| """Structure-viewer payloads (section 13 'interactive 3D scientific universe'). Visualization is kept separate |
| from evidence: the payload carries the evidence state as explicit text labels; colours encode elements only.""" |
| from __future__ import annotations |
|
|
| from typing import Optional |
|
|
| from ase.data import atomic_numbers, covalent_radii |
| from ase.data.colors import jmol_colors |
|
|
| from core.representation import MatterStructure |
| from core.schemas import MATURITY_LABELS |
|
|
|
|
| def _hex(sym: str) -> str: |
| r, g, b = jmol_colors[atomic_numbers[sym]] |
| return "#%02x%02x%02x" % (int(r * 255), int(g * 255), int(b * 255)) |
|
|
|
|
| def structure_payload(app, candidate_id: str, run_id: Optional[str] = None) -> dict: |
| c = app.repo.get_candidate(candidate_id) |
| ms = MatterStructure.from_candidate(c) |
| trajectory = None |
| forces = None |
| if run_id: |
| run = app.repo.get_run(run_id) |
| from evidence.replication import _final_structure |
| fin = _final_structure(app, run) |
| if fin is not None and fin.n_atoms == ms.n_atoms: |
| trajectory = [ms.positions.tolist(), fin.positions.tolist()] |
| f = run.observables.get("forces") |
| if f: |
| forces = f["value"] |
| g = ms.graph() |
| claims = app.repo.list_claims(candidate_id) |
| return { |
| "candidate_id": candidate_id, "formula": ms.formula(), |
| "atoms": [{"symbol": s, "position": p.tolist(), "color": _hex(s), "radius": float(covalent_radii[atomic_numbers[s]])} |
| for s, p in zip(ms.symbols, ms.positions)], |
| "bonds": [{"a": e["source"], "b": e["target"], "type": e.get("type"), "confidence": e.get("confidence")} for e in g["edges"]], |
| "cell": None if ms.cell is None else ms.cell.tolist(), "periodicity": list(ms.pbc), |
| "overlays": {"graph": {"method": g["method"], "note": g.get("note")}, "symmetry": ms.symmetry(), "fields": ms.fields, |
| "forces": forces, "uncertainty": [u.model_dump() for u in c.uncertainty]}, |
| "trajectory": trajectory, |
| "lineage": {"parents": c.parent_ids, "events": c.lineage, "generation_method": c.generation_method}, |
| "evidence_state": {"maturity": c.maturity, "label": MATURITY_LABELS.get(c.maturity), "validation_status": c.validation_status, |
| "claims": [{"claim_id": cl.claim_id, "maturity": cl.maturity_level, "strength": cl.claim_strength} for cl in claims], |
| "disclaimer": "Rendering style does not imply validation. Evidence state is stated in text only."}, |
| } |
|
|
