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PyChimera: use UCSF Chimera modules in any Python 2.7 project

PyChimera: use UCSF Chimera modules in any Python 2.7 project MotivationUCSF Chimera is a powerful visualization tool remarkably present in the computational chemistry and structural biology communities. Built on a C++ core wrapped under a Python 2.7 environment, one could expect to easily import UCSF Chimera’s arsenal of resources in custom scripts or software projects. Nonetheless, this is not readily possible if the script is not executed within UCSF Chimera due to the isolation of the platform. UCSF ChimeraX, successor to the original Chimera, partially solves the problem but yet major upgrades need to be undergone so that this updated version can offer all UCSF Chimera features.ResultsPyChimera has been developed to overcome these limitations and provide access to the UCSF Chimera codebase from any Python 2.7 interpreter, including interactive programming with tools like IPython and Jupyter Notebooks, making it easier to use with additional third-party software.Availability and implementationPyChimera is LGPL-licensed and available at https://github.com/insilichem/pychimera.Supplementary informationSupplementary data are available at Bioinformatics online. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

PyChimera: use UCSF Chimera modules in any Python 2.7 project

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Publisher
Oxford University Press
Copyright
© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
ISSN
1367-4803
eISSN
1460-2059
DOI
10.1093/bioinformatics/bty021
Publisher site
See Article on Publisher Site

Abstract

MotivationUCSF Chimera is a powerful visualization tool remarkably present in the computational chemistry and structural biology communities. Built on a C++ core wrapped under a Python 2.7 environment, one could expect to easily import UCSF Chimera’s arsenal of resources in custom scripts or software projects. Nonetheless, this is not readily possible if the script is not executed within UCSF Chimera due to the isolation of the platform. UCSF ChimeraX, successor to the original Chimera, partially solves the problem but yet major upgrades need to be undergone so that this updated version can offer all UCSF Chimera features.ResultsPyChimera has been developed to overcome these limitations and provide access to the UCSF Chimera codebase from any Python 2.7 interpreter, including interactive programming with tools like IPython and Jupyter Notebooks, making it easier to use with additional third-party software.Availability and implementationPyChimera is LGPL-licensed and available at https://github.com/insilichem/pychimera.Supplementary informationSupplementary data are available at Bioinformatics online.

Journal

BioinformaticsOxford University Press

Published: May 15, 2018

References