msmbuilder

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Better error detections in trajectories

7

So this is based off my experiences earlier today working with a large dataset. Basically, I was trying to run tICA on a set of contacts and kept getting e-15...

msultan

pandas error in plotting

8

I am attempting to run through the [tutorial ](http://msmbuilder.org/3.7.0/tutorial.html) to ensure that MSMBuilder is working as expected. However, I have run into an error that I have been unable to...

MTZimmermann

When I use `DihedralFeaturizer` on the `FsPeptide` dataset, some features seem to have incorrect descriptions: ```python >> DihedralFeaturizer().describe_features(trajectories[0])[77] {'atominds': array([174, 176, 182, 184]), 'featuregroup': 'psi', 'featurizer': 'Dihedral', 'otherinfo': 'cos', 'resids':...

cxhernandez

tICA default update

4

Change the default tICA options to use all tICs and kinetic mapping

brookehus

support conda-forge

6

We should build packages on conda-forge

mpharrigan

Use stride in clustering step in Pipeline

1

I was wondering if there was a trick one could use to cluster on a subset of frames (strided) during that step in a `Pipeline`, but then use the full...

synapticarbors

@msmbuilder/developers I guess you guys can't merge pull requests when the tests are failing. I can turn that check off, but I'd rather make the tests be able to pass....

mpharrigan

"MacroAssignments_" does not have Macro state labels in APM clustering

1

Hi, I want to use APM clustering for my data (some distance metrics), but I was wondering first why should all trajectories be at the exact same length? And second,...

zshamsi2

Fix sklearn 0.18 failing test

3

Can someone try to debug the test failure in sklearn 0.18 ``` ====================================================================== ERROR: msmbuilder.tests.test_featurizer_subset.test_that_all_featurizers_run ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/travis/miniconda3/conda-bld/conda-recipe_1476298884112/_t_env/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/travis/miniconda3/conda-bld/conda-recipe_1476298884112/_t_env/lib/python3.5/site-packages/msmbuilder-3.7.0.dev0-py3.5-linux-x86_64.egg/msmbuilder/tests/test_featurizer_subset.py",...

mpharrigan

symlink problems

4

Dear all, I installed msmb as it's written in tutorial and tried to explore example, but faced with problem attached. I checked symlinks, they are not broken (when I press...

DanaNew