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Scoria: a Python module for manipulating 3D molecular data
Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption o...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5603467/ https://www.ncbi.nlm.nih.gov/pubmed/29086076 http://dx.doi.org/10.1186/s13321-017-0237-8 |
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author | Ropp, Patrick Friedman, Aaron Durrant, Jacob D. |
author_facet | Ropp, Patrick Friedman, Aaron Durrant, Jacob D. |
author_sort | Ropp, Patrick |
collection | PubMed |
description | Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We present Scoria, a Python package for manipulating three-dimensional molecular data. Unlike similar packages, Scoria requires no dependencies, compilation, or system-wide installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g. NumPy, SciPy), if present, to speed and extend its own functionality. To show its utility, we use Scoria to analyze a molecular dynamics trajectory. Our FootPrint script colors the atoms of one chain by the frequency of their contacts with a second chain. We are hopeful that Scoria will be a useful tool for the computational-biology community. A copy is available for download free of charge (Apache License 2.0) at http://durrantlab.com/scoria/. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-017-0237-8) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5603467 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-56034672017-09-27 Scoria: a Python module for manipulating 3D molecular data Ropp, Patrick Friedman, Aaron Durrant, Jacob D. J Cheminform Software Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We present Scoria, a Python package for manipulating three-dimensional molecular data. Unlike similar packages, Scoria requires no dependencies, compilation, or system-wide installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g. NumPy, SciPy), if present, to speed and extend its own functionality. To show its utility, we use Scoria to analyze a molecular dynamics trajectory. Our FootPrint script colors the atoms of one chain by the frequency of their contacts with a second chain. We are hopeful that Scoria will be a useful tool for the computational-biology community. A copy is available for download free of charge (Apache License 2.0) at http://durrantlab.com/scoria/. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-017-0237-8) contains supplementary material, which is available to authorized users. Springer International Publishing 2017-09-18 /pmc/articles/PMC5603467/ /pubmed/29086076 http://dx.doi.org/10.1186/s13321-017-0237-8 Text en © The Author(s) 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Ropp, Patrick Friedman, Aaron Durrant, Jacob D. Scoria: a Python module for manipulating 3D molecular data |
title | Scoria: a Python module for manipulating 3D molecular data |
title_full | Scoria: a Python module for manipulating 3D molecular data |
title_fullStr | Scoria: a Python module for manipulating 3D molecular data |
title_full_unstemmed | Scoria: a Python module for manipulating 3D molecular data |
title_short | Scoria: a Python module for manipulating 3D molecular data |
title_sort | scoria: a python module for manipulating 3d molecular data |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5603467/ https://www.ncbi.nlm.nih.gov/pubmed/29086076 http://dx.doi.org/10.1186/s13321-017-0237-8 |
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