emmet.core.utils

Define utility functions used across the emmet namespace packages.

Functions

arrow_incompatible	Simple decorator to mark a Pydantic model as being incompatible with serialization using pyarrow.
confirm_molecule	Check that something that we expect to be a molecule is actually a Molecule object, and not a dictionary representation.
convert_datetime	Validate datetime-like objects.
dynamic_import	Import arbitrary module or object.
generate_robocrys_condensed_struct_and_description	Get robocrystallographer description of a structure.
get_flat_models_from_model	Get all sub-models from a pydantic model.
get_graph_hash	Return the Weisfeiler Lehman (WL) graph hash of the MoleculeGraph described by this molecule, using the OpenBabelNN strategy with extension for metal coordinate bonds
get_hash_blocked	Get the hash of a file in byte chunks.
get_molecule_id	Return an MPculeID for a molecule, with the hash component based on a particular attribute of the molecule graph representation.
get_num_formula_units	Get the number of formula units in a dict-like composition.
get_sg	helper function to get spacegroup with a loose tolerance
group_molecules	Groups molecules according to composition, charge, and equality
group_structures	Groups structures according to space group and structure matching
jsanitize	This method cleans an input json-like object, either a list or a dict or some sequence, nested or otherwise, by converting all non-string dictionary keys (such as int and float) to strings, and also recursively encodes all objects using Monty's as_dict() protocol. Args: obj: input json-like object. strict (bool): This parameters sets the behavior when jsanitize encounters an object it does not understand. If strict is True, jsanitize will try to get the as_dict() attribute of the object. If no such attribute is found, an attribute error will be thrown. If strict is False, jsanitize will simply call str(object) to convert the object to a string representation. allow_bson (bool): This parameters sets the behavior when jsanitize encounters an bson supported type such as objectid and datetime. If True, such bson types will be ignored, allowing for proper insertion into MongoDb databases. Returns: Sanitized dict that can be json serialized.
make_mol_graph	Construct a MoleculeGraph using OpenBabelNN with metal_edge_extender and (optionally) Critic2 bonding information.
requires_arrow	Decorator for pyarrow-dependent functionality.
set_msonable_type_adapter	Decorator for MSONables defined in emmet with arrow compatible type hints.
type_override	Pydantic model decorator for declaring a field should be serialized as a type that does not match the type hint for the field.
undeform_structure	Get an undeformed structure by applying transformations in a reverse order.
utcnow	Get UTC time right now.

Classes

TYPE_CHECKING

bool(x) -> bool