Toolkit Wrappers and Registries

The toolkit wrappers provide a simple uniform API for accessing some functionality of cheminformatics toolkits. They are used internally by the OpenFF Toolkit to avoid re-implementing existing scientific algorithms, and can be used by users to specify exactly what software is used for any given section of code.

These toolkit wrappers are generally used through a ToolkitRegistry, which facilitates combining software with different capabilities and can be constructed with a list of toolkit wrappers ordered by precedence.

>>> from openff.toolkit import (
...     ToolkitRegistry,
...     OpenEyeToolkitWrapper,
...     RDKitToolkitWrapper,
...     AmberToolsToolkitWrapper,
... )
>>> toolkit_registry = ToolkitRegistry(
...     [
...         OpenEyeToolkitWrapper,
...         RDKitToolkitWrapper,
...         AmberToolsToolkitWrapper,
...     ]
... )

The toolkit wrappers’ functionality can then be accessed through the registry. The first toolkit in the list that provides a method with the given name will be used:

>>> from openff.toolkit import Molecule
>>> molecule = Molecule.from_smiles('Cc1ccccc1')
>>> smiles = toolkit_registry.call('to_smiles', molecule)

For further details on how this search is performed and how it handles exceptions, see the ToolkitRegistry.call() API docs.

Many functions in the OpenFF Toolkit API include a toolkit_registry argument that can be used to specify the toolkit wrappers used by a call to that function. The value of this argument can be either a single toolkit wrapper instance, or an entire toolkit registry:

>>> smiles = molecule.to_smiles(toolkit_registry=RDKitToolkitWrapper())
>>> smiles = molecule.to_smiles(toolkit_registry=toolkit_registry)

For example, differences in to_smiles functionality between the OpenEye and RDKit can be explored by specifying the desired toolkit wrapper:

>>> molecule.to_smiles(toolkit_registry=RDKitToolkitWrapper())
'[H][c]1[c]([H])[c]([H])[c]([C]([H])([H])[H])[c]([H])[c]1[H]'
>>> molecule.to_smiles(toolkit_registry=OpenEyeToolkitWrapper())
'[H]c1c(c(c(c(c1[H])[H])C([H])([H])[H])[H])[H]'

The default value of this argument is the GLOBAL_TOOLKIT_REGISTRY, which by default includes all the toolkits that OpenFF recommends for everyday use:

>>> from openff.toolkit import GLOBAL_TOOLKIT_REGISTRY
>>> len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits)
4

The toolkit_registry_manager context manager allows GLOBAL_TOOLKIT_REGISTRY to be changed temporarily:

>>> from openff.toolkit.utils import toolkit_registry_manager
>>> print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
4
>>> with toolkit_registry_manager(ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])):
...     print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
2

For more information about modifying GLOBAL_TOOLKIT_REGISTRY, see the GLOBAL_TOOLKIT_REGISTRY API docs.

`ToolkitRegistry`	A registry and precedence list for `ToolkitWrapper` objects.
`ToolkitWrapper`	Base class for wrappers around external software toolkits.
`OpenEyeToolkitWrapper`	OpenEye toolkit wrapper
`RDKitToolkitWrapper`	RDKit toolkit wrapper
`AmberToolsToolkitWrapper`	AmberTools toolkit wrapper
`NAGLToolkitWrapper`	NAGL toolkit wrapper for applying partial charges with a GCN model.
`BuiltInToolkitWrapper`	Built-in ToolkitWrapper for very basic functionality.
`GLOBAL_TOOLKIT_REGISTRY`	The toolkit registry used by default when no registry or wrapper is specified.
`toolkit_registry_manager`	A context manager that temporarily changes the `GLOBAL_TOOLKIT_REGISTRY`.