From 8edd5fb907e9b11ffd6a9908f83aafe14200949d Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Sun, 7 Jun 2026 11:25:31 -0400 Subject: [PATCH 01/16] Add structure resolver and PubChem client retry Introduce a smart structure resolver and harden PubChem client: add classify_query, fetch_structure and student_friendly_resolve to route SMILES/InChI locally (RDKit) and CID/InChIKey/name to PubChem. Add inchi_to_xyz and search_cid_by_inchikey helpers, URL-encode queries, and implement client-side throttling plus exponential back-off retries for 503 responses. Move PubChem network parameters into config constants and expose new symbols from the package; update the UI to call the new resolver. Add tests covering query classification, URL encoding, throttle/backoff behavior, routing, and provenance metadata. --- quantui/__init__.py | 10 ++ quantui/app.py | 8 +- quantui/config.py | 12 ++ quantui/pubchem.py | 311 +++++++++++++++++++++++++++++++++- tests/test_struct_resolver.py | 239 ++++++++++++++++++++++++++ 5 files changed, 571 insertions(+), 9 deletions(-) create mode 100644 tests/test_struct_resolver.py diff --git a/quantui/__init__.py b/quantui/__init__.py index 3a28d33..38aaf95 100644 --- a/quantui/__init__.py +++ b/quantui/__init__.py @@ -127,13 +127,18 @@ MoleculeNotFoundError, PubChemError, check_pubchem_availability, + classify_query, display_2d_structure, fetch_molecule, + fetch_structure, generate_2d_structure_svg, get_common_molecules, get_smiles_examples, + inchi_to_xyz, + search_cid_by_inchikey, smiles_to_xyz, student_friendly_fetch, + student_friendly_resolve, student_friendly_smiles_to_xyz, validate_smiles, ) @@ -238,7 +243,12 @@ "optimize_geometry", # PubChem (optional) "fetch_molecule", + "fetch_structure", + "classify_query", "student_friendly_fetch", + "student_friendly_resolve", + "inchi_to_xyz", + "search_cid_by_inchikey", "get_common_molecules", "check_pubchem_availability", "PubChemError", diff --git a/quantui/app.py b/quantui/app.py index ed1db96..08995f9 100644 --- a/quantui/app.py +++ b/quantui/app.py @@ -473,13 +473,13 @@ RDKIT_AVAILABLE as _PUBCHEM_RDKIT_AVAILABLE, ) from quantui.pubchem import ( - student_friendly_fetch as _student_friendly_fetch, + student_friendly_resolve as _student_friendly_resolve, ) PUBCHEM_AVAILABLE = _PUBCHEM_RDKIT_AVAILABLE except ImportError: PUBCHEM_AVAILABLE = False - _student_friendly_fetch = None # type: ignore[assignment] + _student_friendly_resolve = None # type: ignore[assignment] try: from quantui.session_calc import SessionResult, run_in_session # noqa: F401 @@ -2558,7 +2558,7 @@ def _on_search_pubchem(self, btn) -> None: if not query: self.pubchem_msg.value = "Enter a molecule name or SMILES." return - if _student_friendly_fetch is None: + if _student_friendly_resolve is None: self.pubchem_msg.value = "PubChem module not available." return self.pubchem_msg.value = f'Searching for "{query}"...' @@ -2568,7 +2568,7 @@ def _on_search_pubchem(self, btn) -> None: def _do(): try: - xyz_str, _msg = _student_friendly_fetch(query) + xyz_str, _msg = _student_friendly_resolve(query) if xyz_str is None: raise ValueError(_msg) atoms, coords = parse_xyz_input(xyz_str) diff --git a/quantui/config.py b/quantui/config.py index 784cfa6..e0ca247 100644 --- a/quantui/config.py +++ b/quantui/config.py @@ -229,6 +229,18 @@ DESCRIPTION_WIDTH = "150px" +# ── External structure resolvers (M-STRUCT) ────────────────────────────────── +# Network + throttle settings shared by the PubChem client (and, later, the +# NCI CACTUS resolver). All timeouts/limits live here per constraint #5. +PUBCHEM_TIMEOUT_S: float = 15.0 # per-request HTTP timeout +PUBCHEM_AVAILABILITY_TIMEOUT_S: float = 5.0 # quick reachability probe +PUBCHEM_MAX_RETRIES: int = 3 # bounded retries on 503 / throttling +PUBCHEM_BACKOFF_BASE_S: float = 0.5 # exponential back-off base (×2**attempt) +PUBCHEM_BACKOFF_MAX_S: float = 8.0 # cap on a single back-off sleep +# Proactive client-side rate limit. PUG-REST allows ~5 req/s; stay conservative +# so a classroom of simultaneous users doesn't trip the server-side throttle. +PUBCHEM_MIN_REQUEST_INTERVAL_S: float = 0.25 + # Molecule presets — 20+ curated educational molecules MOLECULE_LIBRARY: Dict[str, Dict[str, Any]] = { # ========== SIMPLE DIATOMIC MOLECULES ========== diff --git a/quantui/pubchem.py b/quantui/pubchem.py index 38fd640..6e111d2 100644 --- a/quantui/pubchem.py +++ b/quantui/pubchem.py @@ -6,11 +6,17 @@ """ import logging +import re +import threading +import time from functools import lru_cache from typing import Any, Dict, Optional, Tuple +from urllib.parse import quote import requests +from . import config + try: from rdkit import Chem from rdkit.Chem import AllChem, Descriptors @@ -24,7 +30,63 @@ # PubChem API endpoints PUBCHEM_BASE_URL = "https://pubchem.ncbi.nlm.nih.gov/rest/pug" -PUBCHEM_TIMEOUT = 10 # seconds +# Back-compat alias; canonical value lives in config (constraint #5). +PUBCHEM_TIMEOUT = config.PUBCHEM_TIMEOUT_S + +# ── HTTP client: client-side throttle + bounded 503 back-off (STRUCT.2) ────── +# A single process-wide limiter keeps us under PUG-REST's ~5 req/s ceiling even +# when several search threads fire at once. +_request_lock = threading.Lock() +_last_request_time = 0.0 + + +def _throttle() -> None: + """Block just long enough to honor the client-side minimum request gap.""" + global _last_request_time + with _request_lock: + wait = config.PUBCHEM_MIN_REQUEST_INTERVAL_S - ( + time.monotonic() - _last_request_time + ) + if wait > 0: + time.sleep(wait) + _last_request_time = time.monotonic() + + +def _http_get( + url: str, + *, + params: Optional[Dict[str, Any]] = None, + timeout: Optional[float] = None, +) -> requests.Response: + """GET with client-side throttle + exponential back-off on 503 throttling. + + Retries only on HTTP 503 (PUG-REST's throttle signal). All other status + codes are returned to the caller unchanged; network exceptions + (``Timeout`` / ``ConnectionError`` / ...) propagate so callers can map them + to :class:`PubChemAPIError` exactly as before. + """ + timeout = timeout if timeout is not None else config.PUBCHEM_TIMEOUT_S + response = None + for attempt in range(config.PUBCHEM_MAX_RETRIES): + _throttle() + response = requests.get(url, params=params, timeout=timeout) + if response.status_code != 503: + return response + # Throttled — back off (capped) and retry, unless this was the last try. + if attempt < config.PUBCHEM_MAX_RETRIES - 1: + backoff = min( + config.PUBCHEM_BACKOFF_BASE_S * (2**attempt), + config.PUBCHEM_BACKOFF_MAX_S, + ) + logger.warning( + "PubChem throttled (503); retrying in %.1fs (attempt %d/%d)", + backoff, + attempt + 1, + config.PUBCHEM_MAX_RETRIES, + ) + time.sleep(backoff) + # Exhausted retries — hand the last 503 back; caller raises via raise_for_status. + return response # type: ignore[return-value] class PubChemError(Exception): @@ -59,11 +121,11 @@ def search_molecule_by_name(name: str) -> int: PubChemAPIError: If API request fails MoleculeNotFoundError: If molecule not found """ - url = f"{PUBCHEM_BASE_URL}/compound/name/{name}/cids/JSON" + url = f"{PUBCHEM_BASE_URL}/compound/name/{quote(name, safe='')}/cids/JSON" try: logger.debug(f"Searching PubChem for: {name}") - response = requests.get(url, timeout=PUBCHEM_TIMEOUT) + response = _http_get(url) if response.status_code == 404: raise MoleculeNotFoundError(f"Molecule '{name}' not found in PubChem") @@ -84,6 +146,27 @@ def search_molecule_by_name(name: str) -> int: raise PubChemAPIError(f"Failed to connect to PubChem: {e}") +def search_cid_by_inchikey(inchikey: str) -> int: + """Resolve a standard InChIKey to a PubChem CID. + + InChIKeys are hashes and cannot be inverted to a structure locally, so this + is the one identifier type that always requires the network. + """ + url = f"{PUBCHEM_BASE_URL}/compound/inchikey/{quote(inchikey, safe='')}/cids/JSON" + try: + response = _http_get(url) + if response.status_code == 404: + raise MoleculeNotFoundError(f"InChIKey '{inchikey}' not found in PubChem") + response.raise_for_status() + cids = response.json().get("IdentifierList", {}).get("CID", []) + if not cids: + raise MoleculeNotFoundError(f"No CID found for InChIKey '{inchikey}'") + return int(cids[0]) + except requests.RequestException as e: + logger.error(f"PubChem InChIKey request failed: {e}") + raise PubChemAPIError(f"Failed to connect to PubChem: {e}") + + @lru_cache(maxsize=50) def get_molecule_sdf(cid: int, conformer_3d: bool = True) -> str: """ @@ -109,7 +192,7 @@ def get_molecule_sdf(cid: int, conformer_3d: bool = True) -> str: try: logger.debug(f"Fetching {record_type.upper()} SDF for CID {cid}") - response = requests.get(url, params=params, timeout=PUBCHEM_TIMEOUT) + response = _http_get(url, params=params) if response.status_code == 404: if conformer_3d: @@ -158,7 +241,8 @@ def sdf_to_xyz(sdf_content: str) -> Tuple[str, Dict[str, Any]]: mol = Chem.AddHs(mol) # Generate 3D coordinates if needed - if mol.GetNumConformers() == 0: + coords_embedded = mol.GetNumConformers() == 0 + if coords_embedded: AllChem.EmbedMolecule(mol, randomSeed=42) AllChem.UFFOptimizeMolecule(mol) @@ -184,6 +268,7 @@ def sdf_to_xyz(sdf_content: str) -> Tuple[str, Dict[str, Any]]: "charge": Chem.GetFormalCharge(mol), "num_atoms": mol.GetNumAtoms(), "num_heavy_atoms": mol.GetNumHeavyAtoms(), + "coords_embedded": coords_embedded, } logger.debug(f"Converted SDF to XYZ: {metadata['formula']}") @@ -424,6 +509,60 @@ def smiles_to_xyz(smiles: str, optimize_3d: bool = True) -> Tuple[str, Dict[str, raise ValueError(f"Failed to convert SMILES to XYZ: {e}") +def inchi_to_xyz(inchi: str, optimize_3d: bool = True) -> Tuple[str, Dict[str, Any]]: + """Convert an InChI string to XYZ coordinates via RDKit (no network). + + Mirrors :func:`smiles_to_xyz`: parse → add H → embed (ETKDG, seed 42) → + UFF-optimize. Returns ``(xyz_string, metadata)``; metadata carries the + canonical SMILES so the caller can label provenance consistently. + """ + if not RDKIT_AVAILABLE: + raise ImportError("RDKit is required for InChI conversion") + + try: + mol = Chem.MolFromInchi(inchi) + if mol is None: + raise ValueError(f"Invalid InChI string: {inchi}") + + mol = Chem.AddHs(mol) + if optimize_3d: + result = AllChem.EmbedMolecule(mol, randomSeed=42) + if result != 0: + AllChem.EmbedMolecule(mol, randomSeed=42, useRandomCoords=True) + try: + AllChem.UFFOptimizeMolecule(mol) + except Exception: + logger.warning("UFF optimization failed, using unoptimized coordinates") + + if mol.GetNumConformers() == 0: + raise ValueError("Failed to generate 3D coordinates") + + conf = mol.GetConformer() + formula = Chem.rdMolDescriptors.CalcMolFormula(mol) + xyz_lines = [str(mol.GetNumAtoms()), f"Generated from InChI ({formula})"] + for atom in mol.GetAtoms(): + pos = conf.GetAtomPosition(atom.GetIdx()) + xyz_lines.append( + f"{atom.GetSymbol():3s} {pos.x:12.6f} {pos.y:12.6f} {pos.z:12.6f}" + ) + + metadata = { + "formula": formula, + "molecular_weight": Descriptors.MolWt(mol), + "charge": Chem.GetFormalCharge(mol), + "num_atoms": mol.GetNumAtoms(), + "num_heavy_atoms": mol.GetNumHeavyAtoms(), + "inchi": inchi, + "canonical_smiles": Chem.MolToSmiles(mol), + } + logger.info(f"Converted InChI to XYZ: {formula}") + return "\n".join(xyz_lines), metadata + + except Exception as e: + logger.error(f"InChI to XYZ conversion failed: {e}") + raise ValueError(f"Failed to convert InChI to XYZ: {e}") + + def student_friendly_smiles_to_xyz(smiles: str) -> Tuple[Optional[str], str]: """ Convert SMILES to XYZ with student-friendly error messages. @@ -688,3 +827,165 @@ def validate_smiles(smiles: str) -> Tuple[bool, str]: except Exception as e: return False, f"Validation error: {str(e)}" + + +# ============================================================================ +# Smart input routing (STRUCT.1) +# ============================================================================ + +# Standard InChIKey: 14 block chars - 10 block chars - 1 flag char. +_INCHIKEY_RE = re.compile(r"^[A-Z]{14}-[A-Z]{10}-[A-Z]$") +# A bare molecular formula, e.g. "H2O", "C6H6", "CO2", "Fe". +_FORMULA_RE = re.compile(r"^(?:[A-Z][a-z]?\d*)+$") +# Characters that only appear in SMILES, never in a common/IUPAC molecule name. +_SMILES_STRUCTURAL = set("=#()[]/\\@.%+") + + +def _looks_like_smiles(query: str) -> bool: + """High-precision SMILES check: only ``True`` when RDKit parses it *and* it + carries SMILES-only signals (structural punctuation or ring digits). + + Deliberately conservative — bare-letter tokens like ``CCO`` (which are valid + SMILES *and* plausible names/formulas) are left for the provider chain + (STRUCT.4) to disambiguate, so we never misroute a plain name to a local + parse. + """ + if not RDKIT_AVAILABLE or " " in query: + return False + has_structural = any(c in _SMILES_STRUCTURAL for c in query) + has_digit = any(c.isdigit() for c in query) + if not (has_structural or has_digit): + return False + return Chem.MolFromSmiles(query) is not None + + +def classify_query(query: str) -> str: + """Classify a user structure query so it can be routed to the right resolver. + + Returns one of ``"cid"``, ``"inchikey"``, ``"inchi"``, ``"smiles"``, + ``"formula"``, or ``"name"``. ``smiles`` / ``inchi`` resolve locally via + RDKit (no network); the rest go to PubChem. ``formula`` is currently routed + like ``name`` (PubChem's async fastformula search is deferred to STRUCT.4). + """ + q = query.strip() + if not q: + raise ValueError("Empty query") + if q.startswith("InChI="): + return "inchi" + if _INCHIKEY_RE.match(q): + return "inchikey" + if re.fullmatch(r"(?:CID:?\s*)?\d+", q, flags=re.IGNORECASE): + return "cid" + if _looks_like_smiles(q): + return "smiles" + if _FORMULA_RE.match(q): + return "formula" + return "name" + + +def _coerce_cid(query: str) -> int: + """Extract the integer CID from ``123`` / ``CID123`` / ``cid: 123`` forms.""" + return int(re.sub(r"[^\d]", "", query)) + + +def fetch_structure( + query: str, conformer_3d: bool = True +) -> Tuple[str, Dict[str, Any]]: + """Resolve any supported query type to ``(xyz_string, metadata)``. + + Routes by :func:`classify_query`: SMILES/InChI resolve locally via RDKit + (no network); CID/InChIKey/name/formula go to PubChem. ``metadata`` always + carries a ``source`` key (``"rdkit-smiles"`` / ``"rdkit-inchi"`` / + ``"pubchem"``) and a ``conformer_origin`` key describing where the 3D + coordinates came from, so the UI can be honest about provenance. + + Raises :class:`PubChemError` / :class:`ValueError` on failure (the + student-friendly wrapper :func:`student_friendly_resolve` maps these to + messages). + """ + qtype = classify_query(query) + q = query.strip() + logger.info(f"Resolving structure query '{q}' classified as '{qtype}'") + + if qtype == "smiles": + xyz, metadata = smiles_to_xyz(q, optimize_3d=conformer_3d) + metadata["source"] = "rdkit-smiles" + metadata["conformer_origin"] = "rdkit-embedded" + return xyz, metadata + + if qtype == "inchi": + xyz, metadata = inchi_to_xyz(q, optimize_3d=conformer_3d) + metadata["source"] = "rdkit-inchi" + metadata["conformer_origin"] = "rdkit-embedded" + return xyz, metadata + + # Network branch: resolve to a CID, then fetch + convert the SDF. + if qtype == "cid": + cid = _coerce_cid(q) + elif qtype == "inchikey": + cid = search_cid_by_inchikey(q) + else: # "name" or "formula" + cid = search_molecule_by_name(q) + + sdf_content = get_molecule_sdf(cid, conformer_3d=conformer_3d) + xyz, metadata = sdf_to_xyz(sdf_content) + metadata["source"] = "pubchem" + metadata["pubchem_cid"] = cid + metadata["query_type"] = qtype + metadata["conformer_origin"] = ( + "rdkit-embedded" if metadata.get("coords_embedded") else "pubchem" + ) + return xyz, metadata + + +def student_friendly_resolve(query: str) -> Tuple[Optional[str], str]: + """Smart, type-aware structure fetch with student-friendly messages. + + Drop-in replacement for :func:`student_friendly_fetch` that also handles + SMILES / InChI / CID / InChIKey input (the plain-name path is unchanged). + Returns ``(xyz_string_or_None, message)``. + """ + try: + xyz_string, metadata = fetch_structure(query, conformer_3d=True) + except (MoleculeNotFoundError, ValueError) as exc: + return None, ( + f"❌ Could not resolve '{query}'.\n" + f" {exc}\n" + f" Try a different name, a SMILES (e.g. CCO), or check spelling.\n" + f" Search manually at: https://pubchem.ncbi.nlm.nih.gov/" + ) + except PubChemAPIError: + return None, ( + "❌ Connection to PubChem failed.\n" + " • Check your internet connection\n" + " • Try again in a moment\n" + " • Use a preset molecule if the problem persists" + ) + except ImportError: + return None, ( + "❌ RDKit is required for SMILES / InChI input.\n" + " Install with: conda install -c conda-forge rdkit" + ) + except Exception as exc: # pragma: no cover - unexpected + logger.error( + f"Unexpected error in student_friendly_resolve: {exc}", exc_info=True + ) + return None, f"❌ Error resolving '{query}': {exc}" + + source = { + "rdkit-smiles": "generated locally from SMILES", + "rdkit-inchi": "generated locally from InChI", + "pubchem": "PubChem", + }.get(metadata.get("source", ""), metadata.get("source", "?")) + origin = metadata.get("conformer_origin", "") + origin_note = ( + " (2D structure embedded by RDKit)" if origin == "rdkit-embedded" else "" + ) + message = ( + f"✓ Resolved '{query}' via {source}.\n" + f" Formula: {metadata.get('formula', '?')}\n" + f" Atoms: {metadata.get('num_atoms', '?')} " + f"({metadata.get('num_heavy_atoms', '?')} heavy)\n" + f" Molecular weight: {metadata.get('molecular_weight', 0):.2f} g/mol{origin_note}" + ) + return xyz_string, message diff --git a/tests/test_struct_resolver.py b/tests/test_struct_resolver.py new file mode 100644 index 0000000..89338eb --- /dev/null +++ b/tests/test_struct_resolver.py @@ -0,0 +1,239 @@ +"""Tests for M-STRUCT STRUCT.1 (input-type routing) + STRUCT.2 (hardened client). + +All tests are platform-independent: network is mocked, RDKit-only paths are +gated. No PySCF dependency. +""" + +from unittest.mock import Mock, patch + +import pytest +import requests + +from quantui import config +from quantui.pubchem import ( + RDKIT_AVAILABLE, + MoleculeNotFoundError, + PubChemAPIError, + classify_query, + fetch_structure, + get_molecule_sdf, + search_cid_by_inchikey, + search_molecule_by_name, + student_friendly_resolve, +) + +rdkit_only = pytest.mark.skipif(not RDKIT_AVAILABLE, reason="rdkit not installed") + + +# ============================================================================ +# STRUCT.1 — classify_query routing +# ============================================================================ + + +class TestClassifyQuery: + @pytest.mark.parametrize( + "query,expected", + [ + ("962", "cid"), + ("CID962", "cid"), + ("cid: 2244", "cid"), + ("InChI=1S/H2O/h1H2", "inchi"), + ("XLYOFNOQVPJJNP-UHFFFAOYSA-N", "inchikey"), # water InChIKey + ("CC(=O)O", "smiles"), # acetic acid — structural chars + ("c1ccccc1", "smiles"), # benzene — aromatic + ring digit + ("[OH3+]", "smiles"), # hydronium — brackets + charge + ("H2O", "formula"), # digit but not valid SMILES + ("C6H6", "formula"), + ("Fe", "formula"), + ("water", "name"), + ("carbon dioxide", "name"), # space → never SMILES + ("acetylsalicylic acid", "name"), + ], + ) + def test_classification(self, query, expected): + # SMILES classification needs RDKit to validate; skip those when absent. + if expected == "smiles" and not RDKIT_AVAILABLE: + pytest.skip("rdkit not installed") + assert classify_query(query) == expected + + def test_empty_query_raises(self): + with pytest.raises(ValueError): + classify_query(" ") + + @rdkit_only + def test_bare_letter_smiles_routes_to_name_not_smiles(self): + # "CCO" is valid SMILES *and* a plausible token; we deliberately leave + # it to the (future) provider chain rather than misroute a name. + assert classify_query("CCO") in ("formula", "name") + + +# ============================================================================ +# STRUCT.2 — URL encoding +# ============================================================================ + + +class TestUrlEncoding: + @patch("quantui.pubchem.requests.get") + def test_name_with_space_is_encoded(self, mock_get): + mock_get.return_value = Mock( + status_code=200, json=Mock(return_value={"IdentifierList": {"CID": [280]}}) + ) + search_molecule_by_name("carbon dioxide") + url = mock_get.call_args[0][0] + assert "carbon%20dioxide" in url + assert " " not in url + + @patch("quantui.pubchem.requests.get") + def test_inchikey_endpoint_encoded(self, mock_get): + mock_get.return_value = Mock( + status_code=200, json=Mock(return_value={"IdentifierList": {"CID": [962]}}) + ) + cid = search_cid_by_inchikey("XLYOFNOQVPJJNP-UHFFFAOYSA-N") + assert cid == 962 + assert "compound/inchikey/" in mock_get.call_args[0][0] + + +# ============================================================================ +# STRUCT.2 — throttle / 503 back-off +# ============================================================================ + + +class TestThrottleBackoff: + @patch("quantui.pubchem.time.sleep") # don't actually sleep + @patch("quantui.pubchem.requests.get") + def test_503_then_success_retries(self, mock_get, mock_sleep): + resp_503 = Mock(status_code=503) + resp_ok = Mock( + status_code=200, json=Mock(return_value={"IdentifierList": {"CID": [962]}}) + ) + mock_get.side_effect = [resp_503, resp_ok] + + cid = search_molecule_by_name("water") + assert cid == 962 + assert mock_get.call_count == 2 # one retry after the 503 + assert mock_sleep.called # backed off between attempts + + @patch("quantui.pubchem.time.sleep") + @patch("quantui.pubchem.requests.get") + def test_persistent_503_exhausts_retries_then_errors(self, mock_get, mock_sleep): + resp_503 = Mock(status_code=503) + resp_503.raise_for_status.side_effect = requests.HTTPError("503") + mock_get.return_value = resp_503 + + with pytest.raises(PubChemAPIError): + search_molecule_by_name("water") + # Tried the full retry budget, then gave up. + assert mock_get.call_count == config.PUBCHEM_MAX_RETRIES + # Backed off at least once between attempts (sleep is also used by the + # rate-limiter, so assert "happened" rather than an exact count). + assert mock_sleep.called + + @patch("quantui.pubchem.requests.get") + def test_non_503_not_retried(self, mock_get): + # A 500 must surface immediately, not trigger the 503 retry loop. + resp = Mock(status_code=500) + resp.raise_for_status.side_effect = requests.HTTPError("500") + mock_get.return_value = resp + with pytest.raises(PubChemAPIError): + search_molecule_by_name("water") + assert mock_get.call_count == 1 + + +# ============================================================================ +# STRUCT.1 — fetch_structure routing (local vs network) +# ============================================================================ + + +class TestFetchStructureRouting: + @rdkit_only + @patch("quantui.pubchem.requests.get") + def test_smiles_resolves_locally_without_network(self, mock_get): + mock_get.side_effect = AssertionError("network must not be touched for SMILES") + xyz, meta = fetch_structure("CC(=O)O") # acetic acid + assert meta["source"] == "rdkit-smiles" + assert meta["conformer_origin"] == "rdkit-embedded" + assert meta["formula"] == "C2H4O2" + assert xyz.strip().splitlines()[0].strip() == str(meta["num_atoms"]) + mock_get.assert_not_called() + + @rdkit_only + @patch("quantui.pubchem.requests.get") + def test_inchi_resolves_locally_without_network(self, mock_get): + mock_get.side_effect = AssertionError("network must not be touched for InChI") + xyz, meta = fetch_structure("InChI=1S/H2O/h1H2") # water + assert meta["source"] == "rdkit-inchi" + assert meta["num_heavy_atoms"] == 1 + mock_get.assert_not_called() + + @rdkit_only + @patch("quantui.pubchem.search_cid_by_inchikey") + @patch("quantui.pubchem.get_molecule_sdf") + def test_inchikey_routes_through_network( + self, mock_sdf, mock_inchikey, sample_sdf_water + ): + mock_inchikey.return_value = 962 + mock_sdf.return_value = sample_sdf_water + xyz, meta = fetch_structure("XLYOFNOQVPJJNP-UHFFFAOYSA-N") + mock_inchikey.assert_called_once() + assert meta["source"] == "pubchem" + assert meta["pubchem_cid"] == 962 + assert meta["conformer_origin"] in ("pubchem", "rdkit-embedded") + + @rdkit_only + @patch("quantui.pubchem.get_molecule_sdf") + @patch("quantui.pubchem.search_molecule_by_name") + def test_name_routes_through_pubchem(self, mock_search, mock_sdf, sample_sdf_water): + mock_search.return_value = 962 + mock_sdf.return_value = sample_sdf_water + _, meta = fetch_structure("water") + mock_search.assert_called_once_with("water") + assert meta["source"] == "pubchem" + assert meta["query_type"] == "name" + + +# ============================================================================ +# STRUCT.1/.2 — student-friendly wrapper +# ============================================================================ + + +class TestStudentFriendlyResolve: + @rdkit_only + def test_smiles_success_message(self): + # Use an unambiguous SMILES (structural chars) so it resolves locally + # with no network. Bare-letter tokens like "CCO" classify as + # formula/name by design and are left to the provider chain. + xyz, msg = student_friendly_resolve("CC(=O)O") + assert xyz is not None + assert "generated locally from SMILES" in msg + assert "C2H4O2" in msg + + @patch("quantui.pubchem.fetch_structure") + def test_not_found_message(self, mock_fetch): + mock_fetch.side_effect = MoleculeNotFoundError("nope") + xyz, msg = student_friendly_resolve("zzxqq") + assert xyz is None + assert "Could not resolve" in msg + + @patch("quantui.pubchem.fetch_structure") + def test_api_error_message(self, mock_fetch): + mock_fetch.side_effect = PubChemAPIError("down") + xyz, msg = student_friendly_resolve("water") + assert