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.

Structure tools¶

Tools for manipulating molecules and structures

Todo

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

`generateSMIRNOFFStructure`	Given an OpenEye molecule (oechem.OEMol), create an OpenMM System and use to generate a ParmEd structure using the SMIRNOFF forcefield parameters.
`generateProteinStructure`	Given an OpenMM PDBFile, create the OpenMM System of the protein using OpenMM’s ForceField and then generate the parametrized ParmEd Structure of the protein.
`combinePositions`	Loops through the positions from the ParmEd structures of the protein and ligand, divides by unit.angstroms which will ensure both positions arrays are in the same units.
`mergeStructure`	Combines the parametrized ParmEd structures of the protein and ligand to create the Structure for the protein:ligand complex, while retaining the SMIRNOFF parameters on the ligand.
`generateTopologyFromOEMol`	Generate an OpenMM Topology object from an OEMol molecule.
`get_testdata_filename`	Get the full path to one of the reference files in testsystems.
`normalize_molecules`	Normalize all molecules in specified set.
`read_molecules`	Read molecules from an OpenEye-supported file.
`setPositionsInOEMol`	Set the positions in an OEMol using a position array with units from simtk.unit, i.e.
`extractPositionsFromOEMol`	Get the positions from an OEMol and return in a position array with units via simtk.unit, i.e.
`read_typelist`	Read a parameter type or decorator list from a file.
`positions_from_oemol`	Extract OpenMM positions from OEMol.
`check_energy_is_finite`	Check the potential energy is not NaN.
`get_energy`	Return the potential energy.
`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.
`getMolParamIDToAtomIndex`	Take a Molecule and a SMIRNOFF forcefield object and return a dictionary, keyed by parameter ID, where each entry is a tuple of ( smirks, [[atom1, …
`merge_system`	Merge two given OpenMM systems.
`save_system_to_amber`	Save an OpenMM System, with provided topology and positions, to AMBER prmtop and coordinate files.
`save_system_to_gromacs`	Save an OpenMM System, with provided topology and positions, to AMBER prmtop and coordinate files.

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.