SciDEX — Task: [UI] Add Mol* 3D protein structure viewer to hypot

IMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features. ## REOPENED TASK — CRITICAL CONTEXT This task was previously marked 'done' but the audit could not verify the work actually landed on main. The original work may have been: - Lost to an orphan branch / failed push - Only a spec-file edit (no code changes) - Already addressed by other agents in the meantime - Made obsolete by subsequent work **Before doing anything else:** 1. **Re-evaluate the task in light of CURRENT main state.** Read the spec and the relevant files on origin/main NOW. The original task may have been written against a state of the code that no longer exists. 2. **Verify the task still advances SciDEX's aims.** If the system has evolved past the need for this work (different architecture, different priorities), close the task with reason "obsolete: " instead of doing it. 3. **Check if it's already done.** Run `git log --grep=''` and read the related commits. If real work landed, complete the task with `--no-sha-check --summary 'Already done in '`. 4. **Make sure your changes don't regress recent functionality.** Many agents have been working on this codebase. Before committing, run `git log --since='24 hours ago' -- ` to see what changed in your area, and verify you don't undo any of it. 5. **Stay scoped.** Only do what this specific task asks for. Do not refactor, do not "fix" unrelated issues, do not add features that weren't requested. Scope creep at this point is regression risk. If you cannot do this task safely (because it would regress, conflict with current direction, or the requirements no longer apply), escalate via `orchestra escalate` with a clear explanation instead of committing.

Git Commits (1)

[Docs] Add spec for eb11ca2a: Mol* viewer already on main via 05a277d62026-04-13

Spec File

[UI] Add Mol* 3D protein structure viewer to hypothesis pages

ID: eb11ca2a-6ff3-48db-b6ba-a92f85422ac9 Priority: 88 Type: one_shot Status: done

Goal

Add interactive 3D protein structure viewers using Mol (molstar.org) to hypothesis detail pages. Keep Mol viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase.

Acceptance Criteria

☑ Mol* 3D viewer embedded in hypothesis_detail() page

☑ Mol* 3D viewer embedded in entity_detail() page

☑ Mol* 3D viewer embedded in challenge_detail() page

☑ Mol* viewer NOT shown on /showcase page

☑ PDB structures loaded for target proteins with known PDB IDs

☑ AlphaFold predicted structures used when experimental PDB not available

☑ Lazy-loading (collapsible) to avoid impacting page performance

Implementation

Files Modified

api.py — Added Mol* viewer HTML/JS to hypothesis_detail(), entity_detail(), and challenge_detail()

Key Implementation Details

Lazy-loaded collapsible viewers — Mol* CSS/JS loaded only when user expands the details panel

PDBe Mol* plugin — Uses https://www.ebi.ac.uk/pdbe/pdb-component-library/js/pdbe-molstar-plugin-3.1.0.js

PDB ID mapping — Curated mapping of 80+ neurodegeneration targets to PDB IDs (lines 27207-27399)

AlphaFold fallback — When no experimental structure exists, uses AlphaFold predicted model via UniProt ID

Gene alias resolution — Targets matched by gene name aliases (TDP-43->TARDBP, APOE4->APOE, Tau->MAPT, etc.)

RCSB PDB API fallback — Dynamic search for structures when neither PDB nor AlphaFold ID is known

Commits on Main

afebddfec — [Demo] Add Mol* 3D protein viewers to walkthrough pages [task:8aba1c2f-6223-4836-bbd8-e0c02e958a44]
db23ef9cf — [Artifacts] Add 8 PDB + 3 UniProt protein mappings for Mol* viewers [task:d271b465-bf6]
7fb8ef909 — [Artifacts] Enrich targets with PDB/UniProt IDs + fix challenge Mol* auto-linking [task:e27b4301-b99b-41ae-ad45-d29b603468c0]
91ec0016e — [Quality] Remove Mol* protein viewer section from /showcase page [task:b278d4d3-7b17-4069-b2a1-320a0247e3f4]

Duplicate task note: This task (eb11ca2a) is functionally identical to task 05a277d6-f4cc-4439-ae7a-71806332e313 (spec: d16_4_molstar_protein_viewer_spec.md). Both ask for Mol* on hypothesis pages with same acceptance criteria. Work was completed via the related task's commits.

Work Log

2026-04-14 00:40 PT — Slot minimax:52

Status: Verified complete on main — implementation already exists
Verification: hypothesis_detail() has Mol* viewer at lines 27404-27560 in api.py
Verification: entity_detail() has Mol* viewer at lines 42626-42833 in api.py
Verification: challenge_detail() has Mol* viewer at lines 56560-56967 in api.py
Verification: /showcase has NO Mol* viewer (correct per requirement)
Result: Task already complete on main via commits afebddfec, db23ef9cf, 7fb8ef909, 91ec0016e (associated with related task 05a277d6)

Payload JSON

{
  "requirements": {
    "coding": 8
  },
  "_stall_skip_providers": [],
  "_stall_requeued_by": "minimax",
  "_stall_requeued_at": "2026-04-14 00:46:56",
  "_stall_skip_at": {},
  "_stall_skip_pruned_at": "2026-04-14T10:37:14.022390+00:00"
}