Function _get_atom_maps_OLD has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def _get_atom_maps_OLD(self, molA, molB, **mode: Unpack[ExtendedFMCSMode]) -> Set[Tuple[Tuple[int, int]]]:
        """
        The ``mode`` are FindMCS arguments.
        """
        warnings.warn('`_get_atom_maps_OLD` is no longer used.', category=DeprecationWarning)

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Function guess_warhead has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def guess_warhead(cls, smiles: str) -> Tuple[str, str]:
        """
        Going backwards by guessing what the warhead is.
        Normally there'd be better data handling so no guessing
        """

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Function _embed has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def _embed(self, trial=0, **embed_args) -> None:
        """
        At trial 0, all fore atoms are okay
        At trial 1, only fore atoms with bonds with original bonding are okay
        At trial 2, only common atoms with bonds with original bonding are okay

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Function is_valid has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def is_valid(self, atom: Chem.Atom, trial: int):
        """
        Is this a constrainable atom?
        """
        if atom.GetAtomicNum() == 1:

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Function unbinarize has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def unbinarize(bin: bytes, ignore_errors:bool=True) -> Union[Chem.Mol, None]:
    """
    This is just a wrapper for ``Chem.Mol(bin)``, with safeguards in case it's not a bytes.
    """
    exception = Exception if ignore_errors else ()

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Function _atom_origin_to_xyz has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def _atom_origin_to_xyz(cls, origins: List[str], atom: Chem.Atom, hits: List[Chem.Mol]):
        points = []
        if len(hits) == 0:
            return  # no hits
        hitdex: Dict[str, Chem.Mol] = {hit.GetProp('_Name'): hit for hit in hits}

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Function from_postera_row has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def from_postera_row(cls, row: pd.Series, results:Optional=None):
        if row.fragments == 'x0072' or str(row.fragments) == 'nan':
            # these are not hit inspired.
            cls.journal.error(f'No valid parent hits for {row.CID}.')
            return None

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Avoid too many return statements within this function.

Open

            return False

Avoid too many return statements within this function.

Open

            return {k: self._remove_negatives(v) for k, v in map.items()}

Avoid too many return statements within this function.

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            return self.mmff_minimize(mol,

Avoid too many return statements within this function.

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            return False

Avoid too many return statements within this function.

Open

            return False

Avoid too many return statements within this function.

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            return False

Avoid too many return statements within this function.

Open

        return super().__call__(parameters, hit, hit_atom_idx, followup, followup_atom_idx)

Avoid too many return statements within this function.

Open

            return False  # too bonded etc.

Avoid too many return statements within this function.

Open

        return {name: flip_mapping(submapping) for name, submapping in mapping.items()}

Avoid too many return statements within this function.

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        return True

Avoid too many return statements within this function.

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            return True

Avoid too many return statements within this function.

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            return False

Avoid too many return statements within this function.

Open

            return {h: f for h, f in map.items() if f >= 0 and h >= 0}