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‎docs/_sources/demo.rst.txt‎

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We designed the IDPET Python package to facilitate the study and analysis of conformational ensembles of intrinsically disordered proteins. These proteins, known for their dynamic and highly variable structures, play a fundamental role in various biological processes.
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Here, we highlight four different types of analyses that can be performed using IDPET.
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Here, we highlight four different types of analyses that can be performed using IDPET. For more details you can also check the jupyter notebooks provided in the github repository.
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.. rubric:: Notebooks Overview
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Here’s a summary of the example notebooks available in the github repository:
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.. grid:: 1 1 2 3
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:gutter: 2
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.. card:: ``comparing_ensembles``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/comparing_ensembles.ipynb
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:link-type: url
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Compare multiple conformational ensembles using selected metrics and visualizations.
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.. card:: ``featurization``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/featurization.ipynb
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:link-type: url
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Generate numerical features from protein ensembles for downstream analysis.
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.. card:: ``kpca_analysis``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/kpca_analysis.ipynb
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:link-type: url
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Perform Kernel PCA to capture non-linear variance in ensemble structures.
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.. card:: ``loading_data``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/loading_data.ipynb
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:link-type: url
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Load and preprocess ensemble data from various formats.
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.. card:: ``pca_analysis``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/pca_analysis.ipynb
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:link-type: url
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Principal Component Analysis (PCA) for dimensionality reduction and visualization.
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.. card:: ``plot_customization``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/plot_customization.ipynb
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:link-type: url
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Customize plots for clarity and publication-quality visualizations.
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.. card:: ``sh3_example``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/sh3_example.ipynb
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:link-type: url
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Case study: global and local analysis of the SH3 domain of the Drkn protein.
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.. card:: ``tsne_analysis``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/tsne_analysis.ipynb
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:link-type: url
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t-SNE embedding of ensemble features to explore local structure.
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.. card:: ``umap_analysis``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/umap_analysis.ipynb
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:link-type: url
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UMAP embedding for global manifold learning and visualization.
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<div style="font-size: 12px; color: #001;">Ensemble Comparison</div>
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‎docs/_sources/index.rst.txt‎

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Changelog
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==========
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*Last updated: June 2024*
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*Last updated: August 2025*
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Indices and tables
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==================

‎docs/_sources/overview.rst.txt‎

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.. rubric:: Notebooks Overview
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Here’s a summary of the example notebooks available in the repository:
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.. grid:: 1 1 2 3
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:gutter: 2
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.. card:: ``comparing_ensembles``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/comparing_ensembles.ipynb
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:link-type: url
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Compare multiple conformational ensembles using selected metrics and visualizations.
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.. card:: ``featurization``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/featurization.ipynb
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:link-type: url
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Generate numerical features from protein ensembles for downstream analysis.
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.. card:: ``kpca_analysis``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/kpca_analysis.ipynb
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:link-type: url
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Perform Kernel PCA to capture non-linear variance in ensemble structures.
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.. card:: ``loading_data``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/loading_data.ipynb
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:link-type: url
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Load and preprocess ensemble data from various formats.
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.. card:: ``pca_analysis``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/pca_analysis.ipynb
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:link-type: url
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Principal Component Analysis (PCA) for dimensionality reduction and visualization.
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.. card:: ``plot_customization``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/plot_customization.ipynb
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:link-type: url
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Customize plots for clarity and publication-quality visualizations.
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.. card:: ``sh3_example``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/sh3_example.ipynb
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:link-type: url
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Case study: global and local analysis of the SH3 domain of the Drkn protein.
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.. card:: ``tsne_analysis``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/tsne_analysis.ipynb
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:link-type: url
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t-SNE embedding of ensemble features to explore local structure.
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.. card:: ``umap_analysis``
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:link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/umap_analysis.ipynb
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UMAP embedding for global manifold learning and visualization.

