Use UCSF Chimera Python API in a standard interpreter
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README.rst

PyChimera

Travis CI status AppVeyor status Documentation Status Citation DOI

docs/img/pychimera.png

Use UCSF Chimera packages in any Python 2.7 interpreter

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.

Citation

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!

@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}
}