charge-molecules command

openfe charge-molecules

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

Usage

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 method to use to charge the molecules (any atom mapper or network generation options will be ignored).

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:

partial_charge:
  method: am1bcc
  settings:
    off_toolkit_backend: ambertools

-o, --output <output>

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

-n, --n-cores <n_cores>

Number of cores to use for multiprocessing.

--overwrite-charges

Overwrite any partial charges present in the input molecules.