`plan-rbfe-network` command#

openfe plan-rbfe-network#

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

This tool is an easy way to set up a RBFE calculation campaign. The JSON files this outputs can be used to run each leg of the campaign. openfe. The generated Network will be stored in a folder containing for each transformation a JSON file, that can be run with quickrun.

By default, this tool makes the following choices:

Atom mappings performed by LOMAP, with settings max3d=1.0 and element_change=False
Minimal spanning network as the network planner, with LOMAP default score as the weight function
Water as solvent, with NaCl counter ions at 0.15 M concentration.
Protocol is the OpenMM-based relative hybrid topology protocol, with default settings.

These choices can be customized by creating a settings yaml file, which is passed in via the -s settings.yaml option, which is detailed in the Options section. For more advanced setups, please consider using the Python layer of openfe.

openfe plan-rbfe-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.

-p, --protein <protein>#: Required ProteinComponent. Can be provided as an PDB or as a PDBx/mmCIF file. string.

-C, --cofactors <cofactors>#: Path to cofactors sdf file. This may contain multiple molecules

-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.

plan-rbfe-network command#

openfe plan-rbfe-network#

`plan-rbfe-network` command#