Quantitative analysis of NMR data.
- Installation There are two ways to run the software. First, one can use the compiled package of the GUI version; however, it only provides limited processing capabilities. The latest version of the software can be downloaded from Google drive. This folder also contains the dataset used in this tutorial and workspaces saved on each step of data processing.
Alternatively, to have access to the full functionality (including the ability to write and execute processing scripts, use GUI for simple analysis tasks, and modify the code), it is recommended to clone the containing GitHub repository to a local machine and work with the code directly. The ‘release’ branch contains the latest stable version of the software.
The software is developed for the Windows 10 operating system and written in Python 3.7. The easiest way to set up a Python environment on a local machine is to use a package manager, such as Anaconda (https://www.anaconda.com/). The GitHub repository contains the virtual environment description file (py37-nmr.yml) with the list of all additional packages to be installed, which can be imported to Anaconda. For this, in Anaconda Navigator, open the Environments tab on the left and click “Import” on the bottom of the screen; select the py37-nmr.yml file, which will download and install a Python instance with all required components. After the installation is complete, ensure that the correct environment is currently selected. In this guide we will use examples of data processing set up in a Jupyter Notebook tutorial.ipynb. A link to run Jupyter can be found in the Home tab in Anaconda, or it can also be launched by clicking on the triangle next to the environment name in the Environments tab and selecting “Open with Jupyter notebook” in the pop-up menu. If the folder structure is preserved as in the original repository, the code in the example notebook should run without any modification. Otherwise, it is necessary to ensure that the main nmrQuant directory is in the Python PATH; if needed, it can be added to the PATH with the following command directly within the notebook: “sys.path.insert(0, ‘absolute_path_to_nmrQuant’)”.
Alternatively, to start the GUI, navigate to the containing folder (using ‘cd dir_path\nmrQuant’) and run the command ‘python main.py’ in the terminal. To ensure that the code is run in the correct python environment, it is recommended to launch the terminal directly from Anaconda by clicking on the triangle next to the environment name and selecting “Open Terminal”.