pyedr

Pyedr and Panedr

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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

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 list
• get_unit_dictionary: Returns a dictionary that holds the units of each energy term found in the EDR file.

Panedr

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.

Example

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"

Install

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

Tests

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

License

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