plan-rbfe-network command#
openfe plan-rbfe-network#
Plan a relative binding free energy network, saved in a dir with multiple JSON files.
This tool is an easy way to setup a RBFE-Calculation Campaign. This can be useful for calculating the relative binding free energies of a given set of compounds to a given protein receptor. Plan-rbfe-network finds a reasonable network of transformations and adds the openfe rbfe protocol of year one to the transformations. The output of the command can be used, in order to run the planned transformations with the quickrun tool. For more sophisticated setups, please consider using the python layer of openfe.
- The tool will parse the input and run the rbfe network planner, which executes following steps:
generate an atom mapping for all possible ligand pairs. (default: Lomap)
score all atom mappings. (default: Lomap default score)
build network form all atom mapping scores (default: minimal spanning graph)
The generated Network will be stored in a folder containing for each transformation a JSON file, that can be run with quickrun (or other future tools).
openfe plan-rbfe-network [OPTIONS]
Options
- -M, --mol-dir <mol_dir>#
Required SmallMoleculeComponents from a folder. Folder needs to contain SDF/MOL2 files string. Any number of sdf paths.
- -p, --protein <protein>#
Required ProteinComponent. Can be provided as an PDB or as a PDBx/mmCIF file. string.
- -o, --output-dir <output_dir>#
Path to the output directory. Defaults to ./alchemicalNetwork.
- --mapper <mapper>#
Atom mapper; can either be a name in the openfe.setup namespace or a custom fully-qualified name. In the openfe.setup namespace currently following options are possible: LomapAtomMapper, PersesAtomMapper