STRC Computational Scripts Inventory

Registry of Python/shell scripts we wrote in ~/STRC/models/ that drive hand-built proofs. Distinct from STRC E1659A Computational Tool Audit — that catalogues 143 third-party prediction tools (AlphaMissense, REVEL, MaxEntScan, etc.) used for variant interpretation. Scripts here are “atoms of computation”; third-party tools they call are “instruments”.

Counts as of 2026-04-23:

• 71 .py scripts in ~/STRC/models/
• 4 .py scripts in ~/STRC/ (root — RBM24 scans + iCloud duplicates)
• 38 JSON outputs (one per finished proof + a few per multi-output scripts)
• 12 PNG figures
• 1 SQLite catalog (third-party tools, separate from this inventory)

Status legend

• active — currently produces results that drive a tier-S/A/B hypothesis
• superseded — a newer script replaces it (note replacement in the row)
• scaffold — TODO body only, never run end-to-end
• orphan — was used once, no longer referenced; candidate for removal
• duplicate — iCloud sync conflict ( 2.py suffix); should be removed but not auto-deleted

h01 — Pharmacochaperone E1659A (A-tier) | h01 hub

Script	Status	Output	Backs	Last successful run
pharmacochaperone_target_prep.py	active	pharmacochaperone_target_prep.json, .png	STRC Pharmacochaperone Virtual Screen E1659A (Phase 0)	2026-04-20
pharmacochaperone_phase1_mutant_pocket.py	active	pharmacochaperone_phase1_results.json, phase1_pocket_{WT,MUT}.pdb, .png	STRC Pharmacochaperone Virtual Screen E1659A (Phase 1)	2026-04-20
pharmacochaperone_phase1b_highconf_realign.py	active	pharmacochaperone_phase1b_results.json, .png	STRC Pharmacochaperone Virtual Screen E1659A (Phase 1B)	2026-04-20
pharmacochaperone_phase2_pocket_scan.py	active	pharmacochaperone_phase2_results.json, phase2_top_pocket.pdb, .png	STRC Pharmacochaperone Virtual Screen E1659A (Phase 2)	2026-04-20
pharmacochaperone_phase2b_subpockets.py	active	pharmacochaperone_phase2b_results.json, phase2b_top_subpocket.pdb, .png	STRC Pharmacochaperone K1141 Fragment Pocket	2026-04-20
pharmacochaperone_phase3a_pharmacophore.py	active	pharmacochaperone_phase3a_pharmacophore.json	STRC Pharmacophore Model K1141 Pocket	2026-04-20
pharmacochaperone_phase3b_virtual_screen.py	active	pharmacochaperone_phase3b_virtual_screen.json	STRC Pharmacochaperone Virtual Screen Ranked Leads	2026-04-20
pharmacochaperone_phase3c_shape_fit.py	active	pharmacochaperone_phase3c_shape_fit.json	STRC Pharmacochaperone Virtual Screen Ranked Leads	2026-04-20
pharmacochaperone_phase4_common.py	active (lib)	— (imported by 4a-4f)	STRC Pharmacochaperone Phase 4 Plan	2026-04-21
pharmacochaperone_phase4a_pocket_reproducibility.py	active	pharmacochaperone_phase4a_pocket_reproducibility.json	STRC Pharmacochaperone Phase 4a Pocket Reproducibility	2026-04-21
