Showing 288 of 347 total issues
Avoid too many return statements within this function. Open
return TrueAvoid too many return statements within this function. Open
return FalseAvoid too many return statements within this function. Open
return FalseAvoid too many return statements within this function. Open
return FalseAvoid too many return statements within this function. Open
return {"version": "0+unknown", "full-revisionid": None,Avoid too many return statements within this function. Open
return {Function observed has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def observed(self, titration_states: List[int]) -> np.float64:
"""Return the histogram count for the supplied state."""
# In case of the one site sams approach, the sams weight is the total weight of every titration state
counts = None- Read upRead up
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 free_energy has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def free_energy(self, titration_states: List[int]) -> float:
"""Return the sams free energy value for the provided titration state.
Parameters
----------- Read upRead up
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 run_proplister has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def run_proplister(input_file_path):
"""Run proplister utility on a file and return its properties.
Parameters
----------- Read upRead up
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 from_lists has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def from_lists(
cls,
g_k,
parameters,
proton_count,- Read upRead up
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_isomers has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def _add_isomers(self):
"""
Add all the isomer specific data to the xml template.
"""
- Read upRead up
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 _propose_random_change has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def _propose_random_change(
self, proposal: _StateProposal, residue_pool: Optional[str] = None
) -> _TitrationAttemptData:
"""Use a given proposal mechanism to propose a titration state update for a given group of residues."""
# Select which titratible residues to update.- Read upRead up
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 run_epik has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def run_epik(
input_file_path,
output_file_path,
max_structures=32,
ph=7.4,- Read upRead up
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_sd_bonds has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def get_sd_bonds(sdfilename: str) -> List[Dict[Tuple[int, int], int]]:
"""Parse an SD file/MDL mol file and return a representation of the bonds.
Parameters
----------- Read upRead up
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 _complete_atom_registry has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def _complete_atom_registry(self):
"""
Registers unique atom names. Store in self._atom_names from Residue
"""
for state in self._input_state_data:- Read upRead up
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 from_lists has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def from_lists(
cls,
g_k: float,
charges: List[float],
proton_count: int,- Read upRead up
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 _find_hydrogen_types_for_tautomers has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def _find_hydrogen_types_for_tautomers(
gafftree: lxml.etree.ElementTree, xmlfftree: lxml.etree.ElementTree
) -> set:
"""
Find all atom types that describe hydrogen atoms.- Read upRead up
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 cli has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def cli() -> None:
"""Command line interface for protons run script."""
args = sys.argv
- Read upRead up
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 from_serialized_xml has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def from_serialized_xml(cls, xmltree):
"""Create a titratable residue from a serialized titratable residue.
Parameters
----------- Read upRead up
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 generate_protons_ffxml has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def generate_protons_ffxml(
inputmol2: str,
isomer_dicts: list,
outputffxml: str,
pH: float,- Read upRead up
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"