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exampleAndTutorials.html
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<title>Examples and tutorials — NMRlipids databank 4.9.2023 documentation</title>
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NMRlipids databank
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<li class="toctree-l1"><a class="reference internal" href="listOfFiles.html">List and descriptions of NMRlipids databank files</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#id1">Plotting basic simulation properties</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#id6">Template for more advance API usage</a></li>
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<section id="examples-and-tutorials">
<h1>Examples and tutorials<a class="headerlink" href="#examples-and-tutorials" title="Link to this heading"></a></h1>
<p>A template project for analyses utilizing the NMRlipids databank is available in <a class="reference external" href="https://github.com/NMRLipids/databank-template/tree/main">here</a> where examples and templates for analyses are available from the <a class="reference external" href="https://github.com/NMRLipids/databank-template/tree/main/scripts">scripts</a> folder.</p>
<section id="id1">
<h2><a class="reference external" href="https://github.com/NMRLipids/databank-template/blob/main/scripts/plotSimulation.ipynb">Plotting basic simulation properties</a><a class="headerlink" href="#id1" title="Link to this heading"></a></h2>
<p>Plots the basic properties of simulation selected based on its NMRlipids databank ID number. In addition to <a class="reference external" href="https://github.com/NMRLipids/databank-template/blob/main/scripts/plotSimulation.ipynb">GitHub</a>, the code can be run at <a class="reference external" href="https://colab.research.google.com/github/NMRLipids/databank-template/blob/main/scripts/plotSimulation.ipynb">Colab</a> without additional setup, and app is available at <a class="reference external" href="https://lolicato-nmrlipids-gui-app-qa2ffe.streamlit.app/">Streamlit</a>.</p>
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<section id="id2">
<h2><a class="reference external" href="https://github.com/NMRLipids/databank-template/blob/main/scripts/plotQuality.ipynb">Show ranking tables of simulations based in their quality against experimental data</a><a class="headerlink" href="#id2" title="Link to this heading"></a></h2>
<p>Shows different kinds of rankings of simulations against experimental data. In addition to <a class="reference external" href="https://github.com/NMRLipids/databank-template/blob/main/scripts/plotQuality.ipynb">GitHub</a>, the code can be run at <a class="reference external" href="https://colab.research.google.com/github/NMRLipids/databank-template/blob/main/scripts/plotQuality.ipynb">Colab</a> without additional setup, and app is available at <a class="reference external" href="https://lolicato-nmrlipids-gui-app-qa2ffe.streamlit.app/">Streamlit</a>.</p>
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<section id="id6">
<h2><a class="reference external" href="https://github.com/NMRLipids/databank-template/blob/main/scripts/template.ipynb">Template for more advance API usage</a><a class="headerlink" href="#id6" title="Link to this heading"></a></h2>
<p>Demonstrates the usage of API by three examples. 1) Selects a random simulation and prints the related databank content in human readable format. 2) Shows the readily analyzed properties for the selected random simulation (area per lipid, membrane thickness, relative equilibration times, X-ray scattering form factors, and C-H bond order parameters). 3) Selects a random simulation with the trajectory size below 100Mb and calculates P-N vector angle with respect to membrane normal for all lipids for which P and N atoms are available in headgroup. In addition to <a class="reference external" href="https://github.com/NMRLipids/databank-template/blob/main/scripts/template.ipynb">GitHub</a>, the code can be run at <a class="reference external" href="https://colab.research.google.com/github/NMRLipids/databank-template/blob/main/scripts/template.ipynb">Colab</a> without additional setup.</p>
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<section id="id9">
<h2><a class="reference external" href="https://github.com/NMRLipids/Databank/blob/main/Scripts/AnalyzeDatabank/stats.ipynb">Showing statistics from the NMRlipids databank</a><a class="headerlink" href="#id9" title="Link to this heading"></a></h2>
<p>Plots distributions of simulation lengths, number of atoms and trajectory sizes, distribution of number of lipid components, available single component bilayers and binary lipid mixtures, and pie diagram of temperatures. In addition to <a class="reference external" href="https://github.com/NMRLipids/Databank/blob/main/Scripts/AnalyzeDatabank/stats.ipynb">GitHub</a>, the code can be run at <a class="reference external" href="https://colab.research.google.com/github/NMRLipids/Databank/blob/main/Scripts/AnalyzeDatabank/stats.ipynb">Colab</a> without additional setup.</p>
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