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Added link to jupyter notebook [skip ci]
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| for the user. The `diffusion distance` between frames i and j is best | ||
| approximated by the euclidean distance between rows i and j of | ||
| self.diffusion_space. A Jupyter notebook providing an analysis of protein | ||
| opening and closing is provided [here.](https://github.com/jdetle/dimension_reduction/blob/master/diffusionMaps/Diffusion_Map_Analysis_of_ADK.ipynb) | ||
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jdetle
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Generally, links on the word "here" are considered poor semantics. Much better to put the link on an actual noun, e.g.
"See also this Jupyter notebook that uses diffusion maps to analyse the opening and closing motion of AdK."
Eventually, such notebooks should be collected somewhere under the MDAnalysis umbrella — see also MDAnalysis/MDAnalysis.github.io#4. If we use a separate notebooks repo for them then we can make them easily available as http://mdanalysis.org/notebooks.