Utilities

Toolkit wrappers

The toolkit wrappers provide a simple uniform API for accessing minimal functionality of cheminformatics toolkits.

These toolkit wrappers are generally used through a ToolkitRegistry, which can be constructed with a desired precedence of toolkits:

from openforcefield.utils.toolkits import ToolkitRegistry
toolkit_registry = ToolkitRegistry()
toolkit_precedence = [OpenEyeToolkitWrapper, RDKitToolkitWrapper, AmberToolsToolkitWrapper]
[ toolkit_registry.register(toolkit) for toolkit in toolkit_precedence if toolkit.is_available() ]

Alternatively, the global toolkit registry (which will attempt to register any available toolkits) can be used:

from openforcefield.utils.toolkits import DEFAULT_TOOLKIT_REGISTRY as toolkit_registry

The toolkit wrappers can then be accessed through the registry:

molecule = Molecule.from_smiles('Cc1ccccc1')
smiles = toolkit_registry.call('to_smiles', molecule)
ToolkitRegistry Registry for ToolkitWrapper objects
ToolkitWrapper Toolkit wrapper base class.
OpenEyeToolkitWrapper OpenEye toolkit wrapper
RDKitToolkitWrapper RDKit toolkit wrapper
AmberToolsToolkitWrapper AmberTools toolkit wrapper

Serialization support

Serializable Mix-in to add serialization and deserialization support via JSON, YAML, BSON, TOML, MessagePack, and XML.

Miscellaneous utilities

Miscellaneous utility functions.

inherit_docstrings Inherit docstrings from parent class
all_subclasses Recursively retrieve all subclasses of the specified class
temporary_cd Context to temporary change the working directory.
temporary_directory Context for safe creation of temporary directories.
get_data_filename Get the full path to one of the reference files in testsystems.

Structure tools

Tools for manipulating molecules and structures

Warning

These methods are deprecated and will be removed and replaced with integrated API methods. We recommend that no new code makes use of these functions.

get_molecule_parameterIDs Process a list of molecules with a specified SMIRNOFF ffxml file and determine which parameters are used by which molecules, returning collated results.