This repository contains software tools which allow to compare nuclear magnetic resonance (NMR) spectra and estimate proportions of components in mixture using the Wasserstein distance.
Magnetstein is a modification of the algorithm from a Python3 package called masserstein (available here).
If you encounter any difficulties during installation or usage of these programs, or if you have any suggestions regarding their functionality, please post a GitHub issue or send an email to b.domzal@mimuw.edu.pl.
To be able to use the software provided in this repository, you will need to have a working Python3 distribution installed on your computer.
To use Magnetstein, clone this repository. In the commandline, this can be done by typing:
git clone https://github.com/BDomzal/magnetstein.git
The above command will create a folder magnetstein in your current working directory. Go to this directory by typing
cd magnetstein/
in the commandline. Then, install the package by running the setup.py file:
python3 setup.py install --user
This will install the masserstein package for the current user (including NMR spectroscopy tool Magnetstein).
You will also need to have the following packages installed (all availiable via pip):
IsoSpecPynumpyscipyPuLP
(For example: if you would like to install pulp, you need to type
pip install PuLP
in the commandline.)
If you are a researcher, we strongly recommend using Gurobi (available for academics at no cost) as your solver in Magnetstein. For more information on license and installation, see Gurobi website. Gurobi is a default solver. If you prefer to use Magnetstein without Gurobi, set solver=LpSolverDefault in estimate_proportions function. Note that using Magnetstein without Gurobi can result in long computation time and, in some cases, incorrect results.
See estimation.ipynb in folder examples/.
Powered by © Gurobi.
If you use tools from this package, please cite:
Domżał, B., Nawrocka, E.K., Gołowicz, D., Ciach, M.A., Miasojedow, B., Kazimierczuk, K., & Gambin, A. (2023). Magnetstein: An Open-Source Tool for Quantitative NMR Mixture Analysis Robust to Low Resolution, Distorted Lineshapes, and Peak Shifts. Analytical Chemistry. DOI: 10.1021/acs.analchem.3c03594.