Index A | B | C | D | F | G | H | I | L | M | O | P | R | S | T | U | V | W A add_interface_state() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) Analyzer (class in ionerdss) (class in ionerdss.analysis) atol (ionerdss.ODEPipelineConfig attribute), [1] B box_size (ionerdss.analysis.SimulationMetadata attribute) build_system_from_pdb() (in module ionerdss) build_system_from_plat() (in module ionerdss) C calculate_progress_percentage() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) complex_histograms (ionerdss.analysis.SimulationData attribute) compute_free_energy() (ionerdss.analysis.Analyzer method) (ionerdss.Analyzer method) compute_size_distribution() (ionerdss.analysis.Analyzer method) (ionerdss.Analyzer method) copy_numbers (ionerdss.analysis.SimulationData attribute) D df_free_energy (ionerdss.analysis.SimulationData attribute) df_size_dist (ionerdss.analysis.SimulationData attribute) F from_dict() (ionerdss.System class method) from_json() (ionerdss.System class method) G get_simulation() (ionerdss.analysis.Analyzer method) (ionerdss.Analyzer method) get_summary() (ionerdss.System method) H hist_comps (ionerdss.analysis.SimulationData attribute) hist_matrix (ionerdss.analysis.SimulationData attribute) hist_times (ionerdss.analysis.SimulationData attribute) I id (ionerdss.analysis.SimulationMetadata attribute) initial_concentrations (ionerdss.ODEPipelineConfig attribute), [1] install_nerdss() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) interface_instances (ionerdss.System attribute) interface_types (ionerdss.System attribute) ionerdss module ionerdss.analysis module ionerdss.model module ionerdss.nerdss_simulation module ionerdss.nerdss_simulation.simulation module L LegacyPlotInterface (class in ionerdss.analysis) lifetimes (ionerdss.analysis.SimulationData attribute) load_simulations() (ionerdss.analysis.Analyzer method) (ionerdss.Analyzer method) M modify_inp_file() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) modify_mol_file() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) module ionerdss ionerdss.analysis ionerdss.model ionerdss.nerdss_simulation ionerdss.nerdss_simulation.simulation molecule_instances (ionerdss.System attribute) molecule_types (ionerdss.System attribute) O ODEPipelineConfig (class in ionerdss) P params (ionerdss.analysis.SimulationMetadata attribute) path (ionerdss.analysis.SimulationMetadata attribute) pdb_id (ionerdss.System attribute) platonic_solid_generator (in module ionerdss) plot (ionerdss.ODEPipelineConfig attribute), [1] plot_figure() (ionerdss.analysis.LegacyPlotInterface method) plot_sample_points (ionerdss.ODEPipelineConfig attribute), [1] plot_species_indices (ionerdss.ODEPipelineConfig attribute), [1] print_inp_file() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) print_mol_parameters() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) pull_mol_file_information() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) pull_parameter_file_information() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) pull_reaction_information() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) R run_new_simulations() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) run_ode_pipeline() (in module ionerdss) run_restart_simulations() (ionerdss.nerdss_simulation.Simulation method) (ionerdss.nerdss_simulation.simulation.Simulation method) (ionerdss.Simulation method) S save_csv (ionerdss.ODEPipelineConfig attribute), [1] Simulation (class in ionerdss) (class in ionerdss.nerdss_simulation) (class in ionerdss.nerdss_simulation.simulation) SimulationData (class in ionerdss.analysis) SimulationMetadata (class in ionerdss.analysis) solver_method (ionerdss.ODEPipelineConfig attribute), [1] species_labels (ionerdss.ODEPipelineConfig attribute), [1] System (class in ionerdss) T t_span (ionerdss.ODEPipelineConfig attribute), [1] to_dict() (ionerdss.System method) to_json() (ionerdss.System method) transitions (ionerdss.analysis.SimulationData attribute) U units (ionerdss.System attribute) V validate_system() (ionerdss.System method) volume (ionerdss.analysis.SimulationMetadata attribute) W work_dir (ionerdss.nerdss_simulation.Simulation attribute) (ionerdss.nerdss_simulation.simulation.Simulation attribute) (ionerdss.Simulation attribute) workspace_path (ionerdss.System attribute)