Overview

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A solver for thermodynamic binding networks

The thermodynamic binding network (TBN) model abstracts the thermodynamics of a chemical system as a tradeoff between maximizing the number of bonds and maximizing the number of separate complexes. This package provides a Mathematica interface to a solver for answering questions about stable configurations of a TBN.

Take a look at guide.pdf for details.

Installing

You will need Linux or MacOS and a C compiler.

  1. Download and build a SAT solver with a standard DIMACS interface like Glucose Syrup. You should now have an executable for it somewhere. Say the path to it is $SAT.

  2. Change to the root directory of this package. Build the C code, and create a symbolic link to your SAT solver executable.

    gcc TBN-encode.c -o TBN-encode
    ln -s "$SAT" satsolver
    

Running

To use this package, you will also need Mathematica. Open SelectedExamplesFromPaper.nb in Mathematica and run it.

License

This project is licensed under the 3-clause BSD license. See the file LICENSE for details.