openforcefield.utils.toolkits.ToolkitRegistry¶

class openforcefield.utils.toolkits.ToolkitRegistry(register_imported_toolkit_wrappers=False, toolkit_precedence=None, exception_if_unavailable=True)[source]¶

Registry for ToolkitWrapper objects

Examples

Register toolkits in a specified order, skipping if unavailable

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

Register specified toolkits, raising an exception if one is unavailable

>>> toolkit_registry = ToolkitRegistry()
>>> toolkits = [OpenEyeToolkitWrapper, AmberToolsToolkitWrapper]
>>> for toolkit in toolkits:
...     toolkit_registry.register_toolkit(toolkit)

Register all available toolkits in arbitrary order

>>> from openforcefield.utils import all_subclasses
>>> toolkits = all_subclasses(ToolkitWrapper)
>>> for toolkit in toolkit_precedence:
...     if toolkit.is_available():
...         toolkit_registry.register_toolkit(toolkit)

Retrieve the global singleton toolkit registry, which is created when this module is imported from all available toolkits:

>>> from openforcefield.utils.toolkits import GLOBAL_TOOLKIT_REGISTRY as toolkit_registry
>>> available_toolkits = toolkit_registry.registered_toolkits

Warning

This API is experimental and subject to change.

Attributes:	registered_toolkits List registered toolkits.

Methods

add_toolkit(toolkit_wrapper)	Append a ToolkitWrapper onto the list of toolkits in this ToolkitRegistry
call(method_name, *args, **kwargs)	Execute the requested method by attempting to use all registered toolkits in order of precedence.
register_toolkit(toolkit_wrapper[, …])	Register the provided toolkit wrapper class, instantiating an object of it.
resolve(method_name)	Resolve the requested method name by checking all registered toolkits in order of precedence for one that provides the requested method.

__init__(register_imported_toolkit_wrappers=False, toolkit_precedence=None, exception_if_unavailable=True)[source]¶

Create an empty toolkit registry.

Parameters:

register_imported_toolkit_wrappers : bool, optional, default=False If True, will attempt to register all imported ToolkitWrapper subclasses that can be found, in no particular order. toolkit_precedence : list, optional, default=None List of toolkit wrapper classes, in order of desired precedence when performing molecule operations. If None, defaults to [OpenEyeToolkitWrapper, RDKitToolkitWrapper, AmberToolsToolkitWrapper]. exception_if_unavailable : bool, optional, default=True If True, an exception will be raised if the toolkit is unavailable

Methods

__init__([…])	Create an empty toolkit registry.
add_toolkit(toolkit_wrapper)	Append a ToolkitWrapper onto the list of toolkits in this ToolkitRegistry
call(method_name, *args, **kwargs)	Execute the requested method by attempting to use all registered toolkits in order of precedence.
register_toolkit(toolkit_wrapper[, …])	Register the provided toolkit wrapper class, instantiating an object of it.
resolve(method_name)	Resolve the requested method name by checking all registered toolkits in order of precedence for one that provides the requested method.

Attributes

registered_toolkits

List registered toolkits.

registered_toolkits¶

List registered toolkits.

Warning

This API is experimental and subject to change.

Todo

Should this return a generator? Deep copies? Classes? Toolkit names?

Returns:	toolkits : iterable of toolkit objects

register_toolkit(toolkit_wrapper, exception_if_unavailable=True)[source]¶

Register the provided toolkit wrapper class, instantiating an object of it.

Warning

This API is experimental and subject to change.

Todo

This method should raise an exception if the toolkit is unavailable, unless an optional argument is specified that silently avoids registration of toolkits that are unavailable.

Parameters:	toolkit_wrapper : instance or subclass of ToolkitWrapper The toolkit wrapper to register or its class. exception_if_unavailable : bool, optional, default=True If True, an exception will be raised if the toolkit is unavailable

add_toolkit(toolkit_wrapper)[source]¶

Append a ToolkitWrapper onto the list of toolkits in this ToolkitRegistry

Warning

This API is experimental and subject to change.

Parameters:	toolkit_wrapper : openforcefield.utils.ToolkitWrapper The ToolkitWrapper object to add to the list of registered toolkits

resolve(method_name)[source]¶

Resolve the requested method name by checking all registered toolkits in order of precedence for one that provides the requested method.

Parameters:	method_name : str The name of the method to resolve
Returns:	method The method of the first registered toolkit that provides the requested method name
Raises:	NotImplementedError if the requested method cannot be found among the registered toolkits

Examples

Create a molecule, and call the toolkit to_smiles() method directly

>>> from openforcefield.topology import Molecule
>>> molecule = Molecule.from_smiles('Cc1ccccc1')
>>> toolkit_registry = ToolkitRegistry(register_imported_toolkit_wrappers=True)
>>> method = toolkit_registry.resolve('to_smiles')
>>> smiles = method(molecule)

Todo

Is there a better way to figure out which toolkits implement given methods by introspection?

call(method_name, *args, **kwargs)[source]¶

Execute the requested method by attempting to use all registered toolkits in order of precedence.

*args and **kwargs are passed to the desired method, and return values of the method are returned

This is a convenient shorthand for toolkit_registry.resolve_method(method_name)(*args, **kwargs)

Parameters:	method_name : str The name of the method to execute
Raises:	NotImplementedError if the requested method cannot be found among the registered toolkits

Examples

Create a molecule, and call the toolkit to_smiles() method directly

>>> from openforcefield.topology import Molecule
>>> molecule = Molecule.from_smiles('Cc1ccccc1')
>>> toolkit_registry = ToolkitRegistry(register_imported_toolkit_wrappers=True)
>>> smiles = toolkit_registry.call('to_smiles', molecule)