Tutorials

Tutorials for itcsimlib are provided as five Jupyter notebooks (https://jupyter.org/) and cover a range of different topics:

Chapter 1

Provides a basic framework for an itcsimlib analysis script, and demonstrates how to use the simulation, model, and theoretical experiment classes (ITCSim, ITCModel, ITCExperimentSynthetic, respectively).

Chapter 2

Demonstrates how to read in empirical data to create experiments using the ITCExperiment class, use an indpendent-modes model such as NModes to fit such data, and how to obtain fit parameter confidence intervals.

Chapter 3

Describes how to use the ITCGrid class to either restrain model parameters to discretely sampled values during fitting, or to sample starting conditions prior to optimization using multidimensional grids.

Chapter 4

Covers the creation of Ising-type binding models based on the Ising model class, using the arrangement of occupied sites in the lattice to determine binding free energy and enthalpies.

Chapter 5

Demonstrates the use of the Manipulator object, which enables the user to change model parameters in real time and see the effect on model fits.

If a given topic of interest isn’t described here, please take a look in the Example Scripts section, where more advanced topics and additional tools provided by itcsimlib are demonstrated.

As always, if you need help or have constructive criticism, please drop the author a line at mail@elihuihms.com.