mdentropy
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msmbuilder
Analyze correlated motions in MD trajectories with only a few lines of Python.
Ubuntu 18.04.4 LTS Anaconda python conda version : 4.8.3 python 3.6 # also tried with 3.7 numpy version 1.12.1 # also tried with newer numpy versions pandas version 0.23.4 mdentropy...
>>> msm_assignments = pipeline.fit_transform(trajectories) Traceback (most recent call last): File "", line 1, in File "/home/midhun/anaconda2/envs/py36/lib/python3.6/site-packages/sklearn/pipeline.py", line 298, in fit_transform Xt, fit_params = self._fit(X, y, **fit_params) File "/home/midhun/anaconda2/envs/py36/lib/python3.6/site-packages/sklearn/pipeline.py", line 230,...
When calculating MI, how do you define alpha angle,contact and dihedral?
There's some IL-2 data that can be used for unit testing
[n2](https://github.com/kakao/n2) seems promising. Will do some benchmarking.
Currently seeking logo ideas. Preferably somehow related to entropy....
Newly implemented (using knn estimator): http://scikit-learn.org/stable/modules/generated/sklearn.feature_selection.mutual_info_regression.html#sklearn.feature_selection.mutual_info_regression Would definitely help with code maintainability.
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,...
In this PR, we add the ability to directly compute transfer entropy with timeseries containing discrete random variables or, equivalently, continuous data that has been pre-binned. This has been accomplished...
reference: http://docs.scikit-nano.org/dev/_modules/sknano/core/analysis/periodic_kdtree.html not entirely necessary, but would definitely improve entropy estimation for dihedrals.
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Analyze correlated motions in MD trajectories with only a few lines of Python.