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Moiety Modeling Implementation

Project description

Current library version Supported Python versions Travis CI status

moiety_modeling package provides facilities for moiety model representation, model optimization and model selection.


Please cite the GitHub repository until our manuscript is accepted for publication:


‘moiety_modeling’ runs under Python 3.6+ and is available through python3-pip. Install via pip or clone the git repo and install the following depencies and you are ready to go!

Install on Linux

Pip installation

python3 -m pip install moiety-modeling

GitHub Package installation

Make sure you have git installed:

git clone


‘moiety_modeling’ requires the following Python libraries:

  • docopt for creating the command-line interface.

  • jsonpickle for saving Python objects in a JSON serializable form and outputting to a file.

  • numpy and matplotlib for visualization of optimized results.

  • scipy for application of optimization methods.

  • SAGA-optimize for parameters optimization.


Using moiety_modeling to optimize parameters of moiety model.

python3 -m moiety_modeling modeling --models=<model_jsonfile> --datasets=<dataset_jsonfile> --optimizations=<optimizationSetting_json> --repetition=100 --split --multiprocess --energyFunction=logDifference

Using moiety_modeling to analyze optimized results and select the optimal model.

python3 -m moiety_modeling analyze optimizations --a <optimizationPaths_txtfile>
python3 -m moiety_modeling analyze rank <analysisPaths_txtfile> --rankCriteria=AICc

Using moiety_modeling to visualize the optimzed results.

python3 -m moiety_modeling plot moiety <analysisResults_jsonfile>


Made available under the terms of The modified Clear BSD License. See full license in LICENSE.


  • Huan Jin

  • Hunter N.B. Moseley

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