.. functions analysis documentation master file, created by
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Demo
==============================================

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.

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.  

.. rubric:: Notebooks Overview


Here’s a summary of the example notebooks available in the github repository:

.. grid:: 1 1 2 3
   :gutter: 2

   .. card:: ``comparing_ensembles``
      :link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/comparing_ensembles.ipynb
      :link-type: url

      Compare multiple conformational ensembles using selected metrics and visualizations.

   .. card:: ``featurization``
      :link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/featurization.ipynb
      :link-type: url

      Generate numerical features from protein ensembles for downstream analysis.

   .. card:: ``kpca_analysis``
      :link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/kpca_analysis.ipynb
      :link-type: url

      Perform Kernel PCA to capture non-linear variance in ensemble structures.

   .. card:: ``loading_data``
      :link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/loading_data.ipynb
      :link-type: url

      Load and preprocess ensemble data from various formats.

   .. card:: ``pca_analysis``
      :link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/pca_analysis.ipynb
      :link-type: url

      Principal Component Analysis (PCA) for dimensionality reduction and visualization.

   .. card:: ``plot_customization``
      :link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/plot_customization.ipynb
      :link-type: url

      Customize plots for clarity and publication-quality visualizations.

   .. card:: ``sh3_example``
      :link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/sh3_example.ipynb
      :link-type: url

      Case study: global and local analysis of the SH3 domain of the Drkn protein.

   .. card:: ``tsne_analysis``
      :link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/tsne_analysis.ipynb
      :link-type: url

      t-SNE embedding of ensemble features to explore local structure.

   .. card:: ``umap_analysis``
      :link: https://github.com/BioComputingUP/EnsembleTools/blob/main/notebooks/umap_analysis.ipynb
      :link-type: url

      UMAP embedding for global manifold learning and visualization.



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     <img src="_static/images/icons/gl_an.png" alt="global analysis" title="The global analysis of a protein's structure focuses on studying its total three-dimensional shape, aiming to understand how proteins fold and group together to form stable and functional structures." onclick="redirectToPage('Global_analysis.html')" style="cursor: pointer;width: 200px; height: 200px;">
     <div style="font-size: 12px; color: #001;">Global analysis</div>
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    <div style="font-size: 12px; color: #001;">Local analysis</div>
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    <div style="font-size: 12px; color: #001;">Dimensionality Reduction analysis</div>
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    <div style="font-size: 12px; color: #001;">Ensemble Comparison</div>
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.. toctree::
   :hidden:

   Global_analysis

   local_analysis

   dimensional_reduction

   comparing_ensambles