nebscape_lib_class

class soda_analyzer.nebscape_lib_class(h5_source)

Inspect persisted NEBScape structures, MinHop history, pathways, and outcomes.

Parameters:

h5_source (str or pathlib.Path or h5py.File) – SODA HDF5 filename or an already open file. Only files opened by this view are closed by its close() method.

h5

Underlying file; borrowed when an open handle was supplied.

Type:

h5py.File

exists

Whether the file contains a NEBScape group.

Type:

bool

Notes

Tables are loaded when this view is created. Missing optional tables are empty. Call close() when finished; an externally supplied HDF5 handle remains open.

Methods

check_minhop_history_equivalence	Compare recorded MinHop result structures within native history scopes.
close	Close the HDF5 file owned by this library view.
export_native_nebscape_format	Export recorded results as a native-style NEBScape analysis folder.
get_accepted_minhop_structures	Return raw accepted-history structures for hopping audits.
get_aligned_fs_relaxation_summaries	Return final-state relaxation summaries with the chosen-structure flag.
get_band_endpoint_analysis	Return band endpoint analysis.
get_band_endpoint_summaries	Return band endpoints and optional ancestry.
get_band_ids_by_reaction	Return band identifiers for a reaction, optionally filtered by selection.
get_band_image_atoms	Return interpolated band input images as ASE structures.
get_band_images	Return interpolated input images for a band.
get_band_metadata	Return band endpoints, ancestry, and optional NEB outcome metadata.
get_bands	Return interpolated bands, including selected and dropped bands.
get_bands_for_pair	Return bands associated with one geometry pair.
get_downstream_work_diagnostics	Summarize dependency scopes and downstream work visible in HDF5.
get_dropped_bands	Return bands dropped during interpolation selection.
get_final_results	Collect NEB results with their optional Sella/IRC refinement outputs.
get_finalized_minhop_structures	Return registered finalized endpoints in native input order.
get_geometry_pair_preparation_summaries	Return geometry-pair preparation summaries with scientific outcome names.
get_geometry_pairs	Return geometry pairs matching the requested reaction, mapping, or job.
get_initial_selected_placements	Return selected placement structures used as MinHop inputs.
get_initial_selected_structures	Return selected placement structures used as MinHop inputs.
get_latest_workflow_checkpoint	Return the matching checkpoint with the greatest checkpoint ID.
get_loadrun_resume_diagnostics	Summarize what a NEBScape loadrun can safely reconstruct.
get_minhop_accepted_minima	Return accepted MinHop history entries, including inactive entries by default.
get_minhop_cost_diagnostics	Return observed search execution cost, separately for each invocation.
get_minhop_decision_records	Return MinHop decisions with candidate and duplicate structure links.
get_minhop_finalization_diagnostics	Count inputs/outcomes and optionally summarize recorded worker timing.
get_minhop_finalization_records	Join pending/completed outcomes to their original source and topology reference.
get_minhop_finalization_work_records	Return registered finalization inputs, including pending prepared starts.
get_minhop_history_scope_diagnostics	Infer MinHop history-scope closure from work-item and decision rows.
get_minhop_invalidation_records	Return MinHop invalidations with replacement structure links.
get_minhop_proposal_records	Return MinHop proposals with decoded audit fields.
get_minhop_reference_records	Return original topology-reference records, filtered by stored fields.
get_minhop_repair_diagnostics	Report retained-history violations and resolved/unresolved causal edges.
get_minhop_result_structures	Return all stored MinHop result structures, including rejected candidates.
get_minhop_run_mode_diagnostics	Summarize MinHop run-mode provenance and optimize-only outcomes.
get_minhop_summaries	Return MinHop job summaries.
get_minima	Return stored structures of kind MinHop minimum.
get_neb_result_images	Return optimized NEB images, before optional Sella/IRC refinement.
get_neb_sella_irc_frames	Return saved Sella refinement and forward/reverse IRC trajectories.
get_neb_summaries	Return recorded NEB summaries for matching bands.
get_partial_neb_result_diagnostics	Summarize completed and pending selected bands in partial NEB output.
get_phase_generation_diagnostics	Return generation-like job records inferred from durable rows.
get_prepare_summaries	Return placement preparation summaries.
get_reaction_lineage_trace	Trace structures, geometry pairs, and bands belonging to one reaction.
get_selected_bands	Return bands retained for NEB evaluation.
get_selected_placements	Return selected placement structures used as MinHop inputs.
get_sorted_interpolation_table	Return interpolation ranking rows in native export order.
get_structures	Return structures matching the requested kind and target.
get_table_counts	Return current row counts for NEBScape tables loaded by the analyzer.
get_uncheckpointed_row_diagnostics	Report committed rows beyond the latest complete checkpoint.
get_workflow_checkpoints	Return workflow checkpoints with decoded phase, status, and table counts.
get_workflow_progress_diagnostics	Return a compact NEBScape progress/loadrun diagnostic report.
has_minhop_history_records	Check whether any MinHop work-item or history table contains rows.
read_band	Read one interpolated band by its stored identifier.
read_band_image	Read one interpolated input image by row index or band-local index.
read_geometry_pair	Read one geometry pair by its stored identifier.
read_minhop_accepted_minimum	Read one accepted-history entry by its stored identifier.
read_minhop_summary	Read one MinHop job summary by its stored identifier.
read_neb_result_image	Read one final NEB result image by row index or band-local index.
read_neb_sella_irc_frame	Read one Sella/IRC frame by row index or band-local index.
read_neb_sella_irc_info	Read one Sella/IRC summary by its stored identifier.
read_neb_summary	Read one NEB summary by its stored identifier.
read_prepare_summary	Read one placement preparation summary by its stored identifier.
read_reaction	Read one reaction by its stored identifier.
read_structure	Read one structure by its stored identifier.
summarize_minhop_rejections	Return the fraction of recorded MinHop candidate results rejected.