charge-molecules command#

openfe charge-molecules#

Generate partial charges for the set of input molecules and write them to file.

openfe charge-molecules [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 in settings is set to openeye)

  • nagl (must have openff-nagl installed)

  • espaloma (must have espaloma_charge installed)

The 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 <output>#

The name of the SDF file the charged ligands should be written to.

-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.