.. image:: https://readthedocs.org/projects/pdb-numpy/badge/?version=latest
:target: https://pdb-numpy.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://dev.azure.com/samuelmurailRPBS/pdb_numpy/_apis/build/status/samuelmurail.pdb_numpy?branchName=main
:target: https://dev.azure.com/samuelmurailRPBS/pdb_numpy/_build/latest?definitionId=1&branchName=main
:alt: Build Status
.. image:: https://codecov.io/gh/samuelmurail/pdb_numpy/branch/main/graph/badge.svg?token=MCVDZ7GD0V
:target: https://codecov.io/gh/samuelmurail/pdb_numpy
:alt: Code coverage
About PDB-numpy
===============
``pdb_numpy`` is a python library designed to facilitate working with PDB files
in the context of structural bioinformatics. The library builds upon the
powerful ``numpy`` library to provide efficient and easy-to-use tools for
reading, manipulating, and analyzing PDB files.
The library includes a number of functions for working with PDB files,
including functions for parsing PDB files and extracting relevant information,
such as atomic coordinates, residue identities, and structural information.
Additionally, ``pdb_numpy`` provides a range of functions for performing common
manipulations on PDB structures, such as aligning structures, superimposing
structures, and calculating RMSD values.
* Source code repository:
https://github.com/samuelmurail/pdb_numpy
Main features:
--------------
- Reading and writing PDB/MMCIF files
- Selecting atoms
- Superimposing structures using sequences alignment
- RMSD calculation
- DockQ calculation
- Secondary Structure calculation (pseudo DSSP)
For more examples and documentation, see the ``pdb_numpy`` documentation at
https://pdb-numpy.readthedocs.io/en/latest/readme.html.
Installation
------------
``pdb_numpy`` is available on PyPI and can be installed using ``pip``:
.. code-block:: bash
pip install pdb_numpy
Alternatively, you can install ``pdb_numpy`` from source:
.. code-block:: bash
git clone https://github.com/samuelmurail/pdb_numpy
cd pdb_numpy
python setup.py install
Dependencies
------------
``pdb_numpy`` requires the following dependencies:
- ``numpy``
- ``scipy``
Contributing
------------
``pdb_numpy`` is an open-source project and contributions are welcome. If
you find a bug or have a feature request, please open an issue on the GitHub
repository at https://github.com/samuelmurail/pdb_numpy. If you would like
to contribute code, please fork the repository and submit a pull request.
Author
--------------
* `Samuel Murail <https://samuelmurail.github.io/PersonalPage/>`_, Associate Professor - `Université Paris Cité <https://u-paris.fr>`_, `CMPLI <http://bfa.univ-paris-diderot.fr/equipe-8/>`_.
See also the list of `contributors <https://github.com/samuelmurail/pdb_numpy/contributors>`_ who participated in this project.
License
--------------
This project is licensed under the GNU General Public License v2.0 - see the ``LICENSE`` file for details.
Raw data
{
"_id": null,
"home_page": "https://github.com/samuelmurail/pdb_numpy",
"name": "pdb-numpy",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.7",
"maintainer_email": "",
"keywords": "pdb_numpy,Python,PDB,Numpy,Coor,Model",
"author": "Samuel Murail",
"author_email": "samuel.murail@u-paris.fr",
"download_url": "https://files.pythonhosted.org/packages/c2/9f/7467ee0f2f05e5ac10209ce12d2e641db8324f06c5c30e916e961a1f4a67/pdb_numpy-0.0.2.tar.gz",
"platform": null,
"description": "\n.. image:: https://readthedocs.org/projects/pdb-numpy/badge/?version=latest\n :target: https://pdb-numpy.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://dev.azure.com/samuelmurailRPBS/pdb_numpy/_apis/build/status/samuelmurail.pdb_numpy?branchName=main\n :target: https://dev.azure.com/samuelmurailRPBS/pdb_numpy/_build/latest?definitionId=1&branchName=main\n :alt: Build Status\n\n.. image:: https://codecov.io/gh/samuelmurail/pdb_numpy/branch/main/graph/badge.svg?token=MCVDZ7GD0V\n :target: https://codecov.io/gh/samuelmurail/pdb_numpy\n :alt: Code coverage\n\nAbout PDB-numpy\n===============\n\n``pdb_numpy`` is a python library designed to facilitate working with PDB files\nin the context of structural bioinformatics. The library builds upon the\npowerful ``numpy`` library to provide efficient and easy-to-use tools for\nreading, manipulating, and analyzing PDB files.