pharmacochaperone_phase4b_vina_gnina_screen.py	active	pharmacochaperone_phase4b_vina_gnina_screen.json (+ docking_runs/)	STRC Pharmacochaperone Phase 4b Smoke Test	2026-04-21
pharmacochaperone_phase4c_wt_decoy.py	active	pharmacochaperone_phase4c_wt_decoy.json	STRC Pharmacochaperone Phase 4c WT Decoy	2026-04-21
pharmacochaperone_phase4d_k1141a_decoy.py	scaffold (skipped per Phase 4c interpretation)	—	flagged in STRC Pharmacochaperone Phase 4 Plan	never
pharmacochaperone_phase4e_offtarget_selectivity.py	active	pharmacochaperone_phase4e_offtarget_selectivity.json	STRC Pharmacochaperone Phase 4e Off-Target Selectivity	2026-04-21
pharmacochaperone_phase4f_interface_rescue.py	method-inadequate	pharmacochaperone_phase4f_interface_rescue.json	STRC Pharmacochaperone Phase 4f Interface Rescue SMOKE	2026-04-22 (SMOKE inconclusive)
pharmacochaperone_phase4g_repurpose_screen.py	active	pharmacochaperone_phase4g_repurpose_screen.json	STRC Pharmacochaperone Phase 4g Repurpose Screen	2026-04-22
pharmacochaperone_phase5_md.py	scaffold	—	STRC Pharmacochaperone Phase 4 Plan (gate 7)	never
pharmacochaperone_phase5a_apo_md_smoke.py	active	pharmacochaperone_phase5a_apo_md_smoke.json, artifacts/phase5a_snapshots/	STRC h01 Phase 5 MD Ensemble Rescoring 2026-04-23	2026-04-23
pharmacochaperone_phase5b_ensemble_redock.py	active	pharmacochaperone_phase5b_ensemble_redock.json	STRC h01 Phase 5 MD Ensemble Rescoring 2026-04-23	2026-04-23
pharmacochaperone_phase5c_cryptic_pocket_detection.py	active	pharmacochaperone_phase5c_cryptic_pocket_detection.json	STRC h01 Phase 5c Cryptic Pocket Analysis 2026-04-23	2026-04-23
pharmacochaperone_phase3c_v2a_library_build.py	active	pharmacochaperone_phase3c_v2a_library_build.json, docking_runs/3c_v2/ligands/*.pdbqt	STRC h01 Phase 3c v2 Expanded Screen 2026-04-23	2026-04-23
pharmacochaperone_phase3c_v2b_ensemble_dock.py	active	pharmacochaperone_phase3c_v2b_ensemble_dock.json	STRC h01 Phase 3c v2 Expanded Screen 2026-04-23	2026-04-23
pharmacochaperone_phase3c_v3_fenamic_covalent_library.py	active	pharmacochaperone_phase3c_v3_fenamic_covalent_library.json, docking_runs/3c_v3/ligands/*.pdbqt	STRC h01 Phase 3c v3b Fenamic + Covalent Screen 2026-04-23 (pending)	2026-04-23
pharmacochaperone_phase3c_v3b_ensemble_dock.py	active	pharmacochaperone_phase3c_v3b_ensemble_dock.json (0 GREEN / 29 YELLOW / 21 RED; ceiling Kd 4.57 µM)	STRC h01 Phase 3c v3b + 5d Delivery 2026-04-24	2026-04-24
pharmacochaperone_phase5d_e1659a_md.py	active	pharmacochaperone_phase5d_e1659a_md.json, artifacts/phase5d_snapshots/snap_000-019.pdb (20 snaps, 2 ns, K1141+E1659A verified)	STRC h01 Phase 3c v3b + 5d Delivery 2026-04-24	2026-04-23
pharmacochaperone_phase5e_mutant_ensemble_redock.py	IN PROGRESS (2026-04-24, 11 ligs × 20 mutant snaps × Vina exh=16, per-snap K1141+ring-Cα centroid box)	pharmacochaperone_phase5e_mutant_ensemble_redock.json	STRC h01 Phase 5e Mutant Ensemble Re-Dock (pending)	2026-04-24

