Core concepts

OpenFF Molecule

A graph representation of a molecule containing enough information to unambiguously parametrize it. Required data fields for a Molecule are:

  • atoms: element (integer), formal_charge (integer), is_aromatic (boolean), stereochemistry ('R'/'S'/None)

  • bonds: order (integer), is_aromatic (boolean), stereochemistry ('E'/'Z'/None)

There are several other optional attributes such as conformers and partial_charges that may be populated in the Molecule data structure. These are considered “optional” because they are not required for system creation, however if those fields are populated, the user MAY use them to override values that would otherwise be generated during system creation.

A dictionary, is exposed, which is a Python dict that can be populated with arbitrary data. This data should be considered cosmetic and should not affect system creation. Whenever possible, molecule serialization or format conversion should preserve this data.

OpenFF Topology

A collection of molecules, as well as optional box vector, positions, and other information. A Topology describes the chemistry of a system, but has no force field parameters.

OpenFF ForceField

An object generated from an OFFXML file (or other source of SMIRNOFF data). Most information from the SMIRNOFF data source is stored in this object’s several ParameterHandlers, however some top-level SMIRNOFF data is stored in the ForceField object itself.

OpenFF Interchange

A Topology that has been parametrized by a ForceField. An Interchange contains all the information needed to calculate an energy or start a simulation. Interchange also provides methods to export this information to MD simulation engines.