panedr 0.1

Read and manipulate Gromacs energy files

Panedr reads a Gromacs EDR file and returns its content as a pandas dataframe. The library exposes one function—the edr_to_df function—that gets the path to an EDR file and returns a pandas dataframe.

The pandas library is required.

Example

import panedr

# Read the EDR file
path = 'ener.edr'
df = panedr.edr_to_edr(path)

# Get the average pressure after the first 10 ns
pressure_avg = df[u'Pressure'][df[u'Time'] > 1000].mean()

Install

The panedr module can be installed from source. The source files are available on Github at https://github.com/jbarnoud/panedr. Once the file downloaded, go to the panedr directory and run:

pip install .

You may not have the permissions to install modules system wide, or you may want to install panedr only for the current user. To install the module user wide only, run:

pip install --user .

You may want to consider virtualenv.

panedr is compatible with Python 2.7 and greater and python 3.3 and greater.

Tests

The panedr module comes with a series of tests. To run these tests, install nose, and run:

nosetests -v panedr

License

Panedr translate in python part of the source code of Gromacs. Therefore, Panedr is distributed under the same GNU Lesser General Public License version 2.1 as Gromacs.

Panedr — a library to manipulate Gromacs EDR file in python

Copyright (C) 2016 Jonathan Barnoud

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA