NMR-EsPy

Simon G. Hulse & Mohammadali Foroozandeh,
 Department of Chemistry,
 University of Oxford

Contents

What is NMR-EsPy?

NMR-EsPy (Nuclear Magnetic Resonance Estimation in Python) is a Python package for the estimation of parameters that describe NMR signals.

As with many packages that do number crunching in Python, NMR-EsPy makes heavy use of the NumPy ecosystem.

NMR-EsPy package is a product of work carried out during Simon’s Ph.D within the former Foroozandeh group in the University of Oxford’s Chemistry Department.

The primary goal behind the NMR-EsPy package is to quantify NMR datasets. It is assumed that raw NMR datasets (called FIDs) comprise a number of sinusoidal oscillators; NMR-EsPy uses numerical techniques in order to estimate the amplitudes, phases, frequencies, and damping rates of these oscillators. Such information can be made use of in various applications.

This version of NMR-EsPy provides the means to estimate both 1D NMR datasets and 2D J-Resolved datasets. Available features include:

  • Importing data acquired on Bruker specrometers.

  • Simulating data using the Spinach Matlab package.

  • Basic pre-processing of NMR data (phasing, baseline correction).

  • Estimation of NMR data using numerical optimisation.

  • Generating parameter tables.

  • Generating result figures.

With 2D-J Resolved datasets, NMR-EsPy can be employed to construct homodecoupled (pure shift) spectra via estimation (a paper outlining this is yet to be released).

In future versions, support for other NMR data types and applications will be included.

Using the Documentation

New to NMR-EsPy? Look at the following:

If you wish to use the API:

  1. Read the installation instructions. If you are not interested in using the GUI, it is possible to skip the section titled Installing the GUI to TopSpin

  2. Read the tutorial on 1D data estimation.

  3. Read further tutorials that are relevant to your interests.

  4. Whenever a moment arises that you wish to understand more about particular features in the package, consult the API reference.

If you wish to use the GUI:

  1. Read the installation instructions. If you are going to be loading the GUI from within TopSpin, it is important to read the section titled Installing the GUI to TopSpin.

  2. Read the instructions on using the GUI.

In you are comfortable with writing Python code, it is recommended that you make use of NMR-EsPy via the API, rather than the GUI, as it is more feature rich.

Issues

If you come across any unexpected behavior/bugs, please get in touch with Simon, via email (see the email icon in the sidebar), or file an issue. This project is no longer actively worked on, but if there are bugs that prevent use of the package I will try to fix them.

Publications

  • Simon G. Hulse, Mohammadali Foroozandeh. Newton meets Ockham: Parameter estimation and model selection of NMR data with NMR-EsPy. J. Magn. Reson. 338 (2022) 107173.
    https://doi.org/10.1016/j.jmr.2022.107173