From 35801c2b003fdf908681f9ac32de04d52e4bfd10 Mon Sep 17 00:00:00 2001
From: "Austin L." <86896075+rvnminers-A-and-N@users.noreply.github.com>
Date: Tue, 30 Jun 2026 17:46:38 +0000
Subject: [PATCH] feat(demo): structures + names on substitution;
dosing/applicability/tox notes
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- Substitution candidates now show a 2D structure thumbnail and the molecule's name
(PubChem Title, cached/best-effort) alongside SMILES + known tastes + % match —
app.py enriches each neighbor via reusable _svg() + _name() helpers; the workbench
renders thumbnail | name/SMILES/tastes | % match.
- Footnote notes (web interface): the trained heads are for ORGANIC molecules
(carbon-free flagged out-of-domain); tox-assay flags are indicative caution-only;
quantitative dosing/odor-activity needs threshold tables (licensed/customer), so it
stays qualitative here.
Signed-off-by: Austin L. <86896075+rvnminers-A-and-N@users.noreply.github.com>
---
training/app.py | 54 +++++++++++++++++++++++++++++------------
training/workbench.html | 27 +++++++++++++++------
2 files changed, 58 insertions(+), 23 deletions(-)
diff --git a/training/app.py b/training/app.py
index 8d23614..bcd1f9d 100644
--- a/training/app.py
+++ b/training/app.py
@@ -18,6 +18,7 @@
prediction core doesn't change.
"""
+from functools import lru_cache
from pathlib import Path
from fastapi import FastAPI
@@ -45,6 +46,37 @@ def _resolve(text: str):
return None
+def _svg(smi, w=320, h=220):
+ """2D structure SVG; None if drawing is unavailable (headless box w/o libXrender)."""
+ mol = Chem.MolFromSmiles(smi) if smi else None
+ if mol is None:
+ return None
+ try:
+ from rdkit.Chem.Draw import rdMolDraw2D
+ d = rdMolDraw2D.MolDraw2DSVG(w, h)
+ d.DrawMolecule(mol)
+ d.FinishDrawing()
+ return d.GetDrawingText()
+ except Exception: # noqa: BLE001 — missing X11 libs etc.; degrade gracefully
+ return None
+
+
+@lru_cache(maxsize=8192)
+def _name(smi):
+ """PubChem common name (Title) for a SMILES — cached, best-effort, short timeout."""
+ import json
+ import urllib.parse
+ import urllib.request
+ url = ("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/"
+ f"{urllib.parse.quote(smi)}/property/Title/JSON")
+ try:
+ with urllib.request.urlopen(url, timeout=4) as r:
+ d = json.load(r)
+ return d["PropertyTable"]["Properties"][0].get("Title")
+ except Exception: # noqa: BLE001 — not found / timeout / throttled
+ return None
+
+
class Query(BaseModel):
smiles: str
k: int = 8
@@ -64,25 +96,17 @@ def api_neighbors(q: Query):
smi = _resolve(q.smiles)
if not smi:
return {"neighbors": []}
- return P.substitute(smi, k=q.k)
+ res = P.substitute(smi, k=q.k)
+ for n in res.get("neighbors", []): # enrich each candidate with a structure + a name
+ n["svg"] = _svg(n["smiles"], 132, 96)
+ n["name"] = _name(n["smiles"])
+ return res
@app.post("/api/structure")
def api_structure(q: Query):
- """2D structure depiction (SVG). Degrades to {svg: None} if RDKit's drawing module
- can't load (e.g. a headless box missing libXrender) — never 500s the demo."""
- smi = _resolve(q.smiles)
- mol = Chem.MolFromSmiles(smi) if smi else None
- if mol is None:
- return {"svg": None}
- try:
- from rdkit.Chem.Draw import rdMolDraw2D
- d = rdMolDraw2D.MolDraw2DSVG(320, 220)
- d.DrawMolecule(mol)
- d.FinishDrawing()
- return {"svg": d.GetDrawingText()}
- except Exception: # noqa: BLE001 — missing X11 libs etc.; degrade gracefully
- return {"svg": None}
+ """2D structure depiction (SVG); {svg: None} if drawing is unavailable."""
+ return {"svg": _svg(_resolve(q.smiles))}
@app.get("/", response_class=HTMLResponse)
diff --git a/training/workbench.html b/training/workbench.html
index abd27dc..f5f1a41 100644
--- a/training/workbench.html
+++ b/training/workbench.html
@@ -49,10 +49,14 @@
.chip{font-family:var(--mono);font-size:12px;padding:5px 11px;border-radius:20px;
border:1px solid var(--line);background:var(--surface)}
.chip.on{color:#fff;border-color:transparent}
- .neighbor{display:flex;justify-content:space-between;align-items:center;gap:12px;
+ .neighbor{display:flex;align-items:center;gap:12px;
padding:11px 0;border-bottom:1px solid var(--line)}
.neighbor:last-child{border-bottom:none}
- .neighbor .s{font-family:var(--mono);font-size:12.5px;word-break:break-all}
+ .neighbor .nb-struct{flex:0 0 auto;width:64px;height:48px;background:#fff;border:1px solid var(--line);border-radius:6px}
+ .neighbor .nb-struct svg{width:64px;height:48px}
+ .neighbor .nb-info{flex:1;min-width:0}
+ .neighbor .nb-name{font-weight:600;font-size:13px;text-transform:capitalize;color:var(--ink)}
+ .neighbor .s{font-family:var(--mono);font-size:12px;color:var(--muted);word-break:break-all}
.neighbor .sim{font-family:var(--mono);font-size:12px;color:var(--accent);white-space:nowrap}
.neighbor .kt{font-family:var(--mono);font-size:11px;color:var(--muted)}
.empty{color:var(--muted);font-size:14px;padding:8px 0}
@@ -127,10 +131,13 @@
Aroma
Bars are model predictions; a measured tag means the molecule is in the
- curated data (ground truth, not a guess). Salty is lookup-only and sour is a
- rule. Substitutions rank by structural similarity (Tanimoto over molecular
- fingerprints). Aroma isn't in the public demo — it trains on your licensed or
- in-house odor data, on-prem. Results are leads for the bench, not verdicts.
+ curated data (ground truth, not a guess). The trained taste/tox heads are fit on
+ organic molecules — carbon-free inputs are flagged out-of-domain. Salty is
+ lookup-only, sour is a rule. Tox-assay flags are indicative, caution-only
+ (Tox21 in-vitro models) — never a determination. Quantitative dosing / odor-activity
+ needs odor-threshold tables (licensed or customer data), so it stays qualitative here.
+ Substitutions rank by structural similarity (Tanimoto). Aroma isn't in the public
+ demo — it trains on your data, on-prem. Results are leads for the bench, not verdicts.