h03 — Mini-STRC Single-Vector AAV (S-tier) | h03 hub

Script	Status	Output	Backs	Last successful run
mini_strc_interface_preservation.py	active	mini_strc_interface_preservation.json	STRC Mini-STRC Truncation Interface Validation	2026-04-21
cpg_depletion_mini_strc.py	active (sibling)	cpg_depletion_mini_strc.json, _v0.fasta, _max.fasta	STRC CpG Depletion Mini-STRC	2026-04-21
cpg_depletion_ultra_mini_strc.py	active	cpg_depletion_ultra_mini_strc.json, _v0.fasta, _max.fasta	STRC Ultra-Mini CpG Depletion	2026-04-21
strc_homodimer_interface_from_cif.py	active	strc_homodimer_interface_from_cif.json	STRC Homodimer Interface From CIF	2026-04-21
ultramini_homodimer_consensus.py	active	ultramini_homodimer_consensus.json	STRC Homodimer Interface From CIF (Ultra-Mini section)	2026-04-21
ultra_mini_promoter_shortlist.py	active	ultra_mini_promoter_shortlist.json	STRC Ultra-Mini Promoter Shortlist	2026-04-21
ultramini_vector_cpg_audit.py	active	ultramini_vector_cpg_audit.json	STRC Ultra-Mini CpG Depletion (full-vector audit appendix)	2026-04-21

h04 — Strategy B mRNA-LNP Full-Length (B-tier) | h04 hub

Script	Status	Output	Backs	Last successful run
strc_mrna_strategy_b_pkpd.py	active	strc_mrna_strategy_b_pkpd.json	STRC mRNA-LNP Strategy B Full-Length (PK/PD core)	2026-04-21
strategy_b_audiogram_rescue.py	active	strategy_b_audiogram_rescue.json	STRC mRNA-LNP Strategy B Full-Length (audiogram appendix)	2026-04-21
mrna_lnp_pkpd_integration.py	active (Strategy A baseline)	mrna_lnp_pkpd_integration.json	STRC mRNA-LNP PKPD Multi-Dose Schedule (Strategy A)	2026-04-21
mrna_lnp_audiogram_rescue.py	active (Strategy A baseline)	mrna_lnp_audiogram_rescue.json	STRC mRNA-LNP PKPD Multi-Dose Schedule (Strategy A audiogram)	2026-04-21
mrna_stability_cochlear_results.json	(no script — manual data)	—	STRC mRNA Stability in Cochlea	2026-04-20

h02 — Piezoelectric TM Bioelectronic Amplifier (S-tier) | h02 hub

Script	Status	Output	Backs	Last successful run
piezo_voltage_budget.py	active	piezo_voltage_budget_results.json, .png	STRC Piezoelectric TM Bioelectronic Amplifier (Phase 1)	2026-04-20
piezo_phase2_frequency_bundle.py	active	piezo_phase2_results.json, .png	STRC Piezoelectric TM Bioelectronic Amplifier (Phase 2)	2026-04-20
piezo_phase3_delivery_feasibility.py	active	piezo_phase3_delivery.json, .png	STRC Piezo Delivery Feasibility OHC Targeting	2026-04-20

h05 — Calcium Oscillation Acoustic Therapy (A-tier) | h05 hub

Script	Status	Output	Backs	Last successful run
ca_oscillation_rbm24_ode.py	active	ca_oscillation_rbm24_results.json, .png	STRC Calcium Oscillation Acoustic Therapy (Phase 1 RBM24 path)	2026-04-20
ca_oscillation_ac1_creb_pivot.py	active	ca_oscillation_ac1_creb_results.json, .png	STRC AC1-CREB Alternative Hypothesis	2026-04-20
ca_oscillation_phase2_sensitivity.py	active	ca_oscillation_phase2_sensitivity.json, .png	STRC Calcium Oscillation Acoustic Therapy (Phase 2)	2026-04-20
ca_oscillation_phase3_bifurcation.py	active	ca_oscillation_phase3_bifurcation.json	STRC Calcium Oscillation Acoustic Therapy (Phase 3)	2026-04-21

h06 — Strategy A mRNA / RBM24 (B-tier, was A) | h06 hub

Shares mrna_lnp_pkpd_integration.py and mrna_lnp_audiogram_rescue.py with Strategy B (above).

