mfoutparser: efficient and convenient parsing of ModelFree output files.
Jupyter Notebook Python
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mfoutparser
.gitignore
INSTALL.md
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py

README.md

mfoutparser

by Arthur G. Palmer, III and Michelle L. Gill

A series of python subroutines to read and extract information from the STAR format mfout file generated by the program ModelFree.

Unlike the BMRB STAR format, the format used by ModelFree uses the data_name field, rather than the save_name field and also allows nested loops. (The mfout file has loops nested to a depth of two only).

Live Demo

The mfoutparser/examples directory contains a demonstration Jupyter notebook and sample input and output files. The notebook can be viewed (non-interactively) on GitHub here.

The interactive demo can also be run live in the web browser by clicking here: Binder. After the page loads in Jupyter, click on the following to get to and load the notebook: mfoutparser --> examples --> MFparser_demo.ipynb.

Local Demo

Once mfoutparser has been installed, the examples directory can be copied to the current path using the following shell command:

python -c 'import mfoutparser as mf; mf.copy_examples()'

Compatibility

mfoutparser has been tested on python 2.7, 3.4, and 3.5. It requires the numpy (tested on version 1.10.1) and pandas (version >= 0.17.1) libraries. IPython/Jupyter notebook (version >= 3.2.1) is required to run the demonstration notebook located in the examples directory. Matplotlib is required if plotting of the data is desired.

Installation

mfoutparser can be installed with the conda and pip package managers or using python's setuptools. See the installation instructions for more information.