interchange_system_creation#

pontibus.utils.system_creation.interchange_system_creation(ffsettings: InterchangeFFSettings, solvation_settings: PackmolSolvationSettings | InterchangeOpenMMSolvationSettings, smc_components: dict[SmallMoleculeComponent, Molecule], protein_component: ProteinComponent | None, solvent_component: SolventComponent | None, solvent_offmol: Molecule | None) → tuple[Interchange, dict[Component, ndarray[tuple[int, ...], dtype[_ScalarType_co]]]]#

Create an Interchange object for a given system, solvating with packmol where necessary.

Parameters:

  • ffsettings (InterchangeFFSettings) – Settings defining how the force field is applied.

  • solvation_settings (PackmolSolvationSettings | InterchangeOpenMMSolvationSettings) – Settings defining how the system will be solvated.

  • smc_components (dict[SmallMoleculeComponent, openff.toolkit.Molecule]`) – Solute SmallMoleculeComponents.

  • protein_component (Optional[ProteinComponent]) – Protein component of the system, if any.

  • solvent_component (Optional[SolventComponent]) – Solvent component of the system, if any.

  • solvent_offmol (Optional[openff.toolkit.Molecule]) – OpenFF Molecule defining the solvent, if necessary

Returns:

  • Interchange (openff.interchange.Interchange) – Interchange object for the created system.

  • comp_resids (dict[Component, npt.NDArray]) – A dictionary defining the residue indices matching various components in the system.