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README.md
earthmover_main.py Runtime improvements: Nov 26, 2019
l2vsemd.py Runtime improvements: Nov 26, 2019
laplacian.py
particle.py
produce_all_figures.py
rotating_shaft_res6.mrc
utils.py
wavetransform.py

README.md

This repository contains code for generating the figures in the manuscript Earthmover-Based Manifold Learning for Analyzing Molecular Conformation Spaces by Nathan Zelesko, Amit Moscovich, Joe Kileel, and Amit Singer.

If you have the prerequsities, you can simply run './produce_all_figures.py' to generate the figures in the paper. This will take a few hours.

Prerequisites:

  • Python 3 with SciPy and scikit-learn. I recommend the Anaconda python distribution.
  • The PyWavelets package (included in Anaconda)
  • The mrcfile Python module, to install it run pip install mrcfile.

For any questions, email nathan@zelesko.com or amit@moscovich.org.

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