File m_rmsd.py has 437 lines of code (exceeds 250 allowed). Consider refactoring.

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from __future__ import annotations
from collections import defaultdict
########################################################################################################################

__doc__ = \

Function from_other_annotated_mols has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.

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    def from_other_annotated_mols(cls,
                            followup: Chem.Mol,
                            hits: Sequence[Chem.Mol],
                            annotated: Chem.Mol,
                            ) -> mRMSD:

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mRMSD has 21 functions (exceeds 20 allowed). Consider refactoring.

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class mRMSD:
    """Mols are non-superposed ('aligned') for the RMSD and in Å.

    The RMSD has been calculated differently.
    The inbuilt RMSD calculations in RDKit (``Chem.rdMolAlign.GetBestRMS``) align the two molecules,

Function _mapping_from_annotated_and_hits has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def _mapping_from_annotated_and_hits(cls,
                                         annotated_followup: Chem.Mol,
                                         hits: Sequence[Chem.Mol]):
        assert cls.is_origin_annotated(annotated_followup), 'This molecules is not annotated.'
        mappings = []

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Function overannotate has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

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    def overannotate(cls, mol: Chem.Mol, hits: List[Chem.Mol], priority=('mol_origin', 'atom_origin', 'xyz')):
        """
        Unfortunately, in an attempt to make users happy, I have to make the code more complicated.
        There are three different annotation systems going on.
        The first is the property '_Origin' in the ``Chem.Mol``.

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Function copy_all_possible_origins has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

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    def copy_all_possible_origins(cls, annotated: Chem.Mol, target: Chem.Mol) -> Tuple[List[Chem.Mol], List[List[int]]]:
        """
        Monster leaves a note of what it did. atom prop _Origin is a json of a list of mol _Name dot AtomIdx.
        However, the atom order seems to be maintained but I dont trust it. Also dummy atoms are stripped.

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Function from_internal_xyz has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

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    def from_internal_xyz(cls, annotated_followup):
        """
        This is an alternative for when the atoms have _x, _y, _z
        
        :param annotated_followup:

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Avoid deeply nested control flow statements.

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                        if rex is not None:
                            h = int(rex.group(1))
                            mapping.append((i, h))
            mappings.append(mapping)

Avoid deeply nested control flow statements.

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                        if xyz:
                            cls._set_xyz(tatom, xyz)
                options.append(option)

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

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    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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Avoid too many return statements within this function.

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            return None

Function __init__ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

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    def __init__(self,
                 followup: Chem.Mol,
                 hits: Sequence[Chem.Mol],
                 mappings: List[List[Tuple[int, int]]]):
        """

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