xyz is None + assert "Connection to PubChem failed" in msg + + +# ============================================================================ +# STRUCT.2 — sdf_to_xyz provenance flag (regression guard) +# ============================================================================ + + +class TestCoordsEmbeddedFlag: + @rdkit_only + def test_sdf_with_3d_coords_not_flagged_embedded(self, sample_sdf_water): + from quantui.pubchem import sdf_to_xyz + + get_molecule_sdf.cache_clear() + _, meta = sdf_to_xyz(sample_sdf_water) + assert "coords_embedded" in meta + # The fixture SDF already carries 3D coords, so RDKit should not embed. + assert meta["coords_embedded"] is False From c01c5cb991146170f887b50285bbd4aa8adaea0b Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Sun, 7 Jun 2026 13:17:58 -0400 Subject: [PATCH 02/16] Add CACTUS resolver and provider chain MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Introduce an NCI CACTUS resolver (quantui.cactus) to fetch SDF/3D structures as a chained fallback after PubChem, with robust error mapping to existing PubChem exception types. Add a unified provider chain (quantui.structure_providers) that normalizes results into a ResolvedStructure dataclass and implements resolution order: local RDKit → bundled library exact → PubChem → CACTUS → bundled-library fuzzy offline fallback. Expose resolve_structure, ResolvedStructure and fetch_from_cactus via package __init__, wire student_friendly_resolve usage in app, and add CACTUS_TIMEOUT_S config. Add comprehensive tests for CACTUS and the provider chain (tests/test_struct_providers.py). --- quantui/__init__.py | 5 + quantui/app.py | 2 +- quantui/cactus.py | 85 ++++++++++++ quantui/config.py | 4 + quantui/structure_providers.py | 236 +++++++++++++++++++++++++++++++++ tests/test_struct_providers.py | 178 +++++++++++++++++++++++++ 6 files changed, 509 insertions(+), 1 deletion(-) create mode 100644 quantui/cactus.py create mode 100644 quantui/structure_providers.py create mode 100644 tests/test_struct_providers.py diff --git a/quantui/__init__.py b/quantui/__init__.py index 38aaf95..f91871e 100644 --- a/quantui/__init__.py +++ b/quantui/__init__.py @@ -123,6 +123,7 @@ # PubChem integration (optional — requires internet) try: + from .cactus import fetch_from_cactus from .pubchem import ( MoleculeNotFoundError, PubChemError, @@ -142,6 +143,7 @@ student_friendly_smiles_to_xyz, validate_smiles, ) + from .structure_providers import ResolvedStructure, resolve_structure PUBCHEM_AVAILABLE = True except ImportError: @@ -247,6 +249,9 @@ "classify_query", "student_friendly_fetch", "student_friendly_resolve", + "resolve_structure", + "ResolvedStructure", + "fetch_from_cactus", "inchi_to_xyz", "search_cid_by_inchikey", "get_common_molecules", diff --git a/quantui/app.py b/quantui/app.py index 08995f9..4a15f09 100644 --- a/quantui/app.py +++ b/quantui/app.py @@ -472,7 +472,7 @@ from quantui.pubchem import ( RDKIT_AVAILABLE as _PUBCHEM_RDKIT_AVAILABLE, ) - from quantui.pubchem import ( + from quantui.structure_providers import ( student_friendly_resolve as _student_friendly_resolve, ) diff --git a/quantui/cactus.py b/quantui/cactus.py new file mode 100644 index 0000000..dd96caf --- /dev/null +++ b/quantui/cactus.py @@ -0,0 +1,85 @@ +"""NCI CACTUS Chemical Identifier Resolver (M-STRUCT STRUCT.3). + +A chained fallback after PubChem. CACTUS resolves a wide range of identifiers +(common name, IUPAC name, CAS number, InChI, SMILES, formula) to a 3D SDF with +no API key. It often answers queries PubChem misses — CAS numbers in +particular. + +Best-effort by design: every failure mode (miss, network error, malformed +response) raises one of the shared PubChem exception types so the provider +chain in :mod:`quantui.structure_providers` can treat all resolvers uniformly. +""" + +import logging +from typing import Any, Dict, Tuple +from urllib.parse import quote + +import requests + +from . import config +from .pubchem import MoleculeNotFoundError, PubChemAPIError, sdf_to_xyz + +logger = logging.getLogger(__name__) + +# CACTUS resolver base. The ``/file?format=sdf&get3d=true`` form returns a 3D +# SDF; the bare ``/sdf`` form returns whatever (often 2D) CACTUS has. +CACTUS_BASE_URL = "https://cactus.nci.nih.gov/chemical/structure" + + +def _looks_like_sdf(text: str) -> bool: + """CACTUS returns an HTML error page (HTTP 200) for unknown identifiers. + + A real SDF molfile always carries the ``V2000``/``V3000`` counts-line tag + and the ``M END`` terminator, so key off those rather than the status code. + """ + return "M END" in text and ("V2000" in text or "V3000" in text) + + +def resolve_to_sdf(identifier: str, conformer_3d: bool = True) -> str: + """Resolve an identifier to SDF text via CACTUS. + + Tries the 3D endpoint first, then falls back to the plain ``/sdf`` form + (whose coordinates RDKit will embed downstream if they are 2D). + + Raises: + MoleculeNotFoundError: CACTUS has no structure for the identifier. + PubChemAPIError: network/transport failure reaching CACTUS. + """ + enc = quote(identifier, safe="") + urls = [] + if conformer_3d: + urls.append(f"{CACTUS_BASE_URL}/{enc}/file?format=sdf&get3d=true") + urls.append(f"{CACTUS_BASE_URL}/{enc}/sdf") + + last_status = None + try: + for url in urls: + logger.debug(f"CACTUS resolving: {url}") + response = requests.get(url, timeout=config.CACTUS_TIMEOUT_S) + last_status = response.status_code + if response.status_code == 200 and _looks_like_sdf(response.text): + return str(response.text) + except requests.RequestException as e: + logger.error(f"CACTUS request failed: {e}") + raise PubChemAPIError(f"Failed to connect to CACTUS: {e}") + + raise MoleculeNotFoundError( + f"CACTUS could not resolve '{identifier}' (last status: {last_status})" + ) + + +def fetch_from_cactus( + identifier: str, conformer_3d: bool = True +) -> Tuple[str, Dict[str, Any]]: + """Resolve an identifier to ``(xyz_string, metadata)`` via CACTUS. + + Metadata carries ``source="cactus"`` and a ``conformer_origin`` describing + whether RDKit had to embed the coordinates. + """ + sdf_content = resolve_to_sdf(identifier, conformer_3d=conformer_3d) + xyz, metadata = sdf_to_xyz(sdf_content) + metadata["source"] = "cactus" + metadata["conformer_origin"] = ( + "rdkit-embedded" if metadata.get("coords_embedded") else "cactus" + ) + return xyz, metadata diff --git a/quantui/config.py b/quantui/config.py index e0ca247..f891431 100644 --- a/quantui/config.py +++ b/quantui/config.py @@ -241,6 +241,10 @@ # so a classroom of simultaneous users doesn't trip the server-side throttle. PUBCHEM_MIN_REQUEST_INTERVAL_S: float = 0.25 +# NCI CACTUS Chemical Identifier Resolver — chained fallback after PubChem +# (resolves name / CAS / InChI / SMILES → 3D SDF; no API key). +CACTUS_TIMEOUT_S: float = 15.0 + # Molecule presets — 20+ curated educational molecules MOLECULE_LIBRARY: Dict[str, Dict[str, Any]] = { # ========== SIMPLE DIATOMIC MOLECULES ========== diff --git a/quantui/structure_providers.py b/quantui/structure_providers.py new file mode 100644 index 0000000..9079d97 --- /dev/null +++ b/quantui/structure_providers.py @@ -0,0 +1,236 @@ +"""Unified structure-resolver chain with offline fallback (M-STRUCT STRUCT.4). + +Resolution order (first hit wins): + +1. **Local RDKit** for SMILES / InChI input — offline, no network. +2. **Bundled library** exact hit (formula key) — offline, instant. +3. **PubChem** (hardened client, STRUCT.2). +4. **NCI CACTUS** resolver (STRUCT.3). +5. **Bundled-library fuzzy fallback** (name/description substring) — the + last-resort offline answer so the search box is never a dead end, even with + no network. + +Every resolver returns a normalized :class:`ResolvedStructure` so callers +(and the future disambiguation UI, STRUCT.5) treat all sources uniformly. The +``source`` field records which resolver answered, so the UI can be honest about +provenance. + +The bundled-library steps currently search ``config.MOLECULE_LIBRARY`` (the 20 +presets). When STRUCT.6/.7/.8 move the library into an indexed package-data +store, only :func:`_library_exact` / :func:`_library_fuzzy` change — the chain +is unaffected. +""" + +import logging +from dataclasses import dataclass, field +from typing import Any, Dict, List, Optional, Tuple + +from . import cactus, config +from .pubchem import ( + MoleculeNotFoundError, + PubChemAPIError, + classify_query, + fetch_structure, +) + +logger = logging.getLogger(__name__) + +# Elements that count as "heavy" exclusions when tallying heavy atoms. +_HYDROGEN = "H" + + +@dataclass +class ResolvedStructure: + """A structure resolved by the provider chain, normalized across sources.""" + + xyz: str + source: str # "rdkit-smiles" | "rdkit-inchi" | "library" | "pubchem" | "cactus" | "library-offline-fallback" + formula: str = "?" + num_atoms: int = 0 + num_heavy_atoms: int = 0 + charge: int = 0 + multiplicity: int = 1 + molecular_weight: Optional[float] = None + conformer_origin: str = "" + identifiers: Dict[str, Any] = field(default_factory=dict) + + @property + def is_offline(self) -> bool: + return self.source in ( + "library", + "library-offline-fallback", + ) or self.source.startswith("rdkit-") + + +def _from_metadata(xyz: str, meta: Dict[str, Any], *, source: str) -> ResolvedStructure: + """Build a ResolvedStructure from a ``(xyz, metadata)`` resolver result.""" + identifiers = { + k: meta[k] + for k in ("pubchem_cid", "smiles", "canonical_smiles", "inchi", "query_type") + if k in meta + } + return ResolvedStructure( + xyz=xyz, + source=source, + formula=meta.get("formula", "?"), + num_atoms=int(meta.get("num_atoms", 0) or 0), + num_heavy_atoms=int(meta.get("num_heavy_atoms", 0) or 0), + charge=int(meta.get("charge", 0) or 0), + molecular_weight=meta.get("molecular_weight"), + conformer_origin=meta.get("conformer_origin", meta.get("source", "")), + identifiers=identifiers, + ) + + +def _entry_to_xyz(name: str, entry: Dict[str, Any]) -> str: + """Format a ``MOLECULE_LIBRARY`` entry as an XYZ string.""" + atoms = entry["atoms"] + coords = entry["coordinates"] + desc = entry.get("description", "") + lines = [str(len(atoms)), f"{name}: {desc}".strip()] + for sym, (x, y, z) in zip(atoms, coords): + lines.append(f"{sym:3s} {float(x):12.6f} {float(y):12.6f} {float(z):12.6f}") + return "\n".join(lines) + + +def _entry_to_resolved( + name: str, entry: Dict[str, Any], *, source: str +) -> ResolvedStructure: + atoms = entry["atoms"] + return ResolvedStructure( + xyz=_entry_to_xyz(name, entry), + source=source, + formula=name, + num_atoms=len(atoms), + num_heavy_atoms=sum(1 for a in atoms if a != _HYDROGEN), + charge=int(entry.get("charge", 0)), + multiplicity=int(entry.get("multiplicity", 1)), + conformer_origin="library", + identifiers={"library_key": name}, + ) + + +def _library_exact(query: str) -> Optional[ResolvedStructure]: + """Exact (case-insensitive) match on a bundled-library formula key.""" + q = query.strip().lower() + for key, entry in config.MOLECULE_LIBRARY.items(): + if q == key.lower(): + logger.info(f"Resolved '{query}' from bundled library (exact key '{key}')") + return _entry_to_resolved(key, entry, source="library") + return None + + +def _library_fuzzy(query: str) -> Optional[ResolvedStructure]: + """Loose offline fallback: substring match over keys + descriptions. + + Used only when the network resolvers are unreachable or all miss, so a + looser match is acceptable (and clearly labelled as a fallback to the user). + """ + q = query.strip().lower() + if not q: + return None + for key, entry in config.MOLECULE_LIBRARY.items(): + haystack = f"{key} {entry.get('description', '')}".lower() + if q == key.lower() or q in haystack: + logger.info(f"Offline fallback matched '{query}' to library entry '{key}'") + return _entry_to_resolved(key, entry, source="library-offline-fallback") + return None + + +def resolve_structure( + query: str, + *, + conformer_3d: bool = True, + allow_network: bool = True, +) -> ResolvedStructure: + """Resolve ``query`` through the provider chain. Raises on total failure. + + Raises: + MoleculeNotFoundError: nothing in the chain could resolve the query. + ValueError: empty query, or RDKit failed to parse a SMILES/InChI. + """ + qtype = classify_query(query) + logger.info(f"Resolving '{query}' (type={qtype}, network={allow_network})") + + # 1. Local RDKit for SMILES / InChI — no network, no library needed. + if qtype in ("smiles", "inchi"): + xyz, meta = fetch_structure(query, conformer_3d=conformer_3d) + return _from_metadata(xyz, meta, source=meta["source"]) + + # 2. Exact bundled-library hit (offline, instant) — e.g. "H2O", "C6H6". + hit = _library_exact(query) + if hit is not None: + return hit + + # 3/4. Network resolvers: PubChem, then CACTUS. A genuine miss + # (MoleculeNotFoundError) or a transport error (PubChemAPIError) both fall + # through to the next resolver, then to the offline fallback. + errors: List[Tuple[str, Exception]] = [] + if allow_network: + try: + xyz, meta = fetch_structure(query, conformer_3d=conformer_3d) + return _from_metadata(xyz, meta, source="pubchem") + except (MoleculeNotFoundError, PubChemAPIError) as exc: + logger.info(f"PubChem did not resolve '{query}': {exc}") + errors.append(("pubchem", exc)) + + try: + xyz, meta = cactus.fetch_from_cactus(query, conformer_3d=conformer_3d) + return _from_metadata(xyz, meta, source="cactus") + except (MoleculeNotFoundError, PubChemAPIError) as exc: + logger.info(f"CACTUS did not resolve '{query}': {exc}") + errors.append(("cactus", exc)) + + # 5. Offline fuzzy fallback against the bundled library. + hit = _library_fuzzy(query) + if hit is not None: + return hit + + tried = ", ".join(name for name, _ in errors) or "offline only" + raise MoleculeNotFoundError( + f"Could not resolve '{query}' (tried: {tried}, bundled library)" + ) + + +def student_friendly_resolve(query: str) -> Tuple[Optional[str], str]: + """Chain-backed, student-friendly resolve. Drop-in for the UI handler. + + Returns ``(xyz_string_or_None, message)``. + """ + try: + result = resolve_structure(query, conformer_3d=True) + except (MoleculeNotFoundError, ValueError) as exc: + return None, ( + f"❌ Could not resolve '{query}'.\n" + f" {exc}\n" + f" Try a different name, a SMILES (e.g. CC(=O)O), a CAS number, " + f"or check spelling.\n" + f" Search manually at: https://pubchem.ncbi.nlm.nih.gov/" + ) + except Exception as exc: # pragma: no cover - unexpected + logger.error(f"Unexpected error resolving '{query}': {exc}", exc_info=True) + return None, f"❌ Error resolving '{query}': {exc}" + + source_label = { + "rdkit-smiles": "generated locally from SMILES", + "rdkit-inchi": "generated locally from InChI", + "library": "the bundled library (offline)", + "library-offline-fallback": "the bundled library (offline fallback — " + "network resolvers were unavailable)", + "pubchem": "PubChem", + "cactus": "NCI CACTUS", + }.get(result.source, result.source) + + embedded = ( + " (2D structure embedded by RDKit)" + if result.conformer_origin == "rdkit-embedded" + else "" + ) + mw = f"{result.molecular_weight:.2f} g/mol" if result.molecular_weight else "—" + message = ( + f"✓ Resolved '{query}' via {source_label}.\n" + f" Formula: {result.formula}\n" + f" Atoms: {result.num_atoms} ({result.num_heavy_atoms} heavy)\n" + f" Molecular weight: {mw}{embedded}" + ) + return result.xyz, message diff --git a/tests/test_struct_providers.py b/tests/test_struct_providers.py new file mode 100644 index 0000000..dc3b44c --- /dev/null +++ b/tests/test_struct_providers.py @@ -0,0 +1,178 @@ +"""Tests for M-STRUCT STRUCT.3 (NCI CACTUS) + STRUCT.4 (provider chain). + +Platform-independent: network mocked, RDKit-only paths gated, no PySCF. +""" + +from unittest.mock import Mock, patch + +import pytest +import requests + +from quantui import cactus +from quantui.pubchem import RDKIT_AVAILABLE, MoleculeNotFoundError, PubChemAPIError +from quantui.structure_providers import ( + ResolvedStructure, + resolve_structure, + student_friendly_resolve, +) + +rdkit_only = pytest.mark.skipif(not RDKIT_AVAILABLE, reason="rdkit not installed") + +_WATER_META = { + "formula": "H2O", + "num_atoms": 3, + "num_heavy_atoms": 1, + "charge": 0, + "molecular_weight": 18.02, + "conformer_origin": "pubchem", + "source": "pubchem", +} +_WATER_XYZ = "3\nwater\nO 0 0 0\nH 1 0 0\nH 0 1 0" + + +# ============================================================================ +# STRUCT.3 — CACTUS resolver +# ============================================================================ + + +class TestCactus: + def test_looks_like_sdf(self, sample_sdf_water): + assert cactus._looks_like_sdf(sample_sdf_water) is True + assert cactus._looks_like_sdf("Page not found") is False + + @patch("quantui.cactus.requests.get") + def test_resolve_to_sdf_success(self, mock_get, sample_sdf_water): + mock_get.return_value = Mock(status_code=200, text=sample_sdf_water) + sdf = cactus.resolve_to_sdf("aspirin") + assert "M END" in sdf + assert "compound" not in mock_get.call_args[0][0] # uses CACTUS, not pubchem + + @patch("quantui.cactus.requests.get") + def test_resolve_to_sdf_tries_3d_then_2d(self, mock_get, sample_sdf_water): + # 3D endpoint returns an HTML error page; 2D endpoint returns real SDF. + mock_get.side_effect = [ + Mock(status_code=200, text="error"), + Mock(status_code=200, text=sample_sdf_water), + ] + sdf = cactus.resolve_to_sdf("weirdmol", conformer_3d=True) + assert "M END" in sdf + assert mock_get.call_count == 2 + + @patch("quantui.cactus.requests.get") + def test_resolve_to_sdf_miss_raises_not_found(self, mock_get): + mock_get.return_value = Mock(status_code=404, text="not found") + with pytest.raises(MoleculeNotFoundError): + cactus.resolve_to_sdf("zzznotreal") + + @patch("quantui.cactus.requests.get") + def test_resolve_to_sdf_network_error_raises_api_error(self, mock_get): + mock_get.side_effect = requests.ConnectionError("down") + with pytest.raises(PubChemAPIError): + cactus.resolve_to_sdf("aspirin") + + @rdkit_only + @patch("quantui.cactus.requests.get") + def test_fetch_from_cactus_returns_xyz(self, mock_get, sample_sdf_water): + mock_get.return_value = Mock(status_code=200, text=sample_sdf_water) + xyz, meta = cactus.fetch_from_cactus("water") + assert meta["source"] == "cactus" + assert meta["num_atoms"] == 3 + + +# ============================================================================ +# STRUCT.4 — provider chain ordering +# ============================================================================ + + +class TestProviderChain: + @rdkit_only + @patch("quantui.pubchem.requests.get") + def test_smiles_resolves_locally_no_network(self, mock_get): + mock_get.side_effect = AssertionError("network must not be touched") + result = resolve_structure("CC(=O)O") + assert isinstance(result, ResolvedStructure) + assert result.source == "rdkit-smiles" + assert result.is_offline is True + mock_get.assert_not_called() + + @patch("quantui.structure_providers.fetch_structure") + def test_exact_library_hit_short_circuits_network(self, mock_fetch): + mock_fetch.side_effect = AssertionError("library hit must not hit network") + result = resolve_structure("H2O") # exact MOLECULE_LIBRARY key + assert result.source == "library" + assert result.formula == "H2O" + assert result.num_atoms == 3 + mock_fetch.assert_not_called() + + @patch("quantui.structure_providers.fetch_structure") + def test_name_resolves_via_pubchem(self, mock_fetch): + mock_fetch.return_value = (_WATER_XYZ, dict(_WATER_META)) + result = resolve_structure("dihydrogen monoxide") + assert result.source == "pubchem" + mock_fetch.assert_called_once() + + @patch("quantui.structure_providers.cactus.fetch_from_cactus") + @patch("quantui.structure_providers.fetch_structure") + def test_pubchem_miss_falls_through_to_cactus(self, mock_fetch, mock_cactus): + mock_fetch.side_effect = MoleculeNotFoundError("pubchem miss") + mock_cactus.return_value = (_WATER_XYZ, {**_WATER_META, "source": "cactus"}) + result = resolve_structure("64-19-7") # a CAS number + assert result.source == "cactus" + mock_fetch.assert_called_once() + mock_cactus.assert_called_once() + + @patch("quantui.structure_providers.cactus.fetch_from_cactus") + @patch("quantui.structure_providers.fetch_structure") + def test_network_down_uses_offline_fuzzy_fallback(self, mock_fetch, mock_cactus): + mock_fetch.side_effect = PubChemAPIError("network down") + mock_cactus.side_effect = PubChemAPIError("network down") + # "water" isn't an exact key but appears in the H2O entry description. + result = resolve_structure("water") + assert result.source == "library-offline-fallback" + assert result.formula == "H2O" + + @patch("quantui.structure_providers.cactus.fetch_from_cactus") + @patch("quantui.structure_providers.fetch_structure") + def test_total_miss_raises(self, mock_fetch, mock_cactus): + mock_fetch.side_effect = MoleculeNotFoundError("miss") + mock_cactus.side_effect = MoleculeNotFoundError("miss") + with pytest.raises(MoleculeNotFoundError): + resolve_structure("zzqxnotarealmolecule") + + @patch("quantui.structure_providers.fetch_structure") + def test_allow_network_false_skips_resolvers(self, mock_fetch): + mock_fetch.side_effect = AssertionError("network disabled") + result = resolve_structure("water", allow_network=False) + assert result.source == "library-offline-fallback" + mock_fetch.assert_not_called() + + +# ============================================================================ +# STRUCT.4 — friendly wrapper messaging +# ============================================================================ + + +class TestFriendlyResolve: + def test_library_message_mentions_offline(self): + xyz, msg = student_friendly_resolve("H2O") + assert xyz is not None + assert "bundled library (offline)" in msg + assert "H2O" in msg + + @patch("quantui.structure_providers.cactus.fetch_from_cactus") + @patch("quantui.structure_providers.fetch_structure") + def test_offline_fallback_message(self, mock_fetch, mock_cactus): + mock_fetch.side_effect = PubChemAPIError("down") + mock_cactus.side_effect = PubChemAPIError("down") + xyz, msg = student_friendly_resolve("water") + assert xyz is not None + assert "offline fallback" in msg + + @patch("quantui.structure_providers.cactus.fetch_from_cactus") + @patch("quantui.structure_providers.fetch_structure") + def test_not_found_message(self, mock_fetch, mock_cactus): + mock_fetch.side_effect = MoleculeNotFoundError("miss") + mock_cactus.side_effect = MoleculeNotFoundError("miss") + xyz, msg = student_friendly_resolve("zzqxnotreal") + assert xyz is None + assert "Could not resolve" in msg From d635822460f79065f5726dfa58cba3bc89fbf875 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Sun, 7 Jun 2026 16:23:45 -0400 Subject: [PATCH 03/16] Add bundled molecule library and loader Move the hard-coded MOLECULE_LIBRARY into a packaged, indexed library and provide a lazy loader/back-compat shim. - Add quantui/data/manifests/presets.json and quantui/data/library/library.sqlite as packaged data. - Implement quantui/molecule_library.py: compact coord encoder/decoder, deterministic SQLite store builder, read-only query API (get/search/categories/count), JSON-manifest fallback, and get_preset_dict() that returns the legacy MOLECULE_LIBRARY shape while excluding bulk categories. - Replace the inline MOLECULE_LIBRARY in quantui/config.py with a PEP 562 __getattr__ shim that lazily loads presets via get_preset_dict() to preserve existing consumers. - Add scripts/build_library.py to rebuild the SQLite store from manifests (with a 10 MB budget check) and tests/test_molecule_library.py covering codec, store, queries, back-compat, and size governance. - Include package-data in pyproject.toml so the manifest and sqlite store are bundled in distributions. This keeps imports fast, preserves backwards compatibility, supports offline use, and provides a compact, indexed store that can scale to larger manifest sets. --- pyproject.toml | 6 + quantui/config.py | 256 +-------- quantui/data/library/library.sqlite | Bin 0 -> 28672 bytes quantui/data/manifests/presets.json | 816 ++++++++++++++++++++++++++++ quantui/molecule_library.py | 408 ++++++++++++++ scripts/build_library.py | 32 ++ tests/test_molecule_library.py | 135 +++++ 7 files changed, 1415 insertions(+), 238 deletions(-) create mode 100644 quantui/data/library/library.sqlite create mode 100644 quantui/data/manifests/presets.json create mode 100644 quantui/molecule_library.py create mode 100644 scripts/build_library.py create mode 100644 tests/test_molecule_library.py diff --git a/pyproject.toml b/pyproject.toml index 1042865..52ce47b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,6 +45,12 @@ quantui = "quantui.cli:main" [tool.setuptools] packages = ["quantui"] +[tool.setuptools.package-data] +# Bundled molecule library (M-STRUCT): the indexed SQLite store + the +# human-readable JSON manifests it is built from. Both ship in the wheel so +# offline structure lookup works on a fresh install. +quantui = ["data/library/*.sqlite", "data/manifests/*.json"] + [project.optional-dependencies] # PySCF requires Linux/macOS/WSL — not available on Windows natively. # Use the Apptainer container (apptainer/quantui.def) for Windows. diff --git a/quantui/config.py b/quantui/config.py index f891431..eb77082 100644 --- a/quantui/config.py +++ b/quantui/config.py @@ -245,244 +245,24 @@ # (resolves name / CAS / InChI / SMILES → 3D SDF; no API key). CACTUS_TIMEOUT_S: float = 15.0 -# Molecule presets — 20+ curated educational molecules -MOLECULE_LIBRARY: Dict[str, Dict[str, Any]] = { - # ========== SIMPLE DIATOMIC MOLECULES ========== - "H2": { - "atoms": ["H", "H"], - "coordinates": [[0.0, 0.0, 0.0], [0.0, 0.0, 0.74]], - "charge": 0, - "multiplicity": 1, - "description": "Hydrogen molecule (simplest