{"id":19423085,"url":"https://github.com/quantori/scip-dockingfactory-bundle","last_synced_at":"2025-02-25T04:28:58.717Z","repository":{"id":105047881,"uuid":"579950916","full_name":"quantori/scip-dockingfactory-bundle","owner":"quantori","description":" Docking Factory is a tool to automate molecular docking runs on an HPC cluster using the Dask framework. DockingFactory provides unified way of running molecular docking with different software backends: AutoDock Vina, Smina, Qvina2, and rDock. ","archived":false,"fork":false,"pushed_at":"2023-01-09T16:54:09.000Z","size":98,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-07T18:52:15.587Z","etag":null,"topics":["dask","docking","drug-discovery","hpc","molecular-docking","python","virtual-screening"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/quantori.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-12-19T10:54:02.000Z","updated_at":"2023-08-09T20:49:21.000Z","dependencies_parsed_at":null,"dependency_job_id":"0dc8047b-8e14-4cc1-8b5f-da16dd9be420","html_url":"https://github.com/quantori/scip-dockingfactory-bundle","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantori%2Fscip-dockingfactory-bundle","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantori%2Fscip-dockingfactory-bundle/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantori%2Fscip-dockingfactory-bundle/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantori%2Fscip-dockingfactory-bundle/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/quantori","download_url":"https://codeload.github.com/quantori/scip-dockingfactory-bundle/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240602809,"owners_count":19827589,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["dask","docking","drug-discovery","hpc","molecular-docking","python","virtual-screening"],"created_at":"2024-11-10T13:36:38.448Z","updated_at":"2025-02-25T04:28:58.675Z","avatar_url":"https://github.com/quantori.png","language":"Python","readme":"# DockingFactory Bundle\n\nCopyright (c) 2022 Quantori.\n\nDocking Factory is a tool to automate molecular docking runs on an HPC cluster using the Dask framework. \n\nThis is the head repo that contains all scripts and references required to build DockingFactory bundle.\n\nDockingFactory provides unified way of running molecular docking with different software backends: AutoDock Vina, Smina, Qvina2, and rDock.\n\nDockingFactory provides the automation of the whole process of molecular docking-based virtual screening of large databases. It allows scientists to work exclusively within their research environments with AWS ParrallelCluster and Jupyter Notebooks. \n\nKey advantages:\n\n- Parallelization - DF allows users to easily configure and run docking for millions of compounds with different docking protocols.\n- Scalability - DF can scale from small runs with a few thousand ligands up to millions without reconfiguration.\n- Customization - Interface libraries are implemented in Python. Advanced users can design their docking protocols and pipelines by themselves.\n- Open-source - Parallelization and cluster interaction are handled by an open-source Dask framework, which allows focusing on integration and improvement of the interface rather than on solving infrastructure tasks.\n\nTech stack includes AWS ParallelCluster, Python, Dask, Slurm, and docking backends written in C++.\n\n## Bundle\n\nThe bundle consists of this head project and the following other projects:\n\n- [DockingFactory](https://github.com/quantori/scip-dockingfactory)\n- [DockingInterface](https://github.com/quantori/scip-dockinginterface)\n- [Vina](https://github.com/quantori/scip-vina)\n- [Smina](https://github.com/quantori/scip-smina)\n- [QVina 2](https://github.com/quantori/scip-qvina)\n- [rDock](https://github.com/quantori/scip-rdock)\n\n## Installation\n\n### Prerequisities\n\nOn a Debian-based system. run:\n\n```\nsudo apt install wget curl libffi-dev libssl-dev libbz2-dev g++ make\n```\n\nOn a Redhat-based system, run:\n\n```\nsudo yum install wget curl libffi-devel libssl-devel libbz2-devel g++ make\n```\n\n\n### Getting submodules\n\n```\ngit submodule init \u0026\u0026 git submodule update\ncd dockinginterface\ngit submodule init \u0026\u0026 git submodule update\ncd ..\n```\n\n### Building bundle\n\nExample build command:\n\n```\nBUNDLE_PATH=/path/to/desired/bundle PARALLEL=8 make all\n```\n\nUpon completion of `make`, the self-contained bundle will appear in `/path/to/desired/bundle`. All the necessary binary libraries, Python modules, and the Python environment will be there.\n\n**Note:** The bundle is not allowed to be moved to another directory after creation. You will have to re-run the installation in order to build the bundle in a different directory.\n\n## Running DockingFactory\n\n### Locally\n\n```\n. /path/to/desired/bundle/dask/bin/activate\ndockingfactory.py [arguments] --local yes\n```\n\n### Via AWS ParallelCluster\n\n```\n. /path/to/desired/bundle/dask/bin/activate\nsrun python -u /path/to/desired/bundle/dask/bin/dockingfactory.py [arguments] \n```\n\nSee the [DockingFactory](https://github.com/quantori/scip-dockingfactory) page for command line arguments and examples.\n\n\n## License\n\nQuantori DockingFactory is released under [Apache License, Version 2.0](LICENSE.md)\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantori%2Fscip-dockingfactory-bundle","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantori%2Fscip-dockingfactory-bundle","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantori%2Fscip-dockingfactory-bundle/lists"}