Script	Status	Output	Backs	Last successful run
mrna_lnp_pkpd_hill_sensitivity.py	active	mrna_lnp_pkpd_hill_sensitivity.json	STRC h06 Hill Sensitivity Sweep 2026-04-23	2026-04-23

h07 — Prime Editing for STRC (C-tier) | h07 hub

Script	Status	Output	Backs	Last successful run
pe_phase1_pegrna_design.py	active	pe_phase1_pegrna_design.json	Prime Editing for STRC (Phase 1 SpCas9-NGG)	2026-04-21
pe_phase2_pam_expansion.py	active	pe_phase2_pam_expansion.json	Prime Editing for STRC (Phase 2 PAM expansion)	2026-04-21
pe_phase3_allele_discrimination.py	active	pe_phase3_allele_discrimination.json	STRC pe_phase3_allele_discrimination	2026-04-21
pe_phase4_cas_offinder.py	active (macOS Apple Silicon numpy fallback)	pe_phase4_cas_offinder.json	STRC PE Phase4 STRCP1 Paralog Off-Target	2026-04-22
pe_phase3_5_strcp1_aware.py	active	pe_phase3_5_strcp1_aware.json	STRC PE Phase 3_5 STRCP1-Aware Redesign	2026-04-23

h08 — ASO Exon Skipping (C-tier) | h08 hub

Script	Status	Output	Backs	Last successful run
aso_phase1_design.py	active	aso_phase1_design.json, aso_phase1_candidates.csv	STRC ASO Phase1 Splice-Switch Design	2026-04-21
(ad-hoc fold check 2026-04-22)	one-shot in conversation log	aso_phase1_fold_check.json	STRC ASO Phase1 Fold Check	2026-04-22 — needs lifting into a proper aso_phase1_fold_check.py if re-run
aso_phase2_strcp1_specificity.py	active (pure-numpy, no external deps)	aso_phase2_strcp1_specificity.json	STRC ASO Phase2 STRCP1 Paralog Cross-Hybridization	2026-04-22
ohc_strcp1_expression_check.py	active (stdlib + urllib only, queries GTEx v8)	ohc_strcp1_expression_check.json	STRC STRCP1 GTEx Expression Check	2026-04-22
mrna_lnp_pkpd_integration_v2_ohc_tropism.py	active (v2: adds 1-3% tropism row + ER/UPR 5× ceiling); v1 superseded for new work but retained for diff	mrna_lnp_pkpd_integration_v2_ohc_tropism.json	STRC mRNA-LNP PKPD v2 OHC Tropism	2026-04-22

h15 — OTOA Paralog Cross-Rescue (D/C-tier) | h15 hub

Script	Status	Output	Backs	Last successful run
otoa_phase1_sequence_alignment.py	active (frozen — hypothesis killed)	otoa_phase1_sequence_alignment.json	STRC OTOA Paralog Cross-Rescue (Phase 1A)	2026-04-20
otoa_phase1b_structure_alignment.py	active (frozen — chimera killed by 13.8 Å RMSD)	otoa_phase1b_structure_alignment.json	STRC OTOA Paralog Cross-Rescue (Phase 1B)	2026-04-20