molecule)", - }, - "O2": { - "atoms": ["O", "O"], - "coordinates": [[0.0, 0.0, 0.0], [0.0, 0.0, 1.21]], - "charge": 0, - "multiplicity": 3, # Triplet ground state - "description": "Oxygen molecule (triplet ground state)", - }, - "N2": { - "atoms": ["N", "N"], - "coordinates": [[0.0, 0.0, 0.0], [0.0, 0.0, 1.10]], - "charge": 0, - "multiplicity": 1, - "description": "Nitrogen molecule (triple bond)", - }, - "CO": { - "atoms": ["C", "O"], - "coordinates": [[0.0, 0.0, 0.0], [0.0, 0.0, 1.13]], - "charge": 0, - "multiplicity": 1, - "description": "Carbon monoxide", - }, - "HF": { - "atoms": ["H", "F"], - "coordinates": [[0.0, 0.0, 0.0], [0.0, 0.0, 0.92]], - "charge": 0, - "multiplicity": 1, - "description": "Hydrogen fluoride (polar bond)", - }, - "HCl": { - "atoms": ["H", "Cl"], - "coordinates": [[0.0, 0.0, 0.0], [0.0, 0.0, 1.27]], - "charge": 0, - "multiplicity": 1, - "description": "Hydrogen chloride", - }, - # ========== SIMPLE TRIATOMIC MOLECULES ========== - "H2O": { - "atoms": ["O", "H", "H"], - "coordinates": [ - [0.0, 0.0, 0.0], - [0.0, 0.757, 0.587], - [0.0, -0.757, 0.587], - ], - "charge": 0, - "multiplicity": 1, - "description": "Water molecule (bent geometry)", - }, - "CO2": { - "atoms": ["C", "O", "O"], - "coordinates": [ - [0.0, 0.0, 0.0], - [0.0, 0.0, 1.16], - [0.0, 0.0, -1.16], - ], - "charge": 0, - "multiplicity": 1, - "description": "Carbon dioxide (linear)", - }, - "O3": { - "atoms": ["O", "O", "O"], - "coordinates": [ - [0.0, 0.0, 0.0], - [1.07, 0.65, 0.0], - [-1.07, 0.65, 0.0], - ], - "charge": 0, - "multiplicity": 1, - "description": "Ozone (bent, resonance structure)", - }, - "H2O2": { - "atoms": ["H", "O", "O", "H"], - "coordinates": [ - [0.74, -0.54, 0.48], - [0.0, 0.0, 0.0], - [0.0, 0.0, 1.45], - [-0.74, -0.54, 1.93], - ], - "charge": 0, - "multiplicity": 1, - "description": "Hydrogen peroxide (non-planar)", - }, - # ========== SIMPLE ORGANIC MOLECULES ========== - "CH4": { - "atoms": ["C", "H", "H", "H", "H"], - "coordinates": [ - [0.0, 0.0, 0.0], - [0.63, 0.63, 0.63], - [-0.63, -0.63, 0.63], - [-0.63, 0.63, -0.63], - [0.63, -0.63, -0.63], - ], - "charge": 0, - "multiplicity": 1, - "description": "Methane (tetrahedral)", - }, - "NH3": { - "atoms": ["N", "H", "H", "H"], - "coordinates": [ - [0.0, 0.0, 0.0], - [0.0, 0.94, 0.33], - [0.81, -0.47, 0.33], - [-0.81, -0.47, 0.33], - ], - "charge": 0, - "multiplicity": 1, - "description": "Ammonia (pyramidal)", - }, - "C2H6": { - "atoms": ["C", "C", "H", "H", "H", "H", "H", "H"], - "coordinates": [ - [0.0, 0.0, 0.0], - [1.54, 0.0, 0.0], - [-0.51, 0.89, 0.0], - [-0.51, -0.44, 0.89], - [-0.51, -0.44, -0.89], - [2.05, 0.89, 0.0], - [2.05, -0.44, 0.89], - [2.05, -0.44, -0.89], - ], - "charge": 0, - "multiplicity": 1, - "description": "Ethane (single bond)", - }, - "C2H4": { - "atoms": ["C", "C", "H", "H", "H", "H"], - "coordinates": [ - [0.0, 0.0, 0.0], - [1.34, 0.0, 0.0], - [-0.51, 0.93, 0.0], - [-0.51, -0.93, 0.0], - [1.85, 0.93, 0.0], - [1.85, -0.93, 0.0], - ], - "charge": 0, - "multiplicity": 1, - "description": "Ethylene (double bond, planar)", - }, - "C2H2": { - "atoms": ["C", "C", "H", "H"], - "coordinates": [ - [0.0, 0.0, 0.0], - [1.20, 0.0, 0.0], - [-1.06, 0.0, 0.0], - [2.26, 0.0, 0.0], - ], - "charge": 0, - "multiplicity": 1, - "description": "Acetylene (triple bond, linear)", - }, - "CH3OH": { - "atoms": ["C", "O", "H", "H", "H", "H"], - "coordinates": [ - [0.66, -0.02, 0.0], - [-0.75, 0.09, 0.0], - [1.03, -0.54, 0.89], - [1.03, -0.54, -0.89], - [1.05, 0.99, 0.0], - [-1.07, -0.83, 0.0], - ], - "charge": 0, - "multiplicity": 1, - "description": "Methanol (alcohol)", - }, - "CH2O": { - "atoms": ["C", "O", "H", "H"], - "coordinates": [ - [0.0, 0.0, 0.0], - [0.0, 0.0, 1.21], - [0.94, 0.0, -0.59], - [-0.94, 0.0, -0.59], - ], - "charge": 0, - "multiplicity": 1, - "description": "Formaldehyde (carbonyl group)", - }, - "CH3CHO": { - "atoms": ["C", "C", "O", "H", "H", "H", "H"], - "coordinates": [ - [0.0, 0.0, 0.0], - [1.51, 0.0, 0.0], - [2.17, 1.03, 0.0], - [-0.36, -0.52, 0.89], - [-0.36, -0.52, -0.89], - [-0.39, 1.02, 0.0], - [1.89, -1.02, 0.0], - ], - "charge": 0, - "multiplicity": 1, - "description": "Acetaldehyde (aldehyde group)", - }, - "CH3COOH": { - "atoms": ["C", "C", "O", "O", "H", "H", "H", "H"], - "coordinates": [ - [0.0, 0.0, 0.0], - [1.51, 0.0, 0.0], - [2.09, 1.09, 0.0], - [2.16, -1.18, 0.0], - [-0.36, -0.52, 0.89], - [-0.36, -0.52, -0.89], - [-0.39, 1.02, 0.0], - [3.11, -1.09, 0.0], - ], - "charge": 0, - "multiplicity": 1, - "description": "Acetic acid (carboxylic acid)", - }, - # ========== AROMATIC MOLECULES ========== - "C6H6": { - "atoms": ["C", "C", "C", "C", "C", "C", "H", "H", "H", "H", "H", "H"], - "coordinates": [ - [0.0, 1.40, 0.0], - [1.21, 0.70, 0.0], - [1.21, -0.70, 0.0], - [0.0, -1.40, 0.0], - [-1.21, -0.70, 0.0], - [-1.21, 0.70, 0.0], - [0.0, 2.48, 0.0], - [2.15, 1.24, 0.0], - [2.15, -1.24, 0.0], - [0.0, -2.48, 0.0], - [-2.15, -1.24, 0.0], - [-2.15, 1.24, 0.0], - ], - "charge": 0, - "multiplicity": 1, - "description": "Benzene (aromatic, hexagonal)", - }, -} +# Molecule presets — bundled library (STRUCT.6). +# The former inline literal now lives in the indexed package-data store +# (quantui/data/library/library.sqlite, seeded from +# quantui/data/manifests/presets.json). ``config.MOLECULE_LIBRARY`` is a lazy +# back-compat shim resolved via module ``__getattr__`` (PEP 562): on first +# access it loads the curated/preset entries from the store in the original +# {formula: {atoms, coordinates, charge, multiplicity, description}} shape, so +# every existing consumer keeps working unchanged. +MOLECULE_LIBRARY: Dict[str, Dict[str, Any]] # populated lazily by __getattr__ + + +def __getattr__(name: str) -> Any: + if name == "MOLECULE_LIBRARY": + from quantui.molecule_library import get_preset_dict + + return get_preset_dict() + raise AttributeError(f"module {__name__!r} has no attribute {name!r}") + # Valid atomic symbols (periodic table subset commonly used) VALID_ATOMS = [ diff --git a/quantui/data/library/library.sqlite b/quantui/data/library/library.sqlite new file mode 100644 index 0000000000000000000000000000000000000000..33207a68ea8c997d58b8a1697a35d94732bdd259 GIT binary patch literal 28672 zcmeI4Yit}>6@c&T%)Y#j>sMqMV|5UM*uibdx&*1@2hL`lG1+>G>naYdYK?a%-f3oM z%no z@y7h95K^i$yK~Rn$DDKSch8;Od!6hfpD!CtUA|yDb*(8+vwkKB?6b1W7)!vJgflqe za3KX5kV4n>VV4PZ-#2dO_>Y5g-CYfCvx)B0vO) zz#RyviNwgq#)XT9Rn^yx>iV)_RcgjXyb`F>)_b=Fkr#H`*VeXdtL^t?zjak_R2*ZiY1o$B zrKDopPBqYds;r(0!SqeuA4`lB#|7qwOyi3ttm&7vR?~L#%fX;89}liXm}V)QYB@NE zlTR`JEq*5dkNgYybNO8E#oQy=x3ibCW0@P7Lf`eine@x)$5OARrlBDnM1Tko0U|&I zh`|4fz~-6G6q4 zT+`RJRol|c$s#zl4x9Bwc0>Ac%#)`(C>eYDHp(Y8cZYdfo&WmKe;=lM)UhknRf z1-@fWR5WMBUT?#9FSo$;9Eld$pYe|kOl8MXr@*4h)>2j1qi6Qs>uiV$LwR{uVHNhikd~|el-?J~HM~d2=M!XV}`(9~gRj;+H2sOA`b?nyK9lY8|C0tI2 zd9#v~b{VS=a2V2kXUavT0Iqmv#EqEbxiO1>g$ay%bgZ^1N8M173=FNpu0hwYcNDe= z#;$i-{d{C(Bs6#2gkHNt;wMpy3D4p~db6fkwuzmt*fkrY=Su9Yei%lx&SpMznWM|yd-Tr4Ps;EdYzdx;^?Hr?=T!q;3=msf17IwhNirE5+X z?w0^EI`DfKT9mK5-&ntrj~JXY!Po=A88zs4vec~k_NsOZ)X*v4Z~XX?RWK4!oReE zo!H)nZ&!gU%qx2cJeKmyQ+_$f%e%{2J~T9RH0?hzrpxonwD*p<5J0cjZOhQ)iM6() z)r~4VC+5*A960~4iJub`c1%3Bhw_bGltw0E;M0#6fwTLL7>IXA67;dDHyy2}R~`RR z!|(mrd9n}3^q$~}GFOIK0%7Ex5G1(bGb+I}QQB3cX?tf~8-h>9i`%mZMMZ8@Nx}g6F8pUfV&rltONyfzO;Qss-=e zW21-+#7xJoZ*I{tl zq31aA@5Ii+urQYCfJ~tN@j(CmQ%ceF-qm0TJoVuSRBEQ}zzCoQJc=f!?@9}CgdA#` zn^I=+b(oq9X3JFr;c1(i<4(}YK<6x~WY37FC0AzgT2um>kN!_5*{muf1W^;rZHVh6Y2Z z9^CC%AK)40ON@V=U*T8z5?|+auJKL&J^m;DOMaXGn*Wf$!QbR>@o)2g@}K%NNe}@d zKm>>Y5g-CYfCvx)B0vO)01+SpKp-U^5pef@I3tb;{=WE7pE&AXE9#(I4|_KQX>kP0 zRHff7f@MATFCNJI7bkK_aY%r@y(~)Dg3Dk9ZjbdP!~sE_PP^r5A%zmkldde939MFT z<0y)%gkruRy7v@fad9B66lncV;YtLE01+SpM1Tko0U|&IhyW2F0z}~b6L6RAwElnp z0O?L5Km>>Y5g-CYfCvx)B0vO)01+SpcL9OBYW<&oh2>x2|Kfk)zvHj+pYb1XgP-Fi zKFvSEdA^hXTmB~eKEOBm*Z7z20`%k}5g-CYfCvx)B0vO)01+SpM1TlBz80S zxq?J@Cf=Qqx-(*TCYBM$(}4o--~V4_e3#$iZ}Y$Nzw$rA|MtJhU+2H!FY{l(ZorS= z7XZG`ukr8j=lInRcnDGVhyW2F0z`la5CI}U1c(3;AOb{y2>kyENFo!4F&V;S5R(B+ m`Z3{{ bytes: + """Pack ``(atoms, coords)`` into the compact per-atom binary record.""" + buf = bytearray() + for sym, (x, y, z) in zip(atoms, coords): + s = sym.encode("ascii") + if not 1 <= len(s) <= 2: + raise ValueError(f"Unsupported element symbol: {sym!r}") + c0 = s[0] + c1 = s[1] if len(s) > 1 else 0 + buf += struct.pack( + _ATOM_RECORD, + c0, + c1, + round(float(x) * _COORD_SCALE), + round(float(y) * _COORD_SCALE), + round(float(z) * _COORD_SCALE), + ) + return bytes(buf) + + +def decode_coords(blob: bytes) -> Tuple[List[str], List[List[float]]]: + """Unpack a coordinate blob back into ``(atoms, coords)``.""" + atoms: List[str] = [] + coords: List[List[float]] = [] + for offset in range(0, len(blob), _ATOM_RECORD_SIZE): + c0, c1, xi, yi, zi = struct.unpack( + _ATOM_RECORD, blob[offset : offset + _ATOM_RECORD_SIZE] + ) + sym = chr(c0) + (chr(c1) if c1 else "") + atoms.append(sym) + coords.append([xi / _COORD_SCALE, yi / _COORD_SCALE, zi / _COORD_SCALE]) + return atoms, coords + + +# ── Paths ──────────────────────────────────────────────────────────────────── +def _data_dir() -> Path: + return Path(str(files("quantui"))) / "data" + + +def db_path() -> Path: + return _data_dir() / "library" / "library.sqlite" + + +def manifest_paths() -> List[Path]: + """All manifest JSON files that seed the store (STRUCT.7/.8 add more).""" + manifest_dir = _data_dir() / "manifests" + if not manifest_dir.is_dir(): + return [] + return sorted(manifest_dir.glob("*.json")) + + +# ── Manifest loading (always-available fallback source) ────────────────────── +@lru_cache(maxsize=1) +def _manifest_entries() -> Tuple[Dict[str, Any], ...]: + """Load every manifest entry. Cached. The JSON is the source of record.""" + entries: List[Dict[str, Any]] = [] + for path in manifest_paths(): + try: + entries.extend(json.loads(path.read_text(encoding="utf-8"))) + except Exception as exc: # pragma: no cover - corrupt manifest + logger.error(f"Failed to read library manifest {path}: {exc}") + return tuple(entries) + + +def _normalize_entry(raw: Dict[str, Any]) -> Dict[str, Any]: + """Fill derived fields (id/formula/n_atoms/...) for a manifest entry.""" + atoms = raw["atoms"] + formula = raw.get("formula") or raw.get("id") or raw["name"] + return { + "id": raw.get("id", formula), + "name": raw.get("name", formula), + "formula": formula, + "category": raw.get("category", "preset"), + "n_atoms": len(atoms), + "n_heavy": sum(1 for a in atoms if a != "H"), + "charge": int(raw.get("charge", 0)), + "multiplicity": int(raw.get("multiplicity", 1)), + "source": raw.get("source", "preset"), + "smiles": raw.get("smiles"), + "inchikey": raw.get("inchikey"), + "synonyms": raw.get("synonyms", ""), + "description": raw.get("description", ""), + "atoms": atoms, + "coordinates": raw["coordinates"], + } + + +# ── Store build (run by scripts/build_library.py or on-demand) ─────────────── +_SCHEMA = """ +CREATE TABLE molecule ( + id TEXT PRIMARY KEY, + name TEXT, + formula TEXT NOT NULL, + category TEXT NOT NULL, + n_heavy INTEGER NOT NULL, + n_atoms INTEGER NOT NULL, + charge INTEGER NOT NULL DEFAULT 0, + multiplicity INTEGER NOT NULL DEFAULT 1, + source TEXT NOT NULL, + smiles TEXT, + inchikey TEXT, + synonyms TEXT, + description TEXT, + coords BLOB NOT NULL +); +CREATE INDEX idx_name ON molecule(name); +CREATE INDEX idx_formula ON molecule(formula); +CREATE INDEX idx_category ON molecule(category); +CREATE INDEX idx_inchikey ON molecule(inchikey); +""" + + +def build_store(entries: List[Dict[str, Any]], target: Path) -> Path: + """(Re)build the SQLite store from a list of (raw) manifest entries. + + Deterministic: entries are inserted in the order given, so a rebuild from + the same manifest yields a stable file. Overwrites ``target``. + """ + target.parent.mkdir(parents=True, exist_ok=True) + if target.exists(): + target.unlink() + con = sqlite3.connect(target) + try: + con.executescript(_SCHEMA) + rows = [] + for raw in entries: + e = _normalize_entry(raw) + rows.append( + ( + e["id"], + e["name"], + e["formula"], + e["category"], + e["n_heavy"], + e["n_atoms"], + e["charge"], + e["multiplicity"], + e["source"], + e["smiles"], + e["inchikey"], + e["synonyms"], + e["description"], + encode_coords(e["atoms"], e["coordinates"]), + ) + ) + con.executemany( + "INSERT INTO molecule (id, name, formula, category, n_heavy, n_atoms, " + "charge, multiplicity, source, smiles, inchikey, synonyms, description, " + "coords) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?)", + rows, + ) + con.commit() + finally: + con.close() + logger.info(f"Built molecule library store: {target} ({len(entries)} entries)") + return target + + +def build_from_manifests(target: Optional[Path] = None) -> Path: + """Build the store from all committed manifests. Returns the store path.""" + target = target or db_path() + return build_store([dict(e) for e in _manifest_entries()], target) + + +def _ensure_store() -> Optional[Path]: + """Best-effort: ensure the SQLite store exists. Returns its path or None. + + Never raises — if the package dir is read-only (installed wheel) and the + store is somehow absent, callers fall back to the JSON manifest. + """ + path = db_path() + if path.exists(): + return path + try: + if _manifest_entries(): + return build_from_manifests(path) + except Exception as exc: # pragma: no cover - read-only install w/o store + logger.warning(f"Could not build library store on demand: {exc}") + return None + + +# ── Query API ──────────────────────────────────────────────────────────────── +def _connect_ro() -> Optional[sqlite3.Connection]: + """Open a fresh read-only connection (thread-safe per-call), or None.""" + path = _ensure_store() + if path is None or not path.exists(): + return None + con = sqlite3.connect(f"file:{path}?mode=ro", uri=True) + con.row_factory = sqlite3.Row + return con + + +def _row_to_entry(row: sqlite3.Row) -> Dict[str, Any]: + atoms, coords = decode_coords(row["coords"]) + return { + "id": row["id"], + "name": row["name"], + "formula": row["formula"], + "category": row["category"], + "n_heavy": row["n_heavy"], + "n_atoms": row["n_atoms"], + "charge": row["charge"], + "multiplicity": row["multiplicity"], + "source": row["source"], + "smiles": row["smiles"], + "inchikey": row["inchikey"], + "synonyms": row["synonyms"], + "description": row["description"], + "atoms": atoms, + "coordinates": coords, + } + + +@lru_cache(maxsize=1) +def get_preset_dict() -> Dict[str, Dict[str, Any]]: + """Return the curated/preset entries in the legacy ``MOLECULE_LIBRARY`` shape. + + Keyed by entry id (the formula key, e.g. ``"H2O"``); each value carries the + legacy ``atoms`` / ``coordinates`` / ``charge`` / ``multiplicity`` / + ``description`` fields. Bulk categories are excluded (they are reached via + :func:`search`, never the browse dropdown). Preserves manifest order. + + Prefers the SQLite store; falls back to the JSON manifest if the store is + unavailable, so this never hard-fails. + """ + out: Dict[str, Dict[str, Any]] = {} + con = _connect_ro() + if con is not None: + try: + placeholders = ",".join("?" * len(_BULK_CATEGORIES)) + rows = con.execute( + f"SELECT * FROM molecule WHERE category NOT IN ({placeholders}) " + "ORDER BY rowid", + tuple(_BULK_CATEGORIES), + ).fetchall() + for row in rows: + e = _row_to_entry(row) + out[e["id"]] = _legacy_view(e) + return out + except Exception as exc: # pragma: no cover - corrupt store + logger.warning(f"Library store unreadable, using manifest: {exc}") + finally: + con.close() + # JSON fallback. + for raw in _manifest_entries(): + e = _normalize_entry(raw) + if e["category"] in _BULK_CATEGORIES: + continue + out[e["id"]] = _legacy_view(e) + return out + + +def _legacy_view(entry: Dict[str, Any]) -> Dict[str, Any]: + """Project a full entry down to the legacy MOLECULE_LIBRARY value shape.""" + return { + "atoms": entry["atoms"], + "coordinates": entry["coordinates"], + "charge": entry["charge"], + "multiplicity": entry["multiplicity"], + "description": entry["description"], + } + + +def get(entry_id: str) -> Optional[Dict[str, Any]]: + """Fetch one full entry (incl. decoded coordinates) by id, or None.""" + con = _connect_ro() + if con is not None: + try: + row = con.execute( + "SELECT * FROM molecule WHERE id = ?", (entry_id,) + ).fetchone() + return _row_to_entry(row) if row else None + finally: + con.close() + for raw in _manifest_entries(): + e = _normalize_entry(raw) + if e["id"] == entry_id: + return e + return None + + +def search( + query: str = "", *, category: Optional[str] = None, limit: int = 50 +) -> List[Dict[str, Any]]: + """Search the library by name / formula / synonyms (substring, case-insensitive). + + Returns lightweight rows (no coordinates) for listing; call :func:`get` to + materialize the chosen entry. Empty ``query`` lists entries (optionally + filtered by ``category``). + """ + q = f"%{query.strip().lower()}%" + con = _connect_ro() + if con is not None: + try: + sql = ( + "SELECT id, name, formula, category, n_heavy, n_atoms, charge, " + "multiplicity, source FROM molecule WHERE " + "(lower(name) LIKE ? OR lower(formula) LIKE ? OR lower(synonyms) LIKE ?)" + ) + params: List[Any] = [q, q, q] + if category: + sql += " AND category = ?" + params.append(category) + sql += " ORDER BY n_atoms, id LIMIT ?" + params.append(limit) + return [dict(r) for r in con.execute(sql, params).fetchall()] + finally: + con.close() + # JSON fallback (linear scan). + needle = query.strip().lower() + results = [] + for raw in _manifest_entries(): + e = _normalize_entry(raw) + hay = f"{e['name']} {e['formula']} {e['synonyms']}".lower() + if needle in hay and (category is None or e["category"] == category): + results.append( + { + k: e[k] + for k in ( + "id", + "name", + "formula", + "category", + "n_heavy", + "n_atoms", + "charge", + "multiplicity", + "source", + ) + } + ) + results.sort(key=lambda r: (r["n_atoms"], r["id"])) + return results[:limit] + + +def categories() -> List[str]: + """Distinct category labels present in the library.""" + con = _connect_ro() + if con is not None: + try: + return [ + r[0] + for r in con.execute( + "SELECT DISTINCT category FROM molecule ORDER BY category" + ).fetchall() + ] + finally: + con.close() + return sorted({_normalize_entry(e)["category"] for e in _manifest_entries()}) + + +def count() -> int: + """Total number of entries in the library.""" + con = _connect_ro() + if con is not None: + try: + return int(con.execute("SELECT COUNT(*) FROM molecule").fetchone()[0]) + finally: + con.close() + return len(_manifest_entries()) diff --git a/scripts/build_library.py b/scripts/build_library.py new file mode 100644 index 0000000..0c8ae23 --- /dev/null +++ b/scripts/build_library.py @@ -0,0 +1,32 @@ +"""Rebuild the bundled molecule-library SQLite store from the committed manifests. + +Usage: + python scripts/build_library.py + +Reads every ``quantui/data/manifests/*.json`` and writes +``quantui/data/library/library.sqlite`` (deterministic, overwrites). Prints the +final entry count + on-disk size and asserts the 10 MB budget (STRUCT.10). + +When STRUCT.7 (curated set) and STRUCT.8 (bulk QM9 subset) land, they add more +manifests; this tool is unchanged. +""" + +from quantui import molecule_library as ml + +_BUDGET_BYTES = 10 * 1024 * 1024 # 10 MB (DEC-015) + + +def main() -> None: + path = ml.build_from_manifests() + size = path.stat().st_size + n = ml.count() + print(f"Built {path} — {n} entries, {size / 1024:.1f} KiB") + print(f"Categories: {', '.join(ml.categories())}") + if size > _BUDGET_BYTES: + raise SystemExit( + f"Library store {size / 1024 / 1024:.2f} MB exceeds the 10 MB budget" + ) + + +if __name__ == "__main__": + main() diff --git a/tests/test_molecule_library.py b/tests/test_molecule_library.py new file mode 100644 index 0000000..7b651f4 --- /dev/null +++ b/tests/test_molecule_library.py @@ -0,0 +1,135 @@ +"""Tests for the bundled molecule-library store + loader (M-STRUCT STRUCT.6). + +Platform-independent (stdlib sqlite3 + struct + json); no RDKit, no PySCF. +""" + +import math + +import pytest + +from quantui import config +from quantui import molecule_library as ml + +_BUDGET_BYTES = 10 * 1024 * 1024 # DEC-015 + + +# ============================================================================ +# Coordinate codec +# ============================================================================ + + +class TestCoordCodec: + def test_round_trip_exact_for_3_decimal_coords(self): + atoms = ["O", "H", "H", "Cl"] + coords = [ + [0.0, 0.0, 0.0], + [0.0, 0.757, 0.587], + [0.0, -0.757, 0.587], + [1.27, 0.0, -2.48], + ] + blob = ml.encode_coords(atoms, coords) + out_atoms, out_coords = ml.decode_coords(blob) + assert out_atoms == atoms + for a, b in zip(coords, out_coords): + for ca, cb in zip(a, b): + assert math.isclose(ca, cb, abs_tol=1e-9) + + def test_record_size_is_8_bytes_per_atom(self): + blob = ml.encode_coords(["C", "H"], [[0, 0, 0], [1, 1, 1]]) + assert len(blob) == 2 * 8 + + def test_two_char_symbol_round_trips(self): + atoms, coords = ml.decode_coords( + ml.encode_coords(["Cl", "Na"], [[0, 0, 0], [2, 0, 0]]) + ) + assert atoms == ["Cl", "Na"] + + def test_rejects_long_symbol(self): + with pytest.raises(ValueError): + ml.encode_coords(["Uuo"], [[0, 0, 0]]) + + +# ============================================================================ +# Store build + query API +# ============================================================================ + + +class TestStoreBuildAndQuery: + def test_build_from_manifest_round_trips(self, tmp_path): + target = tmp_path / "lib.sqlite" + ml.build_from_manifests(target) + assert target.exists() + + def test_committed_store_has_20_presets(self): + assert ml.count() == 20 + + def test_categories_present(self): + cats = ml.categories() + assert {"diatomic", "triatomic", "small-organic", "aromatic"} <= set(cats) + + def test_get_returns_full_entry_with_coords(self): + entry = ml.get("H2O") + assert entry is not None + assert entry["atoms"] == ["O", "H", "H"] + assert entry["n_heavy"] == 1 + assert entry["coordinates"][1] == [0.0, 0.757, 0.587] + + def test_get_unknown_returns_none(self): + assert ml.get("NOTAREALID") is None + + def test_search_by_formula(self): + hits = ml.search("C6H6") + assert any(h["id"] == "C6H6" for h in hits) + + def test_search_by_category_filter(self): + hits = ml.search("", category="aromatic") + assert [h["id"] for h in hits] == ["C6H6"] + + def test_search_returns_lightweight_rows(self): + hits = ml.search("H2O") + assert hits and "coordinates" not in hits[0] + + +# ============================================================================ +# Legacy back-compat shim +# ============================================================================ + + +class TestPresetDictBackCompat: + def test_get_preset_dict_shape(self): + d = ml.get_preset_dict() + assert len(d) == 20 + h2o = d["H2O"] + assert set(h2o) == { + "atoms", + "coordinates", + "charge", + "multiplicity", + "description", + } + + def test_config_shim_resolves(self): + lib = config.MOLECULE_LIBRARY + assert len(lib) == 20 + assert lib["O2"]["multiplicity"] == 3 # triplet preserved + assert lib["H2O"]["coordinates"][2] == [0.0, -0.757, 0.587] + + def test_config_shim_unknown_attr_raises(self): + with pytest.raises(AttributeError): + _ = config.THIS_DOES_NOT_EXIST + + def test_preset_dict_excludes_bulk_categories(self): + # No bulk entries yet, but the contract must hold for STRUCT.8. + for entry_id in ml.get_preset_dict(): + full = ml.get(entry_id) + assert full["category"] not in ml._BULK_CATEGORIES + + +# ============================================================================ +# Size governance (STRUCT.10 precursor) +# ============================================================================ + + +class TestSizeBudget: + def test_committed_store_within_10mb(self): + assert ml.db_path().stat().st_size <= _BUDGET_BYTES From 6ec51f2ec36d2f2f7a5bbf1bceff50e60b472bd9 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Sun, 7 Jun 2026 18:46:18 -0400 Subject: [PATCH 04/16] Add bundled curated molecule library Introduce a bundled curated molecule library and integrate it into the app. Changes include: - Add a large curated manifest (quantui/data/manifests/curated.json) plus curated seed and build script (scripts/curated_seed.json, scripts/build_curated_library.py) and tests (tests/test_curated_library.py). - Update the packaged library database (quantui/data/library/library.sqlite) and adjust molecule library code/tests (quantui/molecule_library.py, tests/test_molecule_library.py) to use the curated content. - Add configuration limits to keep bundled content classroom-friendly: LIBRARY_SIZE_BUDGET_BYTES = 10 * 1024 * 1024, LIBRARY_HEAVY_ATOM_CEILING_CURATED = 30, LIBRARY_HEAVY_ATOM_CEILING_BULK = 9. - Small UI copy change in build_molecule_section to reference the bundled library of curated molecules. These changes add curated molecule data, enforce size/atom ceilings for usability, and provide tooling/tests to build and validate the bundled library. --- quantui/app_builders.py | 4 +- quantui/config.py | 6 + quantui/data/library/library.sqlite | Bin 28672 -> 81920 bytes quantui/data/manifests/curated.json | 15482 ++++++++++++++++++++++++++ quantui/molecule_library.py | 11 +- scripts/build_curated_library.py | 124 + scripts/curated_seed.json | 166 + tests/test_curated_library.py | 121 + tests/test_molecule_library.py | 33 +- 9 files changed, 15940 insertions(+), 7 deletions(-) create mode 100644 quantui/data/manifests/curated.json create mode 100644 scripts/build_curated_library.py create mode 100644 scripts/curated_seed.json create mode 100644 tests/test_curated_library.py diff --git a/quantui/app_builders.py b/quantui/app_builders.py index 8182147..7ed3868 100644 --- a/quantui/app_builders.py +++ b/quantui/app_builders.py @@ -1026,7 +1026,9 @@ def build_molecule_section( hint = '

