Sign upLogin

matteoferla/Fragmenstein

View on GitHub
Star
fragmenstein/monster/_collapse_ring.py

Summary

Maintainability
F
5 days
Test Coverage

File _collapse_ring.py has 862 lines of code (exceeds 250 allowed). Consider refactoring.
Open

########################################################################################################################

__doc__ = \
    """
This is the ring collapsing code.
Severity: Major
Found in fragmenstein/monster/_collapse_ring.py - About 2 days to fix

    Function collapse_ring has a Cognitive Complexity of 44 (exceeds 5 allowed). Consider refactoring.
    Open

        def collapse_ring(self, mol: Chem.Mol) -> Chem.Mol:
        """
        Collapses a ring(s) into a single dummy atom(s).
        Stores data as JSON in the atom.
    Severity: Minor
    Found in fragmenstein/monster/_collapse_ring.py - About 6 hrs to fix

    Cognitive Complexity

    Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

    A method's cognitive complexity is based on a few simple rules:

    • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
    • Code is considered more complex for each "break in the linear flow of the code"
    • Code is considered more complex when "flow breaking structures are nested"

    Further reading

    _MonsterRing has 37 functions (exceeds 20 allowed). Consider refactoring.
    Open

    class _MonsterRing(_MonsterJoinNeigh):

    def collapse_mols(self, mols: List[Chem.Mol]):
        mols = [self.collapse_ring(mol) for mol in mols]
        [self.offset(mol) for mol in mols]
    Severity: Minor
    Found in fragmenstein/monster/_collapse_ring.py - About 4 hrs to fix

      Function _join_internally has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
      Open

          def _join_internally(self, mol: Chem.Mol, severe: bool = False) -> Chem.Mol:
        """
        The last check to see if the mol is connected.
        This differs (and calls) ``join_neighboring_mols``
      Severity: Minor
      Found in fragmenstein/monster/_collapse_ring.py - About 2 hrs to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function _renumber_original_indices has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
      Open

          def _renumber_original_indices(self, mol: Chem.Mol,
                                   mapping: Dict[int, int],
                                   name_restriction: Optional[str] = None):
        """
        Renumbers the indices in the ring virtual atom to new mapping.
      Severity: Minor
      Found in fragmenstein/monster/_collapse_ring.py - About 1 hr to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function _detriangulate has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
      Open

          def _detriangulate(self, mol: Chem.RWMol) -> None:
        """
        Prevents novel cyclopropanes and cyclobutanes.

        :param mol:
      Severity: Minor
      Found in fragmenstein/monster/_collapse_ring.py - About 1 hr to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function _determine_mergers_novel_other_pair has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
      Open

          def _determine_mergers_novel_other_pair(self,
                                            mol: Chem.RWMol,
                                            ringcore: Chem.Atom,
                                            other: Chem.Atom) -> List[Tuple[int, int]]:
        """
      Severity: Minor
      Found in fragmenstein/monster/_collapse_ring.py - About 1 hr to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

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

          def merge_pairing_lists(self,
                            nonunique_pairs: List[Tuple[Chem.Atom, Chem.Atom]],
                            ringcore_first=True) \
            -> List[Tuple[Chem.Atom, Chem.Atom]]:
        # complicated because mol.GetAtomWithIdx(2) == mol.GetAtomWithIdx(2) is False
      Severity: Minor
      Found in fragmenstein/monster/_collapse_ring.py - About 1 hr to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

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

          def _get_novel_other_bonded_pairs(self, rings) -> List[Tuple[Chem.Atom, Chem.Atom]]:
        pairs = []
        for ring in rings:
            # ring: Dict[str, List[Any]]
            ringcore = ring['atom']  # Chem.Atom
      Severity: Minor
      Found in fragmenstein/monster/_collapse_ring.py - About 55 mins to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Avoid deeply nested control flow statements.
      Open

                              if neigh not in morituri:
                            mol.AddBond(center_i, neigh, bt)
                            new_bond = mol.GetBondBetweenAtoms(center_i, neigh)
                            BondProvenance.set_bond(new_bond, 'original')
                        else:
      Severity: Major
      Found in fragmenstein/monster/_collapse_ring.py - About 45 mins to fix

