`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.

Note

To ensure a consistent set of partial charges are used for each molecule across different transformations, this tool will automatically generate charges ahead of planning the network. am1bcc charges will be generated via ambertools, this can also be customized using the settings yaml file.

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-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 a YAML file specifying the atom mapper (mapper), network planning algorithm (network), and/or partial charge method (partial_charge) to use.

Supported atom mapper choices are:

- LomapAtomMapper

- KartografAtomMapper

Supported network planning algorithms include (but are not limited to):

- generate_minimal_spanning_tree
- generate_minimal_redundant_network
- generate_radial_network
- generate_lomap_network

Supported partial charge method choices are:

- am1bcc
- am1bccelf10 (only possible if off_toolkit_backend is openeye)
- nagl (must have openff-nagl installed)
- espaloma (must have espaloma_charge installed)

settings: allows for passing in any keyword arguments of the method’s corresponding Python API.

For example:

mapper:
  method: LomapAtomMapper
  settings:
    element_change: false

network:
  method: generate_minimal_redundant_network
  settings:
    mst_num: 3

partial_charge:
  method: am1bcc
  settings:
    off_toolkit_backend: ambertools

-o, --output-dir <output_dir>#: Path to the output directory. Defaults to ./alchemicalNetwork.

--n-protocol-repeats <n_protocol_repeats>#

Number of independent repeats(s) to be run per execution of a transformation using the openfe quickrun command.

For example:

–n-protocol-repeats=3 means openfe quickrun will execute 3 repeats in serial.

–n-protocol-repeats=1 means openfe quickrun will execute only 1 repeat per call, which allows for individual repeats to be submitted in parallel by calling openfe quickrun on the same input JSON file multiple times.

-n, --n-cores <n_cores>#: The number of cores which should be used for multiprocessing stages.

--overwrite-charges#: If the charges already present in the molecules should be overwritten.

plan-rhfe-network command#

openfe plan-rhfe-network#

`plan-rhfe-network` command#