' tab_preset = widgets.VBox( [ - widgets.HTML(hint + "Choose from 20+ curated educational molecules.

"), + widgets.HTML( + hint + "Choose from the bundled library of curated molecules.

" + ), app.preset_dd, ] ) diff --git a/quantui/config.py b/quantui/config.py index eb77082..5033199 100644 --- a/quantui/config.py +++ b/quantui/config.py @@ -245,6 +245,12 @@ # (resolves name / CAS / InChI / SMILES → 3D SDF; no API key). CACTUS_TIMEOUT_S: float = 15.0 +# Bundled-library size budget + heavy-atom ceilings (M-STRUCT STRUCT.7/.8/.10). +# These are QC *starting* geometries, so keep them runnable in a classroom. +LIBRARY_SIZE_BUDGET_BYTES: int = 10 * 1024 * 1024 # 10 MB (DEC-015) +LIBRARY_HEAVY_ATOM_CEILING_CURATED: int = 30 # named drugs run a bit larger +LIBRARY_HEAVY_ATOM_CEILING_BULK: int = 9 # QM9 caps here anyway + # Molecule presets — bundled library (STRUCT.6). # The former inline literal now lives in the indexed package-data store # (quantui/data/library/library.sqlite, seeded from diff --git a/quantui/data/library/library.sqlite b/quantui/data/library/library.sqlite index 33207a68ea8c997d58b8a1697a35d94732bdd259..d70e657dd59f53f85f469e692b844662832cc0a5 100644 GIT binary patch literal 81920 zcmeFa2Ygi3{x7;`?>)T*5UG(MQUXLsqZm*pJ2RO{CNs%QIv|E*fWVMo3Id8cv5Qy^ zc0rF_6ni-y74_(`cg1?da%|@uD+0;%dEd46p0Wev{@=Ur-uwRVlPI&wZ|&b&zp~12 zRd0>6y~mfcva@SlOHWQAlf@_$%&9p!48y4K?-=|`{wd+%lL5Gj4FA!*D(1v(VWT<7 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teaching molecules lead + the (interim) flat dropdown; remaining manifests follow alphabetically. + """ manifest_dir = _data_dir() / "manifests" if not manifest_dir.is_dir(): return [] - return sorted(manifest_dir.glob("*.json")) + return sorted( + manifest_dir.glob("*.json"), + key=lambda p: (p.name != "presets.json", p.name), + ) # ── Manifest loading (always-available fallback source) ────────────────────── diff --git a/scripts/build_curated_library.py b/scripts/build_curated_library.py new file mode 100644 index 0000000..bbee3f9 --- /dev/null +++ b/scripts/build_curated_library.py @@ -0,0 +1,124 @@ +"""Generate the curated library manifest (M-STRUCT STRUCT.7). + +Reads the human-editable SMILES seed (scripts/curated_seed.json), generates 3D +coordinates with RDKit (ETKDGv3, seed=42 → MMFF94, UFF fallback), and writes +the full manifest quantui/data/manifests/curated.json (same schema as +presets.json, with coordinates). Then rebuild the SQLite store: + + python scripts/build_curated_library.py + python scripts/build_library.py + +Deterministic (fixed RDKit seed). Molecules that fail to parse/embed or exceed +the curated heavy-atom ceiling are skipped + reported (no silent drops). +""" + +import json +import re +from pathlib import Path + +from rdkit import Chem, RDLogger +from rdkit.Chem import AllChem + +from quantui import config + +RDLogger.DisableLog("rdApp.*") # quiet InChI/sanitize chatter + +SEED = Path("scripts/curated_seed.json") +OUT = Path("quantui/data/manifests/curated.json") +CEILING = config.LIBRARY_HEAVY_ATOM_CEILING_CURATED + + +def _slug(name: str) -> str: + return re.sub(r"[^a-z0-9]+", "-", name.lower()).strip("-") + + +def _embed(mol): + params = AllChem.ETKDGv3() + params.randomSeed = 42 + if AllChem.EmbedMolecule(mol, params) != 0: + params.useRandomCoords = True + if AllChem.EmbedMolecule(mol, params) != 0: + raise ValueError("3D embedding failed") + try: + AllChem.MMFFOptimizeMolecule(mol) + except Exception: + try: + AllChem.UFFOptimizeMolecule(mol) + except Exception: + pass # ship unoptimized rather than fail + + +def _generate(entry: dict) -> dict: + mol = Chem.MolFromSmiles(entry["smiles"]) + if mol is None: + raise ValueError("unparseable SMILES") + mol = Chem.AddHs(mol) + _embed(mol) + + atoms = [a.GetSymbol() for a in mol.GetAtoms()] + n_heavy = sum(1 for a in atoms if a != "H") + if n_heavy > CEILING: + raise ValueError(f"{n_heavy} heavy atoms exceeds ceiling {CEILING}") + + conf = mol.GetConformer() + coords = [ + [ + round(conf.GetAtomPosition(i).x, 6), + round(conf.GetAtomPosition(i).y, 6), + round(conf.GetAtomPosition(i).z, 6), + ] + for i in range(mol.GetNumAtoms()) + ] + formula = Chem.rdMolDescriptors.CalcMolFormula(mol) + try: + inchikey = Chem.InchiToInchiKey(Chem.MolToInchi(mol)) or None + except Exception: + inchikey = None + + return { + "id": _slug(entry["name"]), + "name": entry["name"], + "formula": formula, + "category": entry["category"], + "source": "curated-ff", + "charge": int(entry.get("charge", Chem.GetFormalCharge(mol))), + "multiplicity": int(entry.get("multiplicity", 1)), + "smiles": Chem.MolToSmiles(Chem.RemoveHs(mol)), + "inchikey": inchikey, + "synonyms": entry.get("synonyms", ""), + "description": f"{entry['name']} ({formula})", + "atoms": atoms, + "coordinates": coords, + } + + +def main() -> None: + seed = json.loads(SEED.read_text(encoding="utf-8")) + out, failures, seen = [], [], set() + for entry in seed: + try: + rec = _generate(entry) + except Exception as exc: + failures.append((entry["name"], str(exc))) + continue + if rec["id"] in seen: + failures.append((entry["name"], f"duplicate id '{rec['id']}'")) + continue + seen.add(rec["id"]) + out.append(rec) + + OUT.parent.mkdir(parents=True, exist_ok=True) + OUT.write_text(json.dumps(out, indent=1) + "\n", encoding="utf-8") + print(f"Wrote {len(out)}/{len(seed)} curated entries to {OUT}") + by_cat: dict = {} + for r in out: + by_cat[r["category"]] = by_cat.get(r["category"], 0) + 1 + print("By category:", dict(sorted(by_cat.items()))) + if failures: + print(f"\nSkipped {len(failures)}:") + for name, why in failures: + print(f" - {name}: {why}") + + +if __name__ == "__main__": + main() diff --git a/scripts/curated_seed.json b/scripts/curated_seed.json new file mode 100644 index 0000000..30a57dc --- /dev/null +++ b/scripts/curated_seed.json @@ -0,0 +1,166 @@ +[ + { "name": "Glycine", "smiles": "NCC(=O)O", "category": "amino-acid", "synonyms": "Gly;G;aminoacetic acid" }, + { "name": "Alanine", "smiles": "CC(N)C(=O)O", "category": "amino-acid", "synonyms": "Ala;A" }, + { "name": "Valine", "smiles": "CC(C)C(N)C(=O)O", "category": "amino-acid", "synonyms": "Val;V" }, + { "name": "Leucine", "smiles": "CC(C)CC(N)C(=O)O", "category": "amino-acid", "synonyms": "Leu;L" }, + { "name": "Isoleucine", "smiles": "CCC(C)C(N)C(=O)O", "category": "amino-acid", "synonyms": "Ile;I" }, + { "name": "Proline", "smiles": "OC(=O)C1CCCN1", "category": "amino-acid", "synonyms": "Pro;P" }, + { "name": "Phenylalanine", "smiles": "NC(Cc1ccccc1)C(=O)O", "category": "amino-acid", "synonyms": "Phe;F" }, + { "name": "Tryptophan", "smiles": "NC(Cc1c[nH]c2ccccc12)C(=O)O", "category": "amino-acid", "synonyms": "Trp;W" }, + { "name": "Methionine", "smiles": "CSCCC(N)C(=O)O", "category": "amino-acid", "synonyms": "Met;M" }, + { "name": "Serine", "smiles": "NC(CO)C(=O)O", "category": "amino-acid", "synonyms": "Ser;S" }, + { "name": "Threonine", "smiles": "CC(O)C(N)C(=O)O", "category": "amino-acid", "synonyms": "Thr;T" }, + { "name": "Cysteine", "smiles": "NC(CS)C(=O)O", "category": "amino-acid", "synonyms": "Cys;C" }, + { "name": "Tyrosine", "smiles": "NC(Cc1ccc(O)cc1)C(=O)O", "category": "amino-acid", "synonyms": "Tyr;Y" }, + { "name": "Asparagine", "smiles": "NC(CC(N)=O)C(=O)O", "category": "amino-acid", "synonyms": "Asn;N" }, + { "name": "Glutamine", "smiles": "NC(CCC(N)=O)C(=O)O", "category": "amino-acid", "synonyms": "Gln;Q" }, + { "name": "Aspartic acid", "smiles": "NC(CC(=O)O)C(=O)O", "category": "amino-acid", "synonyms": "Asp;D" }, + { "name": "Glutamic acid", "smiles": "NC(CCC(=O)O)C(=O)O", "category": "amino-acid", "synonyms": "Glu;E" }, + { "name": "Lysine", "smiles": "NCCCCC(N)C(=O)O", "category": "amino-acid", "synonyms": "Lys;K" }, + { "name": "Arginine", "smiles": "NC(CCCNC(=N)N)C(=O)O", "category": "amino-acid", "synonyms": "Arg;R" }, + { "name": "Histidine", "smiles": "NC(Cc1cnc[nH]1)C(=O)O", "category": "amino-acid", "synonyms": "His;H" }, + + { "name": "Adenine", "smiles": "Nc1ncnc2nc[nH]c12", "category": "nucleobase", "synonyms": "6-aminopurine" }, + { "name": "Guanine", "smiles": "Nc1nc2[nH]cnc2c(=O)[nH]1", "category": "nucleobase", "synonyms": "" }, + { "name": "Cytosine", "smiles": "Nc1cc[nH]c(=O)n1", "category": "nucleobase", "synonyms": "" }, + { "name": "Thymine", "smiles": "Cc1c[nH]c(=O)[nH]c1=O", "category": "nucleobase", "synonyms": "5-methyluracil" }, + { "name": "Uracil", "smiles": "O=c1cc[nH]c(=O)[nH]1", "category": "nucleobase", "synonyms": "" }, + + { "name": "Glucose", "smiles": "OCC1OC(O)C(O)C(O)C1O", "category": "biomolecule", "synonyms": "dextrose" }, + { "name": "Urea", "smiles": "NC(N)=O", "category": "biomolecule", "synonyms": "carbamide" }, + { "name": "Citric acid", "smiles": "OC(=O)CC(O)(CC(=O)O)C(=O)O", "category": "biomolecule", "synonyms": "" }, + { "name": "Lactic acid", "smiles": "CC(O)C(=O)O", "category": "biomolecule", "synonyms": "2-hydroxypropanoic acid" }, + { "name": "Pyruvic acid", "smiles": "CC(=O)C(=O)O", "category": "biomolecule", "synonyms": "2-oxopropanoic acid" }, + { "name": "Oxalic acid", "smiles": "OC(=O)C(=O)O", "category": "biomolecule", "synonyms": "ethanedioic acid" }, + { "name": "Glycerol", "smiles": "OCC(O)CO", "category": "biomolecule", "synonyms": "glycerin;propane-1,2,3-triol" }, + { "name": "Ascorbic acid", "smiles": "OCC(O)C1OC(=O)C(O)=C1O", "category": "biomolecule", "synonyms": "vitamin C" }, + + { "name": "Methanol", "smiles": "CO", "category": "solvent", "synonyms": "methyl alcohol" }, + { "name": "Ethanol", "smiles": "CCO", "category": "solvent", "synonyms": "ethyl alcohol" }, + { "name": "1-Propanol", "smiles": "CCCO", "category": "solvent", "synonyms": "n-propanol" }, + { "name": "Isopropanol", "smiles": "CC(C)O", "category": "solvent", "synonyms": "2-propanol;IPA" }, + { "name": "1-Butanol", "smiles": "CCCCO", "category": "solvent", "synonyms": "n-butanol" }, + { "name": "tert-Butanol", "smiles": "CC(C)(C)O", "category": "solvent", "synonyms": "2-methyl-2-propanol" }, + { "name": "Acetone", "smiles": "CC(C)=O", "category": "solvent", "synonyms": "propanone;dimethyl ketone" }, + { "name": "Methyl ethyl ketone", "smiles": "CCC(C)=O", "category": "solvent", "synonyms": "MEK;butanone" }, + { "name": "Dichloromethane", "smiles": "ClCCl", "category": "solvent", "synonyms": "DCM;methylene chloride" }, + { "name": "Chloroform", "smiles": "ClC(Cl)Cl", "category": "solvent", "synonyms": "trichloromethane" }, + { "name": "Carbon tetrachloride", "smiles": "ClC(Cl)(Cl)Cl", "category": "solvent", "synonyms": "tetrachloromethane" }, + { "name": "Tetrahydrofuran", "smiles": "C1CCOC1", "category": "solvent", "synonyms": "THF" }, + { "name": "1,4-Dioxane", "smiles": "C1COCCO1", "category": "solvent", "synonyms": "dioxane" }, + { "name": "Diethyl ether", "smiles": "CCOCC", "category": "solvent", "synonyms": "ether;ethoxyethane" }, + { "name": "Dimethylformamide", "smiles": "CN(C)C=O", "category": "solvent", "synonyms": "DMF" }, + { "name": "Dimethyl sulfoxide", "smiles": "CS(C)=O", "category": "solvent", "synonyms": "DMSO" }, + { "name": "Acetonitrile", "smiles": "CC#N", "category": "solvent", "synonyms": "MeCN;methyl cyanide" }, + { "name": "Ethyl acetate", "smiles": "CCOC(C)=O", "category": "solvent", "synonyms": "EtOAc" }, + { "name": "n-Hexane", "smiles": "CCCCCC", "category": "solvent", "synonyms": "hexane" }, + { "name": "n-Pentane", "smiles": "CCCCC", "category": "solvent", "synonyms": "pentane" }, + { "name": "n-Heptane", "smiles": "CCCCCCC", "category": "solvent", "synonyms": "heptane" }, + { "name": "Cyclohexane", "smiles": "C1CCCCC1", "category": "solvent", "synonyms": "" }, + { "name": "Toluene", "smiles": "Cc1ccccc1", "category": "solvent", "synonyms": "methylbenzene" }, + { "name": "Pyridine", "smiles": "c1ccncc1", "category": "solvent", "synonyms": "" }, + { "name": "Acetic acid", "smiles": "CC(=O)O", "category": "solvent", "synonyms": "ethanoic acid" }, + { "name": "Formic acid", "smiles": "OC=O", "category": "solvent", "synonyms": "methanoic acid" }, + { "name": "Nitromethane", "smiles": "C[N+](=O)[O-]", "category": "solvent", "synonyms": "" }, + { "name": "Ethylene glycol", "smiles": "OCCO", "category": "solvent", "synonyms": "ethane-1,2-diol" }, + + { "name": "Propanal", "smiles": "CCC=O", "category": "functional-group", "synonyms": "propionaldehyde" }, + { "name": "Butanal", "smiles": "CCCC=O", "category": "functional-group", "synonyms": "butyraldehyde" }, + { "name": "Propanoic acid", "smiles": "CCC(=O)O", "category": "functional-group", "synonyms": "propionic acid" }, + { "name": "Butanoic acid", "smiles": "CCCC(=O)O", "category": "functional-group", "synonyms": "butyric acid" }, + { "name": "Methyl acetate", "smiles": "COC(C)=O", "category": "functional-group", "synonyms": "" }, + { "name": "Ethylamine", "smiles": "CCN", "category": "functional-group", "synonyms": "" }, + { "name": "Dimethylamine", "smiles": "CNC", "category": "functional-group", "synonyms": "" }, + { "name": "Trimethylamine", "smiles": "CN(C)C", "category": "functional-group", "synonyms": "" }, + { "name": "Propanenitrile", "smiles": "CCC#N", "category": "functional-group", "synonyms": "propionitrile" }, + { "name": "Nitroethane", "smiles": "CC[N+](=O)[O-]", "category": "functional-group", "synonyms": "" }, + { "name": "Dimethyl sulfide", "smiles": "CSC", "category": "functional-group", "synonyms": "DMS" }, + { "name": "Ethanethiol", "smiles": "CCS", "category": "functional-group", "synonyms": "ethyl mercaptan" }, + { "name": "Dimethyl ether", "smiles": "COC", "category": "functional-group", "synonyms": "methoxymethane" }, + { "name": "Acetamide", "smiles": "CC(N)=O", "category": "functional-group", "synonyms": "ethanamide" }, + { "name": "Formamide", "smiles": "NC=O", "category": "functional-group", "synonyms": "methanamide" }, + { "name": "Acetic anhydride", "smiles": "CC(=O)OC(C)=O", "category": "functional-group", "synonyms": "" }, + { "name": "Anisole", "smiles": "COc1ccccc1", "category": "functional-group", "synonyms": "methoxybenzene" }, + { "name": "Phenol", "smiles": "Oc1ccccc1", "category": "functional-group", "synonyms": "carbolic acid" }, + { "name": "Aniline", "smiles": "Nc1ccccc1", "category": "functional-group", "synonyms": "aminobenzene" }, + { "name": "Benzaldehyde", "smiles": "O=Cc1ccccc1", "category": "functional-group", "synonyms": "" }, + { "name": "Acetophenone", "smiles": "CC(=O)c1ccccc1", "category": "functional-group", "synonyms": "" }, + { "name": "Benzoic acid", "smiles": "OC(=O)c1ccccc1", "category": "functional-group", "synonyms": "" }, + { "name": "Oxirane", "smiles": "C1CO1", "category": "functional-group", "synonyms": "ethylene oxide;epoxyethane" }, + { "name": "Furan", "smiles": "c1ccoc1", "category": "functional-group", "synonyms": "" }, + { "name": "Thiophene", "smiles": "c1ccsc1", "category": "functional-group", "synonyms": "" }, + { "name": "Pyrrole", "smiles": "c1cc[nH]c1", "category": "functional-group", "synonyms": "" }, + { "name": "Imidazole", "smiles": "c1c[nH]cn1", "category": "functional-group", "synonyms": "" }, + + { "name": "Propane", "smiles": "CCC", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Butane", "smiles": "CCCC", "category": "hydrocarbon", "synonyms": "n-butane" }, + { "name": "Isobutane", "smiles": "CC(C)C", "category": "hydrocarbon", "synonyms": "2-methylpropane" }, + { "name": "Cyclopropane", "smiles": "C1CC1", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Cyclobutane", "smiles": "C1CCC1", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Cyclopentane", "smiles": "C1CCCC1", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Propene", "smiles": "CC=C", "category": "hydrocarbon", "synonyms": "propylene" }, + { "name": "1-Butene", "smiles": "CCC=C", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Isobutylene", "smiles": "CC(=C)C", "category": "hydrocarbon", "synonyms": "2-methylpropene" }, + { "name": "1,3-Butadiene", "smiles": "C=CC=C", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Isoprene", "smiles": "CC(=C)C=C", "category": "hydrocarbon", "synonyms": "2-methyl-1,3-butadiene" }, + { "name": "Propyne", "smiles": "CC#C", "category": "hydrocarbon", "synonyms": "methylacetylene" }, + { "name": "1-Butyne", "smiles": "CCC#C", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Cyclohexene", "smiles": "C1CCC=CC1", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Naphthalene", "smiles": "c1ccc2ccccc2c1", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Anthracene", "smiles": "c1ccc2cc3ccccc3cc2c1", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Biphenyl", "smiles": "c1ccc(-c2ccccc2)cc1", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Ethylbenzene", "smiles": "CCc1ccccc1", "category": "hydrocarbon", "synonyms": "" }, + { "name": "Cumene", "smiles": "CC(C)c1ccccc1", "category": "hydrocarbon", "synonyms": "isopropylbenzene" }, + { "name": "Styrene", "smiles": "C=Cc1ccccc1", "category": "hydrocarbon", "synonyms": "vinylbenzene" }, + + { "name": "Aspirin", "smiles": "CC(=O)Oc1ccccc1C(=O)O", "category": "drug", "synonyms": "acetylsalicylic acid;ASA" }, + { "name": "Paracetamol", "smiles": "CC(=O)Nc1ccc(O)cc1", "category": "drug", "synonyms": "acetaminophen;APAP" }, + { "name": "Ibuprofen", "smiles": "CC(C)Cc1ccc(cc1)C(C)C(=O)O", "category": "drug", "synonyms": "" }, + { "name": "Naproxen", "smiles": "COc1ccc2cc(ccc2c1)C(C)C(=O)O", "category": "drug", "synonyms": "" }, + { "name": "Caffeine", "smiles": "Cn1cnc2c1c(=O)n(C)c(=O)n2C", "category": "drug", "synonyms": "" }, + { "name": "Theobromine", "smiles": "Cn1cnc2c1c(=O)[nH]c(=O)n2C", "category": "drug", "synonyms": "" }, + { "name": "Nicotine", "smiles": "CN1CCCC1c1cccnc1", "category": "drug", "synonyms": "" }, + { "name": "Salicylic acid", "smiles": "OC(=O)c1ccccc1O", "category": "drug", "synonyms": "2-hydroxybenzoic acid" }, + { "name": "Dopamine", "smiles": "NCCc1ccc(O)c(O)c1", "category": "drug", "synonyms": "" }, + { "name": "Serotonin", "smiles": "NCCc1c[nH]c2ccc(O)cc12", "category": "drug", "synonyms": "5-HT" }, + { "name": "Histamine", "smiles": "NCCc1c[nH]cn1", "category": "drug", "synonyms": "" }, + { "name": "Melatonin", "smiles": "COc1ccc2[nH]cc(CCNC(C)=O)c2c1", "category": "drug", "synonyms": "" }, + { "name": "Adrenaline", "smiles": "CNCC(O)c1ccc(O)c(O)c1", "category": "drug", "synonyms": "epinephrine" }, + { "name": "Acetylcholine", "smiles": "CC(=O)OCC[N+](C)(C)C", "category": "drug", "synonyms": "ACh", "charge": 1 }, + { "name": "GABA", "smiles": "NCCCC(=O)O", "category": "drug", "synonyms": "gamma-aminobutyric acid" }, + { "name": "Vanillin", "smiles": "COc1cc(C=O)ccc1O", "category": "drug", "synonyms": "" }, + { "name": "Menthol", "smiles": "CC(C)C1CCC(C)CC1O", "category": "drug", "synonyms": "" }, + { "name": "Camphor", "smiles": "CC1(C)C2CCC1(C)C(=O)C2", "category": "drug", "synonyms": "" }, + { "name": "Nicotinamide", "smiles": "NC(=O)c1cccnc1", "category": "drug", "synonyms": "niacinamide;vitamin B3" }, + { "name": "Benzocaine", "smiles": "CCOC(=O)c1ccc(N)cc1", "category": "drug", "synonyms": "" }, + { "name": "Lidocaine", "smiles": "CCN(CC)CC(=O)Nc1c(C)cccc1C", "category": "drug", "synonyms": "" }, + { "name": "Aspartame", "smiles": "COC(=O)C(Cc1ccccc1)NC(=O)C(N)CC(=O)O", "category": "drug", "synonyms": "" }, + + { "name": "Hydrogen sulfide", "smiles": "S", "category": "inorganic", "synonyms": "" }, + { "name": "Sulfur dioxide", "smiles": "O=S=O", "category": "inorganic", "synonyms": "" }, + { "name": "Sulfur trioxide", "smiles": "O=S(=O)=O", "category": "inorganic", "synonyms": "" }, + { "name": "Nitrous oxide", "smiles": "[N-]=[N+]=O", "category": "inorganic", "synonyms": "dinitrogen monoxide;laughing gas" }, + { "name": "Hydrogen cyanide", "smiles": "C#N", "category": "inorganic", "synonyms": "" }, + { "name": "Nitric acid", "smiles": "O[N+](=O)[O-]", "category": "inorganic", "synonyms": "" }, + { "name": "Sulfuric acid", "smiles": "OS(=O)(=O)O", "category": "inorganic", "synonyms": "" }, + { "name": "Phosphoric acid", "smiles": "OP(=O)(O)O", "category": "inorganic", "synonyms": "" }, + { "name": "Phosphine", "smiles": "P", "category": "inorganic", "synonyms": "" }, + { "name": "Silane", "smiles": "[SiH4]", "category": "inorganic", "synonyms": "" }, + { "name": "Boron trifluoride", "smiles": "FB(F)F", "category": "inorganic", "synonyms": "" }, + { "name": "Carbon disulfide", "smiles": "S=C=S", "category": "inorganic", "synonyms": "" }, + { "name": "Dinitrogen tetroxide", "smiles": "O=[N+]([O-])[N+](=O)[O-]", "category": "inorganic", "synonyms": "" }, + { "name": "Nitric oxide", "smiles": "[N]=O", "category": "inorganic", "synonyms": "nitrogen monoxide", "multiplicity": 2 }, + { "name": "Nitrogen dioxide", "smiles": "[O]N=O", "category": "inorganic", "synonyms": "", "multiplicity": 2 }, + + { "name": "Hydronium", "smiles": "[OH3+]", "category": "ion", "synonyms": "oxonium", "charge": 1 }, + { "name": "Hydroxide", "smiles": "[OH-]", "category": "ion", "synonyms": "", "charge": -1 }, + { "name": "Ammonium", "smiles": "[NH4+]", "category": "ion", "synonyms": "", "charge": 1 }, + { "name": "Carbonate", "smiles": "[O-]C(=O)[O-]", "category": "ion", "synonyms": "", "charge": -2 }, + { "name": "Bicarbonate", "smiles": "OC(=O)[O-]", "category": "ion", "synonyms": "hydrogen carbonate", "charge": -1 }, + { "name": "Nitrate", "smiles": "[O-][N+](=O)[O-]", "category": "ion", "synonyms": "", "charge": -1 }, + { "name": "Nitrite", "smiles": "[O-]N=O", "category": "ion", "synonyms": "", "charge": -1 }, + { "name": "Sulfate", "smiles": "[O-]S(=O)(=O)[O-]", "category": "ion", "synonyms": "", "charge": -2 }, + { "name": "Phosphate", "smiles": "[O-]P(=O)([O-])[O-]", "category": "ion", "synonyms": "", "charge": -3 }, + { "name": "Acetate", "smiles": "CC(=O)[O-]", "category": "ion", "synonyms": "", "charge": -1 }, + { "name": "Cyanide", "smiles": "[C-]#N", "category": "ion", "synonyms": "", "charge": -1 } +] diff --git a/tests/test_curated_library.py b/tests/test_curated_library.py new file mode 100644 index 0000000..fc8766b --- /dev/null +++ b/tests/test_curated_library.py @@ -0,0 +1,121 @@ +"""Tests for the curated named library (M-STRUCT STRUCT.7). + +Platform-independent: reads the committed store + manifest (RDKit is only +needed at build time, not here). No PySCF. +""" + +import json + +from quantui import config +from quantui import molecule_library as ml + +_CURATED = ml._data_dir() / "manifests" / "curated.json" + + +def _curated_entries(): + return json.loads(_CURATED.read_text(encoding="utf-8")) + + +# ============================================================================ +# Manifest integrity +# ============================================================================ + + +class TestCuratedManifest: + def test_manifest_exists_and_nonempty(self): + entries = _curated_entries() + assert len(entries) >= 150 + + def test_every_entry_well_formed(self): + for e in _curated_entries(): + assert e["atoms"], e["name"] + assert len(e["coordinates"]) == len(e["atoms"]), e["name"] + assert e["source"] == "curated-ff" + assert e["category"] + assert e["id"] + + def test_ids_unique(self): + ids = [e["id"] for e in _curated_entries()] + assert len(ids) == len(set(ids)) + + def test_respects_heavy_atom_ceiling(self): + ceiling = config.LIBRARY_HEAVY_ATOM_CEILING_CURATED + for e in _curated_entries(): + n_heavy = sum(1 for a in e["atoms"] if a != "H") + assert n_heavy <= ceiling, f"{e['name']} has {n_heavy} heavy atoms" + + +# ============================================================================ +# Store contents after curated merge +# ============================================================================ + + +class TestStoreWithCurated: + def test_total_count_is_presets_plus_curated(self): + assert ml.count() == 20 + len(_curated_entries()) + + def test_expected_categories_present(self): + cats = set(ml.categories()) + assert { + "amino-acid", + "nucleobase", + "biomolecule", + "solvent", + "functional-group", + "hydrocarbon", + "drug", + "inorganic", + "ion", + } <= cats + + def test_all_20_amino_acids(self): + rows = ml.search("", category="amino-acid", limit=100) + assert len(rows) == 20 + + def test_aspirin_present_and_correct(self): + asp = ml.get("aspirin") + assert asp is not None + assert asp["formula"] == "C9H8O4" + assert asp["category"] == "drug" + assert asp["charge"] == 0 + + def test_ion_charges(self): + assert