openff-interchange documentation

openff.interchange.components.interchange.Interchange

pydantic model openff.interchange.components.interchange.Interchange

A object for storing, manipulating, and converting molecular mechanics data.

Warning

This object is in an early and experimental state and unsuitable for production.

Warning

This API is experimental and subject to change.

Config

• arbitrary_types_allowed: bool = True

• json_encoders: dict = {<class ‘openff.units.units.Quantity’>: <function custom_quantity_encoder at 0x7fdff3466f70>}

• json_loads: function = <function json_loader at 0x7fdff3459280>

• validate_assignment: bool = True

property handlers

Get the PotentialHandler objects in this Interchange object.

add_handler(handler_name: str, handler)

Add a ParameterHandler to this Interchange object.

remove_handler(handler_name: str)

Remove a PotentialHandler in this Interchange object.

property topology

Get the OpenFF Topology object in this Interchange object.

property positions

Get the positions of all particles.

property box

If periodic, an array representing the periodic boundary conditions.

classmethod from_smirnoff(force_field: openff.toolkit.typing.engines.smirnoff.forcefield.ForceField, topology: openff.interchange.components.mdtraj._OFFBioTop, box=None) → openff.interchange.components.interchange.Interchange

Create a new object by parameterizing a topology with a SMIRNOFF force field.

Parameters

• force_field – The force field to parameterize the topology with.

• topology – The topology to parameterize.

• box – The box vectors associated with the interchange.

Examples

Generate an Interchange object from a single-molecule (OpenFF) topology and OpenFF 1.0.0 “Parsley”

>>> from openff.interchange.components.interchange import Interchange
>>> from openff.interchange.components.mdtraj import _OFFBioTop
>>> from openff.toolkit.topology import Molecule
>>> from openff.toolkit.typing.engines.smirnoff import ForceField
>>> import mdtraj as md
>>> mol = Molecule.from_smiles("CC")
>>> mol.generate_conformers(n_conformers=1)
>>> top = _OFFBioTop.from_molecules([mol])
>>> top.mdtop = md.Topology.from_openmm(top.to_openmm())
>>> parsley = ForceField("openff-1.0.0.offxml")
>>> interchange = Interchange.from_smirnoff(topology=top, force_field=parsley)
>>> interchange
Interchange with 8 atoms, non-periodic topology

to_gro(file_path: Union[pathlib.Path, str], writer='internal', decimal: int = 8)

Export this Interchange object to a .gro file.

to_top(file_path: Union[pathlib.Path, str], writer='internal')

Export this interchange to a .top file.

to_lammps(file_path: Union[pathlib.Path, str], writer='internal')

Export this Interchange to a LAMMPS data file.

to_openmm(combine_nonbonded_forces: bool = False)

Export this interchange to an OpenMM System.

to_prmtop(file_path: Union[pathlib.Path, str], writer='internal')

Export this interchange to an Amber .prmtop file.

to_psf(file_path: Union[pathlib.Path, str])

Export this interchange to a CHARMM-style .psf file.

to_crd(file_path: Union[pathlib.Path, str])

Export this interchange to a CHARMM-style .crd file.

to_inpcrd(file_path: Union[pathlib.Path, str], writer='internal')

Export this interchange to an Amber .inpcrd file.

classmethod from_foyer(topology: _OFFBioTop, force_field: FoyerForcefield, **kwargs) → Interchange

Create an Interchange object from a Foyer force field and an OpenFF topology.

Examples

Generate an Interchange object from a single-molecule (OpenFF) topology and the Foyer implementation of OPLS-AA

>>> from openff.interchange.components.interchange import Interchange
>>> from openff.interchange.components.mdtraj import _OFFBioTop
>>> from openff.toolkit.topology import Molecule
>>> from foyer import Forcefield
>>> import mdtraj as md
>>> mol = Molecule.from_smiles("CC")
>>> mol.generate_conformers(n_conformers=1)
>>> top = _OFFBioTop.from_molecules([mol])
>>> top.mdtop = md.Topology.from_openmm(top.to_openmm())
>>> oplsaa = Forcefield(name="oplsaa")
>>> interchange = Interchange.from_foyer(topology=top, force_field=oplsaa)
>>> interchange
Interchange with 8 atoms, non-periodic topology

classmethod from_gromacs(topology_file: Union[pathlib.Path, str], gro_file: Union[pathlib.Path, str], reader='intermol') → openff.interchange.components.interchange.Interchange

Create an Interchange object from GROMACS files.