Fitting with the API

Workflow

• Integrate raw power curves using Origin or NITPIC, creating files containing heats per shot. A collection of demo heat files are available on github.
• Load heat files.
• Choose model describing experiment.
• Choose the fitter.
• Link individual fit parameters to global parameters.
• Fit the model to the data.
• Evaluate the fit statistics.
• Export the results, which will save a csv file and pdf files showing the fit and corner plot.

API demos

We have posted a collection of Jupyter notebooks that demonstrate working with the API: https://github.com/harmslab/pytc-demos. The topics covered are listed below.

Fitter choice

• Using maximum likelihood to fit a model. 00_fit-single-site.ipynb.
• Using a Bayesian sampler. 01_single-site-Bayesian.ipynb.
• Comparision of maximum likelihood, bootstrap, or Bayesian methods. 04_ml-v-bootstrap-v-bayesian.ipynb.

Model choice

• Fit a single-site model. 00_fit-single-site.ipynb.
• Fit a binding polynomial. 02_fit-binding-polynomial.ipynb.
• Fit a competitor binding model. 03_fit-competitor-model.ipynb.

Fitting options

• Change fit guesses or fix parameters. 05_change-param-guess-fix.ipynb.
• Choose the best model using AIC. 11_use-aic-choose-model.ipynb.

Global fits

• Global fit of a single site model to a blank and experimental titration. 07_simultaneous-fit-blank-experiment.ipynb.
• Global fit of a single site model to a blank and three replicate experimental titrations 06_global-fit-three-replicates-and-blank.ipynb.
• Global connector: fit the same binding reaction measured in different buffers to extract ionization enthalpy and num protons 08_global-fit-with-NumProtons-connector.ipynb.
• Global connector: fit the same binding reaction measured at different temperatures to extract van’t Hoff enthalpy 09_global-fit-for-vant-hoff-enthalpy.ipynb.
• Global connector: implement a custom global connector 10_implement-custom-global-connector.ipynb.