{"id":18524273,"url":"https://github.com/mdanalysis/panedr","last_synced_at":"2025-04-06T03:05:47.074Z","repository":{"id":37056936,"uuid":"49365749","full_name":"MDAnalysis/panedr","owner":"MDAnalysis","description":"Reads Gromacs EDR file to populate a pandas dataframe","archived":false,"fork":false,"pushed_at":"2024-11-11T11:04:34.000Z","size":31107,"stargazers_count":32,"open_issues_count":2,"forks_count":7,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-03-30T00:23:07.053Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-2.1","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MDAnalysis.png","metadata":{"files":{"readme":"README.rst","changelog":"ChangeLog","contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-01-10T12:23:58.000Z","updated_at":"2025-03-29T22:58:58.000Z","dependencies_parsed_at":"2023-07-19T07:28:44.333Z","dependency_job_id":"4371ca54-186f-48bf-ab9b-13d7a96eee5e","html_url":"https://github.com/MDAnalysis/panedr","commit_stats":{"total_commits":131,"total_committers":9,"mean_commits":"14.555555555555555","dds":0.549618320610687,"last_synced_commit":"a13d17dbab44f04174db1672458df210e47101f1"},"previous_names":["jbarnoud/panedr"],"tags_count":14,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fpanedr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fpanedr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fpanedr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fpanedr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MDAnalysis","download_url":"https://codeload.github.com/MDAnalysis/panedr/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247427005,"owners_count":20937200,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-06T17:40:21.484Z","updated_at":"2025-04-06T03:05:47.057Z","avatar_url":"https://github.com/MDAnalysis.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Pyedr and Panedr\n================\n\n|Build Status| |cov|\n\nThis repository hosts the source files for both the Pyedr and Panedr packages.\n\n``pyedr`` and ``panedr`` are compatible with Python 3.6 and greater.\n\nPyedr\n-----\n\nPyedr provides a means of reading a `Gromacs EDR`_ binary XDR file and\nreturn its contents as a dictionary of `numpy`_ arrays. Pyedr exposes\nthe following functions:\n\n- ``edr_to_dict``: returns a dictionary of NumPy arrays keyed by the energy\n  type from a given path to an EDR file.\n- ``read_edr``: parses an EDR file and returns the energy terms\n  in a nested list\n- ``get_unit_dictionary``: Returns a dictionary that holds the units of each\n  energy term found in the EDR file.\n\n\nPanedr\n------\n\nPanedr uses the Pyedr library to read a `Gromacs EDR`_ binary energy XDR file\nand returns its contents as a pandas_ dataframe. Panedr exposes the\nfollowing functions:\n\n- ``edr_to_df``: which gets the path to an EDR file and returns a\n  pandas DataFrame.\n- ``get_unit_dictionary``: Returns a dictionary that holds the units of each\n  energy term found in the EDR file.\n\n\nExample\n-------\n\nUsing ``pyedr``:\n\n\n.. code:: python\n\n    import pyedr\n\n    # Read the EDR file\n    path = 'ener.edr'\n    dic = pyedr.edr_to_dict(path)\n\n    # The `verbose` optional parameter can be set to True to display the\n    # progress on stderr\n    dic = pyedr.edr_to_dict(path, verbose=True)\n\n    # Get the average pressure after the first 10 ns\n    pressure_avg = dic['Pressure'][dic['Time'] \u003e 10000].mean()\n\n    # Get the units of the EDR entries\n    unit_dict = pyedr.get_unit_dictionary(path)\n    unit_dict[\"Temperature\"]  # returns \"K\"\n\n\nUsing ``panedr``:\n\n\n.. code:: python\n\n    import panedr\n\n    # Read the EDR file\n    path = 'ener.edr'\n    df = panedr.edr_to_df(path)\n\n    # The `verbose` optional parameter can be set to True to display the\n    # progress on stderr\n    df = panedr.edr_to_df(path, verbose=True)\n\n    # Get the average pressure after the first 10 ns\n    pressure_avg = df['Pressure'][df['Time'] \u003e 10000].mean()\n\n    # Get the units of the EDR entries\n    unit_dict = panedr.get_unit_dictionary(path)\n    unit_dict[\"Temperature\"]  # returns \"K\"\n\n\nInstall\n-------\n\nYou can install ``pyedr`` and ``panedr`` using ``pip``:\n\n.. code:: bash\n\n    pip install pyedr\n\n    # installing panedr automatically installs pyedr\n    pip install panedr\n\n\nIf you are using `conda`_ and `conda-forge`_, you can install with:\n\n.. code:: bash\n\n    conda install -c conda-forge pyedr\n\n    # install panedr automatically installs pyedr\n    conda install -c conda-forge panedr\n\n\nTests\n-----\n\nThe ``pyedr`` and ``panedr`` repositories contains a series of tests.\nIf you downloaded or cloned the code from the repository, you can run\nthe tests. To do so, install `pytest`_, and, in the directory of the\npanedr source code, run:\n\nFor ``pyedr``:\n\n\n.. code:: bash\n\n    pytest -v pyedr/pyedr/tests\n\n\nFor ``panedr``:\n\n\n.. code:: bash\n\n    pytest -v panedr/panedr/tests\n\n\nLicense\n-------\n\nPyedr and Panedr translate part of the source code of Gromacs into Python.\nTherefore, Panedr is distributed under the same GNU Lesser General\nPublic License version 2.1 as Gromacs. See the `license`_ for more details.\n\n\n.. |Build Status| image:: https://github.com/MDAnalysis/panedr/actions/workflows/gh-ci.yaml/badge.svg\n   :alt: Github Actions Build Status\n   :target: https://github.com/MDAnalysis/panedr/actions/workflows/gh-ci.yaml\n\n.. |cov|   image:: https://codecov.io/gh/MDAnalysis/panedr/branch/master/graph/badge.svg\n   :alt: Coverage Status\n   :target: https://codecov.io/gh/MDAnalysis/panedr\n\n.. _`Gromacs EDR`: https://manual.gromacs.org/documentation/current/reference-manual/file-formats.html#edr\n.. _numpy: https://numpy.org/\n.. _pandas: https://pandas.pydata.org/\n.. _conda: https://docs.conda.io\n.. _`conda-forge`: https://conda-forge.org/\n.. _pytest: https://docs.pytest.org/\n.. _license: https://github.com/MDAnalysis/panedr/blob/master/LICENSE.txt\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fpanedr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmdanalysis%2Fpanedr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fpanedr/lists"}