Example Jupyter notebook illustrating how mdciao can be used in API mode.
<p>In this case we compute the Gα-β2AR-interface contact frequencies. The 12 notebook cells are shown in two panels next to each other, A) cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref001" target="_blank">1&...
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2025
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| Summary: | <p>In this case we compute the Gα-β2AR-interface contact frequencies. The 12 notebook cells are shown in two panels next to each other, A) cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref001" target="_blank">1</a>] to [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref007" target="_blank">7</a>] and B) cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref008" target="_blank">8</a>] to [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref012" target="_blank">12</a>]. The outputs of cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref003" target="_blank">3</a>] and [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref005" target="_blank">5</a>] have been edited out ([…]) but are analogous to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.g002" target="_blank">Fig 2A</a>) and can be found in the online documentation and the <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.s001" target="_blank">S1</a> Notebook. The main computation is the generation of the mdciao object, intf, in cell [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref005" target="_blank">5</a>] which can later be used to generate multiple text, tabular, and graphic reports of the frequencies, distributions, and time-traces anywhere else in the notebook. A full version of this notebook, with full outputs and high-res pictures can be found in the <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.s001" target="_blank">S1</a> Notebook, and an online version can be found at <a href="https://proteinformatics.uni-leipzig.de/mdciao/gallery.html#examples" target="_blank">https://proteinformatics.uni-leipzig.de/mdciao/gallery.html#examples</a>. Locally, mdciao users can access this notebook (and others) by invoking the CLT mdc_notebooks.py (cf. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.t001" target="_blank">Table 1</a>).</p> |
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