Index A | B | C | D | E | F | G | H | I | M | N | P | R | S | T | V | W A accepted_for_pairing (soda_analyzer.nebscape_minhop_accepted_minimum_class attribute) active (soda_analyzer.nebscape_minhop_accepted_minimum_class attribute) agent_id (soda_analyzer.ezga_generation_commit_class attribute) (soda_analyzer.ezga_structure_class attribute) analyze_process_product_states() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) atom (soda_analyzer.environment_class property) atomID (soda_analyzer.environment_class attribute) atoms (soda_analyzer.environment_class property) (soda_analyzer.ezga_structure_class attribute) (soda_analyzer.nebscape_structure_class attribute) (soda_analyzer.state_class property) B band_id (soda_analyzer.nebscape_band_class attribute) barrier_list (soda_analyzer.process_class attribute) (soda_analyzer.state_class property) build_decaf_model() (soda_analyzer.environment_lib_class method) build_decaf_model_from_h5() (in module soda_analyzer) C cell (soda_analyzer.state_class property) check_ape_cluster_member_distances() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) check_duplicate_processes() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) check_duplicate_states() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) check_minhop_history_equivalence() (soda_analyzer.nebscape_lib_class method) check_nebscape_minhop_history_equivalence() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) check_soda_run_folder() (in module soda_analyzer) close() (soda_analyzer.ezga_lib_class method) (soda_analyzer.nebscape_lib_class method) (soda_analyzer.soda_lib_class method) commit_id (soda_analyzer.ezga_generation_commit_class attribute) compare_nebscape_fairchem_config_runtime() (in module soda_analyzer) compare_nebscape_fairchem_native_outputs() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) compare_nebscape_native_downstream_outputs() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) compare_nebscape_optimize_only_native_outputs() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) convert_ezga_soda_xyz_fixed_flags() (in module soda_analyzer) convert_hdf5_to_current() (in module soda_analyzer) convert_native_ezga_multi_agent_run_setup_to_soda() (in module soda_analyzer) convert_native_ezga_run_setup_to_soda() (in module soda_analyzer) convert_native_ezga_xyz_to_soda() (in module soda_analyzer) convert_native_nebscape_calculator_to_soda_config() (in module soda_analyzer) convert_native_nebscape_run_setup_to_soda() (in module soda_analyzer) convert_native_nebscape_xyz_to_soda() (in module soda_analyzer) convert_soda_xyz_to_native_ezga() (in module soda_analyzer) convert_soda_xyz_to_native_nebscape() (in module soda_analyzer) D detect_workflow() (soda_analyzer.soda_lib_class method) E embedded_descriptor (soda_analyzer.environment_class property) energies (soda_analyzer.process_class attribute) energy (soda_analyzer.nebscape_structure_class attribute) (soda_analyzer.state_class property) env_list (soda_analyzer.environment_lib_class attribute) environment_class (class in soda_analyzer) environment_lib (soda_analyzer.soda_lib_class attribute) environment_lib_class (class in soda_analyzer) exists (soda_analyzer.ezga_lib_class attribute) (soda_analyzer.nebscape_lib_class attribute) export_cluster_members() (soda_analyzer.environment_lib_class method) export_native_nebscape_format() (soda_analyzer.nebscape_lib_class method) export_nebscape_native_format() (in module soda_analyzer) ezga (soda_analyzer.soda_lib_class attribute) ezga_blob_class (class in soda_analyzer) ezga_generation_commit_class (class in soda_analyzer) ezga_lib_class (class in soda_analyzer) ezga_reactivity_irc_path_class (class in soda_analyzer) ezga_sage_structure_payload_class (class in soda_analyzer) ezga_simulation_frame_class (class in soda_analyzer) ezga_structure_class (class in soda_analyzer) F fixed_list (soda_analyzer.process_class attribute) (soda_analyzer.state_class property) flip_nebscape_soda_xyz_tags() (in module soda_analyzer) force_calls (soda_analyzer.state_class property) format_ape_cluster_member_distance_report() (in module soda_analyzer) format_descriptor_registry_provenance_report() (in module soda_analyzer) format_descriptor_sampling_flags_report() (in module soda_analyzer) format_duplicate_process_report() (in module soda_analyzer) format_duplicate_state_report() (in module soda_analyzer) format_ezga_setup_conversion_report() (in module soda_analyzer) format_nebscape_fairchem_hdf5_numeric_sanity_report() (in module soda_analyzer) format_nebscape_fairchem_native_comparison_report() (in module soda_analyzer) format_nebscape_fairchem_runtime_report() (in module soda_analyzer) format_nebscape_hpc_acceptance_report() (in module soda_analyzer) format_nebscape_native_downstream_comparison_report() (in module soda_analyzer) format_nebscape_optimize_only_native_comparison_report() (in module soda_analyzer) format_nebscape_setup_conversion_report() (in module soda_analyzer) format_process_product_state_report() (in module soda_analyzer) format_soda_run_check_report() (in module soda_analyzer) format_soda_run_command_suggestion() (in module soda_analyzer) full_descriptor (soda_analyzer.environment_class property) full_descriptors (soda_analyzer.environment_lib_class attribute) G generation (soda_analyzer.ezga_generation_commit_class attribute) get_accepted_minhop_structures() (soda_analyzer.nebscape_lib_class method) get_agent_ids() (soda_analyzer.ezga_lib_class method) get_aligned_fs_relaxation_summaries() (soda_analyzer.nebscape_lib_class method) get_atom() (soda_analyzer.environment_class method) (soda_analyzer.environment_lib_class method) get_atomic_numbers_list() (in module soda_analyzer) get_atoms() (in module soda_analyzer) (soda_analyzer.environment_class method) (soda_analyzer.environment_lib_class method) (soda_analyzer.process_class method) (soda_analyzer.state_class method) get_atoms_by_trace() (soda_analyzer.environment_lib_class method) get_audit_record() (soda_analyzer.nebscape_minhop_accepted_minimum_class method) get_band_endpoint_analysis() (soda_analyzer.nebscape_lib_class method) get_band_endpoint_summaries() (soda_analyzer.nebscape_lib_class method) get_band_ids_by_reaction() (soda_analyzer.nebscape_lib_class method) get_band_image_atoms() (soda_analyzer.nebscape_lib_class method) get_band_images() (soda_analyzer.nebscape_lib_class method) get_band_metadata() (soda_analyzer.nebscape_lib_class method) get_bands() (soda_analyzer.nebscape_lib_class method) get_bands_for_pair() (soda_analyzer.nebscape_lib_class method) get_barrier() (in module soda_analyzer) (soda_analyzer.process_class method) get_barrier_list() (in module soda_analyzer) (soda_analyzer.process_class method) (soda_analyzer.state_class method) get_blobs() (soda_analyzer.ezga_lib_class method) get_cell() (in module soda_analyzer) (soda_analyzer.process_class method) (soda_analyzer.state_class method) get_cluster_birth_cycle() (soda_analyzer.environment_lib_class method) get_cluster_birth_cycles() (soda_analyzer.environment_lib_class method) get_cluster_ids() (soda_analyzer.environment_lib_class method) get_cluster_member_count() (soda_analyzer.environment_lib_class method) get_cluster_member_traces() (soda_analyzer.environment_lib_class method) get_cluster_members() (soda_analyzer.environment_lib_class method) get_cluster_model_member_rows() (soda_analyzer.environment_lib_class method) get_clustering_member_rows() (soda_analyzer.environment_lib_class method) get_clusters_for_structure() (soda_analyzer.environment_lib_class method) get_committed_table_prefix() (soda_analyzer.ezga_lib_class method) get_complete_commits() (soda_analyzer.ezga_lib_class