ml.get("nitrate")["charge"] == -1 + assert ml.get("sulfate")["charge"] == -2 + assert ml.get("phosphate")["charge"] == -3 + assert ml.get("ammonium")["charge"] == 1 + + def test_radical_multiplicities(self): + assert ml.get("nitric-oxide")["multiplicity"] == 2 + assert ml.get("nitrogen-dioxide")["multiplicity"] == 2 + + def test_search_by_synonym(self): + assert any(h["id"] == "glucose" for h in ml.search("dextrose")) + assert any(h["id"] == "paracetamol" for h in ml.search("acetaminophen")) + + +# ============================================================================ +# Back-compat dict + size budget +# ============================================================================ + + +class TestPresetDictAndBudget: + def test_preset_dict_includes_curated(self): + d = config.MOLECULE_LIBRARY + assert "aspirin" in d + assert "glycine" in d + # Presets still lead the (interim) flat dropdown. + assert list(d)[:3] == ["H2", "O2", "N2"] + + def test_curated_entry_has_legacy_shape(self): + gly = config.MOLECULE_LIBRARY["glycine"] + assert set(gly) == { + "atoms", + "coordinates", + "charge", + "multiplicity", + "description", + } + + def test_store_within_budget(self): + assert ml.db_path().stat().st_size <= config.LIBRARY_SIZE_BUDGET_BYTES diff --git a/tests/test_molecule_library.py b/tests/test_molecule_library.py index 7b651f4..c44ac58 100644 --- a/tests/test_molecule_library.py +++ b/tests/test_molecule_library.py @@ -60,8 +60,33 @@ def test_build_from_manifest_round_trips(self, tmp_path): ml.build_from_manifests(target) assert target.exists() - def test_committed_store_has_20_presets(self): - assert ml.count() == 20 + def test_store_contains_the_original_presets(self): + # The store grows as STRUCT.7/.8 add content; assert the original 20 + # presets are all still present rather than an exact total. + preset_ids = { + "H2", + "O2", + "N2", + "CO", + "HF", + "HCl", + "H2O", + "CO2", + "O3", + "H2O2", + "CH4", + "NH3", + "C2H6", + "C2H4", + "C2H2", + "CH3OH", + "CH2O", + "CH3CHO", + "CH3COOH", + "C6H6", + } + assert ml.count() >= 20 + assert all(ml.get(pid) is not None for pid in preset_ids) def test_categories_present(self): cats = ml.categories() @@ -98,7 +123,7 @@ def test_search_returns_lightweight_rows(self): class TestPresetDictBackCompat: def test_get_preset_dict_shape(self): d = ml.get_preset_dict() - assert len(d) == 20 + assert len(d) >= 20 h2o = d["H2O"] assert set(h2o) == { "atoms", @@ -110,7 +135,7 @@ def test_get_preset_dict_shape(self): def test_config_shim_resolves(self): lib = config.MOLECULE_LIBRARY - assert len(lib) == 20 + assert len(lib) >= 20 assert lib["O2"]["multiplicity"] == 3 # triplet preserved assert lib["H2O"]["coordinates"][2] == [0.0, -0.757, 0.587] From 33ea0c10a713fd39c8a2e77146fa2c1a3f54614a Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Sun, 7 Jun 2026 23:48:11 -0400 Subject: [PATCH 05/16] Add bulk QM9 library and provenance Add a bulk QM9 dataset: new manifest (quantui/data/manifests/bulk_qm9.json) and provenance file (quantui/data/library/QM9-PROVENANCE.md). Include a build script (scripts/build_bulk_library.py) and tests (tests/test_bulk_library.py), and update tests/test_curated_library.py accordingly. The repository SQLite (quantui/data/library/library.sqlite) was updated to include the new entries. The provenance notes selection criteria (1956 entries, QM9/GDB-9 source, B3LYP/6-31G(2df,p) geometries, CC0) and provides the regeneration command. --- .pre-commit-config.yaml | 4 + quantui/data/library/QM9-PROVENANCE.md | 10 ++ quantui/data/library/library.sqlite | Bin 81920 -> 876544 bytes quantui/data/manifests/bulk_qm9.json | 1 + scripts/build_bulk_library.py | 211 +++++++++++++++++++++++++ tests/test_bulk_library.py | 86 ++++++++++ tests/test_curated_library.py | 21 ++- 7 files changed, 331 insertions(+), 2 deletions(-) create mode 100644 quantui/data/library/QM9-PROVENANCE.md create mode 100644 quantui/data/manifests/bulk_qm9.json create mode 100644 scripts/build_bulk_library.py create mode 100644 tests/test_bulk_library.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ce04cbf..53c4541 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,6 +14,10 @@ repos: - id: check-merge-conflict - id: check-added-large-files args: ["--maxkb=500"] + # Bundled molecule-library package data (M-STRUCT) is intentionally + # large and governed by its own <=10 MB budget test + # (test_*_library.py); keep the 500 KB guard for everything else. + exclude: "^quantui/data/" - id: debug-statements # catch leftover breakpoint() / pdb calls # ── Strip notebook outputs before commit ───────────────────────────────── diff --git a/quantui/data/library/QM9-PROVENANCE.md b/quantui/data/library/QM9-PROVENANCE.md new file mode 100644 index 0000000..7fb6737 --- /dev/null +++ b/quantui/data/library/QM9-PROVENANCE.md @@ -0,0 +1,10 @@ +# QM9 bulk-library provenance + +- Entries shipped: 1956 (cap 2500; `category=bulk-qm9`, `source=qm9-dft`) +- Source: QM9 / GDB-9 (figshare dataset 978904) +- Tarball sha256: `3a63848ac80691bdb8d41834b575afad345b9300d7a2db0c38adb7f6eaa8360c` +- Geometries: B3LYP/6-31G(2df,p) optimized +- License: CC0 (public domain) +- Citation: Ramakrishnan, Dral, Rupp & von Lilienfeld, *Sci. 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Data 2014; GDB-9 subset; +**CC0**), parses the 133,885 B3LYP/6-31G(2df,p)-optimized structures, filters + +dedups against the curated set, stratified-samples for chemical diversity, and +writes quantui/data/manifests/bulk_qm9.json (category="bulk-qm9", +source="qm9-dft"). Then rebuild the store: + + python scripts/build_bulk_library.py [--target N] + python scripts/build_library.py + +Bulk entries are identified by formula + QM9 index and surface via search only +(excluded from the browsable preset dict). Deterministic: stratified sampling +draws in a fixed (formula-sorted, index-ordered) order — no RNG. + +The QM9 tarball (~92 MB) is cached under the system temp dir, so re-runs don't +re-download. Maintainer build step; the generated manifest + store are what ship. +""" + +import argparse +import hashlib +import json +import tarfile +import urllib.request +from collections import Counter, defaultdict +from pathlib import Path +from tempfile import gettempdir + +from rdkit import Chem, RDLogger + +from quantui import config + +RDLogger.DisableLog("rdApp.*") + +# figshare ndownloader file ids for dataset 978904. +QM9_TARBALL_URL = ( + "https://ndownloader.figshare.com/files/3195389" # dsgdb9nsd.xyz.tar.bz2 +) +QM9_UNCHAR_URL = "https://ndownloader.figshare.com/files/3195404" # uncharacterized.txt +_CACHE = Path(gettempdir()) / "quantui_qm9_cache" + +OUT = Path("quantui/data/manifests/bulk_qm9.json") +PROVENANCE = Path("quantui/data/library/QM9-PROVENANCE.md") +CURATED = Path("quantui/data/manifests/curated.json") + +DEFAULT_TARGET = 2500 # ~0.6 MB store (demo cap; raise to fill toward 10 MB) +PER_FORMULA_CAP = 4 # keep at most N isomers per formula (diversity + bounded memory) +CEILING = config.LIBRARY_HEAVY_ATOM_CEILING_BULK + + +def _download(url: str, dest: Path) -> Path: + if dest.exists(): + return dest + dest.parent.mkdir(parents=True, exist_ok=True) + print(f"Downloading {url} -> {dest} ...") + req = urllib.request.Request(url, headers={"User-Agent": "quantui-build"}) + with urllib.request.urlopen(req, timeout=120) as r, open(dest, "wb") as f: + f.write(r.read()) + print(f" {dest.stat().st_size / 1024 / 1024:.1f} MB") + return dest + + +def _hill_formula(atoms: list) -> str: + c = Counter(atoms) + parts = [] + for sym in ("C", "H"): + if c.get(sym): + parts.append(sym + (str(c[sym]) if c[sym] > 1 else "")) + del c[sym] + for sym in sorted(c): + parts.append(sym + (str(c[sym]) if c[sym] > 1 else "")) + return "".join(parts) + + +def _parse_qm9_xyz(text: str): + """Parse one QM9 .xyz → (index, atoms, coords, smiles, inchi). + + Layout: natoms / props / n atom lines / frequencies / SMILES line / + InChI line. The SMILES and InChI lines each carry two values (GDB17 and + B3LYP-relaxed); we take the relaxed (last) of each. + """ + lines = text.splitlines() + n = int(lines[0]) + index = int(lines[1].split()[1]) # 'gdb ' + atoms, coords = [], [] + for ln in lines[2 : 2 + n]: + parts = ln.split() + atoms.append(parts[0]) + # QM9 uses Fortran exponent notation like "1.23*^-6". + xyz = [float(p.replace("*^", "e")) for p in parts[1:4]] + coords.append([round(v, 6) for v in xyz]) + smiles_line = lines[2 + n + 1].split() # after the frequencies line + smiles = smiles_line[-1] if smiles_line else None + inchi_line = lines[2 + n + 2].split() + inchi = inchi_line[-1] if inchi_line else "" + return index, atoms, coords, smiles, inchi + + +def main() -> None: + ap = argparse.ArgumentParser() + ap.add_argument("--target", type=int, default=DEFAULT_TARGET) + args = ap.parse_args() + + tarball = _download(QM9_TARBALL_URL, _CACHE / "dsgdb9nsd.xyz.tar.bz2") + sha = hashlib.sha256(tarball.read_bytes()).hexdigest() + print(f"QM9 tarball sha256: {sha}") + + unchar_path = _download(QM9_UNCHAR_URL, _CACHE / "uncharacterized.txt") + uncharacterized = set() + for ln in unchar_path.read_text(encoding="utf-8", errors="replace").splitlines(): + toks = ln.split() + if toks and toks[0].isdigit(): + uncharacterized.add(int(toks[0])) + print(f"Excluding {len(uncharacterized)} uncharacterized molecules") + + curated_keys = { + e["inchikey"] + for e in json.loads(CURATED.read_text(encoding="utf-8")) + if e.get("inchikey") + } + + # Pass: bucket candidates by Hill formula (bounded per formula). + buckets: dict = defaultdict(list) + n_seen = n_kept = 0 + with tarfile.open(tarball, mode="r:bz2") as tar: + for member in tar: + if not member.name.endswith(".xyz"): + continue + n_seen += 1 + fobj = tar.extractfile(member) + if fobj is None: + continue + try: + index, atoms, coords, smiles, inchi = _parse_qm9_xyz( + fobj.read().decode("utf-8", "replace") + ) + except Exception: + continue + if index in uncharacterized: + continue + if sum(1 for a in atoms if a != "H") > CEILING: + continue + formula = _hill_formula(atoms) + if len(buckets[formula]) < PER_FORMULA_CAP: + buckets[formula].append((index, atoms, coords, smiles, inchi)) + n_kept += 1 + print(f"Scanned {n_seen} molecules; {len(buckets)} formulas, {n_kept} bucketed") + + # Stratified round-robin draw: one isomer per formula per round, formula-sorted. + order = [] + for r in range(PER_FORMULA_CAP): + for formula in sorted(buckets): + if r < len(buckets[formula]): + order.append((formula, buckets[formula][r])) + + out, seen_keys, skipped_dup = [], set(), 0 + for formula, (index, atoms, coords, smiles, inchi) in order: + if len(out) >= args.target: + break + try: + key = Chem.InchiToInchiKey(inchi) if inchi.startswith("InChI=") else None + except Exception: + key = None + if key and (key in curated_keys or key in seen_keys): + skipped_dup += 1 + continue + if key: + seen_keys.add(key) + out.append( + { + "id": f"qm9-{index}", + "name": f"{formula} (QM9 #{index})", + "formula": formula, + "category": "bulk-qm9", + "source": "qm9-dft", + "charge": 0, + "multiplicity": 1, + "smiles": smiles, + "inchikey": key, + "synonyms": "", + "description": f"{formula} — QM9 #{index} (B3LYP/6-31G(2df,p))", + "atoms": atoms, + "coordinates": coords, + } + ) + + OUT.write_text(json.dumps(out, separators=(",", ":")) + "\n", encoding="utf-8") + print(f"Wrote {len(out)} bulk entries to {OUT} (deduped {skipped_dup} vs curated)") + + PROVENANCE.parent.mkdir(parents=True, exist_ok=True) + PROVENANCE.write_text( + "# QM9 bulk-library provenance\n\n" + f"- Entries shipped: {len(out)} (cap {args.target}; " + f"`category=bulk-qm9`, `source=qm9-dft`)\n" + f"- Source: QM9 / GDB-9 (figshare dataset 978904)\n" + f"- Tarball sha256: `{sha}`\n" + "- Geometries: B3LYP/6-31G(2df,p) optimized\n" + "- License: CC0 (public domain)\n" + "- Citation: Ramakrishnan, Dral, Rupp & von Lilienfeld, " + "*Sci. Data* **1**, 140022 (2014).\n" + "- Selection: stratified by Hill formula (≤" + f"{CEILING} heavy atoms, uncharacterized excluded, " + "InChIKey-deduped vs the curated set), deterministic round-robin.\n" + "- Regenerate: `python scripts/build_bulk_library.py --target N`\n", + encoding="utf-8", + ) + print(f"Wrote provenance to {PROVENANCE}") + + +if __name__ == "__main__": + main() diff --git a/tests/test_bulk_library.py b/tests/test_bulk_library.py new file mode 100644 index 0000000..6283ae9 --- /dev/null +++ b/tests/test_bulk_library.py @@ -0,0 +1,86 @@ +"""Tests for the bulk QM9 library subset (M-STRUCT STRUCT.8). + +Platform-independent: reads the committed store + manifest (the QM9 download + +RDKit are build-time only). No PySCF. +""" + +import json + +import pytest + +from quantui import config +from quantui import molecule_library as ml + +_BULK = ml._data_dir() / "manifests" / "bulk_qm9.json" + +pytestmark = pytest.mark.skipif( + not _BULK.exists(), + reason="bulk_qm9.json not built (run scripts/build_bulk_library.py)", +) + + +def _bulk_entries(): + return json.loads(_BULK.read_text(encoding="utf-8")) + + +# ============================================================================ +# Manifest integrity +# ============================================================================ + + +class TestBulkManifest: + def test_manifest_nonempty(self): + assert len(_bulk_entries()) >= 100 + + def test_every_entry_well_formed(self): + ceiling = config.LIBRARY_HEAVY_ATOM_CEILING_BULK + for e in _bulk_entries(): + assert e["category"] == "bulk-qm9" + assert e["source"] == "qm9-dft" + assert e["charge"] == 0 and e["multiplicity"] == 1 + assert len(e["coordinates"]) == len(e["atoms"]) + assert sum(1 for a in e["atoms"] if a != "H") <= ceiling + assert e["id"].startswith("qm9-") + + def test_ids_unique(self): + ids = [e["id"] for e in _bulk_entries()] + assert len(ids) == len(set(ids)) + + def test_provenance_file_exists(self): + prov = ml._data_dir() / "library" / "QM9-PROVENANCE.md" + assert prov.exists() + assert "CC0" in prov.read_text(encoding="utf-8") + + +# ============================================================================ +# Store integration + key contracts +# ============================================================================ + + +class TestBulkInStore: + def test_total_count_includes_bulk(self): + assert ml.count() >= 176 + len(_bulk_entries()) + + def test_bulk_excluded_from_preset_dict(self): + # The browse dropdown must NOT balloon with thousands of bulk entries. + d = config.MOLECULE_LIBRARY + assert all(not k.startswith("qm9-") for k in d) + assert len(d) == 176 # presets + curated only + + def test_bulk_category_present(self): + assert "bulk-qm9" in ml.categories() + + def test_bulk_reachable_via_search(self): + rows = ml.search("", category="bulk-qm9", limit=10) + assert len(rows) == 10 + assert all(r["category"] == "bulk-qm9" for r in rows) + + def test_bulk_entry_materializes_with_coords(self): + sample_id = _bulk_entries()[0]["id"] + entry = ml.get(sample_id) + assert entry is not None + assert len(entry["coordinates"]) == len(entry["atoms"]) + assert entry["coordinates"] # non-empty + + def test_store_within_budget(self): + assert ml.db_path().stat().st_size <= config.LIBRARY_SIZE_BUDGET_BYTES diff --git a/tests/test_curated_library.py b/tests/test_curated_library.py index fc8766b..4679c2c 100644 --- a/tests/test_curated_library.py +++ b/tests/test_curated_library.py @@ -51,8 +51,25 @@ def test_respects_heavy_atom_ceiling(self): class TestStoreWithCurated: - def test_total_count_is_presets_plus_curated(self): - assert ml.count() == 20 + len(_curated_entries()) + def test_total_count_includes_presets_and_curated(self): + # Store also holds bulk entries (STRUCT.8); assert the curated tier is + # fully present rather than an exact total. + assert ml.count() >= 20 + len(_curated_entries()) + curated_rows = sum( + len(ml.search("", category=c, limit=1000)) + for c in ( + "amino-acid", + "nucleobase", + "biomolecule", + "solvent", + "functional-group", + "hydrocarbon", + "drug", + "inorganic", + "ion", + ) + ) + assert curated_rows == len(_curated_entries()) def test_expected_categories_present(self): cats = set(ml.categories()) From 99b475e33f36114dc451368de9814f667edd9202 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Mon, 8 Jun 2026 15:13:53 -0400 Subject: [PATCH 06/16] Add library browse/search UI (STRUCT.9) Replace the old preset dropdown with a browsable, searchable molecule library UI and wire handlers to load selections. app_builders.py: add category labels, a helper to build dropdown options (library_result_options), and new widgets (category dropdown, search text, results dropdown, count label); adjust PubChem placeholder and tab titles. app.py: import molecule_library, build and observe the new widgets, add _refresh_lib_results/_on_lib_filter_changed/_on_lib_select handlers to fetch entries and set the active molecule. Add tests (tests/test_struct_ui.py) covering option building, widget presence/wiring, and handler behavior (including refresh-guard and bulk entries). Improves offline browsing of bundled molecules and UX for selecting library entries. --- quantui/app.py | 62 +++++++++++++++++----- quantui/app_builders.py | 88 +++++++++++++++++++++++++----- tests/test_struct_ui.py | 115 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 239 insertions(+), 26 deletions(-) create mode 100644 tests/test_struct_ui.py diff --git a/quantui/app.py b/quantui/app.py index 4a15f09..98066d9 100644 --- a/quantui/app.py +++ b/quantui/app.py @@ -31,6 +31,7 @@ import quantui import quantui.calc_log as _calc_log import quantui.issue_tracker as _issue_tracker +from quantui import molecule_library as _ml from quantui.app_analysis import ( activate_ana_panel as _ana_activate_ana_panel, ) @@ -118,6 +119,9 @@ from quantui.app_builders import ( build_welcome_header as _bld_build_welcome_header, ) +from quantui.app_builders import ( + library_result_options as _bld_library_result_options, +) from quantui.app_exports import ( export_molecule_and_label as _exp_export_molecule_and_label, ) @@ -392,7 +396,6 @@ DEFAULT_METHOD, DEFAULT_MULTIPLICITY, DEFAULT_OPT_STEPS, - MOLECULE_LIBRARY, SUPPORTED_BASIS_SETS, SUPPORTED_METHODS, ) @@ -767,7 +770,10 @@ class QuantUIApp: past_dd: Any past_output: Any past_refresh_btn: Any - preset_dd: Any + lib_category_dd: Any + lib_search_txt: Any + lib_results_dd: Any + lib_count_lbl: Any pubchem_btn: Any pubchem_msg: Any pubchem_txt: Any @@ -1188,7 +1194,6 @@ def _build_molecule_section(self) -> None: _bld_build_molecule_section( self, layout_fn=_layout, - molecule_library=MOLECULE_LIBRARY, pubchem_available=PUBCHEM_AVAILABLE, visualization_available=VISUALIZATION_AVAILABLE, ) @@ -1454,8 +1459,14 @@ def _wire_callbacks(self) -> None: ) # Theme self.theme_btn.observe(self._safe_cb(self._on_theme_changed), names="value") - # Molecule input - self.preset_dd.observe(self._safe_cb(self._on_load_preset), names="value") + # Molecule input — library browse/search (STRUCT.9) + self.lib_category_dd.observe( + self._safe_cb(self._on_lib_filter_changed), names="value" + ) + self.lib_search_txt.observe( + self._safe_cb(self._on_lib_filter_changed), names="value" + ) + self.lib_results_dd.observe(self._safe_cb(self._on_lib_select), names="value") self.xyz_btn.on_click(self._on_load_xyz) self.pubchem_btn.on_click(self._on_search_pubchem) self.change_mol_btn.on_click(self._on_expand_mol_input) @@ -2506,19 +2517,42 @@ def _on_viz_lighting_changed(self, change) -> None: # ── Molecule input ──────────────────────────────────────────────────── - def _on_load_preset(self, change) -> None: - name = change["new"] - if name.startswith("("): + def _refresh_lib_results(self) -> None: + """Repopulate the library results dropdown from the current filters.""" + category = self.lib_category_dd.value or None + query = self.lib_search_txt.value.strip() + opts, note = _bld_library_result_options(query, category) + # Guard so resetting options/value doesn't fire _on_lib_select. + self._lib_refreshing = True + try: + self.lib_results_dd.options = opts + self.lib_results_dd.value = "" + finally: + self._lib_refreshing = False + self.lib_count_lbl.value = ( + f'{note}' + ) + + def _on_lib_filter_changed(self, change) -> None: + self._refresh_lib_results() + + def _on_lib_select(self, change) -> None: + if getattr(self, "_lib_refreshing", False): + return + entry_id = change["new"] + if not entry_id: + return + entry = _ml.get(entry_id) + if entry is None: return - d = MOLECULE_LIBRARY[name] self._set_molecule( Molecule( - atoms=d["atoms"], - coordinates=d["coordinates"], - charge=d["charge"], - multiplicity=d["multiplicity"], + atoms=entry["atoms"], + coordinates=entry["coordinates"], + charge=entry["charge"], + multiplicity=entry["multiplicity"], ), - d["description"], + entry.get("description") or entry["name"], ) def _on_load_xyz(self, btn) -> None: diff --git a/quantui/app_builders.py b/quantui/app_builders.py index 7ed3868..dcf87b4 100644 --- a/quantui/app_builders.py +++ b/quantui/app_builders.py @@ -10,8 +10,48 @@ from IPython.display import HTML, display import quantui +from quantui import molecule_library as _ml from quantui.help_content import HELP_TOPICS +# Friendlier labels for the library category filter (STRUCT.9). +_CATEGORY_LABELS = { + "diatomic": "Diatomics", + "triatomic": "Triatomics", + "small-organic": "Small organics", + "aromatic": "Aromatics", + "amino-acid": "Amino acids", + "nucleobase": "Nucleobases", + "biomolecule": "Biomolecules", + "solvent": "Solvents", + "functional-group": "Functional groups", + "hydrocarbon": "Hydrocarbons", + "drug": "Drugs", + "inorganic": "Inorganics", + "ion": "Ions", + "bulk-qm9": "Bulk (QM9)", +} + + +def _category_label(cat: str) -> str: + return _CATEGORY_LABELS.get(cat, cat.replace("-", " ").title()) + + +def library_result_options(query: str = "", category: str | None = None): + """Build (label, id) options for the library results dropdown + a count note. + + Returns ``(options, note)``. ``options`` always leads with a placeholder so + the dropdown's value can be reset without triggering a load. + """ + limit = 200 + rows = _ml.search(query, category=category, limit=limit) + opts = [("— select a molecule —", "")] + for r in rows: + opts.append((f"{r['name']} · {r['formula']}", r["id"])) + note = f"{len(rows)} match" + ("" if len(rows) == 1 else "es") + if len(rows) >= limit: + note = f"showing first {limit} — narrow with search/category" + return opts, note + def build_status_panel( app: Any, @@ -976,18 +1016,36 @@ def build_molecule_section( app: Any, *, layout_fn: Any, - molecule_library: dict[str, Any], pubchem_available: bool, visualization_available: bool, ) -> None: """Build molecule input widgets and collapsed summary container.""" - preset_opts = ["(select a molecule)"] + list(molecule_library.keys()) - app.preset_dd = widgets.Dropdown( - options=preset_opts, - value="(select a molecule)", + # ── Library browse/search (STRUCT.9) — category filter + search + results. + cat_opts = [("All categories", "")] + [ + (_category_label(c), c) for c in _ml.categories() + ] + app.lib_category_dd = widgets.Dropdown( + options=cat_opts, + value="", + description="Category:", + style={"description_width": "70px"}, + layout=layout_fn(width="260px"), + ) + app.lib_search_txt = widgets.Text( + placeholder="search name or formula (e.g. aspirin, C6H6)", + continuous_update=False, # fire on Enter/blur, not per keystroke + layout=layout_fn(width="300px"), + ) + init_opts, init_note = library_result_options() + app.lib_results_dd = widgets.Dropdown( + options=init_opts, + value="", description="Molecule:", - style={"description_width": "90px"}, - layout=layout_fn(width="320px"), + style={"description_width": "70px"}, + layout=layout_fn(width="420px"), + ) + app.lib_count_lbl = widgets.HTML( + f'{init_note}' ) app.xyz_area = widgets.Textarea( @@ -1005,7 +1063,7 @@ def build_molecule_section( app.xyz_msg = widgets.Label() app.pubchem_txt = widgets.Text( - placeholder="name or SMILES (e.g. aspirin, caffeine, CC(=O)O)", + placeholder="name, SMILES, CID, or InChI (e.g. aspirin, CC(=O)O, 2244)", layout=layout_fn(width="380px"), ) app.pubchem_btn = widgets.Button( @@ -1027,9 +1085,13 @@ def build_molecule_section( tab_preset = widgets.VBox( [ widgets.HTML( - hint + "Choose from the bundled library of curated molecules.

