https://github.com/mdanalysis/panedr
Reads Gromacs EDR file to populate a pandas dataframe
https://github.com/mdanalysis/panedr
Last synced: about 1 year ago
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Reads Gromacs EDR file to populate a pandas dataframe
- Host: GitHub
- URL: https://github.com/mdanalysis/panedr
- Owner: MDAnalysis
- License: lgpl-2.1
- Created: 2016-01-10T12:23:58.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2024-11-11T11:04:34.000Z (over 1 year ago)
- Last Synced: 2025-03-30T00:23:07.053Z (about 1 year ago)
- Language: Python
- Size: 29.7 MB
- Stars: 32
- Watchers: 7
- Forks: 7
- Open Issues: 2
-
Metadata Files:
- Readme: README.rst
- Changelog: ChangeLog
- License: LICENSE.txt
- Authors: AUTHORS
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README
Pyedr and Panedr
================
|Build Status| |cov|
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.
.. |Build Status| image:: https://github.com/MDAnalysis/panedr/actions/workflows/gh-ci.yaml/badge.svg
:alt: Github Actions Build Status
:target: https://github.com/MDAnalysis/panedr/actions/workflows/gh-ci.yaml
.. |cov| image:: https://codecov.io/gh/MDAnalysis/panedr/branch/master/graph/badge.svg
:alt: Coverage Status
:target: https://codecov.io/gh/MDAnalysis/panedr
.. _`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