SMILES Mutation Search
=======================

The molecule-domain counterpart to :doc:`Single Mutant Search </api/alf_tools/optimizer/search/single_mutant_search/index>`:
a search protocol that proposes novel SMILES each round by mutating the top-K best-labelled
training molecules, filtered for RDKit validity. Unlike protein sequences, most single-character
SMILES edits are structurally invalid, so this filtering step is required. RDKit's error logger
is silenced, since invalid mutations are expected and handled internally.

Mutating only the single current best (``top_k=1``) makes the search a pure hill-climb: once no
neighbour of the incumbent beats it, the same neighbourhood is regenerated every round and the
loop stalls in that local optimum. Setting ``top_k`` higher keeps several regions of the search
space open at once, so a stall in one neighbourhood doesn't stall the whole search.

.. automodule:: alf_tools.optimizer.search.smiles_mutation_search
   :members:
   :show-inheritance:
   :undoc-members: