Metadata-Version: 2.1
Name: cmdtools
Version: 1.0.1
Summary: A collection of tools relating to transfer operators
Home-page: https://github.com/zib-cmd/cmdtools
Author: Alexander Sikorski
Author-email: sikorski@zib.de
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: scikit-learn
Provides-Extra: slepc
Requires-Dist: slepc4py ; extra == 'slepc'
Provides-Extra: tests
Requires-Dist: pytest ; extra == 'tests'
Requires-Dist: pytest-cov ; extra == 'tests'
Requires-Dist: pytest-benchmark ; extra == 'tests'

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# cmdtools

This Python library implements a suite of tools used and/or developed in the [Computational Molecular Design](https://www.zib.de/numeric/cmd) group of the Zuse Institute Berlin.


## Installation

Install with `pip install cmdtools`
    (If you want to use the SLEPc library for sparse Schur decompositions install cmdtools with the extra slepc, i.e. `pip install "cmdtools[slepc]"`)

## Contents
*  `pcca`: An implementation of (generalized) PCCA⁺ using the Schur decomposition
*  `ajc`: A sparse implementation of the augmented jump chain
*  `diffusionmaps`: Diffusionmaps with sparse support and out of sample extensions
*  `galerkin`: Trajectory based estimation of the transfer operator using a Galerkin projection onto Gaussian RBFs
*  `gillespie`: Trajectory simulation from a generator
*  `newton_generator`: Multi-step estimation of the generator via the Newton polynomial
*  `picking_algorithm`: Given a set of datapoints, pick n points such that they are distributed as evenly / equidistant as possible
*  `sqra`: The Square Root approximation, estimating the generator for the diffusion in a given potential
*  `voronoi`: Voronoi clustering of trajectories and estimation of the transfer operator with different metrics and center strategies.
*  `diffusion`: A collection of dynamical systems (So far the double- and triple-well)


