msmbuilder

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Implement Path Lumping Algorithm

1

From Xuhui's group http://aip.scitation.org/doi/abs/10.1063/1.4995558 (h/t @msultan)

cxhernandez

bad magic number in libdistance when running develop

1

I'm getting this error: ``` ImportError: bad magic number in 'msmbuilder.libdistance': b'\x03\xf3\r\n' ``` when I run `python setup.py develop`, but not when I run `python setup.py install`.

brookehus

Inconsistency Between msmb commands and save_trajs function

1

I think there is an inconsistency in the formatting of the filenames that are saved when using subcommands from the `msmb` command line functionality and the `save_trajs` function of the...

jeiros

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...

cing

GMRQ test score error

10

Hi, I'm using Pipeline and ShuffleSplit with msmbuilder3.7.0 to perform cross validation of different parameters. I'm iterating through the different parameters and printing the gmrq score of each ShuffleSplit fold...

LaurenReid94

Omnia channel is being deprecated

mpharrigan

retire the msmbuilder email list?

2

How do the @msmbuilder/developers feel about retiring the email list? I think the github issue tracker is probably a better way since the issues are indexed by google and easier...

msultan

sample_msm: api change?

3

I'm trying to draw samples from an msm generated with msmbuilder, but I run into an error with the command shown in `microstate-traj.py`: ```python inds = sample_msm(ttrajs, kmeans.cluster_centers_, msm, n_steps=200,...

smsaladi

Different tICA results from different versions of msmbuilder

1

Hi, Please check out the attachment. I did these tICA analyses on the same system but different versions of msmbuilders (3.0 and 3.7); However, it showed a "shifted" folding behaviors....

juanmit

e.g. (implicitly) recommended practices for implied timescales are different in the [example notebooks](https://github.com/msmbuilder/msmbuilder/blob/master/examples/advanced/implied-timescales.ipynb), and the [tutorial](https://github.com/msmbuilder/msmbuilder/blob/master/msmbuilder/project_templates/msm/timescales-plot.py). I think we should probably update the old/"advanced" example notebooks.

brookehus