‎docs/demo.html‎

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<section id="demo">
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<h1>Demo<a class="headerlink" href="#demo" title="Link to this heading"></a></h1>
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<p>We designed the IDPET Python package to facilitate the study and analysis of conformational ensembles of intrinsically disordered proteins. These proteins, known for their dynamic and highly variable structures, play a fundamental role in various biological processes.</p>
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<p>Here, we highlight four different types of analyses that can be performed using IDPET.</p>
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<p>Here, we highlight four different types of analyses that can be performed using IDPET. For more details you can also check the jupyter notebooks provided in the github repository.</p>
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<p class="rubric">Notebooks Overview</p>
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<p>Here’s a summary of the example notebooks available in the github repository:</p>
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<div class="sd-container-fluid sd-sphinx-override sd-mb-4 docutils">
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<div class="sd-row sd-row-cols-1 sd-row-cols-xs-1 sd-row-cols-sm-1 sd-row-cols-md-2 sd-row-cols-lg-3 sd-g-2 sd-g-xs-2 sd-g-sm-2 sd-g-md-2 sd-g-lg-2 docutils">
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<code class="docutils literal notranslate"><span class="pre">comparing_ensembles</span></code></div>
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<p class="sd-card-text">Compare multiple conformational ensembles using selected metrics and visualizations.</p>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/comparing_ensembles.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/comparing_ensembles.ipynb</span></a></div>
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<code class="docutils literal notranslate"><span class="pre">featurization</span></code></div>
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<p class="sd-card-text">Generate numerical features from protein ensembles for downstream analysis.</p>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/featurization.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/featurization.ipynb</span></a></div>
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<div class="sd-card-body docutils">
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<div class="sd-card-title sd-font-weight-bold docutils">
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<code class="docutils literal notranslate"><span class="pre">kpca_analysis</span></code></div>
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<p class="sd-card-text">Perform Kernel PCA to capture non-linear variance in ensemble structures.</p>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/kpca_analysis.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/kpca_analysis.ipynb</span></a></div>
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<div class="sd-card sd-sphinx-override sd-mb-3 sd-shadow-sm sd-card-hover docutils">
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<div class="sd-card-body docutils">
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<div class="sd-card-title sd-font-weight-bold docutils">
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<code class="docutils literal notranslate"><span class="pre">loading_data</span></code></div>
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<p class="sd-card-text">Load and preprocess ensemble data from various formats.</p>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/loading_data.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/loading_data.ipynb</span></a></div>
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<div class="sd-card sd-sphinx-override sd-mb-3 sd-shadow-sm sd-card-hover docutils">
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<div class="sd-card-title sd-font-weight-bold docutils">
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<code class="docutils literal notranslate"><span class="pre">pca_analysis</span></code></div>
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<p class="sd-card-text">Principal Component Analysis (PCA) for dimensionality reduction and visualization.</p>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/pca_analysis.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/pca_analysis.ipynb</span></a></div>
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<div class="sd-card sd-sphinx-override sd-mb-3 sd-shadow-sm sd-card-hover docutils">
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<div class="sd-card-body docutils">
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<div class="sd-card-title sd-font-weight-bold docutils">
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<code class="docutils literal notranslate"><span class="pre">plot_customization</span></code></div>
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<p class="sd-card-text">Customize plots for clarity and publication-quality visualizations.</p>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/plot_customization.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/plot_customization.ipynb</span></a></div>
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<div class="sd-card sd-sphinx-override sd-mb-3 sd-shadow-sm sd-card-hover docutils">
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<div class="sd-card-title sd-font-weight-bold docutils">
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<code class="docutils literal notranslate"><span class="pre">sh3_example</span></code></div>
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<p class="sd-card-text">Case study: global and local analysis of the SH3 domain of the Drkn protein.</p>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/sh3_example.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/sh3_example.ipynb</span></a></div>
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<div class="sd-card-title sd-font-weight-bold docutils">
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<code class="docutils literal notranslate"><span class="pre">tsne_analysis</span></code></div>
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<p class="sd-card-text">t-SNE embedding of ensemble features to explore local structure.</p>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/tsne_analysis.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/tsne_analysis.ipynb</span></a></div>
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<code class="docutils literal notranslate"><span class="pre">umap_analysis</span></code></div>
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<p class="sd-card-text">UMAP embedding for global manifold learning and visualization.</p>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/umap_analysis.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/umap_analysis.ipynb</span></a></div>
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‎docs/index.html‎

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<p><em>Last updated: August 2025</em></p>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/comparing_ensembles.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/comparing_ensembles.ipynb</span></a></div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/featurization.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/featurization.ipynb</span></a></div>
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</div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/kpca_analysis.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/kpca_analysis.ipynb</span></a></div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/loading_data.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/loading_data.ipynb</span></a></div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/pca_analysis.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/pca_analysis.ipynb</span></a></div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/plot_customization.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/plot_customization.ipynb</span></a></div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/sh3_example.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/sh3_example.ipynb</span></a></div>
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<a class="sd-stretched-link sd-hide-link-text reference external" href="https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/tsne_analysis.ipynb"><span>https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/tsne_analysis.ipynb</span></a></div>
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