Showing 120 of 121 total issues
Function __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, store_directory, **analyzer_kwargs):
# Convert analyzer string quantities into variables.
for key, value in analyzer_kwargs.items():
try:
quantity = utils.quantity_from_string(value)- 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_equilibration_plots has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def generate_equilibration_plots(self, discard_from_start=1):
"""
Create the equilibration scatter plots showing the trend lines, correlation time,
and number of effective samples
- 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 resnames has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def resnames(self):
"""Iterate over the names of all the molecules in the file (read-only).
This assumes that each molecule in the mol2 file has a single residue name.
- 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 _validate_samplers has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def _validate_samplers(self, yaml_content):
"""Validate samplers section."""
sampler_descriptions = yaml_content.get('samplers', None)
if sampler_descriptions is None:
return {}- 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 pack_transformation has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def pack_transformation(mol1_pos, mol2_pos, min_distance, max_distance):
"""Compute an affine transformation that solve clashes and fit mol2 in the box.
The method randomly shifts and rotates mol2 until all its atoms are within
min_distance and max_distance from mol1. The position of mol1 is kept fixed.- 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 extract_analyzer_kwargs has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def extract_analyzer_kwargs(args, quantities_as_strings=False):
import simtk.unit as unit
"""Return a dictionary with the keyword arguments to pass to the analyzer."""- 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_free_energy has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def generate_free_energy(self):
fe_data = self.get_experiment_free_energy_data()
delta_f = fe_data['free_energy_diff']
delta_h = fe_data['enthalpy_diff']
delta_f_err = fe_data['free_energy_diff_error']- 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 create_alchemical_phase has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def create_alchemical_phase(self):
"""
Create the alchemical phase based on all the options
This only creates it, but does nothing else to prepare for simulations. The ``initialize_alchemical_phase``- 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 setup_all_systems has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def setup_all_systems(self):
"""Setup all molecules and systems in the database.
The method supports parallelization through MPI.
- 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 __init__ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, script=None, job_id=None, n_jobs=None):
"""
Constructor.
"""- 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 write_version_py has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def write_version_py(filename='Yank/version.py'):
cnt = """
# This file is automatically generated by setup.py
short_version = '{base_version:s}'
version = '{version:s}'- 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 git_version has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def git_version():
# Return the git revision as a string
# copied from numpy setup.py
def _minimal_ext_cmd(cmd):
# construct minimal environment- 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_oe_mol_positions has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def get_oe_mol_positions(molecule, conformer_idx=0):
"""
Get the molecule positions from an OpenEye Molecule
Requires OpenEye Toolkit- 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_general_simulation_data has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def get_general_simulation_data(self):
"""
General purpose simulation data on number of iterations, number of states, and number of atoms.
This just prints out this data in a regular, formatted pattern.
- 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_experiments_protocols has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def _generate_experiments_protocols(self):
"""Go through all experiments and generate 'auto' alchemical paths."""
# Find all experiments that have at least one phase whose
# alchemical path needs to be generated automatically.
experiments_to_generate = []- 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 _resume_thermodynamic_trailblazing has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def _resume_thermodynamic_trailblazing(checkpoint_dir_path, initial_protocol):
"""Resume a previously-run trailblaze execution.
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 _determine_restraint_parameters has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def _determine_restraint_parameters(self, sampler_states, topography):
"""Determine restraint parameters.
Currently, all equilibrium values are measured from the initial structure,
while spring constants are set to 20 kcal/(mol A**2) or 20 kcal/(mol rad**2)- 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_leaves has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def _find_leaves(self):
"""Traverse a dict tree and find the leaf nodes.
Returns
-------- 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 round_charge has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def round_charge(self):
"""Round the net charge to the nearest integer to 6-digit precision.
Raises
------- 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 save_unit has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def save_unit(self, unit_name, output_path):
"""
Write a LEaP unit to file.
Accepts either ``*.prmtop``, ``*.inpcrd``, or ``*.pdb`` files- 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"