedral_backbone()` will return an incorrect value if there's a gap the protein backbone, i.e. it fails `biotite.structure.check_res_id_continuity()`. For example in the...