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Parameter Optimisation by Iterative Spectral Evaluation, a TopSpin-compatible NMR package

Project description

Parameter Optimisation by Iterative Spectral Evaluation

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Jonathan Yong and Mohammadali Foroozandeh, University of Oxford

Anal. Chem. 2021, 93 (31), 10735–10739. DOI: 10.1021/acs.analchem.1c01767


Overview

POISE is a Python package for the numerical optimisation of NMR parameters. It works by iteratively acquiring NMR spectra with different parameters and using a cost function to determine the optimal point.

The software comprises two parts:

  • the user-facing frontend, which runs in Bruker's TopSpin software. It can be executed from the TopSpin command line, or called from an AU or Python script (the documentation contains more instructions on this).

  • the backend, which is hidden from the user; it runs on a system installation of Python 3.6+.


Installation

To install POISE, you will need:

  • TopSpin. The minimum tested version is 3.6; however, this should work on any version of TopSpin that has Python 2.7 internally bundled (older versions of Python 2 are not currently supported). To check which version of Python comes with TopSpin, follow these instructions.

    Note that other instrument manufacturers are not currently supported.

  • Python 3.6 or later. This refers to a system installation, which is entirely separate from that in TopSpin. Please download and install that (many instructions are available online).

POISE can then be installed using pip (which uses the system installation of Python):

python -m pip install nmrpoise   # or 'python3'

If any errors occur, please see the documentation, or contact us.

To upgrade or reinstall POISE use:

python -m pip install --upgrade nmrpoise --no-cache-dir

Note that the --no-cache-dir flag is necessary if you are reinstalling (its purpose is explained in the documentation).


Documentation

The documentation is hosted at https://foroozandehgroup.github.io/nmrpoise; it contains complete instructions on how to set POISE up and use it.

There is also a video guide available at https://www.youtube.com/watch?v=QTCeSCRZs4I.


Contact us

Any feedback, questions, or bugs? Please create a GitHub issue or email us: we can be reached at firstname.lastname@chem.ox.ac.uk.

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nmrpoise-1.2.3.tar.gz (22.7 MB view hashes)

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