Outputs#

Core analysis outputs#

SimulationSet.run() writes this bundle by default — see Output location and default artifacts below for exactly when and where. Under output_dir/raw_data/:

  • ``*_hbonds.csv`` — frame-level donor/hydrogen/acceptor indices, frame, bond label

  • ``*_occupancy.csv`` — present-frame counts and occupancy fractions

  • ``*_pivot.csv`` — bond-label × frame matrices for heatmaps and comparisons

  • ``manifest.json`` — run metadata (inputs, sub_frames, resid_range, backbone_only, …)

  • ``qc_report.json`` — present when QC was enabled

And directly under output_dir:

  • ``plots/`` — per-replicate heatmaps, an aggregated heatmap, and (when bond_statistics_threshold is set) lifetime/break-frequency bar plots

  • ``structure_bfactors.pdb`` — frame-0 reference structure colored by per-residue H-bond variance across replicates (see Output location and default artifacts for where “frame 0” comes from on each input path)

Differential / comparison outputs#

ComparisonSet.compare() writes this bundle by default too (see Output location and default artifacts) — no need to call export_comparison_artifacts or plot_difference yourself:

  • ``raw_data/comparison.csv``, ``manifest.json`` — per-donor occupancy in each condition, raw and clipped difference (clipped to [-1, 1] for visualization / B-factors); see export_comparison_artifacts()

  • ``plots/difference.png`` — plot_difference() with manual or autocorrelation-based thresholds

  • ``plots/heatmaps/`` — aligned per-replicate heatmaps for both sets, via plot_heatmaps_both()

  • ``structure_bfactors_diff.pdb`` — differential B-factors (label_b − label_a) on set_a’s frame-0 reference structure

Opt-in only (not part of the default bundle, since they need a graph_mode/threshold choice): Connectivity HTML — residue graphs from occupancy or Δ occupancy (export_connectivity_graph_html(), community-aware variant available).

Default location#

A fresh, timestamped directory under ./phenom_outputs/ (or $PHENOMS_OUTPUT_DIR) per run — see Output location and default artifacts for the exact naming and how to override it with output_dir= / --output-dir, or disable default writing entirely with output_dir=False.