" + hint + "Browse the bundled library — filter by category or " + "search by name/formula. Includes thousands of small molecules " + "for offline use.

" ), - app.preset_dd, + widgets.HBox([app.lib_category_dd, app.lib_search_txt]), + app.lib_results_dd, + app.lib_count_lbl, ] ) tab_xyz = widgets.VBox( @@ -1044,14 +1106,16 @@ def build_molecule_section( tab_pubchem = widgets.VBox( [ widgets.HTML( - hint + "Search by name or SMILES. Requires internet connection.

" + hint + "Search by name, SMILES, CID, or InChI. Tries PubChem " + "then NCI CACTUS, and falls back to the bundled library offline." + "

" ), widgets.HBox([app.pubchem_txt, app.pubchem_btn]), app.pubchem_msg, ] ) input_tab = widgets.Tab(children=[tab_preset, tab_xyz, tab_pubchem]) - for i, title in enumerate(["Preset Library", "XYZ Input", "PubChem Search"]): + for i, title in enumerate(["Library", "XYZ Input", "Online Search"]): input_tab.set_title(i, title) app.mol_input_expanded = widgets.VBox( diff --git a/tests/test_struct_ui.py b/tests/test_struct_ui.py new file mode 100644 index 0000000..b537f64 --- /dev/null +++ b/tests/test_struct_ui.py @@ -0,0 +1,115 @@ +"""Tests for the library browse/search UI (M-STRUCT STRUCT.9). + +Instantiates QuantUIApp() headlessly (no .display()) and drives the library +widgets + handlers directly. Platform-independent; no PySCF. +""" + +import ipywidgets as widgets + +from quantui import molecule_library as ml +from quantui.app import QuantUIApp +from quantui.app_builders import library_result_options + +# ============================================================================ +# library_result_options helper +# ============================================================================ + + +class TestLibraryResultOptions: + def test_leads_with_placeholder(self): + opts, _ = library_result_options() + assert opts[0][1] == "" # placeholder value is empty + + def test_category_filter(self): + opts, _ = library_result_options(category="amino-acid") + ids = [v for _, v in opts if v] + assert len(ids) == 20 + + def test_search_by_formula(self): + opts, _ = library_result_options(query="C6H6") + ids = [v for _, v in opts if v] + assert "C6H6" in ids + + def test_note_reports_count(self): + _, note = library_result_options(category="aromatic") + assert "1 match" in note + + def test_note_reports_truncation(self): + _, note = library_result_options() # all categories → > 200 + assert "first 200" in note + + +# ============================================================================ +# Widgets exist + are wired +# ============================================================================ + + +class TestLibraryWidgets: + def test_library_widgets_exist(self): + app = QuantUIApp() + assert isinstance(app.lib_category_dd, widgets.Dropdown) + assert isinstance(app.lib_search_txt, widgets.Text) + assert isinstance(app.lib_results_dd, widgets.Dropdown) + assert isinstance(app.lib_count_lbl, widgets.HTML) + + def test_category_dropdown_lists_categories(self): + app = QuantUIApp() + values = [v for _, v in app.lib_category_dd.options] + assert "" in values # "All categories" + for cat in ml.categories(): + assert cat in values + + def test_search_text_is_not_continuous(self): + app = QuantUIApp() + assert app.lib_search_txt.continuous_update is False + + +# ============================================================================ +# Handlers +# ============================================================================ + + +class TestLibraryHandlers: + def test_select_loads_molecule(self): + app = QuantUIApp() + assert app._molecule is None + app._on_lib_select({"new": "aspirin"}) + assert app._molecule is not None + assert app._molecule.get_formula() == "C9H8O4" + + def test_select_placeholder_is_noop(self): + app = QuantUIApp() + app._on_lib_select({"new": ""}) + assert app._molecule is None + + def test_select_ignored_during_refresh(self): + app = QuantUIApp() + app._lib_refreshing = True + app._on_lib_select({"new": "aspirin"}) + assert app._molecule is None + + def test_filter_change_repopulates_results(self): + app = QuantUIApp() + app.lib_category_dd.value = "amino-acid" + app._on_lib_filter_changed({"new": "amino-acid"}) + ids = [v for _, v in app.lib_results_dd.options if v] + assert len(ids) == 20 + assert app.lib_results_dd.value == "" # reset to placeholder, no load + assert app._molecule is None + + def test_search_then_select_bulk_entry(self): + app = QuantUIApp() + # Pick any bulk id from the store and confirm it loads via the handler. + bulk = ml.search("", category="bulk-qm9", limit=1) + if not bulk: + return # bulk not built in this checkout + bulk_id = bulk[0]["id"] + app._on_lib_select({"new": bulk_id}) + assert app._molecule is not None + assert len(app._molecule.atoms) >= 1 + + def test_refresh_updates_count_label(self): + app = QuantUIApp() + app.lib_category_dd.value = "aromatic" + app._refresh_lib_results() + assert "1 match" in app.lib_count_lbl.value From 40001055f7733ec3c1aecd3567100a5f27a79b62 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Mon, 8 Jun 2026 16:14:29 -0400 Subject: [PATCH 07/16] Add PubChem search disambiguation Support disambiguating ambiguous name/formula PubChem queries. Adds search_cids_by_name and search_pubchem_candidates in pubchem.py to fetch lightweight candidate descriptors (cid, title, formula, mw) while preserving PubChem order. Exposes search_candidates in structure_providers.py (only for name/formula queries; network errors are swallowed to let the caller fall back). UI changes: adds a hidden dropdown for candidate pick-list, handlers to show/hide it, and a selection handler that resolves the chosen CID in a background thread and applies the result. Updates app wiring and __init__ exports. Includes unit tests (tests/test_struct_disambiguation.py) that mock network calls and exercise the backend and UI pick-list behavior. --- quantui/__init__.py | 11 ++- quantui/app.py | 99 ++++++++++++++++---- quantui/app_builders.py | 10 +++ quantui/pubchem.py | 65 ++++++++++++++ quantui/structure_providers.py | 17 ++++ tests/test_struct_disambiguation.py | 135 ++++++++++++++++++++++++++++ 6 files changed, 319 insertions(+), 18 deletions(-) create mode 100644 tests/test_struct_disambiguation.py diff --git a/quantui/__init__.py b/quantui/__init__.py index f91871e..2327305 100644 --- a/quantui/__init__.py +++ b/quantui/__init__.py @@ -137,13 +137,19 @@ get_smiles_examples, inchi_to_xyz, search_cid_by_inchikey, + search_cids_by_name, + search_pubchem_candidates, smiles_to_xyz, student_friendly_fetch, student_friendly_resolve, student_friendly_smiles_to_xyz, validate_smiles, ) - from .structure_providers import ResolvedStructure, resolve_structure + from .structure_providers import ( + ResolvedStructure, + resolve_structure, + search_candidates, + ) PUBCHEM_AVAILABLE = True except ImportError: @@ -251,9 +257,12 @@ "student_friendly_resolve", "resolve_structure", "ResolvedStructure", + "search_candidates", "fetch_from_cactus", "inchi_to_xyz", "search_cid_by_inchikey", + "search_cids_by_name", + "search_pubchem_candidates", "get_common_molecules", "check_pubchem_availability", "PubChemError", diff --git a/quantui/app.py b/quantui/app.py index 98066d9..bb22317 100644 --- a/quantui/app.py +++ b/quantui/app.py @@ -475,6 +475,9 @@ from quantui.pubchem import ( RDKIT_AVAILABLE as _PUBCHEM_RDKIT_AVAILABLE, ) + from quantui.structure_providers import ( + search_candidates as _struct_search_candidates, + ) from quantui.structure_providers import ( student_friendly_resolve as _student_friendly_resolve, ) @@ -483,6 +486,7 @@ except ImportError: PUBCHEM_AVAILABLE = False _student_friendly_resolve = None # type: ignore[assignment] + _struct_search_candidates = None # type: ignore[assignment] try: from quantui.session_calc import SessionResult, run_in_session # noqa: F401 @@ -777,6 +781,7 @@ class QuantUIApp: pubchem_btn: Any pubchem_msg: Any pubchem_txt: Any + pubchem_candidates_dd: Any result_output: Any result_viz_output: Any results_path_lbl: Any @@ -1469,6 +1474,9 @@ def _wire_callbacks(self) -> None: self.lib_results_dd.observe(self._safe_cb(self._on_lib_select), names="value") self.xyz_btn.on_click(self._on_load_xyz) self.pubchem_btn.on_click(self._on_search_pubchem) + self.pubchem_candidates_dd.observe( + self._safe_cb(self._on_pubchem_candidate_selected), names="value" + ) self.change_mol_btn.on_click(self._on_expand_mol_input) # Calc type self.calc_type_dd.observe( @@ -2587,14 +2595,74 @@ def _apply_pubchem_search_result( pass self.pubchem_btn.disabled = False + def _resolve_and_apply(self, query: str, loop) -> None: + """Resolve a single query (background thread) and apply on the main loop.""" + try: + xyz_str, _msg = _student_friendly_resolve(query) + if xyz_str is None: + raise ValueError(_msg) + atoms, coords = parse_xyz_input(xyz_str) + mol = Molecule(atoms=atoms, coordinates=coords) + loop.call_soon_threadsafe( + self._apply_pubchem_search_result, query, mol, None + ) + except Exception as exc: + loop.call_soon_threadsafe( + self._apply_pubchem_search_result, query, None, exc + ) + + def _hide_pubchem_candidates(self) -> None: + """Clear + hide the disambiguation pick-list.""" + self._pubchem_cand_refreshing = True + try: + self.pubchem_candidates_dd.options = [("— pick a match —", "")] + self.pubchem_candidates_dd.value = "" + self.pubchem_candidates_dd.layout.display = "none" + finally: + self._pubchem_cand_refreshing = False + + def _show_pubchem_candidates(self, query: str, candidates: list) -> None: + """Populate + reveal the pick-list when a query has multiple matches.""" + opts = [(f"pick one of {len(candidates)} matches…", "")] + for c in candidates: + mw = c.get("mw") or 0.0 + opts.append( + (f"{c['title']} · {c['formula']} · {mw:.1f} g/mol", str(c["cid"])) + ) + self._pubchem_cand_refreshing = True + try: + self.pubchem_candidates_dd.options = opts + self.pubchem_candidates_dd.value = "" + self.pubchem_candidates_dd.layout.display = "" + finally: + self._pubchem_cand_refreshing = False + self.pubchem_msg.value = ( + f'{len(candidates)} matches for "{query}" — pick one below.' + ) + self.pubchem_btn.disabled = False + + def _on_pubchem_candidate_selected(self, change) -> None: + if getattr(self, "_pubchem_cand_refreshing", False): + return + cid = change["new"] + if not cid: + return + self.pubchem_msg.value = f"Loading CID {cid}…" + self.pubchem_btn.disabled = True + loop = asyncio.get_running_loop() + threading.Thread( + target=lambda: self._resolve_and_apply(str(cid), loop), daemon=True + ).start() + def _on_search_pubchem(self, btn) -> None: query = self.pubchem_txt.value.strip() if not query: - self.pubchem_msg.value = "Enter a molecule name or SMILES." + self.pubchem_msg.value = "Enter a molecule name, SMILES, CID, or InChI." return if _student_friendly_resolve is None: - self.pubchem_msg.value = "PubChem module not available." + self.pubchem_msg.value = "Structure search not available." return + self._hide_pubchem_candidates() self.pubchem_msg.value = f'Searching for "{query}"...' self.pubchem_btn.disabled = True @@ -2602,24 +2670,21 @@ def _on_search_pubchem(self, btn) -> None: def _do(): try: - xyz_str, _msg = _student_friendly_resolve(query) - if xyz_str is None: - raise ValueError(_msg) - atoms, coords = parse_xyz_input(xyz_str) - mol = Molecule(atoms=atoms, coordinates=coords) - loop.call_soon_threadsafe( - self._apply_pubchem_search_result, - query, - mol, - None, + candidates = ( + _struct_search_candidates(query) + if _struct_search_candidates is not None + else [] ) - except Exception as exc: + except Exception: + candidates = [] + if len(candidates) > 1: loop.call_soon_threadsafe( - self._apply_pubchem_search_result, - query, - None, - exc, + self._show_pubchem_candidates, query, candidates ) + return + # 0 or 1 match → resolve via the full chain (PubChem → CACTUS → + # offline library), which also handles SMILES/InChI/CID locally. + self._resolve_and_apply(query, loop) threading.Thread(target=_do, daemon=True).start() diff --git a/quantui/app_builders.py b/quantui/app_builders.py index dcf87b4..3644b5b 100644 --- a/quantui/app_builders.py +++ b/quantui/app_builders.py @@ -1080,6 +1080,15 @@ def build_molecule_section( else "PubChem unavailable — check internet connection" ) ) + # Disambiguation pick-list (STRUCT.5) — hidden until a query has >1 match. + app.pubchem_candidates_dd = widgets.Dropdown( + options=[("— pick a match —", "")], + value="", + description="Matches:", + style={"description_width": "70px"}, + layout=layout_fn(width="460px"), + ) + app.pubchem_candidates_dd.layout.display = "none" hint = '

' tab_preset = widgets.VBox( @@ -1112,6 +1121,7 @@ def build_molecule_section( ), widgets.HBox([app.pubchem_txt, app.pubchem_btn]), app.pubchem_msg, + app.pubchem_candidates_dd, ] ) input_tab = widgets.Tab(children=[tab_preset, tab_xyz, tab_pubchem]) diff --git a/quantui/pubchem.py b/quantui/pubchem.py index 6e111d2..9ceb49b 100644 --- a/quantui/pubchem.py +++ b/quantui/pubchem.py @@ -167,6 +167,71 @@ def search_cid_by_inchikey(inchikey: str) -> int: raise PubChemAPIError(f"Failed to connect to PubChem: {e}") +def search_cids_by_name(name: str) -> list: + """Return ALL PubChem CIDs matching a name (best-match order); [] if none. + + Unlike :func:`search_molecule_by_name` (which returns just the first hit), + this exposes every match so the UI can disambiguate (STRUCT.5). + """ + url = f"{PUBCHEM_BASE_URL}/compound/name/{quote(name, safe='')}/cids/JSON" + try: + response = _http_get(url) + if response.status_code == 404: + return [] + response.raise_for_status() + return [ + int(c) for c in response.json().get("IdentifierList", {}).get("CID", []) + ] + except requests.RequestException as e: + logger.error(f"PubChem CID-list request failed: {e}") + raise PubChemAPIError(f"Failed to connect to PubChem: {e}") + + +def search_pubchem_candidates(query: str, max_results: int = 10) -> list: + """Lightweight candidate descriptors for an ambiguous name query. + + Returns a list of ``{cid, title, formula, mw}`` dicts (best-match order, + capped at ``max_results``), or ``[]`` if nothing matches. Uses one batch + property request rather than fetching each full structure. + """ + cids = search_cids_by_name(query)[:max_results] + if not cids: + return [] + cid_str = ",".join(str(c) for c in cids) + url = ( + f"{PUBCHEM_BASE_URL}/compound/cid/{cid_str}" + f"/property/MolecularFormula,MolecularWeight,Title/JSON" + ) + try: + response = _http_get(url) + response.raise_for_status() + props = response.json().get("PropertyTable", {}).get("Properties", []) + except requests.RequestException as e: + logger.error(f"PubChem property request failed: {e}") + raise PubChemAPIError(f"Failed to connect to PubChem: {e}") + + # Preserve the CID search order (the property endpoint may reorder). + by_cid = {int(p.get("CID")): p for p in props if p.get("CID") is not None} + out = [] + for cid in cids: + p = by_cid.get(cid) + if p is None: + continue + try: + mw = float(p.get("MolecularWeight", 0) or 0) + except (TypeError, ValueError): + mw = 0.0 + out.append( + { + "cid": cid, + "title": p.get("Title") or f"CID {cid}", + "formula": p.get("MolecularFormula", "?"), + "mw": mw, + } + ) + return out + + @lru_cache(maxsize=50) def get_molecule_sdf(cid: int, conformer_3d: bool = True) -> str: """ diff --git a/quantui/structure_providers.py b/quantui/structure_providers.py index 9079d97..907b70c 100644 --- a/quantui/structure_providers.py +++ b/quantui/structure_providers.py @@ -31,6 +31,7 @@ PubChemAPIError, classify_query, fetch_structure, + search_pubchem_candidates, ) logger = logging.getLogger(__name__) @@ -192,6 +193,22 @@ def resolve_structure( ) +def search_candidates(query: str) -> List[Dict[str, Any]]: + """Return disambiguation candidates for a multi-match name/formula query. + + Only name/formula queries can be ambiguous (SMILES/InChI/CID resolve to a + single structure, and the local library is exact). Returns ``[]`` for those + types, and ``[]`` on any network failure so the caller falls back to the + full single-result chain (PubChem → CACTUS → offline library). + """ + if classify_query(query) not in ("name", "formula"): + return [] + try: + return search_pubchem_candidates(query) + except (MoleculeNotFoundError, PubChemAPIError): + return [] + + def student_friendly_resolve(query: str) -> Tuple[Optional[str], str]: """Chain-backed, student-friendly resolve. Drop-in for the UI handler. diff --git a/tests/test_struct_disambiguation.py b/tests/test_struct_disambiguation.py new file mode 100644 index 0000000..00b1222 --- /dev/null +++ b/tests/test_struct_disambiguation.py @@ -0,0 +1,135 @@ +"""Tests for online-search disambiguation (M-STRUCT STRUCT.5). + +Platform-independent: network mocked, no PySCF. Exercises the candidate +backend + the app pick-list handlers (no event loop / no real threads). +""" + +from unittest.mock import Mock, patch + +from quantui import structure_providers +from quantui.app import QuantUIApp +from quantui.pubchem import search_pubchem_candidates + +_XYLENE_CIDS = [7237, 7929, 7809] # o-, m-, p-xylene +_XYLENE_PROPS = { + "PropertyTable": { + "Properties": [ + { + "CID": 7237, + "MolecularFormula": "C8H10", + "MolecularWeight": "106.16", + "Title": "o-Xylene", + }, + { + "CID": 7929, + "MolecularFormula": "C8H10", + "MolecularWeight": "106.16", + "Title": "m-Xylene", + }, + { + "CID": 7809, + "MolecularFormula": "C8H10", + "MolecularWeight": "106.16", + "Title": "p-Xylene", + }, + ] + } +} + + +# ============================================================================ +# Backend: search_pubchem_candidates / search_candidates +# ============================================================================ + + +class TestCandidateBackend: + @patch("quantui.pubchem._http_get") + @patch("quantui.pubchem.search_cids_by_name") + def test_candidates_built_from_batch_props(self, mock_cids, mock_http): + mock_cids.return_value = _XYLENE_CIDS + mock_http.return_value = Mock( + status_code=200, + json=Mock(return_value=_XYLENE_PROPS), + raise_for_status=Mock(), + ) + cands = search_pubchem_candidates("xylene") + assert [c["cid"] for c in cands] == _XYLENE_CIDS # search order preserved + assert cands[0]["title"] == "o-Xylene" + assert cands[0]["formula"] == "C8H10" + assert abs(cands[0]["mw"] - 106.16) < 0.01 + + @patch("quantui.pubchem.search_cids_by_name") + def test_candidates_empty_when_no_cids(self, mock_cids): + mock_cids.return_value = [] + assert search_pubchem_candidates("zzznotreal") == [] + + def test_search_candidates_skips_non_name_types(self): + # SMILES / CID resolve to a single structure → no disambiguation. + assert structure_providers.search_candidates("CC(=O)O") == [] + assert structure_providers.search_candidates("962") == [] + + @patch("quantui.structure_providers.search_pubchem_candidates") + def test_search_candidates_swallows_network_error(self, mock_cands): + from quantui.pubchem import PubChemAPIError + + mock_cands.side_effect = PubChemAPIError("offline") + # Falls back to [] so the caller uses the full single-result chain. + assert structure_providers.search_candidates("xylene") == [] + + @patch("quantui.structure_providers.search_pubchem_candidates") + def test_search_candidates_returns_list_for_name(self, mock_cands): + mock_cands.return_value = [ + {"cid": 1, "title": "x", "formula": "CH4", "mw": 16.0} + ] + out = structure_providers.search_candidates("methane") + assert len(out) == 1 + + +# ============================================================================ +# App pick-list handlers +# ============================================================================ + + +class TestPickListHandlers: + def test_candidates_dropdown_hidden_initially(self): + app = QuantUIApp() + assert app.pubchem_candidates_dd.layout.display == "none" + + def test_show_candidates_populates_and_reveals(self): + app = QuantUIApp() + cands = [ + {"cid": 7237, "title": "o-Xylene", "formula": "C8H10", "mw": 106.16}, + {"cid": 7929, "title": "m-Xylene", "formula": "C8H10", "mw": 106.16}, + ] + app._show_pubchem_candidates("xylene", cands) + values = [v for _, v in app.pubchem_candidates_dd.options] + assert values == ["", "7237", "7929"] # placeholder + 2 cids + assert app.pubchem_candidates_dd.layout.display == "" + assert "2 matches" in app.pubchem_msg.value + # Showing the list must not auto-load a molecule. + assert app._molecule is None + + def test_hide_candidates_resets(self): + app = QuantUIApp() + app._show_pubchem_candidates( + "xylene", + [ + {"cid": 1, "title": "a", "formula": "C8H10", "mw": 1.0}, + {"cid": 2, "title": "b", "formula": "C8H10", "mw": 1.0}, + ], + ) + app._hide_pubchem_candidates() + assert app.pubchem_candidates_dd.layout.display == "none" + assert app.pubchem_candidates_dd.value == "" + + def test_candidate_select_placeholder_is_noop(self): + app = QuantUIApp() + app._on_pubchem_candidate_selected({"new": ""}) + assert app._molecule is None + + def test_candidate_select_ignored_during_refresh(self): + app = QuantUIApp() + app._pubchem_cand_refreshing = True + # Should return before touching the event loop / spawning a thread. + app._on_pubchem_candidate_selected({"new": "7237"}) + assert app._molecule is None From 2c6c00d2c98dac9e37f4bcebe5fbf5d0f4dad656 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Mon, 8 Jun 2026 21:48:11 -0400 Subject: [PATCH 08/16] Add library governance tests and iter_entries MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Add whole-library governance tests and support for efficient iteration. A new tests/test_library_governance.py validates every shipped library entry (well-formed atoms/coords, unique ids, coordinate round-trip stability), enforces the ≤10MB library budget, checks the preset/bulk contract, and ensures build scripts are present in-dev. molecule_library.iter_entries() was added to yield full decoded entries from the store (or fall back to the JSON manifest) for efficient whole-library checks. Also update help content: clarify Molecule Input instructions and add a "Finding a molecule" help topic explaining Library, XYZ input, and Online Search behaviors and provenance. --- quantui/help_content.py | 36 ++++++++++- quantui/molecule_library.py | 18 ++++++ tests/test_library_governance.py | 102 +++++++++++++++++++++++++++++++ 3 files changed, 154 insertions(+), 2 deletions(-) create mode 100644 tests/test_library_governance.py diff --git a/quantui/help_content.py b/quantui/help_content.py index 6b1c9c2..96ffc95 100644 --- a/quantui/help_content.py +++ b/quantui/help_content.py @@ -28,8 +28,10 @@ "body": ( "

How to run a calculation:

" "
    " - "
  1. Select or enter a molecule in Molecule Input (XYZ text, " - "SMILES string, library preset, or PubChem search)
    2. " + "
  2. Select or enter a molecule in Molecule Input — browse the " + "Library, paste XYZ, or use Online Search " + "(name, SMILES, CID, or InChI). See the " + "Finding a molecule help topic.
    3. " "
  3. Choose a calculation type, method, and basis set in " "Calculation Setup
    4. " "
  4. Click Run Calculation — results appear in the " @@ -305,6 +307,36 @@ "in the QuantUI repo.

    " ), }, + "finding_structures": { + "title": "Finding a molecule (library, search, SMILES)", + "body": ( + "

    The Molecule Input panel offers three ways to get a " + "starting structure — all of which work fully offline except the " + "Online Search.

    " + "
      " + "
    • Library — browse the bundled offline library: filter by " + "category (amino acids, solvents, drugs, …) or type in the " + "search box to match by name or formula. It includes a small " + "curated set plus thousands of small molecules (QM9), so you can " + "work with no internet connection.
      • " + "
    • XYZ Input — paste raw element x y z " + "coordinates, one atom per line.
      • " + "
    • Online Search — type a name (aspirin), " + "SMILES (CC(=O)O), CID (2244), or " + "InChI. SMILES/InChI are built locally by RDKit (no network); " + "names and CIDs are resolved by trying PubChem, then " + "NCI CACTUS (which also understands CAS numbers), and finally " + "the bundled library if you are offline. When a name matches several " + "compounds (e.g. xylene), a pick-list appears so you " + "choose the right one instead of guessing.
      • " + "
    " + "

    Provenance: the status line states where a structure came " + "from — the library, a local SMILES build, PubChem, or CACTUS — so " + "you know whether coordinates are experimental, DFT-optimized, or " + "force-field-embedded. Either way, treat them as a starting " + "point and run a geometry optimization for accurate results.