method) get_count() (soda_analyzer.process_class method) get_descriptor_bandwidths() (in module soda_analyzer) get_descriptor_clustering_members() (in module soda_analyzer) get_descriptor_embedding_members() (in module soda_analyzer) get_descriptor_embedding_operator() (in module soda_analyzer) get_descriptor_full_id_from_registry_row() (in module soda_analyzer) get_descriptor_meta_dict() (in module soda_analyzer) get_descriptor_registries_table() (in module soda_analyzer) get_downstream_work_diagnostics() (soda_analyzer.nebscape_lib_class method) get_dropped_bands() (soda_analyzer.nebscape_lib_class method) get_embedded_descriptor() (soda_analyzer.environment_class method) (soda_analyzer.environment_lib_class method) get_embedded_descriptors() (soda_analyzer.environment_lib_class method) get_embedded_descriptors_by_cluster() (soda_analyzer.environment_lib_class method) get_embedded_descriptors_by_registry_rows() (soda_analyzer.environment_lib_class method) get_embedding_member_rows() (soda_analyzer.environment_lib_class method) get_endpoint_analysis() (soda_analyzer.nebscape_band_class method) get_endpoint_structures() (soda_analyzer.ezga_reactivity_irc_path_class method) get_endpoint_summary() (soda_analyzer.nebscape_band_class method) (soda_analyzer.nebscape_geometry_pair_class method) get_energies() (soda_analyzer.process_class method) get_energy() (in module soda_analyzer) (soda_analyzer.process_class method) (soda_analyzer.state_class method) get_final_results() (soda_analyzer.nebscape_lib_class method) (soda_analyzer.soda_lib_class method) get_finalized_minhop_structures() (soda_analyzer.nebscape_lib_class method) get_fixed_list() (in module soda_analyzer) (soda_analyzer.process_class method) (soda_analyzer.state_class method) get_force_calls() (soda_analyzer.state_class method) get_frames() (soda_analyzer.ezga_reactivity_irc_path_class method) (soda_analyzer.nebscape_sella_irc_info_class method) get_frames_by_kind() (soda_analyzer.ezga_reactivity_irc_path_class method) (soda_analyzer.nebscape_sella_irc_info_class method) get_full_descriptor() (soda_analyzer.environment_class method) (soda_analyzer.environment_lib_class method) get_full_descriptor_id() (soda_analyzer.environment_lib_class method) get_full_descriptor_ids_by_registry_rows() (soda_analyzer.environment_lib_class method) get_full_descriptors_by_cluster() (soda_analyzer.environment_lib_class method) get_full_descriptors_by_registry_rows() (soda_analyzer.environment_lib_class method) get_full_descriptors_table() (in module soda_analyzer) get_generation_commits() (soda_analyzer.ezga_lib_class method) get_generations() (soda_analyzer.ezga_lib_class method) get_geometry_pair() (soda_analyzer.nebscape_band_class method) get_geometry_pair_preparation_summaries() (soda_analyzer.nebscape_lib_class method) get_geometry_pairs() (soda_analyzer.nebscape_lib_class method) get_hise_stages() (soda_analyzer.ezga_lib_class method) get_images() (soda_analyzer.nebscape_band_class method) get_initial_selected_placements() (soda_analyzer.nebscape_lib_class method) get_initial_selected_structures() (soda_analyzer.nebscape_lib_class method) get_latest_complete_commit() (soda_analyzer.ezga_lib_class method) get_latest_workflow_checkpoint() (soda_analyzer.nebscape_lib_class method) get_lineage() (soda_analyzer.nebscape_structure_class method) get_lineage_summary() (soda_analyzer.nebscape_structure_class method) get_loadrun_resume_diagnostics() (soda_analyzer.nebscape_lib_class method) get_minhop_accepted_minima() (soda_analyzer.nebscape_lib_class method) get_minhop_cost_diagnostics() (soda_analyzer.nebscape_lib_class method) get_minhop_decision_records() (soda_analyzer.nebscape_lib_class method) get_minhop_finalization_diagnostics() (soda_analyzer.nebscape_lib_class method) get_minhop_finalization_records() (soda_analyzer.nebscape_lib_class