Index A | B | C | D | F | G | H | I | L | M | O | P | R | S | T | U | V | W A 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 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] interface_instances (ionerdss.System attribute) interface_types (ionerdss.System attribute) ionerdss module ionerdss.analysis module ionerdss.model module L LegacyPlotInterface (class in ionerdss.analysis) lifetimes (ionerdss.analysis.SimulationData attribute) load_simulations() (ionerdss.analysis.Analyzer method) (ionerdss.Analyzer method) M module ionerdss ionerdss.analysis ionerdss.model 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] R run_ode_pipeline() (in module ionerdss) S save_csv (ionerdss.ODEPipelineConfig attribute), [1] 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 workspace_path (ionerdss.System attribute)