\n\nThe library includes a number of functions for working with PDB files,\nincluding functions for parsing PDB files and extracting relevant information,\nsuch as atomic coordinates, residue identities, and structural information.\nAdditionally, ``pdb_numpy`` provides a range of functions for performing common\nmanipulations on PDB structures, such as aligning structures, superimposing\nstructures, and calculating RMSD values.\n\n\n* Source code repository:\n https://github.com/samuelmurail/pdb_numpy\n\n\nMain features:\n--------------\n\n- Reading and writing PDB/MMCIF files\n- Selecting atoms\n- Superimposing structures using sequences alignment\n- RMSD calculation\n- DockQ calculation\n- Secondary Structure calculation (pseudo DSSP)\n\nFor more examples and documentation, see the ``pdb_numpy`` documentation at\nhttps://pdb-numpy.readthedocs.io/en/latest/readme.html.\n\nInstallation\n------------\n\n``pdb_numpy`` is available on PyPI and can be installed using ``pip``:\n\n.. code-block:: bash\n\n pip install pdb_numpy\n\nAlternatively, you can install ``pdb_numpy`` from source:\n\n.. code-block:: bash\n\n git clone https://github.com/samuelmurail/pdb_numpy\n cd pdb_numpy\n python setup.py install\n\nDependencies\n------------\n\n``pdb_numpy`` requires the following dependencies:\n\n- ``numpy``\n- ``scipy``\n\n\nContributing\n------------\n\n``pdb_numpy`` is an open-source project and contributions are welcome. If\nyou find a bug or have a feature request, please open an issue on the GitHub\nrepository at https://github.com/samuelmurail/pdb_numpy. If you would like\nto contribute code, please fork the repository and submit a pull request.\n\nAuthor\n--------------\n\n* `Samuel Murail <https://samuelmurail.github.io/PersonalPage/>`_, Associate Professor - `Universit\u00e9 Paris Cit\u00e9 <https://u-paris.fr>`_, `CMPLI <http://bfa.univ-paris-diderot.fr/equipe-8/>`_.\n\nSee also the list of `contributors <https://github.com/samuelmurail/pdb_numpy/contributors>`_ who participated in this project.\n\nLicense\n--------------\n\nThis project is licensed under the GNU General Public License v2.0 - see the ``LICENSE`` file for details.\n",
"bugtrack_url": null,
"license": "GNUv2.0",
"summary": "Pdb_Numpy is a python library allowing simple operations on pdb coor files.",
"version": "0.0.2",
"project_urls": {
"Homepage": "https://github.com/samuelmurail/pdb_numpy"
},
"split_keywords": [
"pdb_numpy",
"python",
"pdb",
"numpy",
"coor",
"model"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "bfd2a5fba32c9a69bbbfcdec9407ebbe70481165c81567ae08f1c2c16083c294",
"md5": "11e8d0335b651528d5672e7901b49646",
"sha256": "a2f44b161b2681b6db85bb8f398b8a48a770010cc92a632c74e1ee5c58bbbb74"
},
"downloads": -1,
"filename": "pdb_numpy-0.0.2-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "11e8d0335b651528d5672e7901b49646",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": ">=3.7",
"size": 67189,
"upload_time": "2023-11-20T11:46:11",
"upload_time_iso_8601": "2023-11-20T11:46:11.186960Z",
"url": "https://files.pythonhosted.org/packages/bf/d2/a5fba32c9a69bbbfcdec9407ebbe70481165c81567ae08f1c2c16083c294/pdb_numpy-0.0.2-py2.py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "c29f7467ee0f2f05e5ac10209ce12d2e641db8324f06c5c30e916e961a1f4a67",
"md5": "8567973060e0c1f7d12758763938adf8",
"sha256": "36a44361f60a768d93f5787fb2268aaf16a041c292095019aef56a489169ca70"
},
"downloads": -1,
"filename": "pdb_numpy-0.0.2.tar.gz",
"has_sig": false,
"md5_digest": "8567973060e0c1f7d12758763938adf8",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7",
"size": 59816,
"upload_time": "2023-11-20T11:46:12",
"upload_time_iso_8601": "2023-11-20T11:46:12.537569Z",
"url": "https://files.pythonhosted.org/packages/c2/9f/7467ee0f2f05e5ac10209ce12d2e641db8324f06c5c30e916e961a1f4a67/pdb_numpy-0.0.2.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-11-20 11:46:12",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "samuelmurail",
"github_project": "pdb_numpy",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"requirements": [
{
"name": "numpy",
"specs": [
[
">=",
"1.2"
]
]
},
{
"name": "scipy",
"specs": [
[
">=",
"1.5"
]
]
}
],
"lcname": "pdb-numpy"
}
JSON
