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.
panedr is compatible with python 2.7 and greater, and with python 3.5 and greater.
import panedr # Read the EDR file path = 'ener.edr' df = panedr.edr_to_df(path) # The `verbose` optional parameter can be set to True to display the # progress on stderr df = panedr.edr_to_df(path, verbose=True) # Get the average pressure after the first 10 ns pressure_avg = df[u'Pressure'][df[u'Time'] > 10000].mean()
pip install panedr
The panedr repository contains a series of tests. If you downloaded or cloned the code from the repository, you can run the tests. To do so, install pytest, and, in the directory of the panedr source code, run:
pytest -v tests
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
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