https://github.com/janjoswig/msmlangerin

Contribution to SciPy John Hunter Excellence in Plotting Competition 2020
https://github.com/janjoswig/msmlangerin

Last synced: 7 days ago
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Contribution to SciPy John Hunter Excellence in Plotting Competition 2020

• Host: GitHub
• URL: https://github.com/janjoswig/msmlangerin
• Owner: janjoswig
• Created: 2020-05-18T08:32:29.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-05-18T09:12:27.000Z (over 4 years ago)
• Last Synced: 2024-10-28T15:03:41.793Z (about 2 months ago)
• Language: Jupyter Notebook
• Size: 7.71 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
Markov-state model of an endocytic pattern recognition receptor

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SciPy John Hunter Excellence in Plotting Competition 2020

Submitted by Jan-Oliver Joswig, PhD student in the Molecular Dynamics Group at Freie Universität Berlin, Germany

Plot

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The notebook in this repository produces an interactive plot, with this default view:

![default](default_view.png)

Clicking on the cluster icons in the legend or on the lines in the lower left plot, changes the illustration:

![cluster7](cluster7_view.png)

Files

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 - msm.ipynb : Jupyter notebook, containing a description of the background of this contribution, pre-requirements to draw the interactive plot, and the interactive plot itself.

 - data/ :

    - dG.npy, x.npy, y.npy : free energy surface (histogram) and bin mids in two dimensions.

    - dG_<*cluster*>.npy, x_<*cluster*>.npy, y_<*cluster*>.npy : free energy surfaces for clusters of conformations.

    - E_<*process*>.npy, x_e<*cluster*>.npy, y_e<*cluster*>.npy : eigenvector surface for the transition processes.

    - its.npy : implied time scales, corresponding to lag times of the MSMs.

    - lags.npy : lag times for estimated MSMs.

    - conf.png : image of langerin (default).

    - cl<*cluster*>.png : image of a representative structure for the clusters.

 - default_view.png : Picture of the default state of the interactive plot.

 - cluster7_view.png : Picture of the interactive plot were cluster 7 and process 4 were picked.

 - screencast.mp4 : Video demonstrating the interactive plot.

 - matplotlibrc : Matplotlib plot configuration file to ensure a sensible layout in the notebook.