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This repository hosts the source files for both the Pyedr and Panedr packages.
pyedr
and panedr
are compatible with Python 3.6 and greater.
Pyedr provides a means of reading a Gromacs EDR
binary XDR file and
return its contents as a dictionary of numpy
arrays. Pyedr exposes
the following functions:
edr_to_dict
: returns a dictionary of NumPy arrays keyed by the energy
type from a given path to an EDR file.read_edr
: parses an EDR file and returns the energy terms
in a nested listget_unit_dictionary
: Returns a dictionary that holds the units of each
energy term found in the EDR file.Panedr uses the Pyedr library to read a Gromacs EDR
binary energy XDR file
and returns its contents as a pandas dataframe. Panedr exposes the
following functions:
edr_to_df
: which gets the path to an EDR file and returns a
pandas DataFrame.get_unit_dictionary
: Returns a dictionary that holds the units of each
energy term found in the EDR file.Using pyedr
:
.. code:: python
import pyedr
# Read the EDR file
path = 'ener.edr'
dic = pyedr.edr_to_dict(path)
# The `verbose` optional parameter can be set to True to display the
# progress on stderr
dic = pyedr.edr_to_dict(path, verbose=True)
# Get the average pressure after the first 10 ns
pressure_avg = dic['Pressure'][dic['Time'] > 10000].mean()
# Get the units of the EDR entries
unit_dict = pyedr.get_unit_dictionary(path)
unit_dict["Temperature"] # returns "K"
Using panedr
:
.. code:: python
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['Pressure'][df['Time'] > 10000].mean()
# Get the units of the EDR entries
unit_dict = panedr.get_unit_dictionary(path)
unit_dict["Temperature"] # returns "K"
You can install pyedr
and panedr
using pip
:
.. code:: bash
pip install pyedr
# installing panedr automatically installs pyedr
pip install panedr
If you are using conda
and conda-forge
, you can install with:
.. code:: bash
conda install -c conda-forge pyedr
# install panedr automatically installs pyedr
conda install -c conda-forge panedr
The pyedr
and panedr
repositories 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:
For pyedr
:
.. code:: bash
pytest -v pyedr/pyedr/tests
For panedr
:
.. code:: bash
pytest -v panedr/panedr/tests
Pyedr and Panedr translate part of the source code of Gromacs into Python.
Therefore, Panedr is distributed under the same GNU Lesser General
Public License version 2.1 as Gromacs. See the license
_ for more details.
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.. _Gromacs EDR
: https://manual.gromacs.org/documentation/current/reference-manual/file-formats.html#edr
.. _numpy: https://numpy.org/
.. _pandas: https://pandas.pydata.org/
.. conda: https://docs.conda.io
.. conda-forge
: https://conda-forge.org/
.. _pytest: https://docs.pytest.org/
.. _license: https://github.com/MDAnalysis/panedr/blob/master/LICENSE.txt