h09 — Synthetic Peptide Hydrogel HTC (A-tier) | h09 hub

Script	Status	Output	Backs	Last successful run
hydrogel_phase1_self_assembly.py	active	hydrogel_phase1_self_assembly.json	STRC Hydrogel HTC Phase 1 Self-Assembly (Phase 1)	2026-04-23
af3_jobs_2026-04-23b_hydrogel_builder.py	active	af3_jobs_2026-04-23b_hydrogel/ (6 JSONs)	STRC Hydrogel HTC Phase 1 Self-Assembly (Phase 2)	2026-04-23
af3_jobs_2026-04-23b_hydrogel/analysis_summary.py	active	af3_jobs_2026-04-23b_hydrogel/analysis_summary.json	STRC Hydrogel HTC Phase 1 Self-Assembly (Phase 2 results)	2026-04-23
af3_jobs_2026-04-23c_hydrogel_retool_builder.py	active	af3_jobs_2026-04-23c_hydrogel_retool/ (3 JSONs)	STRC Hydrogel HTC Phase 1 Self-Assembly (Phase 3)	2026-04-23
af3_jobs_2026-04-23c_hydrogel_retool/analysis_summary.py	active	af3_jobs_2026-04-23c_hydrogel_retool/analysis_summary.json	STRC Hydrogel HTC Phase 1 Self-Assembly (Phase 3 results)	2026-04-23
af3_jobs_2026-04-23e_hydrogel_phase3b_builder.py	active	af3_jobs_2026-04-23e_hydrogel_phase3b/ (4 JSONs)	STRC Hydrogel HTC Phase 1 Self-Assembly (Phase 3b)	2026-04-23
af3_jobs_2026-04-23e_hydrogel_phase3b/analysis_summary.py	active	af3_jobs_2026-04-23e_hydrogel_phase3b/analysis_summary.json	STRC Hydrogel HTC Phase 1 Self-Assembly (Phase 3b results)	2026-04-23
hydrogel_phase4a_cif_interface_forensics.py	active	hydrogel_phase4a_cif_interface_forensics.json	STRC Hydrogel Phase 4 Computational Campaign (4a)	2026-04-23
af3_jobs_2026-04-23f_hydrogel_phase4b_builder.py	active	af3_jobs_2026-04-23f_hydrogel_phase4b/ (8 JSONs)	STRC Hydrogel Phase 4 Computational Campaign (4b batch)	2026-04-23
hydrogel_phase4c_sequence_liabilities.py	active	hydrogel_phase4c_sequence_liabilities.json	STRC Hydrogel Phase 4 Computational Campaign (4c)	2026-04-23
hydrogel_phase4d_factin_bundling_model.py	active	hydrogel_phase4d_factin_bundling_model.json	STRC Hydrogel Phase 4 Computational Campaign (4d)	2026-04-23
hydrogel_phase4e_cochlear_pkpd.py	active	hydrogel_phase4e_cochlear_pkpd.json	STRC Hydrogel Phase 4 Computational Campaign (4e)	2026-04-23
hydrogel_phase4f_mhc_immunogenicity.py	active	hydrogel_phase4f_mhc_immunogenicity.json	STRC Hydrogel Phase 4 Computational Campaign (4f)	2026-04-23
hydrogel_phase4g_spps_feasibility.py	active	hydrogel_phase4g_spps_feasibility.json	STRC Hydrogel Phase 4 Computational Campaign (4g)	2026-04-23
hydrogel_phase4h_endogenous_strc_competition.py	active	hydrogel_phase4h_endogenous_strc_competition.json	STRC Hydrogel Phase 4 Computational Campaign (4h)	2026-04-23
hydrogel_phase4e_v2_blend_scaffold.py	active	hydrogel_phase4e_v2_blend_scaffold.json	STRC h09 Phase 4e_v2 Blend Scaffold	2026-04-23
hydrogel_phase4i_kd_sensitivity.py	active	hydrogel_phase4i_kd_sensitivity.json	STRC h09 Phase 4i Kd Sensitivity Sweep 2026-04-23	2026-04-23

h26 — Engineered Homodimer Avidity (B-tier) | h26 hub

Script	Status	Output	Backs	Last successful run
af3_jobs_2026-04-23d_engineered_homodimer_builder.py	active	af3_jobs_2026-04-23d_engineered_homodimer/ (5 JSONs)	STRC Engineered Homodimer Avidity (Phase 1)	2026-04-23
af3_jobs_2026-04-23d_engineered_homodimer_forensics.py	active	hypotheses/h26-engineered-homodimer/artifacts/phase1_af3_2026-04-23/af3_jobs_2026-04-23d_engineered_homodimer_analysis.json	STRC Engineered Homodimer Phase 1 Results	2026-04-23
engineered_homodimer_phase1c_contact_cluster.py	active	engineered_homodimer_phase1c_contact_cluster.json	STRC h26 Phase 1c Contact Re-Cluster 2026-04-23	2026-04-23

