normalize_molecule

openff.nagl.toolkits.openff.normalize_molecule(molecule: Molecule, max_iter: int = 200, inplace: bool = False, toolkit_registry=NAGL_TOOLKIT_REGISTRY) → Molecule[source]

Normalize the bond orders and charges of a molecule by applying a series of transformations to it.

Parameters:

  • molecule (openff.toolkit.topology.Molecule) – The molecule to normalize.

  • max_iter (int, default 200) – The maximum number of iterations to perform for each transformation. This parameter is only used with the RDKit ToolkitWrapper, as the OpenEyeToolkitWrapper applies each normalization reaction exhaustively.

  • inplace (bool, default False) – If the molecule should be normalized in place or a new molecule should be returned. If a new molecule is returned, atoms remain ordered like the original molecule.

  • toolkit_registry (openff.toolkit.utils.toolkits.ToolkitRegistry or) – lopenff.toolkit.utils.toolkits.ToolkitWrapper, default=GLOBAL_TOOLKIT_REGISTRY ToolkitRegistry or ToolkitWrapper to use to perform normalization reactions.

Returns:

normalized_molecule (openff.toolkit.topology.Molecule)