Kyle Beauchamp comments

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                                            Kyle Beauchamp

Update tICA docs

Also: IMHO eliminate the ProjectInfo.yaml inputs to scripts, as they get set by default. I think that will help people stay focused on the tICA-specific details.

Update tICA docs

If you do end up merging the theory + applications into a single sphinx file, could you move the link to sit under the "Documentation" section on the main docs...

Update tICA docs

Again, let me know if you run out of time and I can file a PR for some of this stuff.

Update tICA docs

So should I use k-centers or k-medoids when clustering my tICA results? Because we're working in the eigenvector space, I imagine that either one of the following is true: 1....

Update tICA docs

Thanks. Have you ever done k-means? E.g. do I have to update Cluster.py?

Update tICA docs

I think I answered my own question ``` Cluster.py tica atompairs: error: argument alg: invalid choice: 'kmeans' (choose from 'kcenters', 'hybrid', 'clarans', 'sclarans', 'hierarchical') ```

Update tICA docs

We do have a commented-out KMeans class in `clustering.py`...

Update tICA docs

IMHO it looks _highly_ suspicious.

Update tICA docs

If we want kmeans, we should definitely just wrap sklearn.

Update tICA docs

Hey our tICA pipeline is 100% streaming, which is a huge memory advantage over the previous RMSD-based pipeline. This is a huge win that we should advertise.