itcsimlib

itcsimlib uses statistical thermodynamics (ST) models to simulate and fit binding data, in particular those obtained from isothermal titration calorimetry (ITC). Because statistical thermodynamics models can calculate the prevalence of individual lattice+ligand configurations, itcsimlib can be readily adapted to fit mass spectrometry data as well.

itcsimlib also provides a number of tools for understanding / analyzing Ising ST models that may be of general interest to those studing complex binding processes. These include automated generation of partition functions and figures depicting lattice + ligand configuration with their degeneracies.

Getting Started

  • Installation instructions for required dependencies and optional compilation.
  • Tutorials that demonstrate basic itcsimlib usage and script development.
  • Example Scripts for additional functionality, tools, and advanced topics.

Reference

itcsimlib doesn’t possess a GUI. You will need to write scripts in Python that make use of the itcsimlib classes described below.

Essentials

itcsimlib.itc_sim Essential simulator for generating or fitting data with binding models.
itcsimlib.itc_experiment Core classes for handling simulated and empirical data.
itcsimlib.model_independent Non-ising type binding models for itcsimlib.

Fitting

itcsimlib.itc_fit Provides model parameter optimization to fit experimental data.
itcsimlib.itc_grid Provides discrete sample parameter values selection during data fitting.
itcsimlib.manipulator Primitive GUI elements to modify model parameters in real time.

Model Development

itcsimlib.itc_model Basic itcsimlib model class.
itcsimlib.model_ising Provides Ising type lattice+ligand binding models for itcsimlib.
itcsimlib.model_drakon Helper classes and functions that permit use of DRAKON to build statistical thermodynamics models.
itcsimlib.model_trap Binding models for the undecameric TRAP + tryptophan system, demonstrating the use of models written in C via DLLs.
itcsimlib.mass_spec Extension of Ising classes for fitting mass spectrometry data.

Nuts and Bolts

itcsimlib.thermo Basic thermodynamic transform/conversion functions.
itcsimlib.utilities Utilities for file input/output.
itcsimlib.itc_calc Base itc calculation routines for handling multiprocessing.

Indices