Encodermap

For a quick intro have a look at the following video:

Encodermap is a neural-network autoencoder based approach to dimensionality reduction.

Start with the tutorials

You can access all EncoderMap tutorials online on mybinder.org:

Getting started

For installation instructions, and FAQs refer this section.

User guide

The user guide contains more in-depth information about concepts and use cases.

API reference

Collection of all code documentation.

Developer guide

The developer guide helps you in contributing to encodermap.

Test and Coverage Reports

Reports of unittests

Code coverage

Citations

You can find more information in these two articles. Please cite one or both if you use EncoderMap in your project. [LP19] and [LBJP19]

[LBJP19]

Tobias Lemke, Andrej Berg, Alok Jain, and Christine Peter. Encodermap (ii): visualizing important molecular motions with improved generation of protein conformations. Journal of Chemical Information and Modeling, 59(11):4550–4560, 2019.

[LP19]

Tobias Lemke and Christine Peter. Encodermap: dimensionality reduction and generation of molecule conformations. Journal of chemical theory and computation, 15(2):1209–1215, 2019.