shared / cross-hypothesis

Script	Status	Output	Backs	Last successful run
ipsae_strc_reassess.sh	active	artifacts/ipsae/*.txt (6 jobs × 3 outputs each)	STRC ipSAE Cross-Complex Reassessment 2026-04-23 — h09 gate 3 narrowing + #26 Mech 3→2	2026-04-23
af3_jobs_2026-04-22_builder.py	active	af3_jobs_2026-04-22/ (4 JSONs + MANIFEST)	STRC SpyCatcher Assembly Phase 1 Geometry, STRC TECTA Chimera Phase 1 Fold Check	2026-04-22
af3_jobs_2026-04-22/analysis_summary.py	active	af3_jobs_2026-04-22/analysis_summary.json	STRC SpyCatcher Assembly Phase 1 Geometry (Phase 1a), STRC TECTA Chimera Phase 1 Fold Check	2026-04-23
af3_jobs_2026-04-23_builder.py	active	af3_jobs_2026-04-23/ (2 JSONs + MANIFEST)	STRC SpyCatcher Assembly Phase 1 Geometry (Phase 1b, aa 700 split)	2026-04-23
af3_jobs_2026-04-23/analysis_summary.py	active	af3_jobs_2026-04-23/analysis_summary.json	STRC SpyCatcher Assembly Phase 1 Geometry (Phase 1b results)	2026-04-23
strc_aav_lnp_stack_pkpd.py	active	strc_aav_lnp_stack_pkpd.json	STRC AAV-LNP Stack PKPD (h03+h04 joint)	2026-04-23
ca_osc_maternal_allele_only.py	active	ca_osc_maternal_allele_only.json	STRC Ca Oscillation Maternal-Only PD (h05 Misha-specific)	2026-04-23

ref — Misha-specific therapy integration

Script	Status	Output	Backs	Last successful run
misha_compound_het_stack_model.py	active	misha_compound_het_stack_model.json	Misha Compound-Het Therapy Stack Model	2026-04-23

shared / uncategorized — Reference supporting models

Script	Status	Output	Backs	Last successful run
abr_transfer_model.py	active (referenced from audiogram models)	abr_transfer_results.json	STRC ABR Transfer Function Model	2026-04-17
stereocilia_bundle_mechanics.py	active (referenced from Piezo + Mini-STRC)	bundle_mechanics_results.json	STRC Stereocilia Bundle Mechanics Model	2026-04-17
therapeutic_window_model.py	active (referenced from multiple)	therapeutic_window_results.json	Adult Treatment Window STRC	2026-04-17
rescue_threshold_model.py	active (combined therapeutic window + ABR)	rescue_threshold_results.json	STRC Rescue Threshold	2026-04-17
dual_vector_otof_calibration.py	active (calibration anchor for AAV models)	dual_vector_otof_results.json	STRC Dual-Vector vs Single-Vector Transduction	2026-04-17
sonoporation_model.py	active (sonogenetic delivery sub-model)	(no JSON output found?)	Sonogenetic STRC Computational Proof (paused C-tier)	2026-04-17

Ad-hoc data extracts (no formal driver script)

