Example Scripts

These examples provide a number of real-life applications of itcsimlib or show off specialized usage that may not be covered in the Tutorials. The author can provide no assurances regarding their quality or suitability.

Note that the examples/data directory contains the six experimental TRAP+Tryptophan titrations used in the author’s 2017 Biophysical Journal paper, and provide a good example of the file format itcsimlib uses.

dilution.py

Provides an example of a brute force method to estimate heat-of-dilutions in the case of poor baseline control. Should be used as a last resort, and not recommended for poorly-constrained models.

drakon

Demonstrates how the graphical programming language DRAKON (https://drakonhub.com/) may be used to construct Ising-type binding models for use in itcsimlib.

estimate.py

Compares the two different methods for estimating fit parameter uncertainties in itcsimlib; critical chi-square or bootstrapping (jackknife).

hill.py

Generates a hill-like binding isotherm by expanding a model to write the free ligand and lattice saturation (theta) at each titration point.

ising_plotter.py

Shows off itcsimlib’s ability to make figures enumerating the different lattice + ligand configurations for linear and circular lattices, as well as their energetic degeneracy at different model parameters.

mass_spec.ipynb

Extends an Ising model to simulate and fit mass spectrometry data, as well as generate useful population plots.

neighbors.py

Provides an example of how a model may be expanded in order to provide statistics about the number of sites that are empty, or have 0, 1, or 2 neighbors in the system lattices.

populations.py

Extends a model to provide data for comparing the best-fit populations/abundancies of different lattice+ligand stoichiometries at different experimental temperatures.

If you’d like to contribute your own example of itcsimlib usage, please contact the author at mail@elihuihms.com.