qrunch.chemistry.embedded_atoms.embedded_atoms_selector_protocols

Active site selection based on coordination environment changes and partial charge changes during a reaction.

Classes

EmbeddedAtomsExtender

Extends an existing embedded atoms selection with additional atoms.

PrimaryEmbeddedAtomsSelector

Identifies the core set of active atoms from a reaction.
class EmbeddedAtomsExtender

Bases: Protocol

Extends an existing embedded atoms selection with additional atoms.

__init__(*args, **kwargs)
extend(active_indices: set[int], reaction: Reaction) → set[int]

Return additional atom indices to include based on the current active set.

The returned set should contain all new atoms to add (not including the input set).

Parameters:

  • active_indices (set[int]) – The current set of active atom indices.

  • reaction (Reaction) – The reaction being analyzed.

Return type:

set[int]

class PrimaryEmbeddedAtomsSelector

Bases: Protocol

Identifies the core set of active atoms from a reaction.

__init__(*args, **kwargs)
scores(reaction: Reaction, prepared_data: Sequence[PreparedRestrictedData] | Sequence[PreparedUnrestrictedData] | None = None, molecular_configurations: Sequence[MolecularConfiguration] | None = None) → ndarray[tuple[Any, ...], dtype[float64]]

Compute a normalized per-atom score for the reaction.

The returned array has one entry per atom, with values in [0.0, 1.0] where the highest-scoring atom is 1.0. This shared scale lets the scores of different selectors be summed to rank atoms against one another, for example to enforce a maximum number of embedded atoms. This method is only consulted when the selection must be reduced to fit max_number_of_embedded_atoms.

Parameters:

  • reaction (Reaction) – The reaction to analyze.

  • prepared_data (Sequence[PreparedRestrictedData] | Sequence[PreparedUnrestrictedData] | None) – Optional sequence of prepared data (one per reaction image) from the mean-field and localization stages. Required by selectors that depend on electronic structure information.

  • molecular_configurations (Sequence[MolecularConfiguration] | None) – Optional sequence of molecular configurations (one per reaction image). Required by selectors that need basis set information (e.g., for IAO construction).

Return type:

ndarray[tuple[Any, …], dtype[float64]]

select(reaction: Reaction, prepared_data: Sequence[PreparedRestrictedData] | Sequence[PreparedUnrestrictedData] | None = None, molecular_configurations: Sequence[MolecularConfiguration] | None = None) → set[int]

Select the core active atom indices for the reaction.

Parameters:

  • reaction (Reaction) – The reaction to analyze.

  • prepared_data (Sequence[PreparedRestrictedData] | Sequence[PreparedUnrestrictedData] | None) – Optional sequence of prepared data (one per reaction image) from the mean-field and localization stages. Required by selectors that depend on electronic structure information.

  • molecular_configurations (Sequence[MolecularConfiguration] | None) – Optional sequence of molecular configurations (one per reaction image). Required by selectors that need basis set information (e.g., for IAO construction).

Return type:

set[int]