Function get_system_files_paths has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def get_system_files_paths(self, system_id):
        """Return the paths to the systems files.

        Parameters
        ----------

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Function process_tool_directive has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def process_tool_directive(directives, option, dispatch, allowed_values, yields_value=False):
    """Process a directive.

    Parameters
    ----------

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Avoid deeply nested control flow statements.

Open

                    if previous_thermo_state is not None:
                        computed_thermo_states.append(previous_thermo_state)
                else:

Avoid deeply nested control flow statements.

Open

                        if v in combinatorial_id_nodes:
                            i = expanded_tree[update_node_key].index(v)
                            expanded_tree[update_node_key][i:i+1] = combinatorial_id_nodes[v]
                elif update_node_val in combinatorial_id_nodes:

Avoid deeply nested control flow statements.

Open

                        if len(line_fields) > 1:
                            smiles_str = line_fields[1].strip()
                        else:
                            smiles_str = line_fields[0].strip()

Function _expand_experiments has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def _expand_experiments(self):
        """Generates all possible combinations of experiment.

        Each generated experiment is uniquely named. If job_id and n_jobs are
        set, this returns only the experiments assigned to this particular job.

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Function create has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def create(self, thermodynamic_state, sampler_states, storage,

Avoid deeply nested control flow statements.

Open

                        if not utils.is_openeye_installed(oetools=('oechem',)):
                            err_msg = 'Molecule {}: Cannot "select" from {} file without OpenEye toolkit'
                            raise RuntimeError(err_msg.format(comb_mol_name, extension))
                        n_models = len(utils.load_oe_molecules(comb_molecule['filepath']))

Function _minimize_sampler_state has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def _minimize_sampler_state(sampler_state_id, sampler_states, thermodynamic_state,
                                tolerance, max_iterations):
        """Minimize the specified sampler state at the given thermodynamic state.
        """
        sampler_state = sampler_states[sampler_state_id]

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

Open

def call_constructor(parent_cls, constructor_description, special_conversions=None,

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

Open

def process_tool_directive(directives, option, dispatch, allowed_values, yields_value=False):

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

Open

def read_system_files(positions_file_path, parameters_file_path, system_options,

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

Open

    def _numerical_torsion_integrand(self, phi, phi0, spring_constant, kt):

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

Open

def _cache_trailblaze_data(checkpoint_dir_path, optimal_protocol, states_stds,

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

Open

    def __init__(self, restrained_receptor_atoms=None, restrained_ligand_atoms=None,

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

Open

    def _numerical_angle_integrand(self, theta, theta0, spring_constant, kt):

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

Open

    def _numerical_distance_integrand(self, r, r0, spring_constant, kt):

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``

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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']

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

Open

    def _build_default_alchemical_region(system, topography, protocol):
        """Create a default AlchemicalRegion if the user hasn't provided one."""
        # TODO: we should probably have a second region that annihilate sterics of counterions.
        alchemical_region_kwargs = {}

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