usage: liggrep.py [-h] [-m MODE] [-o BABEL_EXEC] [-f FILE] [-v] [--num_processors N] [--job_manager {serial,multiprocessing,mpi}] [-t] [-i] receptor ligands filters
LigGrep 1.0.0, a free, open-source program for identifying docked poses that participate in user-specified receptor/ligand interactions. As input, LigGrep accepts a protein receptor file (PDB, PDBQT), a directory containing many docked-compound files (PDB, PDBQT, SDF), and a list of user-specified filters (JSON). It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters.
positional arguments: receptor PDBQT file containing receptor information. ligands Directory of PDBQT files containing the docked-ligand files. filters JSON file containing filters, which are formatted as a list of dictionaries.
optional arguments: -h, --help show this help message and exit -m MODE, --mode MODE Optional user-specified bond-order mode. If OPENBABEL, LigGrep will assign bond orders using the open-babel executable specified via the --babel_exec parameter. If SMILES, LigGrep will use SMILES files to assign bond orders. These files must be in the same directory as the docked-ligand files, and they must be similarly named (except with the .smi extension). If NONE, LigGrep will not attempt to assign bond orders. The docked ligands must either be in a format that itself specifies bond orders (e.g., SDF), or the user- specified filters must not depend on bond orders. Default: NONE -o BABEL_EXEC, --babel_exec BABEL_EXEC Optional path to the OpenBabel executable. -f FILE, --file FILE The name of the file were LigGrep analysis should be saved. Defaults to "output.txt". -v, --verbose Indicate why molecules and poses are rejected (standard output). --num_processors N, -p N Number of processors to use for parallel calculations. Defaults to 1. --job_manager {serial,multiprocessing,mpi} Determine what style of multiprocessing to use: serial, mpi, or multiprocessing. Serial will override the num_processors flag, forcing it to be one. MPI mode requires mpi4py 2.1.0 or higher. Defaults to serial. -t, --test Run optional tests to verify that code updates don't break functionality. -i, --internal_test (Optional parameter used for internal testing.)
EXAMPLES OF USE:
- Prepare a virtual library and save all 3D models to a single SDF file in the present directory:
python liggrep.py ./liggrep/examples/receptors/receptor.pdb
"./liggrep/examples/ligands/sdf/*.sdf" ./liggrep/examples/filters.json
- Assign bond orders to PDBQT-formatted ligands using SMI files in the same directory:
python liggrep.py ./liggrep/examples/receptors/receptor.pdbqt
"./liggrep/examples/ligands/pdb/*.pdb" ./liggrep/examples/filters.json
--mode SMILES
- Or use Open Babel to assign bond orders:
python liggrep.py ./liggrep/examples/receptors/receptor.pdbqt
"./liggrep/examples/ligands/pdb/*.pdb" ./liggrep/examples/filters.json
--mode OPENBABEL --babel_exec /usr/local/bin/obabel
- By default, LigGrep saves the names of the poses that pass all filters to "output.txt". You can optionally specify a different output file:
python liggrep.py ./liggrep/examples/receptors/receptor.pdb
"./liggrep/examples/ligands/sdf/*.sdf" ./liggrep/examples/filters.json
--file other_output.txt
- You can tell LigGrep to output why each ligand/pose is accepted or rejected:
python liggrep.py ./liggrep/examples/receptors/receptor.pdb
"./liggrep/examples/ligands/sdf/*.sdf" ./liggrep/examples/filters.json
--verbose
- By default, LigGrep runs in serial mode, meaning it runs on only one processor. You can also use multiple processors to speed the process. Requesting -1 processors means all processors will be used.
python liggrep.py ./liggrep/examples/receptors/receptor.pdb
"./liggrep/examples/ligands/sdf/*.sdf" ./liggrep/examples/filters.json
--job_manager multiprocessing --num_processors -1