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

Currently it can contain sections for customising the atom mapper and network planning algorithm, these are addressed using a mapper: or network: key in the yaml file. The algorithm to be used for these sections is then specified by the method: key. For choosing mappers, either the LomapAtomMapper or KartografAtomMapper are allowed choices, while for the network planning algorithm either the generate_minimal_spanning_tree or generate_minimal_redundant_network options are allowed. Finally, a settings: key can be given to customise the algorithm, with allowable options corresponding to the keyword arguments of the Python API for these algorithms.

For example, this is a valid settings yaml file to specify that the Lomap atom mapper should be used forbidding element changes, while the generate_minimal_redundant_network function used to plan the network

mapper:
  method: LomapAtomMapper
  settings:
    element_change: false

network:
  method: generate_minimal_redundant_network
  settings:
    mst_num: 3
-o, --output-dir <output_dir>#

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