.. Dock2D documentation master file, created by sphinx-quickstart on Fri May 6 16:28:20 2022. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Dock2D Doc(k)umentation ================================== The library is used to build a toy protein dataset and models to solve the tasks for molecular recognition: .. glossary:: Interaction Pose (IP): Solve for a specific pose between two proteins known to interact. This is the pose generated from the lowest energy transformation that brings a ligand spatially proximal to a receptor. Fact-of-Interaction (FI): Solve for whether two proteins meaningfully interact, if at all. This is the probability of two proteins interacting using the free energy of possible transformations. Directory Reference ------------------- The library is structured into five directories: * :doc:`Dock2D.DatasetGeneration ` Generate a protein pool to create IP and FI datasets. * :doc:`Dock2D.Models ` Four models, two :doc:`BruteForce ` and two :doc:`Sampling ` models for the IP and FI tasks each. * :doc:`Dock2D.Tests ` Testing scripts to check dataset, algorithm, and model functionality. * :doc:`Dock2D.Utility ` Utility classes ranging from data loading to plotting. .. toctree:: :maxdepth: 2 :caption: Contents: api/Dock2D.DatasetGeneration api/Dock2D.Models api/Dock2D.Tests api/Dock2D.Utility Cite Us ------- This code is part of the work done in `our paper `_ . Please cite us if you use this code in your own work: .. code-block:: text @article{Dock2D, title={{Dock2D: Synthetic datasets for the molecular recognition problem}}, author={Bhadra-Lobo, Derevyanko, Lamoureux}, journal={arXiv preprint arxiv:2212.03456}, year={2022}, } Indices and tables ------------------ * :ref:`genindex`