SimTk/msmbuilder — pull request #240 by schwancr (2013-09-25 17:55:29+00:00)
Title: Tica mle

Code for doing tICA in msmbuilder

Major changes/additions:

1) src/python/tICA.py : library for calculating the matrices
2) scripts/python/tICA_train.py : script for interfacing with the above library
3) src/python/parsers.py : I had to add the ability to "layer" metrics, so now to specify you want to cluster with tica, you have to do something like Cluster.py tica positions kcenters , because tica needs to work on top of a vectorized representation. This will change in MSMB3, however, when we use "featurizers."
4) src/python/metrics/positions.py : this metric just uses the a distance in R^3N on conformations that are globally aligned to a single structure. This uses lprmsd to do the alignment.