nmrPype

Python implementation of command-line program nmrpipe, using linux pipelines to process NMR data.

• Documentation: https://phimykah.github.io/nmrpype
• NMRPipe Website: https://www.ibbr.umd.edu/nmrpipe
• Source Code: https://github.com/PhiMykah/nmrPype
• Bug Reports: https://github.com/PhiMykah/nmrPype/issues

Installation

Installing nmrPype can be done by through pip:

# Install prerequisites
pip install numpy scipy
# Install program
pip install nmrPype

A virtual environment or conda environment is recommended for using nmrPype. If using conda, numpy and scipy can be installed using conda install.

Note

This is made for Python 3.10 or above. Some of the code requires Python 3.10's features such as match-case statements.

Python 3.12 is recommended as development is done with 3.12, but testing is done to assure that 3.10 is supported.

Usage

nmrPype can be used in through two methods: Command-line and Script

Command-line

nmrPype -in [inFile] -fn fnName -out [outFile] [-ov]

Functions:

FT                  Perform a Fourier transform (FT) on the data
ZF                  Perform a Zero Fill (ZF) Operation on the data
SP (SINE)           Adjustable Sine Bell
PS                  Perform a Phase Correction (PS) on the data
YTP (TP, XY2YX)     2D Plane Transpose
ZTP (XYZ2ZYX)       3D Matrix Transpose
ATP (XYZA2AYZX)     4D Matrix Transpose (unimplemented)
NULL                Null Function, does not apply any function

Run the nmrPype --help command to see a list of more options.

Script

In a Python script or jupyter notebook use the following line:

import nmrPype

I recommend setting the import as pype for simplification.

Example

import nmrPype as pype

df = pype.DataFrame("h.fid") # Load NMR data file into script
df.array() # Display spectral data array

Building From Source

Building using Pip

1. Install prerequisites

pip install numpy scipy

2. Clone the repository

git clone https://github.com/PhiMykah/nmrPype

3. Install in development mode with pip:

cd nmrPype
pip install -e .

Building using Conda

With conda, the environment.yml file can be used to obtain the development environment.

1. Clone the repository

git clone https://github.com/PhiMykah/nmrPype

2. Copy the source conda environment

cd nmrPype
conda env create -f environment.yml --name nmrpype

• You can set the name to anything you wish, but typically my convention is to have the environments lowercase

3. Install in development mode with pip:

pip install -e .