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https://github.com/unixjunkie/ligprep

LigGrep is a program for identifying docked poses that participate in user-specified receptor/ligand interactions. It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters.
https://github.com/unixjunkie/ligprep

docking post-processing sbvs

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LigGrep is a program for identifying docked poses that participate in user-specified receptor/ligand interactions. It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters.

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LigGrep 1.0.0

=============



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:



1. 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



2. 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



3. 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



4. 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



5. 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



6. 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