Avoid deeply nested control flow statements.

Open

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

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

Open

    def _find_similar_sampler_states(sampler_states):
        """Groups SamplerStates that have the same positions.

        Returns
        -------

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Avoid deeply nested control flow statements.

Open

                        if char_per_str != 0:
                            idx = sorted_vals[i][0]
                            filtered_vals[idx] = filtered_vals[idx][:-char_per_str]
                        length_diff -= char_per_str

Avoid deeply nested control flow statements.

Open

                        if is_processed and not resume_setup:
                            err_msg = 'molecule {} file'.format(molecule_id)
                            break

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

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

Open

def find_alchemical_counterions(system, topography, region_name):
    """Return the atom indices of the ligand or solute counter ions.

    In periodic systems, the solvation box needs to be neutral, and
    if the decoupled molecule is charged, it will cause trouble. This

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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 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:

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

Open

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

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

Open

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

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

Open

def call_constructor(parent_cls, constructor_description, special_conversions=None,

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

Open

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

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 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."""

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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 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.

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