Output JSON	Source	Backs
af3_ultramini_results_2026-04-21.json	manual collation of AF3 server outputs	STRC AF3 Ultra-Mini Multimer Validation
strc_e1_conservation_nmd_motifs.json	one-shot conservation extract	STRC E1 Conservation and NMD Motifs
strc_exon_protein_mapping.json	one-shot mapping	STRC RBM24 Exon Mapping to Human Protein
strc_tmem145_interface_from_cif.json	older variant of strc_homodimer_interface_from_cif.py (predecessor; now superseded by mini_strc_interface_preservation.py for the TMEM145 zone)	(legacy reference — superseded)
rbm24_mrna_dose_response_results.json	older Strategy A dose-response, retained as historical	STRC mRNA Therapy Hypothesis
rbm24_sd03_splicing_analysis.json	one-shot Sun et al. 2026 SD03 ingestion	STRC RBM24 Exon Splicing Quantification
pharmacochaperone_phase3b_virtual_screen.json (×2 entries — Phase 3B output collated)	by Phase 3B script	as Phase 3B above
aso_phase1_fold_check.json	ad-hoc 2026-04-22 (this conversation)	STRC ASO Phase1 Fold Check

Outside the canonical models/ directory

Script	Location	Status	Notes
rbm24_scan.py	./ (root)	active (older RBM24 motif scan)	predecessor of ca_oscillation_rbm24_ode.py; retained for replication
rbm24_scan_v2.py	./ (root)	active (refactored RBM24 motif scan)	sibling of rbm24_scan.py
rbm24_scan 2.py	./ (root)	duplicate (iCloud sync conflict)	identical to rbm24_scan.py; flagged for cleanup, do not auto-delete
rbm24_scan_v2 2.py	./ (root)	duplicate (iCloud sync conflict)	identical to rbm24_scan_v2.py; flagged for cleanup
pharmacochaperone_phase4f_interface_rescue.py	also at ~/Desktop/strc-jobs-2026-04-22/	bundle copy	the canonical version lives in models/; bundle copy is for taildrop transfer
pe_phase4_cas_offinder.py	also at ~/Desktop/strc-jobs-2026-04-22/	bundle copy	as above

Audit findings (2026-04-22)

Scaffolds that never ran (kill if not advancing in 30 days):

• pharmacochaperone_phase4d_k1141a_decoy.py — explicitly skipped per Phase 4c interpretation; safe to delete after Phase 4f closes if 4f passes.
• pharmacochaperone_phase5_md.py — Phase 5 GROMACS MD; deferred until Phase 4f result lands. Keep as scaffold reservation; flesh out once 4f closes.

Duplicates (iCloud sync conflicts):

• rbm24_scan 2.py, rbm24_scan_v2 2.py — same content as their no-suffix siblings. Keep flagged here; remove manually after a diff confirms identity.

Possibly orphaned outputs (no clear note backref or older than 4 days without update):

• strc_tmem145_interface_from_cif.json — predecessor of mini-STRC interface preservation; data is interesting but not currently referenced in any active proof. Decide: re-link to a note or move to _archive/.

Things missing that probably should exist:

• aso_phase1_fold_check.py — the ASO fold check 2026-04-22 was an ad-hoc conversation one-shot. If the check needs re-running on revised ASOs, lift it into a proper script.
• pe_phase3_5_strcp1_aware_redesign.py — does not exist yet; required by the next step on the Prime Editing for STRC row in STRC Hypothesis Ranking.
• aso_phase3a_morpholino_design.py — required by the next step on STRC ASO Exon Skipping row (escape path 2 from STRC ASO Phase2 STRCP1 Paralog Cross-Hybridization).
• aso_phase3b_allele_specific_gapmer_c4976.py — required by the next step on STRC ASO Exon Skipping row (escape path 5 from STRC ASO Phase2 STRCP1 Paralog Cross-Hybridization).

Things that should be moved to a proper inventory:

• This note is the inventory. Future scripts go here.

Connections

• [part-of] STRC Research Portal
• STRC E1659A Computational Tool Audit — that one tracks 143 third-party prediction tools; this one tracks our hand-written drivers
• STRC Hypothesis Ranking — every script ultimately backs a row in the ranking
• [applies] Misha — every active script targets Misha’s variant or paternal deletion