{"id":17255131,"url":"https://github.com/unixjunkie/ligprep","last_synced_at":"2025-07-29T21:32:25.492Z","repository":{"id":144782438,"uuid":"318054923","full_name":"UnixJunkie/ligprep","owner":"UnixJunkie","description":"LigGrep is a program for identifying docked poses that participate in user-specified receptor/ligand interactions. 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As input, LigGrep\naccepts a protein receptor file (PDB, PDBQT), a directory containing many\ndocked-compound files (PDB, PDBQT, SDF), and a list of user-specified filters\n(JSON). It evaluates each docked pose and outputs the names of the compounds\nwith poses that pass all filters.\n\npositional arguments:\n  receptor              PDBQT file containing receptor information.\n  ligands               Directory of PDBQT files containing the docked-ligand\n                        files.\n  filters               JSON file containing filters, which are formatted as a\n                        list of dictionaries.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -m MODE, --mode MODE  Optional user-specified bond-order mode. If OPENBABEL,\n                        LigGrep will assign bond orders using the open-babel\n                        executable specified via the --babel_exec parameter.\n                        If SMILES, LigGrep will use SMILES files to assign\n                        bond orders. These files must be in the same directory\n                        as the docked-ligand files, and they must be similarly\n                        named (except with the .smi extension). If NONE,\n                        LigGrep will not attempt to assign bond orders. The\n                        docked ligands must either be in a format that itself\n                        specifies bond orders (e.g., SDF), or the user-\n                        specified filters must not depend on bond orders.\n                        Default: NONE\n  -o BABEL_EXEC, --babel_exec BABEL_EXEC\n                        Optional path to the OpenBabel executable.\n  -f FILE, --file FILE  The name of the file were LigGrep analysis should be\n                        saved. Defaults to \"output.txt\".\n  -v, --verbose         Indicate why molecules and poses are rejected\n                        (standard output).\n  --num_processors N, -p N\n                        Number of processors to use for parallel calculations.\n                        Defaults to 1.\n  --job_manager {serial,multiprocessing,mpi}\n                        Determine what style of multiprocessing to use:\n                        serial, mpi, or multiprocessing. Serial will override\n                        the num_processors flag, forcing it to be one. MPI\n                        mode requires mpi4py 2.1.0 or higher. Defaults to\n                        serial.\n  -t, --test            Run optional tests to verify that code updates don't\n                        break functionality.\n  -i, --internal_test   (Optional parameter used for internal testing.)\n\nEXAMPLES OF USE:\n\n1. Prepare a virtual library and save all 3D models to a single SDF file in\n   the present directory:\n\npython liggrep.py ./liggrep/examples/receptors/receptor.pdb \\\n    \"./liggrep/examples/ligands/sdf/*.sdf\" ./liggrep/examples/filters.json\n\n2. Assign bond orders to PDBQT-formatted ligands using SMI files in the same\n   directory:\n\npython liggrep.py ./liggrep/examples/receptors/receptor.pdbqt \\\n    \"./liggrep/examples/ligands/pdb/*.pdb\" ./liggrep/examples/filters.json \\\n    --mode SMILES\n\n3. Or use Open Babel to assign bond orders:\n\npython liggrep.py ./liggrep/examples/receptors/receptor.pdbqt \\\n    \"./liggrep/examples/ligands/pdb/*.pdb\" ./liggrep/examples/filters.json \\\n    --mode OPENBABEL --babel_exec /usr/local/bin/obabel\n\n4. By default, LigGrep saves the names of the poses that pass all filters to\n   \"output.txt\". You can optionally specify a different output file:\n\npython liggrep.py ./liggrep/examples/receptors/receptor.pdb \\\n    \"./liggrep/examples/ligands/sdf/*.sdf\" ./liggrep/examples/filters.json \\\n    --file other_output.txt\n\n5. You can tell LigGrep to output why each ligand/pose is accepted or\n   rejected:\n\npython liggrep.py ./liggrep/examples/receptors/receptor.pdb \\\n    \"./liggrep/examples/ligands/sdf/*.sdf\" ./liggrep/examples/filters.json \\\n    --verbose\n\n6. By default, LigGrep runs in serial mode, meaning it runs on only one\n   processor. You can also use multiple processors to speed the process.\n   Requesting -1 processors means all processors will be used.\n\npython liggrep.py ./liggrep/examples/receptors/receptor.pdb \\\n    \"./liggrep/examples/ligands/sdf/*.sdf\" ./liggrep/examples/filters.json \\\n    --job_manager multiprocessing --num_processors -1\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fligprep","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Fligprep","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fligprep/lists"}