Function fix_columns has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

    def fix_columns(self, df: pd.DataFrame, preferred_name: str, options: List[str]):
        if preferred_name not in df.columns:
            for name_col in options:
                for variant_fx in [str.lower, str.upper, str.title]:
                    alt = variant_fx(name_col)  # noqa

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Function categorize has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

    def categorize(self,
                   row: pd.Series,
                   size_tolerance: int=0,
                   move_cutoff:float=1.,
                   ddG_cutoff:float=0.,

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Function create_polygon has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def create_polygon(n=6, radius=1.5,

Function _combine_ops has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def _combine_ops(cls,

Function get_color_origins has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def get_color_origins(self) -> Dict[str, Dict[int, str]]:
        """
        Get for the hits and followup the color of the origin
        as seen in show_comparison
        :return:

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Function make_maps has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def make_maps(cls, target: Chem.Mol, mols: List[Chem.Mol], mode: Optional[Dict[str, Any]] = None) \
            -> Dict[str, List[Dict[int, int]]]:
        """
        This is basically if someone is using this class outside of Monster

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Function guess_origins has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def guess_origins(self, mol: Chem.Mol = None, hits: Optional[List[Chem.Mol]] = None):
        """
        Given a positioned mol guess its origins...

        :param mol:

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Function make_coordinate_constraints_for_combination has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def make_coordinate_constraints_for_combination(self):
        """
        See also ``cls.make_coordinate_constraints_for_placement``.
        This operates based on ``atom.HasProp('_Novel')``, not origins!
        :return:

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Function find_attachment has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

def find_attachment(pdb: Chem.Mol, ligand_resn: str) -> Tuple[Union[Chem.Atom, None], Union[Chem.Atom, None]]:
    """
    Finds the two atoms in a crosslink bond without looking at LINK record

    :param pdb: a rdkit Chem object

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Function _add_bonds has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def _add_bonds(self):
        """
        Add bonds from aft to mod, a copy of fore.
        Called by combine().
        Will add property 'provenance' to bonds, with values 'fore' or 'aft' or 'common' or 'semicommon'.

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Function _con_embed has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def _con_embed(self, trial: int = 0) -> None:
        slimmed = Chem.RWMol(self.positioned_mol)
        keepers = []
        unkeepers = []
        for atom in slimmed.GetAtoms():

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Function transmute_FindMCS_parameters has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def transmute_FindMCS_parameters(
        **mode: Unpack[ExtendedFMCSMode]) -> rdFMCS.MCSParameters:  # noqa lowercase not applicable
    """
    The function ``rdFMCS.FindMCS`` has two ways of being used.
    In one, a series of arguments are passed,

Function get_possible_map has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def get_possible_map(self,

Consider simplifying this complex logical expression.

Open

        if dummy_w_dummy and \
                zeroth.GetSymbol() == '*' and \
                first.GetSymbol() == '*':
            distance = 9999
            dummy_distance = measure_distance(confs[0].GetAtomPosition(i), confs[1].GetAtomPosition(j))

Consider simplifying this complex logical expression.

Open

                if len(followup_hetero_neighs) == 1 and len(hit_hetero_neighs) == 1:
                    followup_old, hit_old = followup_atom, hit_atom
                    followup_atom = followup_hetero_neighs[0]
                    hit_atom = hit_hetero_neighs[0]
                    custom_map[hit_name][hit_atom.GetIdx()] = followup_atom.GetIdx()

Consider simplifying this complex logical expression.

Open

        if residue is None:
            ## assuming it is LIG then.
            ligand_selector = pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector()
            ligand_selector.set_residue_name3('LIG')
            m = self._vector2residues(ligand_selector.apply(self.pose))  # noqa its in Igor_min

Consider simplifying this complex logical expression.

Open

    if len(mapping) == 0:
        return mapping
    # Sequence[Tuple[int, int]] (basic)
    elif isinstance(mapping, Sequence) and isinstance(mapping[0], tuple) and isinstance(mapping[0][1], int):
        return [(b, a) for a, b in mapping]

Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self,

Function extract_mol has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def extract_mol(cls,

Function display_energy has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def display_energy(self,
                       minimized_mol: Union[Chem.Mol, None],
                       term: Union[str, Enum]='all',
                       scorefxn: Optional[pyrosetta.ScoreFunction]=None,
                       colorMap:str='coolwarm') -> Dict[str, float]:

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