method) get_minhop_finalization_work_records() (soda_analyzer.nebscape_lib_class method) get_minhop_history_scope_diagnostics() (soda_analyzer.nebscape_lib_class method) get_minhop_invalidation_records() (soda_analyzer.nebscape_lib_class method) get_minhop_proposal_records() (soda_analyzer.nebscape_lib_class method) get_minhop_reference_records() (soda_analyzer.nebscape_lib_class method) get_minhop_repair_diagnostics() (soda_analyzer.nebscape_lib_class method) get_minhop_result_structures() (soda_analyzer.nebscape_lib_class method) get_minhop_run_mode_diagnostics() (soda_analyzer.nebscape_lib_class method) get_minhop_summaries() (soda_analyzer.nebscape_lib_class method) get_minima() (soda_analyzer.nebscape_lib_class method) get_model_member_registry_rows() (soda_analyzer.environment_lib_class method) get_model_meta() (soda_analyzer.environment_lib_class method) get_model_payload() (soda_analyzer.environment_lib_class method) get_neb_result_images() (soda_analyzer.nebscape_band_class method) (soda_analyzer.nebscape_lib_class method) get_neb_sella_irc_frames() (soda_analyzer.nebscape_band_class method) (soda_analyzer.nebscape_lib_class method) get_neb_sella_irc_info() (soda_analyzer.nebscape_band_class method) get_neb_summaries() (soda_analyzer.nebscape_lib_class method) get_neb_summary() (soda_analyzer.nebscape_band_class method) get_nebscape_workflow_progress_diagnostics() (soda_analyzer.soda_lib_class method) get_parent_structure() (soda_analyzer.nebscape_structure_class method) get_partial_neb_result_diagnostics() (soda_analyzer.nebscape_lib_class method) get_phase_generation_diagnostics() (soda_analyzer.nebscape_lib_class method) get_population_memberships() (soda_analyzer.ezga_lib_class method) get_pos() (in module soda_analyzer) (soda_analyzer.process_class method) (soda_analyzer.state_class method) get_prefactor() (in module soda_analyzer) (soda_analyzer.process_class method) get_prefactor_list() (in module soda_analyzer) (soda_analyzer.process_class method) (soda_analyzer.state_class method) get_prepare_summaries() (soda_analyzer.nebscape_lib_class method) get_proc_list() (soda_analyzer.state_class method) get_process_product_states_table() (in module soda_analyzer) get_process_table() (in module soda_analyzer) get_rate() (in module soda_analyzer) get_rates() (soda_analyzer.process_class method) get_reaction_lineage_trace() (soda_analyzer.nebscape_lib_class method) get_reactivity_irc_paths() (soda_analyzer.ezga_lib_class method) get_refst() (soda_analyzer.process_class method) get_registry_members() (soda_analyzer.environment_lib_class method) get_registry_row() (soda_analyzer.environment_class method) (soda_analyzer.environment_lib_class method) get_registry_table() (soda_analyzer.environment_class method) get_rejected_structures() (soda_analyzer.ezga_lib_class method) get_representative_environment() (soda_analyzer.environment_lib_class method) get_result_images() (soda_analyzer.nebscape_neb_summary_class method) get_row_dicts() (soda_analyzer.ezga_lib_class method) get_rows() (soda_analyzer.ezga_lib_class method) get_rsp_atoms() (in module soda_analyzer) (soda_analyzer.process_class method) get_rsp_count() (soda_analyzer.process_class method) get_rsp_pos() (in module soda_analyzer) (soda_analyzer.process_class method) get_rsp_refst() (soda_analyzer.process_class method) get_sage_structure_payloads() (soda_analyzer.ezga_lib_class method) get_search_ids() (soda_analyzer.state_class method) get_selected_bands() (soda_analyzer.nebscape_lib_class method) get_selected_placements() (soda_analyzer.nebscape_lib_class method) get_sella_irc_frames() (soda_analyzer.nebscape_neb_summary_class method) get_sella_irc_info() (soda_analyzer.nebscape_neb_summary_class method) get_sorted_interpolation_table() (soda_analyzer.nebscape_lib_class method) get_species_list() (in