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 3.3 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 stdout 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'] > 1000].mean()
pip install panedr
The panedr module comes with a series of tests. To run these tests, install nose, and run:
nosetests -v panedr
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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