https://github.com/insilichem/pychimera

Use UCSF Chimera Python API in a standard interpreter
https://github.com/insilichem/pychimera

conda-recipe python-2 python27 ucsf-chimera

Last synced: about 2 months ago
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Use UCSF Chimera Python API in a standard interpreter

• Host: GitHub
• URL: https://github.com/insilichem/pychimera
• Owner: insilichem
• License: lgpl-3.0
• Created: 2016-01-24T21:49:11.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2019-03-28T15:39:52.000Z (about 6 years ago)
• Last Synced: 2025-03-23T18:38:52.250Z (2 months ago)
• Topics: conda-recipe, python-2, python27, ucsf-chimera
• Language: Python
• Homepage: http://pychimera.readthedocs.io
• Size: 1.42 MB
• Stars: 58
• Watchers: 7
• Forks: 10
• Open Issues: 4
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
PyChimera

=========

.. image:: https://travis-ci.org/insilichem/pychimera.svg?branch=master

   :target: https://travis-ci.org/insilichem/pychimera

   :alt: Travis CI status

.. image:: https://ci.appveyor.com/api/projects/status/fwp3uum6be7tcfqn/branch/master?svg=true

   :target: https://ci.appveyor.com/project/jaimergp/pychimera

   :alt: AppVeyor status

.. image:: https://readthedocs.org/projects/pychimera/badge/?version=latest

   :target: http://pychimera.readthedocs.io/en/latest/?badge=latest

   :alt: Documentation Status

.. image:: https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbty021-blue.svg

   :target: http://dx.doi.org/10.1093/bioinformatics/bty021

   :alt: Citation DOI

.. image:: docs/img/pychimera.png

**Use UCSF Chimera packages in any Python 2.7 interpreter**

.. image:: docs/img/pychimera.gif

With PyChimera you can…

-  Run scripts depending on chimera **from CLI** with ``pychimera script.py``.

-  Enable ``import chimera`` in interactive coding sessions **outside UCSF Chimera**,

   including IPython and Jupyter Notebooks.

-  Launch a standard UCSF Chimera instance, with the benefit of importing all

   your ``conda`` or ``virtualenv`` packages with ``pychimera --gui``.

I hope it’s useful! Feedback is appreciated!

Documentation

-------------

The updated documentation is always available at `readthedocs`_.

Acknowledgments

---------------

Largely based on ideas by `Greg Couch at chimera-users`_.

.. _UCSF Chimera: https://www.cgl.ucsf.edu/chimera/

.. _latest UCSF Chimera: http://www.cgl.ucsf.edu/chimera/download.html

.. _Greg Couch at chimera-users: http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html

.. _readthedocs: http://pychimera.readthedocs.io

Citation

--------

.. image:: https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbty021-blue.svg

   :target: http://dx.doi.org/10.1093/bioinformatics/bty021

PyChimera is scientific software, funded by public research grants

(Spanish MINECO's project ``CTQ2014-54071-P``, Generalitat de Catalunya's

project ``2014SGR989`` and research grant ``2017FI_B2_00168``, COST Action ``CM1306``).

If you make use of PyChimera in scientific publications, please cite it. It will help

measure the impact of our research and secure future funding!

.. code-block:: latex

   @article{pychimera2018,

     author = {Rodríguez-Guerra Pedregal, Jaime and Maréchal, Jean-Didier},

     title = {PyChimera: use UCSF Chimera modules in any Python 2.7 project},

     journal = {Bioinformatics},

     volume = {34},

     number = {10},

     pages = {1784-1785},

     year = {2018},

     doi = {10.1093/bioinformatics/bty021},

     URL = {http://dx.doi.org/10.1093/bioinformatics/bty021},

     eprint = {/oup/backfile/content_public/journal/bioinformatics/34/10/10.1093_bioinformatics_bty021/1/bty021.pdf}

   }