{"id":19423092,"url":"https://github.com/quantori/scip-dockingfactory","last_synced_at":"2026-04-22T09:06:30.305Z","repository":{"id":105047865,"uuid":"579990388","full_name":"quantori/scip-dockingfactory","owner":"quantori","description":"Docking Factory is a tool to automate molecular docking runs on an HPC cluster using the Dask framework. 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Other projects that are also parts of the bundle are:\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\nSee the [DockingFactory Bundle](https://github.com/quantori/scip-dockingfactory-bundle) repo for installation instructions.\n\n## Quick Start\n\n```\ncd tests/test1local\ndockingfactory.py --config config.yml --local yes\n```\n\n## Usage\n\n```\nusage: dockingfactory.py [-h] [--config CONFIG] [--handler HANDLER]\n                         [--handler_config HANDLER_CONFIG]\n                         [--input_path INPUT_PATH] [--receptor RECEPTOR]\n                         [--output_folder OUTPUT_FOLDER]\n                         [--rdock_protocol RDOCK_PROTOCOL]\n                         [--rdock_recdef RDOCK_RECDEF]\n                         [--rdock_nruns RDOCK_NRUNS] [--rdock_root RDOCK_ROOT]\n                         [--rdock_home RDOCK_HOME] [--csv_out CSV_OUT]\n                         [--output OUTPUT] [--address ADDRESS]\n                         [--maximum_scale MAXIMUM_SCALE] [--name NAME]\n                         [--partition PARTITION]\n                         [--worker_instance_type WORKER_INSTANCE_TYPE]\n                         [--scheduler_instance_type SCHEDULER_INSTANCE_TYPE]\n                         [--server_mode SERVER_MODE]\n                         [--failed_ligand_out FAILED_LIGAND_OUT]\n                         [--error_msg_out ERROR_MSG_OUT]\n                         [--errors_aws ERRORS_AWS] [--restart RESTART]\n                         [--cost_per_cpu COST_PER_CPU] [--debug DEBUG]\n                         [--local LOCAL]\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --config CONFIG       Main config file (.yml)\n  --handler HANDLER     Name of handler (usually smina)\n  --handler_config HANDLER_CONFIG\n                        Path to config file for handler (.txt)\n  --input_path INPUT_PATH\n                        Path to folder with ligands (.pdbqt, subdirectories\n                        are searched automatically)\n  --receptor RECEPTOR   Path to receptor (.pdbqt)\n  --output_folder OUTPUT_FOLDER\n                        Path to output folder for docked .pdbqt\n  --rdock_protocol RDOCK_PROTOCOL\n                        Protocol for rDock (.prm)\n  --rdock_recdef RDOCK_RECDEF\n                        Receptor definition for rDock (.prm)\n  --rdock_nruns RDOCK_NRUNS\n                        Number of runs for rdock\n  --rdock_root RDOCK_ROOT\n                        Root directory of rDock files\n  --rdock_home RDOCK_HOME\n                        Home directory of rDock files\n  --csv_out CSV_OUT     Path to output .csv file\n  --output OUTPUT       Path to output folder with .csv, ligands, errors, and\n                        etc.\n  --address ADDRESS     Dask cluster address\n  --maximum_scale MAXIMUM_SCALE\n                        Dask cluster maximum scale\n  --name NAME           Dask cluster name\n  --partition PARTITION\n                        Partition for Dask cluster\n  --worker_instance_type WORKER_INSTANCE_TYPE\n                        Type of worker instance for Dask cluster\n  --scheduler_instance_type SCHEDULER_INSTANCE_TYPE\n                        Type of scheduler instance for Dask cluster\n  --server_mode SERVER_MODE\n                        Keep running after all ligands have been processed\n  --failed_ligand_out FAILED_LIGAND_OUT\n                        Output file containing failed ligand filenames (.csv)\n  --error_msg_out ERROR_MSG_OUT\n                        Output file containing error messages that come from\n                        docking engine (.txt)\n  --errors_aws ERRORS_AWS\n                        Output file containing error messages that come from\n                        AWS (.txt)\n  --restart RESTART     Run leftover unprocessed files\n  --cost_per_cpu COST_PER_CPU\n                        Cost per AWS CPU\n  --debug DEBUG         Write debug files (for development only)\n  --local LOCAL         Run dockingfactory in local mode\n```\n\n### Waiting for the script to finish\n\nThe script prints lines, one line per second, with the current statistics, for example:\n```\n3675/245/0/12223 clusters: 1, workers: 2, CPUs: 128, Elapsed: 27 min 04 s, Left: 62 min, Rate: 2.26 lig/sec, Current cost: $1.54, Cost estimate: $6.14\n```\nHere, 3675 is the number of processed ligands (both successes and failures), 245 is the number of failures, and 12223 is the total number of ligands. The zero is the number of ligands that have failed due to technical reason.\n\nAs soon as all ligands are processed, the script terminates (unless you specified `--server_mode=true`).\n\n\n## Configuration File\n\nYou can have a YAML configuration file, or specify parameters as the script’s command line arguments, or both. Command line arguments take precedence over configuration file.\n\n### Example\n\nExample `config.yaml`:\n\n```\naddress: http://10.2.34.23:8000\nmaximum_scale: 1\nname: cluster-arm\npartition: compute-cpu\nworker_instance_type: c6g.16xlarge\nscheduler_instance_type: c6g.medium\n\nhandler: smina\nhandler_config: /home/username/docking/dockingfactory/ZINC/smina_zinc.txt\ninput_path: /home/username/docking/dockingfactory/ZINC/viva_VFVS_100\nreceptor: /home/userame/docking/dockingfactory/ZINC/receptor/AR_5JJ_Bside_protonated.pdbqt\noutput: /home/username/docking/dockingfactory/ZINC/zinc_out\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","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantori%2Fscip-dockingfactory","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantori%2Fscip-dockingfactory/lists"}