remove dead code

Author: esoteric-ephemera

mp_api/client/routes/molecules/bonds.py

@@ -1,8 +1,8 @@
 """Define core molecules functionality.
 
-Note that these classes are not currently working.
-The `MoleculeRester` methods: `search`, `find_molecule`, `get_molecule_by_mpculeid`,
-all return 404s when attempting to use them.
+Note that the `MoleculeRester`, unlike the `MaterialsRester`,
+has no API functionality beyond serving as an access point for
+the JCESR and summary resters.
 """
 
 from __future__ import annotations
@@ -15,185 +15,9 @@
 from mp_api.client.core.utils import validate_ids
 from mp_api.client.routes.molecules import MOLECULES_RESTERS
 
-
-class BaseMoleculeRester(CoreRester):
+class MoleculeRester(CoreRester):
+    """Define molecules stub for accessing JCESR and summary data."""
     document_model = MoleculeDoc
     primary_key = "molecule_id"
-
-    def get_molecule_by_mpculeid(
-        self, mpcule_id: str, final: bool = True
-    ) -> Molecule | list[Molecule]:
-        """Get a molecule object for a given Materials Project molecules ID (MPculeID).
-
-        Arguments:
-            mpcule_id (str): Materials project molecule ID
-            final (bool): Whether to get the final (optimized) molecule, or the list of initial
-                (pre-optimized) structures. Defaults to True.
-
-        Returns:
-            molecule (Union[Molecule, List[Molecule]]): Pymatgen Molecule object or list of
-                pymatgen Molecule objects.
-        """
-        field = "molecule" if final else "initial_molecules"
-
-        response = self.search(molecule_ids=[mpcule_id], fields=[field])  # type: ignore
-        return response[0][field] if (response and response[0]) else response  # type: ignore
-
-    def find_molecule(
-        self,
-        filename_or_molecule: str | Molecule,
-        charge: int | None = None,
-        spin_multiplicity: int | None = None,
-        tolerance: float = 0.01,
-        allow_multiple_results: bool = False,
-    ) -> list[str] | str:
-        """Finds matching molecules from the Materials Project molecules database (MPcules).
-
-        Multiple results may be returned of "similar" molecules based on
-        distance using the pymatgen MoleculeMatcher algorithm.
-
-        Args:
-            filename_or_molecule: filename or Molecule object
-            charge: Molecule charge. Default is None, meaning that the charge will not be used to
-                restrict the output.
-            spin_multiplicity: Molecule's spin multiplicity. Default is None, meaning that the output will
-                not be restricted by spin multiplicity.
-            tolerance: RMSD difference threshold for MoleculeMatcher
-            allow_multiple_results: changes return type for either
-            a single mpcule_id or list of mpcule_ids
-        Returns:
-            A matching mpcule_id if one is found or list of results if allow_multiple_results
-            is True
-        Raises:
-            MPRestError
-        """
-        if isinstance(filename_or_molecule, str):
-            m = Molecule.from_file(filename_or_molecule)
-        elif isinstance(filename_or_molecule, Molecule):
-            m = filename_or_molecule
-        else:
-            raise MPRestError("Provide filename or Structure object.")
-
-        results = self._post_resource(
-            body=m.as_dict(),
-            params={
-                "tolerance": tolerance,
-                "charge": charge,
-                "spin_multiplicity": spin_multiplicity,
-            },
-            suburl="find_molecule",
-            use_document_model=False,
-        ).get("data")
-
-        if len(results) > 1:  # type: ignore
-            if not allow_multiple_results:
-                raise ValueError(
-                    "Multiple matches found for this combination of tolerances, but "
-                    "`allow_multiple_results` set to False."
-                )
-            return results  # type: ignore
-
-        return results[0]["molecule_id"] if (results and results[0]) else []
-
-    def search(
-        self,
-        charge: tuple[int, int] | None = None,
-        spin_multiplicity: tuple[int, int] | None = None,
-        nelements: tuple[int, int] | None = None,
-        chemsys: str | list[str] | None = None,
-        deprecated: bool | None = None,
-        elements: list[str] | None = None,
-        exclude_elements: list[str] | None = None,
-        formula: str | list[str] | None = None,
-        molecule_ids: MPculeID | list[MPculeID] | None = None,
-        task_ids: str | list[str] | None = None,
-        num_chunks: int | None = None,
-        chunk_size: int = 1000,
-        all_fields: bool = True,
-        fields: list[str] | None = None,
-    ):
-        """Query molecule docs using a variety of search criteria.
-
-        Arguments:
-            charge (Tuple[int, int]): Minimum and maximum charge for the molecule.
-            spin_multiplicity (Tuple[int, int]): Minimum and maximum spin for the molecule.
-            nelements (Tuple[int, int]): Minimum and maximum number of elements
-            chemsys (str, List[str]): A chemical system, list of chemical systems
-                (e.g., Li-C-O, [C-O-H-N, Li-N]).
-            deprecated (bool): Whether the material is tagged as deprecated.
-            elements (List[str]): A list of elements.
-            exclude_elements (List(str)): List of elements to exclude.
-            formula (str, List[str]): An alphabetical formula or list of formulas
-                (e.g. "C2 Li2 O4", ["C2 H4", "C2 H6"]).
-            molecule_ids (MPculeID, List[MPculeID]): List of Materials Project Molecule IDs (MPculeIDs) to return data
-                for.
-            task_ids (str, List[str]): List of Materials Project IDs to return data for.
-            num_chunks (int): Maximum number of chunks of data to yield. None will yield all possible.
-            chunk_size (int): Number of data entries per chunk.
-            all_fields (bool): Whether to return all fields in the document. Defaults to True.
-            fields (List[str]): List of fields in MoleculeDoc to return data for.
-                Default is molecule_id, last_updated, and formula_alphabetical if all_fields is False.
-
-        Returns:
-            ([MoleculeDoc]) List of molecules documents
-        """
-        query_params: dict = {"deprecated": deprecated}
-
-        if molecule_ids:
-            if isinstance(molecule_ids, str):
-                molecule_ids = [molecule_ids]
-
-            query_params.update({"molecule_ids": ",".join(molecule_ids)})
-
-        if charge:
-            query_params.update({"charge": charge})
-
-        if spin_multiplicity:
-            query_params.update({"spin_multiplicity": spin_multiplicity})
-
-        if formula:
-            if isinstance(formula, str):
-                formula = [formula]
-
-            query_params.update({"formula": ",".join(formula)})
-
-        if chemsys:
-            if isinstance(chemsys, str):
-                chemsys = [chemsys]
-
-            query_params.update({"chemsys": ",".join(chemsys)})
-
-        if elements:
-            query_params.update({"elements": ",".join(elements)})
-
-        if exclude_elements:
-            query_params.update({"exclude_elements": ",".join(exclude_elements)})
-
-        if task_ids:
-            if isinstance(task_ids, str):
-                task_ids = [task_ids]
-
-            query_params.update({"task_ids": ",".join(validate_ids(task_ids))})
-
-        query_params = {
-            entry: query_params[entry]
-            for entry in query_params
-            if query_params[entry] is not None
-        }
-
-        return super()._search(
-            num_chunks=num_chunks,
-            chunk_size=chunk_size,
-            all_fields=all_fields,
-            fields=fields,
-            **query_params,
-        )
-
-
-class AssociatedMoleculeRester(BaseMoleculeRester):
-    suffix = "molecules/assoc"
-
-
-class MoleculeRester(BaseMoleculeRester):
     suffix = "molecules/core"
     _sub_resters = MOLECULES_RESTERS