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.
You will need Linux or MacOS and a C compiler.
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
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
To use this package, you will also need Mathematica. Open SelectedExamplesFromPaper.nb in Mathematica and run it.
This project is licensed under the 3-clause BSD license. See the file LICENSE for details.