Forcefield typing tools¶

Chemical environments¶

Tools for representing and operating on chemical environments

Warning

This class is largely redundant with the same one in the Chemper package, and will likely be removed.

ChemicalEnvironment

Chemical environment abstract base class that matches an atom, bond, angle, etc.

Forcefield typing engines¶

Engines for applying parameters to chemical systems

The SMIRks-Native Open Force Field (SMIRNOFF)¶

A reference implementation of the SMIRNOFF specification for parameterizing biomolecular systems

ForceField¶

The ForceField class is a primary part of the top-level toolkit API. ForceField objects are initialized from SMIRNOFF data sources (e.g. an OFFXML file). For a basic example of system creation using a ForceField, see examples/SMIRNOFF_simulation.

ForceField

A factory that assigns SMIRNOFF parameters to a molecular system

Parameter Type¶

ParameterType objects are representations of individual SMIRKS-based SMIRNOFF parameters. These are usually initialized during ForceField creation, and can be inspected and modified by users via the Python API. For more information, see examples/forcefield_modification.

`ParameterType`	Base class for SMIRNOFF parameter types.
`BondHandler.BondType`	A SMIRNOFF bond type
`AngleHandler.AngleType`	A SMIRNOFF angle type.
`ProperTorsionHandler.ProperTorsionType`	A SMIRNOFF torsion type for proper torsions.
`ImproperTorsionHandler.ImproperTorsionType`	A SMIRNOFF torsion type for improper torsions.
`vdWHandler.vdWType`	A SMIRNOFF vdWForce type.

Parameter Handlers¶

Each ForceField primarily consists of several ParameterHandler objects, which each contain the machinery to add one energy component to a system. During system creation, each ParameterHandler registered to a ForceField has its assign_parameters() function called..

`ParameterList`	Parameter list that also supports accessing items by SMARTS string.
`ParameterHandler`	Base class for parameter handlers.
`BondHandler`	Handle SMIRNOFF `<Bonds>` tags
`AngleHandler`	Handle SMIRNOFF `<AngleForce>` tags
`ProperTorsionHandler`	Handle SMIRNOFF `<ProperTorsionForce>` tags
`ImproperTorsionHandler`	Handle SMIRNOFF `<ImproperTorsionForce>` tags
`vdWHandler`	Handle SMIRNOFF `<vdW>` tags
`ElectrostaticsHandler`	Handles SMIRNOFF `<Electrostatics>` tags.
`ToolkitAM1BCCHandler`	Handle SMIRNOFF `<ToolkitAM1BCC>` tags

Parameter I/O Handlers¶

ParameterIOHandler objects handle reading and writing of serialzied SMIRNOFF data sources.

`ParameterIOHandler`	Base class for handling serialization/deserialization of SMIRNOFF ForceField objects
`XMLParameterIOHandler`	Handles serialization/deserialization of SMIRNOFF ForceField objects from OFFXML format.