plan-rhfe-network command#

openfe plan-rhfe-network#

Plan a relative hydration free energy network, saved as JSON files for the quickrun command.

This tool is an easy way to setup a RHFE-Calculation Campaign. This can be useful for testing our tools. Plan-rhfe-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:

  1. generate an atom mapping for all possible ligand pairs. (default: Lomap)

  2. score all atom mappings. (default: Lomap default score)

  3. 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-rhfe-network [OPTIONS]

Options

-M, --molecules <molecules>#

Required A directory or file containing all molecules to be loaded, either as a single SDF or multiple MOL2/SDFs. Any number of sdf paths.

-s, --settings <yaml_settings>#

Path to planning settings yaml file.

-o, --output-dir <output_dir>#

Path to the output directory. Defaults to ./alchemicalNetwork.