Customising CLI planning with YAML settings

The planning commands in the CLI can be made more powerful by supplying YAML-formatted files to customise the planning algorithms.

This settings file has a series of sections for customising the different algorithms. For example, the settings file which re-specifies the default behaviour would look like

network:
  method: plan_minimal_spanning_tree
mapper:
  method: LomapAtomMapper
  settings:
    time: 1
    threed: True
    max3d: 0.95
    element_change: True

The name of the algorithm is given behind the method: key and the arguments to the algorithm are then optionally given behind the settings: key. Both the network: and mapper: sections are optional.

The settings YAML file is then provided to the -s option of openfe plan-rbfe-network:

openfe plan-rbfe-network -M molecules.sdf -P protein.pdb -s settings.yaml

Customising the atom mapper

There is a choice to be made as to which atom mapper is used, currently included are the LomapAtomMapper and the KartografAtomMapper (full details in the Kartograf documentation.)

For example, to switch to using the Kartograf atom mapper, this settings YAML could be used

mapper:
  method: KartografAtomMapper
  settings:
    atom_max_distance: 0.95
    atom_map_hydrogens: True
    map_hydrogens_on_hydrogens_only: False
    map_exact_ring_matches_only: True

Customising the network planner

There are a variety of network planning options available, including generate_radial_network(), generate_minimal_spanning_network(), and generate_minimal_redundant_network().

For example, to plan a radial network using a ligand called ‘CHEMBL1078774’ as the central ligand, this settings YAML could be given

network:
  method: generate_radial_network
  settings:
    central_ligand: CHEMBL1078774

Where the required central_ligand argument has been passed inside the settings: section.

Note that there is a subtle distinction when ligand names could be interpreted as integers. To select the first ligand, the integer 0 can be given

network:
  method: generate_radial_network
  settings:
    central_ligand: 0

Whereas if we wanted to specify the ligand named “0”, we would instead explicitly pass this as a string to the YAML settings file

network:
  method: generate_radial_network
  settings:
    central_ligand: '0'