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

    def reanimate(self) -> float:
        """
        Calls Igor recursively until the ddG is negative or zero.
        igor.minimize does a good job. this is just to get everything as a normal molecule
Severity: Minor
Found in fragmenstein/victor/_victor_igor.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_constraint has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _get_constraint(self, extra_constraint: Optional[str] = None) -> Union[Constraints, None]:
        # deal with covalent and non covalent separately
        if self.is_covalent:
            self.journal.debug(f'{self.long_name} - is covalent.')
            constraint = self._fix_covalent()
Severity: Minor
Found in fragmenstein/victor/_victor_common.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 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 _validate_custom_map has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _validate_custom_map(self):
        """
        What on earth has the user submitted as custom_map?

        :return:
Severity: Minor
Found in fragmenstein/monster/_place.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 propagate_alternatives has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def propagate_alternatives(self, fewer: List[Chem.Mol]) -> int:
        """
        Given the alt atoms strored in the Chem.Atom property ``_AltSymbol`` try those
        """
        pt = Chem.GetPeriodicTable()
Severity: Minor
Found in fragmenstein/monster/_place_modes/_refine.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 _harmonize_warhead_combine has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _harmonize_warhead_combine(self):
        """
        Runs self.harmonize_warheads on the hits, but also determines covalency

        :return:
Severity: Minor
Found in fragmenstein/victor/_victor_combine.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 sample_new_conformation has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def sample_new_conformation(self, random_seed=None):
        """This method is intended for Multivictor.
        It generates a new conformation based on different random seeds.
        """
        scaffold = self.modifications["chimera"]
Severity: Minor
Found in fragmenstein/monster/_place_modes/_refine.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 measure_map has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def measure_map(self, mol: Chem.Mol, mapping: Dict[int, int]) -> np.array:
        """
        Returns a vector with the distances but not of length len(mapping)
        This used by offness to score how bad the mapping is
Severity: Minor
Found in fragmenstein/monster/unmerge_mapper.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 _closest__is_ring_atom has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _closest__is_ring_atom(atom):
        if atom.GetIsAromatic():
            return True
        elif atom.HasProp('_ori_i') and atom.GetIntProp('_ori_i') == -1:
            if atom.HasProp('_bonds') and 'AROMATIC' in atom.GetProp('_bonds'):
Severity: Minor
Found in fragmenstein/monster/_communal.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

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

    def __call__(self, row):
        with contextlib.suppress(cli_default_settings['supressed_exceptions']):
            penalty = 0
            if row.outcome != 'acceptable':
                return float('inf')
Severity: Minor
Found in fragmenstein/laboratory/_score.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_n_filtered_mols has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def get_n_filtered_mols(cls, amount: int, **cutoffs) -> List[Chem.Mol]:
        """Get ``amount`` of the mols (Chem.Mol) randomly
         that match a cutoff criterion.
        As listed in ``get_filtered_mol``"""
        mols = []
Severity: Minor
Found in fragmenstein/demo/_base_dataset_holder.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 _ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _(self,
          mol: Chem.Mol,
          long_name: str = 'ligand',
          merging_mode='expansion',
          atomnames: Optional[Dict[int, str]] = None,
Severity: Minor
Found in fragmenstein/victor/_victor_place.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 decompose has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def decompose(self, mol: Chem.Mol) -> List[Chem.Mol]:
        name = mol.GetProp('_Name')
        index = mol.GetIntProp('decompose_index')
        for atom in mol.GetAtoms():
            atom.SetProp('ori_name', str(name))
Severity: Minor
Found in fragmenstein/faux_victors/brics.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 shift_ligand has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def shift_ligand(self, simulation: mma.Simulation, amount: Union[mmu.Quantity, mm.Vec3, float]):
        if isinstance(amount, float):
            amount: mmu.Quantity = mm.Vec3(amount, 0, 0) * mmu.angstrom
        elif isinstance(amount, mm.Vec3):
            amount: mmu.Quantity = amount * mmu.angstrom
Severity: Minor
Found in fragmenstein/openmm/fritz.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 __init__ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self,
                 followup: Chem.Mol,
                 hits: Sequence[Chem.Mol],
                 mappings: List[List[Tuple[int, int]]]):
        """
Severity: Minor
Found in fragmenstein/m_rmsd.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 _assert_placement_inputs has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _assert_placement_inputs(self):
        if '*' in self.smiles and (self.covalent_resi is None or self.covalent_resn is None):
            raise ValueError(f'{self.long_name} - is covalent but without known covalent residues')
            # TODO '*' in self.smiles is bad. user might start with a mol file.
        elif '*' in self.smiles:
Severity: Minor
Found in fragmenstein/victor/_victor_place.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 _clean_up has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _clean_up(self):
        """
        `.flat_combo`` is ``.mod`` withoout Hs and coordinates.
        `.rectified`` is ``.flat_combo`` after rectification.
        the returned will be `.positioned_mol`` ie. ``.rectified`` with Hs.
Severity: Minor
Found in fragmenstein/faux_victors/mcs_monster.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

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