.. _utils :: 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 :class:`ToolkitRegistry`, which can be constructed with a desired precedence of toolkits: .. code-block:: python 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: .. code-block:: python from openforcefield.utils.toolkits import DEFAULT_TOOLKIT_REGISTRY as toolkit_registry The toolkit wrappers can then be accessed through the registry: .. code-block:: python molecule = Molecule.from_smiles('Cc1ccccc1') smiles = toolkit_registry.call('to_smiles', molecule) .. currentmodule:: openforcefield.utils.toolkits .. autosummary:: :nosignatures: :toctree: api/generated/ ToolkitRegistry ToolkitWrapper OpenEyeToolkitWrapper RDKitToolkitWrapper AmberToolsToolkitWrapper Serialization support --------------------- .. currentmodule:: openforcefield.utils.serialization .. autosummary:: :nosignatures: :toctree: api/generated/ Serializable Miscellaneous utilities ----------------------- Miscellaneous utility functions. .. currentmodule:: openforcefield.utils.utils .. autosummary:: :nosignatures: :toctree: api/generated/ inherit_docstrings all_subclasses temporary_cd temporary_directory get_data_file_path convert_0_1_smirnoff_to_0_2 convert_0_2_smirnoff_to_0_3 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. .. currentmodule:: openforcefield.utils.structure .. autosummary:: :nosignatures: :toctree: api/generated/ get_molecule_parameterIDs