aa_properties           Amino acid properties
annotate_cleavage_sites
                        Annotate cleavage-site efficiency
batch_compare_enzymes   Compare multiple enzymes across a full proteome
batch_evaluate          Batch-evaluate multiple proteins
calculate_peptide_mass
                        Calculate peptide mass or m/z
calculate_pI            Calculate peptide isoelectric point
compare_digests         Compare multiple enzymes on a single protein
digest_protein          Simulate a proteolytic digest
digest_report           Print a compact console report for a
                        proteolytic digest
evaluate_digest         Evaluate a proteolytic digest
export_peptide_list     Export a peptide list for downstream tools
pepvet_check            Quick digest check for a single protein
pepvet_plot_config      Configure pepVet plot appearance
pepvet_plot_config_reset
                        Reset pepVet plot configuration to defaults
pepvet_preset           Return a named scoring preset
pepvet_save_figure      Save a pepVet figure with publication-ready
                        defaults
pepvet_theme_manuscript
                        pepVet manuscript theme
pepvet_theme_presentation
                        pepVet presentation theme
plot_batch_comparison   Multi-enzyme proteome comparison
plot_cleavage_map       Cleavage Site Map
plot_coverage_map       Protein Coverage Map
plot_digest_profile     Four-Panel Digest Diagnostic Plot
plot_enzyme_comparison
                        Enzyme Comparison Chart
plot_gravy_landscape    GRAVY Landscape: 2D Scatter of Peptide Length
                        vs. Hydrophobicity
plot_length_distribution
                        Standalone Peptide Length Distribution
plot_missed_cleavage_impact
                        Missed Cleavage Impact Plot
plot_mz_distribution    Precursor m/z Distribution
plot_peptide_overlap_map
                        Amino-Acid Peptide Overlap Map
plot_pI_distribution    pI Distribution: Histogram of Peptide
                        Isoelectric Points
plot_proteome_overview
                        Proteome digest overview
plot_score_diagnostics
                        Plot score diagnostics
plot_weight_sensitivity
                        Plot weight sensitivity
recommend_enzyme        Return the highest-scoring enzyme for a single
                        protein
score_diagnostics       Score diagnostics for pepVet scoring models
score_peptides          Score digested peptides for pre-acquisition
                        review
sensitivity_analysis    Weight sensitivity analysis
summarize_batch         Summarize a batch digest evaluation
triage_proteins         Triage proteins from a batch evaluation
