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Showing 254 of 254 total issues

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

    def _calculate_thermo_common(self):
        """
        This method is common to both combination and placement and is unique to Wictor
        as both ``_calculate_combination_thermo`` and ``_calculate_placement_thermo`` are overridden
        and do the same here.
Severity: Minor
Found in fragmenstein/faux_victors/no_pyrosetta.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 make_covalent has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def make_covalent(cls, smiles: str,
                      warhead_name: Optional[str] = None) -> Union[str, None]:
        """
        Convert a unreacted warhead to a reacted one in the SMILES
Severity: Minor
Found in fragmenstein/victor/_victor_utils.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 add_mol has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def add_mol(self, mol: Chem.Mol, carbon_color: str = '', colorValue:str='') -> ComponentViewer:
        """
        Add a rdkit.Chem to an NGLWidget.
        This function is used by Walton and Monster
Severity: Minor
Found in fragmenstein/ngl_display.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_restraining_atom_indices has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _get_restraining_atom_indices(self) -> List[int]:
        # Place has '_Stdev': 1.887379141862766e-15, '_Origin': '["x0395.9", "x0434.6"]', '_Max': 0.37818712299601354}
        # Combine has '_ori_i': 100, '_ori_name': 'x0395', '_x': 9.309, '_y': -5.402, '_z': 26.27
        # and occassionally '_ring_i'
        # The problem stemming from the collasing business
Severity: Minor
Found in fragmenstein/openmm/openvictor.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 summarize has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def summarize(self):
        if self.error_msg:
            if self.monster is None:
                N_constrained_atoms = float('nan')
                N_unconstrained_atoms = float('nan')
Severity: Minor
Found in fragmenstein/victor/_victor_utils.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,
                 iterator: Iterator,
                 fun: Callable,
                 n_cores: int = -1,
                 timeout: int = 240,
Severity: Minor
Found in fragmenstein/laboratory/_base.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 summarize has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def summarize(self):
        if self.error_msg:
            if self.monster is None:
                N_constrained_atoms = float('nan')
                N_unconstrained_atoms = float('nan')
Severity: Minor
Found in fragmenstein/openmm/openvictor.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 rotate has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def rotate(self, mol_idx: int, theta: float, axis: str, degrees: bool = True):
        """
        Rotate a molecule around a give angle on an axis.
        This is coded terribly.
Severity: Minor
Found in fragmenstein/walton/_movements.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 convert_to_origins has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def convert_to_origins(self, mol: Chem.Mol, both=False):
        """
        In this class the 'provenance' are marked as common, aft, fore, rectified (semicommon is bond)
        """
        fore_name = self.fore.GetProp('_Name')
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

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

    def __call__(self, cutoff: int = 0, max_mergers: int = 10_000, maxDepth: int = 4) -> pd.DataFrame:
        self.fragments = []
        for hit in self.hits.values():
            self.fragments.extend(self.decompose(hit))
        self.info['N_fragments'] = len(self.fragments)
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 _safely_do has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _safely_do(self,
                   execute: Optional[Callable] = None,
                   resolve: Optional[Callable] = None,
                   reject: Optional[Callable] = None):
        """
Severity: Minor
Found in fragmenstein/victor/_victor_safety.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 _add_atoms has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

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

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

    def combine(self,
                mols: Sequence[Chem.Mol],
                permute: bool = True,
                combination_size: int = 2,
                **kwargs) -> Union[pebble.ProcessMapFuture, pd.DataFrame]:
Severity: Minor
Found in fragmenstein/laboratory/_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 add_dummy_to_mol has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def add_dummy_to_mol(ligand: Chem.Mol,
                     ligand_resn: str,
                     holo: Chem.Mol,
                     dummy_name: str = 'CONN') -> Chem.Mol:
    """
Severity: Minor
Found in fragmenstein/extraction_funs.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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