module soda_analyzer) (soda_analyzer.process_class method) (soda_analyzer.state_class method) get_stat_repeats() (soda_analyzer.process_class method) get_stat_repeats_list() (soda_analyzer.state_class method) get_state_id_list() (in module soda_analyzer) get_state_process_id_list() (in module soda_analyzer) get_structure() (soda_analyzer.ezga_simulation_frame_class method) get_structures() (soda_analyzer.ezga_lib_class method) (soda_analyzer.nebscape_lib_class method) get_table() (soda_analyzer.ezga_lib_class method) get_table_counts() (soda_analyzer.nebscape_lib_class method) get_termination_ids() (soda_analyzer.state_class method) get_trace() (soda_analyzer.environment_lib_class method) get_uncheckpointed_row_diagnostics() (soda_analyzer.nebscape_lib_class method) get_workflow_checkpoints() (soda_analyzer.nebscape_lib_class method) get_workflow_progress_diagnostics() (soda_analyzer.nebscape_lib_class method) group_cluster_members_by_structure() (soda_analyzer.environment_lib_class method) H h5 (soda_analyzer.ezga_lib_class attribute) (soda_analyzer.nebscape_lib_class attribute) (soda_analyzer.soda_lib_class attribute) (soda_analyzer.state_class attribute) has_minhop_history_records() (soda_analyzer.nebscape_lib_class method) I is_selected_for_neb (soda_analyzer.nebscape_band_class attribute) M meta (soda_analyzer.environment_lib_class attribute) N nebscape (soda_analyzer.soda_lib_class attribute) nebscape_band_class (class in soda_analyzer) nebscape_band_image_class (class in soda_analyzer) nebscape_geometry_pair_class (class in soda_analyzer) nebscape_lib_class (class in soda_analyzer) nebscape_minhop_accepted_minimum_class (class in soda_analyzer) nebscape_minhop_summary_class (class in soda_analyzer) nebscape_molecule_class (class in soda_analyzer) nebscape_neb_result_image_class (class in soda_analyzer) nebscape_neb_summary_class (class in soda_analyzer) nebscape_prepare_summary_class (class in soda_analyzer) nebscape_reaction_class (class in soda_analyzer) nebscape_reaction_side_class (class in soda_analyzer) nebscape_sella_irc_frame_class (class in soda_analyzer) nebscape_sella_irc_info_class (class in soda_analyzer) nebscape_structure_class (class in soda_analyzer) normalize_descriptor_embed_op_for_decaf() (in module soda_analyzer) P pair_id (soda_analyzer.nebscape_band_class attribute) parent_structure_id (soda_analyzer.nebscape_structure_class attribute) pos (soda_analyzer.state_class property) potential_energy (soda_analyzer.ezga_structure_class attribute) prefactor_list (soda_analyzer.process_class attribute) (soda_analyzer.state_class property) preload() (soda_analyzer.state_class method) proc_list (soda_analyzer.state_class attribute) proc_num (soda_analyzer.state_class property) process_class (class in soda_analyzer) procID (soda_analyzer.environment_class attribute) (soda_analyzer.process_class attribute) R read_agent_metadata() (soda_analyzer.ezga_lib_class method) read_band() (soda_analyzer.nebscape_lib_class method) read_band_image() (soda_analyzer.nebscape_lib_class method) read_blob() (soda_analyzer.ezga_lib_class method) read_con() (in module soda_analyzer) read_descriptor_model_from_h5() (in module soda_analyzer) read_dynamics() (soda_analyzer.soda_lib_class method) read_env() (soda_analyzer.environment_lib_class method) read_environmentlib() (soda_analyzer.soda_lib_class method) read_envlist() (soda_analyzer.environment_lib_class method) read_ezga() (soda_analyzer.soda_lib_class method) read_geometry_pair() (soda_analyzer.nebscape_lib_class method) read_meta() (soda_analyzer.environment_lib_class method) (soda_analyzer.soda_lib_class method) read_minhop_accepted_minimum() (soda_analyzer.nebscape_lib_class method) read_minhop_summary() (soda_analyzer.nebscape_lib_class method) read_neb_result_image() (soda_analyzer.nebscape_lib_class