        Consider simplifying this complex logical expression.
        Open

                    if ringcore_first and atom_a.HasProp('_current_is') and not atom_b.HasProp('_current_is'):
                ringcore = ai
                other = bi
                pairing = f'{ringcore}-{other}'
            elif ringcore_first and atom_b.HasProp('_current_is') and not atom_a.HasProp('_current_is'):
        Severity: Major
        Found in fragmenstein/monster/_collapse_ring.py - About 40 mins to fix

          Function _restore_bond has 5 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def _restore_bond(self, mol: Chem.RWMol,
          Severity: Minor
          Found in fragmenstein/monster/_collapse_ring.py - About 35 mins to fix

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

                def _get_merging_penalties(self, mol, shape: Tuple[int, int], indices_ring):
        """
        confusingly this is a different set of penalties to `_get_joining_penalties` which is for joining
        :param mol:
        :param shape:
            Severity: Minor
            Found in fragmenstein/monster/_collapse_ring.py - About 35 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

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

                def _place_ring_atoms(self, mol, rings: List[Dict[str, Union[Chem.Atom, List[Any]]]]):
        """
        Plase all atoms stored in rings.

        :param mol:
            Severity: Minor
            Found in fragmenstein/monster/_collapse_ring.py - About 35 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

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

                def expand_ring(self, mol: Chem.Mol) -> Chem.Mol:
        """
        Undoes collapse ring

        :param mol: untouched.
            Severity: Minor
            Found in fragmenstein/monster/_collapse_ring.py - About 35 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

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

                def _get_new_index(self, mol: Chem.Mol, old: int, search_collapsed=True,
                       name_restriction: Optional[str] = None) -> int:
        """
        Given an old index check in ``_ori_i`` for what the current one is.
        NB. ring placeholder will be -1 and these also have ``_ori_is``. a JSON of the ori_i they summarise.
            Severity: Minor
            Found in fragmenstein/monster/_collapse_ring.py - About 35 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

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

                def _determine_mergers_novel_ringcore_pair(self,
                                               mol: Chem.RWMol,
                                               ringcore_A: Chem.Atom,
                                               ringcore_B: Chem.Atom) -> List[Tuple[int, int]]:
        """
            Severity: Minor
            Found in fragmenstein/monster/_collapse_ring.py - About 35 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

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

                def offset(self, mol: Chem.Mol):
        """
        This is to prevent clashes.
        The numbers of the ori indices stored in collapsed rings are offset by the class variable (_collapsed_ring_offset)
        multiples of 100. (autoincrements to avoid dramas)
            Severity: Minor
            Found in fragmenstein/monster/_collapse_ring.py - About 25 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

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

                def _restore_original_bonding(self, mol: Chem.RWMol, rings: List[Dict[str, List[Any]]]) -> None:
        """
        Restore the bonding stored in the ringcore.

        The data of each collapsed atom is given by ``self._get_expansion_for_atom(ring, i)``
            Severity: Minor
            Found in fragmenstein/monster/_collapse_ring.py - About 25 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

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

                def _get_novel_ringcore_bonded_pairs(self, rings):
        """
        called by _get_novel_ringcore_pairs alongside _get_close_novel_ringcores
        Opposite of _get_novel_other_bonded_pairs
            Severity: Minor
            Found in fragmenstein/monster/_collapse_ring.py - About 25 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

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

                def _get_expansion_for_atom(self, ring: Dict[str, List[Any]], i: int) -> Dict[str, Any]:
        """
        ``_get_expansion_data`` returns from a mol the "expansion data for the rings"
        ``_get_expansion_for_atom`` given one of the list of the data from the latter (representing a ring core)
        and an index of which of the internal atoms that were collapsed return a dictionary of details
            Severity: Minor
            Found in fragmenstein/monster/_collapse_ring.py - About 25 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            There are no issues that match your filters.

            Category
            Status