nmrglue

Version: 0.6-dev

Short description

nmrglue: a module for working with NMR data in Python.

Description

Nmrglue is a module for working with NMR data in Python. When used with the NumPy, SciPy, and matplotlib packages nmrglue provides a robust environment for rapidly developing new methods for processing, analyzing, and visualizing NMR data. Nmrglue also provides a framework for connecting existing NMR software packages.

Key features

Nmrglue has the ability to read, write and convert between a number of NMR file formats including Agilent/Varian, Bruker, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit files. The files, which are represented in Python as dictionaries of spectral parameters and NumPy ndarray objects, can be easily examined, modified and processed as desired.

Nmrglue provides a number of functions for processing NMR data such as apodization, spectral shifting, Fourier and other transformations, baseline smoothing and flattening, and linear prediction modeling and extrapolation. In addition new processing schemes can be implemented easily using the nmrglue provided functions and the multitude of numerical routines provided by the NumPy and SciPy packages.

When used in conjunction with the matplotlib (or other) python plotting library nmrglue can be used to create publication quality figures of NMR spectrum or examine data interactively. For example:

Nmrglue can be used to analysis NMR data, with routines to perform peak picking, multidimensional lineshape fitting (peak fitting), and peak integration provided within the package. New analysis methods can be rapidly developed and tested in Python or by integrating Fortran and C/C++ code.

Tool Authors

• Jonathan J. Helmus

Container Contributors

• Kristian Peters (IPB-Halle)
• Pabo Moreno (EMBL-EBI)

Website

• http://www.nmrglue.com
• http://github.com/jjhelmus/nmrglue

Git Repository

• https://github.com/phnmnl/container-nmrglue.git

Installation

For local individual installation:

docker pull docker-registry.phenomenal-h2020.eu/phnmnl/nmrglue

Usage Instructions

For direct docker usage:

docker run docker-registry.phenomenal-h2020.eu/phnmnl/nmrglue ...

Publications

• J.J. Helmus, C.P. Jaroniec, Nmrglue: An open source Python package for the analysis of multidimensional NMR data, J. Biomol. NMR 2013, 55, 355-367. doi:10.1007/s10858-013-9718-x