method) read_neb_sella_irc_frame() (soda_analyzer.nebscape_lib_class method) read_neb_sella_irc_info() (soda_analyzer.nebscape_lib_class method) read_neb_summary() (soda_analyzer.nebscape_lib_class method) read_nebscape() (soda_analyzer.soda_lib_class method) read_prepare_summary() (soda_analyzer.nebscape_lib_class method) read_process_product_states() (soda_analyzer.soda_lib_class method) read_reaction() (soda_analyzer.nebscape_lib_class method) read_reactivity_irc_path() (soda_analyzer.ezga_lib_class method) read_sage_structure_payload() (soda_analyzer.ezga_lib_class method) read_state() (soda_analyzer.soda_lib_class method) read_state_struct_array() (in module soda_analyzer) read_statelist() (soda_analyzer.soda_lib_class method) read_structure() (soda_analyzer.ezga_lib_class method) (soda_analyzer.nebscape_lib_class method) registry_row_id (soda_analyzer.environment_class attribute) registry_table (soda_analyzer.environment_lib_class attribute) repair_con_file() (in module soda_analyzer) rsp_atoms (soda_analyzer.process_class attribute) rsp_pos (soda_analyzer.process_class attribute) S sage_structure_field_policy (soda_analyzer.ezga_lib_class attribute) search_id_list (soda_analyzer.state_class property) search_stats (soda_analyzer.state_class property) soda_lib_class (class in soda_analyzer) species_list (soda_analyzer.state_class property) stat_repeats_list (soda_analyzer.state_class property) state_class (class in soda_analyzer) state_id_list (soda_analyzer.soda_lib_class attribute) state_list (soda_analyzer.soda_lib_class attribute) state_num (soda_analyzer.soda_lib_class attribute) stateID (soda_analyzer.environment_class attribute) (soda_analyzer.process_class attribute) (soda_analyzer.state_class attribute) status_name (soda_analyzer.ezga_generation_commit_class attribute) structure (soda_analyzer.nebscape_minhop_accepted_minimum_class attribute) structure_id (soda_analyzer.ezga_structure_class attribute) (soda_analyzer.nebscape_structure_class attribute) structure_kind_name (soda_analyzer.nebscape_structure_class attribute) structures_are_equivalent() (in module soda_analyzer) suggest_soda_run_command() (in module soda_analyzer) summarize() (soda_analyzer.ezga_lib_class method) summarize_clusters() (soda_analyzer.environment_lib_class method) summarize_descriptor_registry_provenance() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) summarize_descriptor_sampling_flags() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) summarize_minhop_rejections() (soda_analyzer.nebscape_lib_class method) summarize_nebscape_fairchem_hdf5_numeric_sanity() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) summarize_nebscape_fairchem_runtime() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) summarize_nebscape_fairchem_soda_config() (in module soda_analyzer) summarize_nebscape_geometry_pair_preparation_logs() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) summarize_nebscape_hpc_acceptance() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) summarize_nebscape_minhop_finalization_timing() (in module soda_analyzer) summarize_nebscape_minhop_rejections() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) summarize_nebscape_minhop_run_modes() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) summarize_nebscape_workflow_progress() (in module soda_analyzer) (soda_analyzer.soda_lib_class method) T termination_list (soda_analyzer.state_class property) to_dict() (soda_analyzer.ezga_blob_class method) (soda_analyzer.ezga_generation_commit_class method) (soda_analyzer.ezga_reactivity_irc_path_class method) (soda_analyzer.ezga_sage_structure_payload_class method) (soda_analyzer.ezga_simulation_frame_class method) (soda_analyzer.ezga_structure_class method) V validate_sage_structure_payloads() (soda_analyzer.ezga_lib_class method) W workflow (soda_analyzer.soda_lib_class attribute)