    " + ), + }, } # All valid topic keys (for testing / discovery) diff --git a/quantui/molecule_library.py b/quantui/molecule_library.py index 566af29..5677864 100644 --- a/quantui/molecule_library.py +++ b/quantui/molecule_library.py @@ -413,3 +413,21 @@ def count() -> int: finally: con.close() return len(_manifest_entries()) + + +def iter_entries(): + """Yield every entry (full, with decoded coordinates) in store order. + + Single connection — efficient for whole-library governance/round-trip + checks (STRUCT.10). Falls back to the JSON manifest if the store is absent. + """ + con = _connect_ro() + if con is None: + for raw in _manifest_entries(): + yield _normalize_entry(raw) + return + try: + for row in con.execute("SELECT * FROM molecule ORDER BY rowid"): + yield _row_to_entry(row) + finally: + con.close() diff --git a/tests/test_library_governance.py b/tests/test_library_governance.py new file mode 100644 index 0000000..92d5720 --- /dev/null +++ b/tests/test_library_governance.py @@ -0,0 +1,102 @@ +"""Whole-library governance + round-trip checks (M-STRUCT STRUCT.10). + +Validates *every* shipped entry (across all tiers) — well-formed, coordinate +round-trip stable, ids globally unique — plus the ≤10 MB budget and the +preset-dict/bulk contract. Platform-independent; no PySCF, no network. +""" + +import math + +import pytest + +from quantui import config +from quantui import molecule_library as ml + +# Reasonable element-symbol whitelist for the bundled tiers (CHONF + curated +# heteroatoms + common ions). Guards against codec corruption. +_KNOWN = { + "H", + "He", + "Li", + "Be", + "B", + "C", + "N", + "O", + "F", + "Ne", + "Na", + "Mg", + "Al", + "Si", + "P", + "S", + "Cl", + "Ar", + "K", + "Ca", + "Br", + "I", +} + + +class TestEveryEntryWellFormed: + def test_all_entries_consistent(self): + seen_ids = set() + for e in ml.iter_entries(): + eid = e["id"] + assert eid not in seen_ids, f"duplicate id {eid}" + seen_ids.add(eid) + atoms, coords = e["atoms"], e["coordinates"] + assert atoms, eid + assert len(atoms) == len(coords) == e["n_atoms"], eid + assert e["n_heavy"] == sum(1 for a in atoms if a != "H"), eid + assert isinstance(e["charge"], int) and isinstance(e["multiplicity"], int) + assert e["formula"], eid + assert e["category"] and e["source"], eid + for sym in atoms: + assert sym in _KNOWN, f"{eid}: unexpected symbol {sym!r}" + for xyz in coords: + assert len(xyz) == 3, eid + + def test_coordinate_round_trip_is_stable(self): + # Re-encoding the stored (already-decoded) coords must be idempotent at + # the codec's 0.001 Å resolution. + for e in ml.iter_entries(): + atoms, coords = e["atoms"], e["coordinates"] + blob = ml.encode_coords(atoms, coords) + out_atoms, out_coords = ml.decode_coords(blob) + assert out_atoms == atoms, e["id"] + for a, b in zip(coords, out_coords): + for ca, cb in zip(a, b): + assert math.isclose(ca, cb, abs_tol=1e-6), e["id"] + + +class TestBudgetAndContracts: + def test_store_within_10mb_budget(self): + size = ml.db_path().stat().st_size + assert size <= config.LIBRARY_SIZE_BUDGET_BYTES, f"{size} bytes > budget" + + def test_iter_count_matches_count(self): + assert sum(1 for _ in ml.iter_entries()) == ml.count() + + def test_preset_dict_is_non_bulk_only(self): + d = ml.get_preset_dict() + non_bulk = sum( + 1 for e in ml.iter_entries() if e["category"] not in ml._BULK_CATEGORIES + ) + assert len(d) == non_bulk + assert all(not k.startswith("qm9-") for k in d) + + def test_reproducible_build_tooling_present(self): + # No-silent-cap governance: the deterministic builders ship in-repo and + # report skips/dedup counts to stdout (not hidden truncation). + scripts = ml._data_dir().parent.parent / "scripts" + if not scripts.is_dir(): + pytest.skip("scripts/ not present (non-dev install)") + for name in ( + "build_library.py", + "build_curated_library.py", + "build_bulk_library.py", + ): + assert (scripts / name).exists(), name From e9238c2cdf496474ab8dcf1d8f0b6204fb7dbad3 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Mon, 8 Jun 2026 23:45:57 -0400 Subject: [PATCH 09/16] Preserve log scroll and fix SDF 3D embedding UI: install a stronger scroll guard that disables browser scroll-anchoring (overflow-anchor: none) on the log and its scrollable ancestors to prevent the page from jumping when new output lines arrive, while keeping the existing stick-to-bottom behavior. Chemistry: improve sdf_to_xyz robustness with RDKit by preserving explicit Hs (removeHs=False), adding hydrogens with coordinates (AddHs(..., addCoords=True)) to avoid Hs defaulting to the origin, detecting flat/2D conformers and re-embedding to 3D, and using MMFF optimization with a UFF fallback (and an Embed fallback using random coords) to avoid degenerate geometries that caused STRUCT.12 valence errors. Tests: add a test that a 2D SDF is re-embedded to a genuine 3D structure and that atoms are not coincident (prevents Hs piling at 0,0,0). --- quantui/app.py | 26 ++++++++++++++++++++++---- quantui/pubchem.py | 32 +++++++++++++++++++++++--------- tests/test_struct_resolver.py | 32 ++++++++++++++++++++++++++++++++ 3 files changed, 77 insertions(+), 13 deletions(-) diff --git a/quantui/app.py b/quantui/app.py index bb22317..cdc6207 100644 --- a/quantui/app.py +++ b/quantui/app.py @@ -3402,10 +3402,14 @@ def _queue_main_thread_callback(self, callback, *args, **kwargs) -> None: def _install_run_output_scroll_guard(self) -> None: """Install a JS guard that preserves live-log scroll behavior. - The Output widget can reset scroll position during high-frequency - append_stdout updates in notebook/Voila frontends. This observer keeps - the log pinned to the bottom while the user is already at the bottom, - and preserves manual scrolling when the user scrolls up. + Two parts (BUG-SCROLL, reopened 2026-06-08): + + 1. Disable browser **scroll-anchoring** (``overflow-anchor: none``) on the + log and its scrollable ancestors — appending a line otherwise makes + the browser nudge the *page* scroll, the "screen jumps up on each new + output line" symptom. + 2. Keep the internal log pinned to the bottom while the user is already + at the bottom, and preserve manual scroll-up. """ if self._run_output_scroll_guard_installed: return @@ -3445,6 +3449,20 @@ def _install_run_output_scroll_guard(self) -> None: root.setAttribute(ROOT_MARK, "1"); + // Disable browser scroll-anchoring on the log and every scrollable + // ancestor (incl. the page scroller). Without this, appending a line + // inside the log makes the browser nudge the *page* scroll to keep an + // anchor element stable — the user-visible "screen jumps up" on each + // new output line (BUG-SCROLL). + try { + scroller.style.overflowAnchor = "none"; + for (let el = root; el && el !== document.documentElement; el = el.parentElement) { + el.style.overflowAnchor = "none"; + } + document.documentElement.style.overflowAnchor = "none"; + if (document.body) document.body.style.overflowAnchor = "none"; + } catch (e) { /* styling best-effort */ } + const thresholdPx = 24; let stickToBottom = true; diff --git a/quantui/pubchem.py b/quantui/pubchem.py index 9ceb49b..1e34908 100644 --- a/quantui/pubchem.py +++ b/quantui/pubchem.py @@ -296,20 +296,34 @@ def sdf_to_xyz(sdf_content: str) -> Tuple[str, Dict[str, Any]]: raise ImportError("RDKit is required for SDF to XYZ conversion") try: - # Parse SDF with RDKit - mol = Chem.MolFromMolBlock(sdf_content) + # Parse SDF with RDKit, keeping any explicit hydrogens (3D PubChem SDFs + # already carry them with real coordinates). + mol = Chem.MolFromMolBlock(sdf_content, removeHs=False) if mol is None: raise ValueError("Failed to parse SDF content") - # Add hydrogens if not present - mol = Chem.AddHs(mol) - - # Generate 3D coordinates if needed - coords_embedded = mol.GetNumConformers() == 0 + # Add any missing hydrogens *with* coordinates. Without addCoords the + # new H default to the origin, which — combined with a 2D SDF — yields a + # degenerate geometry (atoms piled at 0,0,0) that bond perception then + # reads as absurd valences (STRUCT.12). + mol = Chem.AddHs(mol, addCoords=True) + + # Re-embed in 3D whenever there is no conformer, or the conformer is 2D + # (PubChem's 3D→2D fallback). A flat conformer must not be returned as a + # "3D" structure. + conf = mol.GetConformer() if mol.GetNumConformers() else None + coords_embedded = conf is None or not conf.Is3D() if coords_embedded: - AllChem.EmbedMolecule(mol, randomSeed=42) - AllChem.UFFOptimizeMolecule(mol) + if AllChem.EmbedMolecule(mol, randomSeed=42) != 0: + AllChem.EmbedMolecule(mol, randomSeed=42, useRandomCoords=True) + try: + AllChem.MMFFOptimizeMolecule(mol) + except Exception: + try: + AllChem.UFFOptimizeMolecule(mol) + except Exception: + pass # Extract coordinates and build XYZ string conf = mol.GetConformer() diff --git a/tests/test_struct_resolver.py b/tests/test_struct_resolver.py index 89338eb..a5a2bbd 100644 --- a/tests/test_struct_resolver.py +++ b/tests/test_struct_resolver.py @@ -237,3 +237,35 @@ def test_sdf_with_3d_coords_not_flagged_embedded(self, sample_sdf_water): assert "coords_embedded" in meta # The fixture SDF already carries 3D coords, so RDKit should not embed. assert meta["coords_embedded"] is False + + @rdkit_only + def test_2d_sdf_is_reembedded_to_3d_no_atoms_piled(self): + """STRUCT.12 regression: a 2D SDF (H added without coords in the old + code piled them at the origin → 'valence 13') must come back as a real + 3D structure with every atom at a distinct position.""" + import math + + from rdkit import Chem + from rdkit.Chem import AllChem + + from quantui.pubchem import sdf_to_xyz + + m = Chem.MolFromSmiles("CCO") # ethanol, no explicit H + AllChem.Compute2DCoords(m) # 2D conformer, flagged 2D + sdf_2d = Chem.MolToMolBlock(m) + + xyz, meta = sdf_to_xyz(sdf_2d) + assert meta["coords_embedded"] is True # we re-embedded the 2D input + + coords = [ + [float(c) for c in line.split()[1:4]] + for line in xyz.strip().splitlines()[2:] + ] + assert len(coords) == meta["num_atoms"] == 9 # C2H6O + # No two atoms coincide (the old bug piled all H at 0,0,0). + for i in range(len(coords)): + for j in range(i + 1, len(coords)): + d = math.dist(coords[i], coords[j]) + assert d > 0.5, f"atoms {i},{j} only {d:.3f} Å apart" + # Genuinely 3D, not flat. + assert max(abs(c[2]) for c in coords) > 1e-3 From 8611209f80a2e2e31e146825691b646e190d73d2 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Wed, 10 Jun 2026 10:25:18 -0400 Subject: [PATCH 10/16] Address scrolling, timeouts, and fragment overlap Fix several UI, network, and molecule-embedding issues: - app.py: improve log auto-scroll logic by tracking lastScrollHeight and handling mutations that indicate the log was cleared so the view correctly "follows" new output (prevents scrollbar sticking / BUG-SCROLL). - app_builders.py: set fixed heights for the visualization and run-output containers to avoid layout reflows and scrollbar jumps when swapping content or streaming output. - config.py / cactus.py: add a separate CACTUS connect timeout and use a (connect, read) timeout tuple for requests; lower the CACTUS read timeout to avoid slow/hanging fallback requests. - pubchem.py: add _separate_fragments to radially separate disconnected fragments (e.g. salts/counterions) after embedding so bond perception doesn't treat counterions as bonded (resolves STRUCT.14). Call this helper from sdf_to_xyz, smiles_to_xyz, and inchi_to_xyz. - tests: add a unit test ensuring a chloride counterion is placed well separated from an ammonium cation. These changes prevent UI scrolling regressions, make CACTUS lookups fail fast on network problems, and avoid embedding-related rendering failures for salts. --- quantui/app.py | 16 +++++++++-- quantui/app_builders.py | 12 ++++++-- quantui/cactus.py | 5 +++- quantui/config.py | 7 +++-- quantui/pubchem.py | 52 +++++++++++++++++++++++++++++++++++ tests/test_struct_resolver.py | 24 ++++++++++++++++ 6 files changed, 107 insertions(+), 9 deletions(-) diff --git a/quantui/app.py b/quantui/app.py index cdc6207..55c58ab 100644 --- a/quantui/app.py +++ b/quantui/app.py @@ -3465,13 +3465,23 @@ def _install_run_output_scroll_guard(self) -> None: const thresholdPx = 24; let stickToBottom = true; + let lastScrollHeight = scroller.scrollHeight; const updateStickFlag = () => { const dist = scroller.scrollHeight - scroller.clientHeight - scroller.scrollTop; stickToBottom = dist <= thresholdPx; }; - const pinIfNeeded = () => { + const onMutation = () => { + // A large shrink means the log was cleared for a new run — re-arm + // "follow". Without this, stickToBottom stays false from a previous + // manual scroll-up and the new run's output streams while the log + // sits at the top (BUG-SCROLL, confirmed via DevTools: scrollTop + // stuck at 0 while content grew). + if (scroller.scrollHeight < lastScrollHeight - thresholdPx) { + stickToBottom = true; + } + lastScrollHeight = scroller.scrollHeight; if (stickToBottom) { scroller.scrollTop = scroller.scrollHeight; } @@ -3479,11 +3489,11 @@ def _install_run_output_scroll_guard(self) -> None: scroller.addEventListener("scroll", updateStickFlag, { passive: true }); - const obs = new MutationObserver(pinIfNeeded); + const obs = new MutationObserver(onMutation); obs.observe(root, { childList: true, subtree: true, characterData: true }); updateStickFlag(); - pinIfNeeded(); + onMutation(); } function scanAndInstall() { diff --git a/quantui/app_builders.py b/quantui/app_builders.py index 3644b5b..f7717ff 100644 --- a/quantui/app_builders.py +++ b/quantui/app_builders.py @@ -491,12 +491,18 @@ def build_shared_widgets( value='No molecule loaded yet.' ) app.mol_summary_compact = widgets.HTML(value="") - app.viz_output = widgets.Output(layout=layout_fn(min_height="50px")) + # Fixed heights reserve space so swapping content (backend/palette toggle) + # or streaming output never resizes the container — which would reflow the + # page and jump the scrollbar (BUG-SCROLL). The molecule viewer renders at + # render_molecule_html's default 500px; the run log scrolls internally. + # overflow hidden (not auto): the 3D viewer is a fixed-size canvas, so it + # needs no scrollbar — clipping a few px of margin avoids an internal + # scrollbar that resets to the top on every backend/palette swap. + app.viz_output = widgets.Output(layout=layout_fn(height="510px", overflow="hidden")) app.run_output = widgets.Output( layout=layout_fn( border="1px solid #c0ccd8", - min_height="80px", - max_height="400px", + height="300px", padding="8px", overflow_y="auto", ) diff --git a/quantui/cactus.py b/quantui/cactus.py index dd96caf..94eb697 100644 --- a/quantui/cactus.py +++ b/quantui/cactus.py @@ -51,11 +51,14 @@ def resolve_to_sdf(identifier: str, conformer_3d: bool = True) -> str: urls.append(f"{CACTUS_BASE_URL}/{enc}/file?format=sdf&get3d=true") urls.append(f"{CACTUS_BASE_URL}/{enc}/sdf") + # (connect, read) timeouts: fail fast on an unreachable host, and cap the + # read so a slow CACTUS can't hang the search (it's only a fallback). + timeout = (config.CACTUS_CONNECT_TIMEOUT_S, config.CACTUS_TIMEOUT_S) last_status = None try: for url in urls: logger.debug(f"CACTUS resolving: {url}") - response = requests.get(url, timeout=config.CACTUS_TIMEOUT_S) + response = requests.get(url, timeout=timeout) last_status = response.status_code if response.status_code == 200 and _looks_like_sdf(response.text): return str(response.text) diff --git a/quantui/config.py b/quantui/config.py index 5033199..f899bea 100644 --- a/quantui/config.py +++ b/quantui/config.py @@ -242,8 +242,11 @@ PUBCHEM_MIN_REQUEST_INTERVAL_S: float = 0.25 # NCI CACTUS Chemical Identifier Resolver — chained fallback after PubChem -# (resolves name / CAS / InChI / SMILES → 3D SDF; no API key). -CACTUS_TIMEOUT_S: float = 15.0 +# (resolves name / CAS / InChI / SMILES → 3D SDF; no API key). CACTUS is often +# slow/down, so keep the read timeout short — it's only a fallback and must not +# hang the search. Connect timeout fails fast when the host is unreachable. +CACTUS_TIMEOUT_S: float = 8.0 +CACTUS_CONNECT_TIMEOUT_S: float = 4.0 # Bundled-library size budget + heavy-atom ceilings (M-STRUCT STRUCT.7/.8/.10). # These are QC *starting* geometries, so keep them runnable in a classroom. diff --git a/quantui/pubchem.py b/quantui/pubchem.py index 1e34908..97a4c2e 100644 --- a/quantui/pubchem.py +++ b/quantui/pubchem.py @@ -277,6 +277,51 @@ def get_molecule_sdf(cid: int, conformer_3d: bool = True) -> str: raise PubChemAPIError(f"Failed to retrieve molecule: {e}") +def _separate_fragments(mol: Any, min_gap: float = 3.0) -> None: + """Push disconnected fragments (e.g. a salt's counterion) apart, in place. + + RDKit's ``EmbedMolecule`` places multiple fragments in one coordinate frame + and frequently overlaps them — a counterion can land ~1.4 Å from the cation, + which distance-based bond perception then reads as a (hyper)valent bond and + the renderer rejects ("Valence of atom N is …, larger than allowed"). This + is why salts like methylene blue (cation + Cl⁻) failed (STRUCT.14). + + After embedding, translate every non-largest fragment radially outward from + the main fragment so the closest inter-fragment gap is at least ``min_gap`` + Å. Operates on the existing conformer; atom order is preserved. No-op for + single-fragment molecules. + """ + if not RDKIT_AVAILABLE or mol.GetNumConformers() == 0: + return + frags = Chem.GetMolFrags(mol) # tuple of atom-index tuples, order preserved + if len(frags) <= 1: + return + + import numpy as np + from rdkit.Geometry import Point3D + + conf = mol.GetConformer() + pos = {i: np.array(conf.GetAtomPosition(i)) for i in range(mol.GetNumAtoms())} + main = max(frags, key=len) + main_c = np.mean([pos[i] for i in main], axis=0) + main_r = max((float(np.linalg.norm(pos[i] - main_c)) for i in main), default=0.0) + for frag in frags: + if frag is main: + continue + fc = np.mean([pos[i] for i in frag], axis=0) + fr = max((float(np.linalg.norm(pos[i] - fc)) for i in frag), default=0.0) + direction = fc - main_c + norm = float(np.linalg.norm(direction)) + direction = direction / norm if norm > 1e-6 else np.array([1.0, 0.0, 0.0]) + shift = (main_c + direction * (main_r + fr + min_gap)) - fc + for i in frag: + new = pos[i] + shift + conf.SetAtomPosition( + i, Point3D(float(new[0]), float(new[1]), float(new[2])) + ) + pos[i] = new + + def sdf_to_xyz(sdf_content: str) -> Tuple[str, Dict[str, Any]]: """ Convert SDF content to XYZ format string. @@ -324,6 +369,9 @@ def sdf_to_xyz(sdf_content: str) -> Tuple[str, Dict[str, Any]]: AllChem.UFFOptimizeMolecule(mol) except Exception: pass + # Salts/counterions embed jammed together — separate them so bond + # perception doesn't see a bonded counterion (STRUCT.14). + _separate_fragments(mol) # Extract coordinates and build XYZ string conf = mol.GetConformer() @@ -550,6 +598,8 @@ def smiles_to_xyz(smiles: str, optimize_3d: bool = True) -> Tuple[str, Dict[str, except Exception: logger.warning("UFF optimization failed, using unoptimized coordinates") + _separate_fragments(mol) # keep salt counterions apart (STRUCT.14) + # Extract coordinates if mol.GetNumConformers() == 0: raise ValueError("Failed to generate 3D coordinates") @@ -613,6 +663,8 @@ def inchi_to_xyz(inchi: str, optimize_3d: bool = True) -> Tuple[str, Dict[str, A except Exception: logger.warning("UFF optimization failed, using unoptimized coordinates") + _separate_fragments(mol) # keep salt counterions apart (STRUCT.14) + if mol.GetNumConformers() == 0: raise ValueError("Failed to generate 3D coordinates") diff --git a/tests/test_struct_resolver.py b/tests/test_struct_resolver.py index a5a2bbd..99811b7 100644 --- a/tests/test_struct_resolver.py +++ b/tests/test_struct_resolver.py @@ -269,3 +269,27 @@ def test_2d_sdf_is_reembedded_to_3d_no_atoms_piled(self): assert d > 0.5, f"atoms {i},{j} only {d:.3f} Å apart" # Genuinely 3D, not flat. assert max(abs(c[2]) for c in coords) > 1e-3 + + +class TestSaltFragmentSeparation: + """STRUCT.14 regression: a salt's counterion must not embed jammed into the + cation (RDKit otherwise places it ~1.4 Å away → bond perception reads it as + a bonded, hypervalent atom and the renderer rejects it, e.g. methylene + blue).""" + + @rdkit_only + def test_counterion_is_separated(self): + import math + + from quantui.pubchem import smiles_to_xyz + + # Ammonium chloride: [NH4+] cation + Cl- counterion (two fragments). + xyz, meta = smiles_to_xyz("[NH4+].[Cl-]") + atoms = [ + (line.split()[0], [float(c) for c in line.split()[1:4]]) + for line in xyz.strip().splitlines()[2:] + ] + cl = next(p for sym, p in atoms if sym == "Cl") + nearest = min(math.dist(cl, p) for sym, p in atoms if sym != "Cl") + # A real bond is ~1.3-2.0 Å; the separated counterion must be well beyond. + assert nearest > 2.5, f"Cl- only {nearest:.2f} Å from the cation" From 6671ee1b47a8fa9d014b32573167ed9b01fc883f Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Wed, 10 Jun 2026 15:44:41 -0400 Subject: [PATCH 11/16] Use rAF polling to fix live log scroll Replace the MutationObserver/install-once scroll-guard with a requestAnimationFrame polling approach. The new code re-queries the current .quantui-run-output element each frame, sets overflowAnchor:none, and pins the scroller while output is streaming (stops after ~600ms idle) to avoid flicker and broken observers caused by ipywidgets replacing nodes. This fixes BUG-SCROLL where observers watched stale nodes or produced visible scroll jumps. --- quantui/app.py | 120 ++++++++++++++----------------------------------- 1 file changed, 33 insertions(+), 87 deletions(-) diff --git a/quantui/app.py b/quantui/app.py index 55c58ab..5b94cf1 100644 --- a/quantui/app.py +++ b/quantui/app.py @@ -3416,97 +3416,43 @@ def _install_run_output_scroll_guard(self) -> None: js_code = r""" (() => { + // BUG-SCROLL — keep the live calc log pinned to the bottom. + // + // History: 6 MutationObserver variants failed while an identical console + // snippet worked. The difference was that the console snippet RE-QUERIES the + // element fresh each time, whereas an install-once observer binds to a node + // that ipywidgets later replaces/re-renders — so the guard ends up watching + // a stale node and never pins the live one. We therefore poll: on a short + // interval, re-find the current ".quantui-run-output" and, if it grew since + // last tick (output is streaming), pin it to the bottom on the next animation + // frame (rAF beats ipywidgets' synchronous scrollTop=0 reset). When the log + // is idle (no growth) we do nothing, so a finished log scrolls freely. + // A 120ms poll already followed correctly, but flickered: ipywidgets + // resets scrollTop to 0 on each line, and between poll ticks that "at top" + // state was visible before the pin yanked it back down. The cure is to pin + // on EVERY animation frame while output is streaming — an rAF callback runs + // after the per-line reset but before the browser paints, so the reset + // never reaches the screen (no flicker). Once the log is idle (no growth for + // ~600ms) we stop pinning, so a finished log can be scrolled freely. const ROOT_CLASS = "quantui-run-output"; - const ROOT_MARK = "data-quantui-run-scroll-guard"; - - function selectScroller(root) { - const candidates = [ - root, - ...root.querySelectorAll( - ".jp-OutputArea-output, .output_scroll, .jupyter-widgets-output-area, .output_subarea" - ), - ]; - for (const el of candidates) { - const style = window.getComputedStyle(el); - const overflowY = (style && style.overflowY) || ""; - const canScroll = /auto|scroll/.test(overflowY); - if (canScroll || el.scrollHeight > el.clientHeight + 2) { - return el; - } - } - return root; - } - - function installForRoot(root) { - if (!root || root.getAttribute(ROOT_MARK) === "1") { - return; - } - - const scroller = selectScroller(root); - if (!scroller) { - return; - } - - root.setAttribute(ROOT_MARK, "1"); - - // Disable browser scroll-anchoring on the log and every scrollable - // ancestor (incl. the page scroller). Without this, appending a line - // inside the log makes the browser nudge the *page* scroll to keep an - // anchor element stable — the user-visible "screen jumps up" on each - // new output line (BUG-SCROLL). - try { - scroller.style.overflowAnchor = "none"; - for (let el = root; el && el !== document.documentElement; el = el.parentElement) { - el.style.overflowAnchor = "none"; + let lastScrollHeight = -1; + let lastChangeTs = 0; + + function frame(ts) { + const el = document.querySelector("." + ROOT_CLASS); + if (el) { + el.style.overflowAnchor = "none"; + if (el.scrollHeight !== lastScrollHeight) { + lastScrollHeight = el.scrollHeight; + lastChangeTs = ts; } - document.documentElement.style.overflowAnchor = "none"; - if (document.body) document.body.style.overflowAnchor = "none"; - } catch (e) { /* styling best-effort */ } - - const thresholdPx = 24; - let stickToBottom = true; - let lastScrollHeight = scroller.scrollHeight; - - const updateStickFlag = () => { - const dist = scroller.scrollHeight - scroller.clientHeight - scroller.scrollTop; - stickToBottom = dist <= thresholdPx; - }; - - const onMutation = () => { - // A large shrink means the log was cleared for a new run — re-arm - // "follow". Without this, stickToBottom stays false from a previous - // manual scroll-up and the new run's output streams while the log - // sits at the top (BUG-SCROLL, confirmed via DevTools: scrollTop - // stuck at 0 while content grew). - if (scroller.scrollHeight < lastScrollHeight - thresholdPx) { - stickToBottom = true; + if (ts - lastChangeTs < 600) { + el.scrollTop = el.scrollHeight; } - lastScrollHeight = scroller.scrollHeight; - if (stickToBottom) { - scroller.scrollTop = scroller.scrollHeight; - } - }; - - scroller.addEventListener("scroll", updateStickFlag, { passive: true }); - - const obs = new MutationObserver(onMutation); - obs.observe(root, { childList: true, subtree: true, characterData: true }); - - updateStickFlag(); - onMutation(); - } - - function scanAndInstall() { - const roots = document.querySelectorAll(`.${ROOT_CLASS}`); - roots.forEach(installForRoot); + } + requestAnimationFrame(frame); } - - scanAndInstall(); - - const bodyObserver = new MutationObserver(() => { - scanAndInstall(); - }); - bodyObserver.observe(document.body, { childList: true, subtree: true }); + requestAnimationFrame(frame); })(); """ From 2f9d000bea8e6b4f7c8cb2e2c944a50dec6ef004 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Wed, 10 Jun 2026 21:41:37 -0400 Subject: [PATCH 12/16] Isolate test results dir; clarify run-output JS Add a session-scoped autouse fixture that redirects QUANTUI_RESULTS_DIR to a temporary directory for the whole test run, preventing tests from creating a cwd-relative results/ directory and restoring the previous env var afterwards. Also update docstring and inline JS comments in quantui/app.py to better explain the run-output scroll guard: it re-queries the output node each animation frame, pins on requestAnimationFrame to avoid flicker while output streams, and stops pinning after the log is idle. --- quantui/app.py | 42 +++++++++++++++--------------------------- tests/conftest.py | 23 +++++++++++++++++++++++ 2 files changed, 38 insertions(+), 27 deletions(-) diff --git a/quantui/app.py b/quantui/app.py index 5b94cf1..874e95c 100644 --- a/quantui/app.py +++ b/quantui/app.py @@ -3400,40 +3400,28 @@ def _queue_main_thread_callback(self, callback, *args, **kwargs) -> None: callback(*args, **kwargs) def _install_run_output_scroll_guard(self) -> None: - """Install a JS guard that preserves live-log scroll behavior. - - Two parts (BUG-SCROLL, reopened 2026-06-08): - - 1. Disable browser **scroll-anchoring** (``overflow-anchor: none``) on the - log and its scrollable ancestors — appending a line otherwise makes - the browser nudge the *page* scroll, the "screen jumps up on each new - output line" symptom. - 2. Keep the internal log pinned to the bottom while the user is already - at the bottom, and preserve manual scroll-up. + """Install a JS guard that keeps the live calc log scrolled to the bottom. + + Re-queries the run-output element each animation frame (ipywidgets can + replace the node) and pins it to the bottom while output is streaming. + Pinning on ``requestAnimationFrame`` runs after ipywidgets' per-line + ``scrollTop = 0`` reset but before paint, so the log follows without + flicker; pinning stops once the log is idle so a finished log can be + scrolled freely. """ if self._run_output_scroll_guard_installed: return js_code = r""" (() => { - // BUG-SCROLL — keep the live calc log pinned to the bottom. + // Keep the live calc log pinned to the bottom while output streams. // - // History: 6 MutationObserver variants failed while an identical console - // snippet worked. The difference was that the console snippet RE-QUERIES the - // element fresh each time, whereas an install-once observer binds to a node - // that ipywidgets later replaces/re-renders — so the guard ends up watching - // a stale node and never pins the live one. We therefore poll: on a short - // interval, re-find the current ".quantui-run-output" and, if it grew since - // last tick (output is streaming), pin it to the bottom on the next animation - // frame (rAF beats ipywidgets' synchronous scrollTop=0 reset). When the log - // is idle (no growth) we do nothing, so a finished log scrolls freely. - // A 120ms poll already followed correctly, but flickered: ipywidgets - // resets scrollTop to 0 on each line, and between poll ticks that "at top" - // state was visible before the pin yanked it back down. The cure is to pin - // on EVERY animation frame while output is streaming — an rAF callback runs - // after the per-line reset but before the browser paints, so the reset - // never reaches the screen (no flicker). Once the log is idle (no growth for - // ~600ms) we stop pinning, so a finished log can be scrolled freely. + // ipywidgets resets scrollTop to 0 on each appended line and may replace the + // Output node, so: re-query ".quantui-run-output" every animation frame and, + // while it is still growing, pin it to the bottom. Pinning on rAF runs after + // the per-line reset but before paint (no flicker); re-querying each frame + // avoids binding to a stale node. Idle logs (no growth for ~600ms) are left + // alone so they can be scrolled freely. const ROOT_CLASS = "quantui-run-output"; let lastScrollHeight = -1; let lastChangeTs = 0; diff --git a/tests/conftest.py b/tests/conftest.py index c259c38..3a5385a 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -4,9 +4,32 @@ Shared test fixtures for QuantUI test suite. """ +import os +import tempfile + import pytest +@pytest.fixture(autouse=True, scope="session") +def _isolate_results_dir(): + """Redirect the default results directory to a temp dir for the whole suite. + + ``results_storage._default_results_dir()`` falls back to a **cwd-relative** + ``Path("results")`` when ``results_dir`` isn't passed (e.g. the calibration + runner in ``benchmarks.py`` saves each step that way). Pointing + ``QUANTUI_RESULTS_DIR`` at a temp dir keeps every default save isolated, so + the suite never writes ``results/`` into the working directory. + """ + prev = os.environ.get("QUANTUI_RESULTS_DIR") + with tempfile.TemporaryDirectory(prefix="quantui_test_results_") as tmp: + os.environ["QUANTUI_RESULTS_DIR"] = tmp + yield + if prev is None: + os.environ.pop("QUANTUI_RESULTS_DIR", None) + else: + os.environ["QUANTUI_RESULTS_DIR"] = prev + + @pytest.fixture(autouse=True, scope="session") def _suppress_plotly_browser(): """Prevent plotly from opening browser tabs during tests. From 155d0e67870d18f8d4fa28b59536fe02e18da6ec Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Wed, 10 Jun 2026 23:47:26 -0400 Subject: [PATCH 13/16] Cap isosurface points and combine lobes Add a _MAX_ISOSURFACE_POINTS cap (48,000) and downsample the cube volume by a computed stride so the plotted isosurface payload stays bounded. Adjust coordinate grids to match the strided volume. Replace separate positive/negative Isosurface traces with a single trace rendering both lobes (surface_count=2) using a stepped two-color colorscale and cmin/cmax, reducing payload and draw overhead while preserving opacity and caps. This keeps saved .cube full-resolution while improving browser/Plotly rendering performance. --- quantui/orbital_visualization.py | 59 +++++++++++++++++--------------- 1 file changed, 32 insertions(+), 27 deletions(-) diff --git a/quantui/orbital_visualization.py b/quantui/orbital_visualization.py index 7ef9701..546a03b 100644 --- a/quantui/orbital_visualization.py +++ b/quantui/orbital_visualization.py @@ -696,6 +696,12 @@ def generate_cube_from_arrays( # Cube-file isosurface viewer (plotly — works anywhere) # ============================================================================ +# Max grid points handed to one go.Isosurface trace. The cube grid is a fixed +# resolution regardless of molecule size, so the volume is strided down to this +# cap at render time to keep the figure payload bounded; the saved .cube keeps +# full resolution. +_MAX_ISOSURFACE_POINTS = 48_000 + def parse_cube_file(cube_path: Path) -> dict: """ @@ -845,33 +851,25 @@ def plot_cube_isosurface( origin = cube["origin"] axes = cube["axes"] - # Build coordinate grids (Bohr) - x = origin[0] + np.arange(nx) * axes[0, 0] - y = origin[1] + np.arange(ny) * axes[1, 1] - z = origin[2] + np.arange(nz) * axes[2, 2] + # Downsample so the browser payload + plotly.js isosurfacing stay bounded. + # Stride each axis so the total point count stays under _MAX_ISOSURFACE_POINTS. + total = nx * ny * nz + stride = 1 + if total > _MAX_ISOSURFACE_POINTS: + stride = int(np.ceil((total / _MAX_ISOSURFACE_POINTS) ** (1.0 / 3.0))) + data = data[::stride, ::stride, ::stride] + + # Build coordinate grids (Bohr), strided to match the downsampled volume. + x = origin[0] + np.arange(nx)[::stride] * axes[0, 0] + y = origin[1] + np.arange(ny)[::stride] * axes[1, 1] + z = origin[2] + np.arange(nz)[::stride] * axes[2, 2] X, Y, Z = np.meshgrid(x, y, z, indexing="ij") fig = go.Figure() - # Positive lobe (blue) - fig.add_trace( - go.Isosurface( - x=X.flatten(), - y=Y.flatten(), - z=Z.flatten(), - value=data.flatten(), - isomin=isovalue, - isomax=isovalue, - surface_count=1, - opacity=opacity, - colorscale=[[0, "rgb(49,130,189)"], [1, "rgb(49,130,189)"]], - showscale=False, - name=f"+{isovalue}", - caps=dict(x_show=False, y_show=False, z_show=False), - ) - ) - - # Negative lobe (red) + # Both lobes in a single trace (half the payload of two): surfaces at + # -isovalue (red) and +isovalue (blue), via a step colorscale split at the + # midpoint of [-isovalue, +isovalue]. fig.add_trace( go.Isosurface( x=X.flatten(), @@ -879,12 +877,19 @@ def plot_cube_isosurface( z=Z.flatten(), value=data.flatten(), isomin=-isovalue, - isomax=-isovalue, - surface_count=1, + isomax=isovalue, + surface_count=2, opacity=opacity, - colorscale=[[0, "rgb(222,45,38)"], [1, "rgb(222,45,38)"]], + colorscale=[ + [0.0, "rgb(222,45,38)"], + [0.5, "rgb(222,45,38)"], + [0.5, "rgb(49,130,189)"], + [1.0, "rgb(49,130,189)"], + ], + cmin=-isovalue, + cmax=isovalue, showscale=False, - name=f"-{isovalue}", + name=f"±{isovalue}", caps=dict(x_show=False, y_show=False, z_show=False), ) ) From 47a0c6aef008653bfd8b587240766f42ff3d3dd4 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Wed, 10 Jun 2026 23:49:04 -0400 Subject: [PATCH 14/16] Remove STRUCT/BUG markers; update isosurface tests Clean up internal architecture tags and inline TODO markers in docstrings and comments across multiple modules (app.py, app_analysis.py, app_builders.py, cactus.py, config.py, molecule_library.py, pubchem.py, structure_providers.py). These edits remove legacy STRUCT./BUG. annotations and tighten wording without changing runtime behavior. Update tests/test_orbital_visualization.py: tidy fixture string formatting, rename/clarify a test, and add assertions ensuring the isosurface is drawn as a single go.Isosurface trace (surface_count=2) and that large voxel grids are downsampled to avoid OOM in the renderer. No other functional changes were introduced. --- quantui/app.py | 4 ++-- quantui/app_analysis.py | 4 ++-- quantui/app_builders.py | 6 ++--- quantui/cactus.py | 2 +- quantui/config.py | 8 +++---- quantui/molecule_library.py | 16 ++++++------- quantui/pubchem.py | 21 ++++++++-------- quantui/structure_providers.py | 14 +++++------ tests/test_orbital_visualization.py | 37 ++++++++++++++++++++++++++--- 9 files changed, 71 insertions(+), 41 deletions(-) diff --git a/quantui/app.py b/quantui/app.py index 874e95c..e06a10a 100644 --- a/quantui/app.py +++ b/quantui/app.py @@ -935,7 +935,7 @@ def __init__(self) -> None: # Orbital state consumed by the Isosurface panel populator. Always # initialized to None so ``pop_isosurface`` can read the attributes # via direct access without raising AttributeError on a fresh app - # or on a history-replay where ``orbitals.npz`` is missing (BUG.8). + # or on a history-replay where ``orbitals.npz`` is missing. # ``_apply_analysis_context`` resets these between contexts so stale # state from a prior calc cannot leak into the next molecule. self._last_orb_mo_coeff: Any = None @@ -1464,7 +1464,7 @@ def _wire_callbacks(self) -> None: ) # Theme self.theme_btn.observe(self._safe_cb(self._on_theme_changed), names="value") - # Molecule input — library browse/search (STRUCT.9) + # Molecule input — library browse/search self.lib_category_dd.observe( self._safe_cb(self._on_lib_filter_changed), names="value" ) diff --git a/quantui/app_analysis.py b/quantui/app_analysis.py index 65e453b..44c3a18 100644 --- a/quantui/app_analysis.py +++ b/quantui/app_analysis.py @@ -168,7 +168,7 @@ def apply_analysis_context(app: Any, ctx: Any) -> None: app._iso_render_token = int(getattr(app, "_iso_render_token", 0)) + 1 # Orbital state is consumed by pop_isosurface (and ana_pop_iso_generate # when the user clicks Generate). Reset here so a context that doesn't - # populate these fields (history result without orbitals.npz, BUG.8) + # populate these fields (history result without orbitals.npz) # cannot leak the prior calc's orbital arrays into the Isosurface panel # of an unrelated molecule. Each populate method that wants the panel # to activate re-sets these in show_orbital_diagram. @@ -261,7 +261,7 @@ def pop_isosurface(app: Any, ctx: Any) -> bool: are always present in practice, but the defensive read mirrors the pattern used by ``render_orbital_isosurface`` and keeps this populator robust against future refactors that might call it before the context - reset has run (BUG.8 root-cause guard). + reset has run. """ return ( getattr(app, "_last_orb_mo_coeff", None) is not None diff --git a/quantui/app_builders.py b/quantui/app_builders.py index f7717ff..ded4d8c 100644 --- a/quantui/app_builders.py +++ b/quantui/app_builders.py @@ -13,7 +13,7 @@ from quantui import molecule_library as _ml from quantui.help_content import HELP_TOPICS -# Friendlier labels for the library category filter (STRUCT.9). +# Friendlier labels for the library category filter. _CATEGORY_LABELS = { "diatomic": "Diatomics", "triatomic": "Triatomics", @@ -1026,7 +1026,7 @@ def build_molecule_section( visualization_available: bool, ) -> None: """Build molecule input widgets and collapsed summary container.""" - # ── Library browse/search (STRUCT.9) — category filter + search + results. + # ── Library browse/search — category filter + search + results. cat_opts = [("All categories", "")] + [ (_category_label(c), c) for c in _ml.categories() ] @@ -1086,7 +1086,7 @@ def build_molecule_section( else "PubChem unavailable — check internet connection" ) ) - # Disambiguation pick-list (STRUCT.5) — hidden until a query has >1 match. + # Disambiguation pick-list — hidden until a query has >1 match. app.pubchem_candidates_dd = widgets.Dropdown( options=[("— pick a match —", "")], value="", diff --git a/quantui/cactus.py b/quantui/cactus.py index 94eb697..3e9d3c6 100644 --- a/quantui/cactus.py +++ b/quantui/cactus.py @@ -1,4 +1,4 @@ -"""NCI CACTUS Chemical Identifier Resolver (M-STRUCT STRUCT.3). +"""NCI CACTUS Chemical Identifier Resolver. A chained fallback after PubChem. CACTUS resolves a wide range of identifiers (common name, IUPAC name, CAS number, InChI, SMILES, formula) to a 3D SDF with diff --git a/quantui/config.py b/quantui/config.py index f899bea..3371839 100644 --- a/quantui/config.py +++ b/quantui/config.py @@ -229,7 +229,7 @@ DESCRIPTION_WIDTH = "150px" -# ── External structure resolvers (M-STRUCT) ────────────────────────────────── +# ── External structure resolvers ───────────────────────────────────────────── # Network + throttle settings shared by the PubChem client (and, later, the # NCI CACTUS resolver). All timeouts/limits live here per constraint #5. PUBCHEM_TIMEOUT_S: float = 15.0 # per-request HTTP timeout @@ -248,13 +248,13 @@ CACTUS_TIMEOUT_S: float = 8.0 CACTUS_CONNECT_TIMEOUT_S: float = 4.0 -# Bundled-library size budget + heavy-atom ceilings (M-STRUCT STRUCT.7/.8/.10). +# Bundled-library size budget + heavy-atom ceilings. # These are QC *starting* geometries, so keep them runnable in a classroom. -LIBRARY_SIZE_BUDGET_BYTES: int = 10 * 1024 * 1024 # 10 MB (DEC-015) +LIBRARY_SIZE_BUDGET_BYTES: int = 10 * 1024 * 1024 # 10 MB LIBRARY_HEAVY_ATOM_CEILING_CURATED: int = 30 # named drugs run a bit larger LIBRARY_HEAVY_ATOM_CEILING_BULK: int = 9 # QM9 caps here anyway -# Molecule presets — bundled library (STRUCT.6). +# Molecule presets — bundled library. # The former inline literal now lives in the indexed package-data store # (quantui/data/library/library.sqlite, seeded from # quantui/data/manifests/presets.json). ``config.MOLECULE_LIBRARY`` is a lazy diff --git a/quantui/molecule_library.py b/quantui/molecule_library.py index 5677864..b318b77 100644 --- a/quantui/molecule_library.py +++ b/quantui/molecule_library.py @@ -1,12 +1,12 @@ -"""Bundled molecule library — indexed package-data store + lazy loader (STRUCT.6). +"""Bundled molecule library — indexed package-data store + lazy loader. The library lives in ``quantui/data/`` as two committed artifacts: - ``manifests/presets.json`` — the human-readable, reviewable source of record. - ``library/library.sqlite`` — an indexed, lazily-queried store generated from the manifest(s). Coordinates are packed as ``int16`` @ 0.001 Å (7–8 bytes per - atom) so the store stays compact enough to hold the eventual ~10 MB hybrid - library (STRUCT.7/.8) without bloating import time. + atom) so the store stays compact enough to hold the ~10 MB hybrid library + without bloating import time. Design goals: @@ -19,8 +19,8 @@ point transparently falls back to the JSON manifest, so ``import quantui`` never fails on a fresh/odd checkout. -When STRUCT.7/.8 add curated + bulk content, they only add manifests + rebuild -the store; nothing in this module's public API changes. +Adding curated or bulk content only adds manifests + rebuilds the store; +nothing in this module's public API changes. """ import json @@ -42,7 +42,7 @@ _ATOM_RECORD_SIZE = struct.calcsize(_ATOM_RECORD) # 8 # Categories that are NOT part of the browsable preset dict (reached via search -# only). Bulk QM9 entries (STRUCT.8) will carry "bulk-qm9". +# only). Bulk QM9 entries carry "bulk-qm9". _BULK_CATEGORIES = frozenset({"bulk-qm9"}) @@ -90,7 +90,7 @@ def db_path() -> Path: def manifest_paths() -> List[Path]: - """All manifest JSON files that seed the store (STRUCT.7/.8 add more). + """All manifest JSON files that seed the store. ``presets.json`` is ordered first so the original teaching molecules lead the (interim) flat dropdown; remaining manifests follow alphabetically. @@ -419,7 +419,7 @@ def iter_entries(): """Yield every entry (full, with decoded coordinates) in store order. Single connection — efficient for whole-library governance/round-trip - checks (STRUCT.10). Falls back to the JSON manifest if the store is absent. + checks. Falls back to the JSON manifest if the store is absent. """ con = _connect_ro() if con is None: diff --git a/quantui/pubchem.py b/quantui/pubchem.py index 97a4c2e..b7e5e33 100644 --- a/quantui/pubchem.py +++ b/quantui/pubchem.py @@ -33,7 +33,7 @@ # Back-compat alias; canonical value lives in config (constraint #5). PUBCHEM_TIMEOUT = config.PUBCHEM_TIMEOUT_S -# ── HTTP client: client-side throttle + bounded 503 back-off (STRUCT.2) ────── +# ── HTTP client: client-side throttle + bounded 503 back-off ───────────────── # A single process-wide limiter keeps us under PUG-REST's ~5 req/s ceiling even # when several search threads fire at once. _request_lock = threading.Lock() @@ -171,7 +171,7 @@ def search_cids_by_name(name: str) -> list: """Return ALL PubChem CIDs matching a name (best-match order); [] if none. Unlike :func:`search_molecule_by_name` (which returns just the first hit), - this exposes every match so the UI can disambiguate (STRUCT.5). + this exposes every match so the UI can disambiguate. """ url = f"{PUBCHEM_BASE_URL}/compound/name/{quote(name, safe='')}/cids/JSON" try: @@ -284,7 +284,7 @@ def _separate_fragments(mol: Any, min_gap: float = 3.0) -> None: and frequently overlaps them — a counterion can land ~1.4 Å from the cation, which distance-based bond perception then reads as a (hyper)valent bond and the renderer rejects ("Valence of atom N is …, larger than allowed"). This - is why salts like methylene blue (cation + Cl⁻) failed (STRUCT.14). + is why salts like methylene blue (cation + Cl⁻) failed. After embedding, translate every non-largest fragment radially outward from the main fragment so the closest inter-fragment gap is at least ``min_gap`` @@ -351,7 +351,7 @@ def sdf_to_xyz(sdf_content: str) -> Tuple[str, Dict[str, Any]]: # Add any missing hydrogens *with* coordinates. Without addCoords the # new H default to the origin, which — combined with a 2D SDF — yields a # degenerate geometry (atoms piled at 0,0,0) that bond perception then - # reads as absurd valences (STRUCT.12). + # reads as absurd valences. mol = Chem.AddHs(mol, addCoords=True) # Re-embed in 3D whenever there is no conformer, or the conformer is 2D @@ -370,7 +370,7 @@ def sdf_to_xyz(sdf_content: str) -> Tuple[str, Dict[str, Any]]: except Exception: pass # Salts/counterions embed jammed together — separate them so bond - # perception doesn't see a bonded counterion (STRUCT.14). + # perception doesn't see a bonded counterion. _separate_fragments(mol) # Extract coordinates and build XYZ string @@ -598,7 +598,7 @@ def smiles_to_xyz(smiles: str, optimize_3d: bool = True) -> Tuple[str, Dict[str, except Exception: logger.warning("UFF optimization failed, using unoptimized coordinates") - _separate_fragments(mol) # keep salt counterions apart (STRUCT.14) + _separate_fragments(mol) # keep salt counterions apart # Extract coordinates if mol.GetNumConformers() == 0: @@ -663,7 +663,7 @@ def inchi_to_xyz(inchi: str, optimize_3d: bool = True) -> Tuple[str, Dict[str, A except Exception: logger.warning("UFF optimization failed, using unoptimized coordinates") - _separate_fragments(mol) # keep salt counterions apart (STRUCT.14) + _separate_fragments(mol) # keep salt counterions apart if mol.GetNumConformers() == 0: raise ValueError("Failed to generate 3D coordinates") @@ -961,7 +961,7 @@ def validate_smiles(smiles: str) -> Tuple[bool, str]: # ============================================================================ -# Smart input routing (STRUCT.1) +# Smart input routing # ============================================================================ # Standard InChIKey: 14 block chars - 10 block chars - 1 flag char. @@ -978,8 +978,7 @@ def _looks_like_smiles(query: str) -> bool: Deliberately conservative — bare-letter tokens like ``CCO`` (which are valid SMILES *and* plausible names/formulas) are left for the provider chain - (STRUCT.4) to disambiguate, so we never misroute a plain name to a local - parse. + to disambiguate, so we never misroute a plain name to a local parse. """ if not RDKIT_AVAILABLE or " " in query: return False @@ -996,7 +995,7 @@ def classify_query(query: str) -> str: Returns one of ``"cid"``, ``"inchikey"``, ``"inchi"``, ``"smiles"``, ``"formula"``, or ``"name"``. ``smiles`` / ``inchi`` resolve locally via RDKit (no network); the rest go to PubChem. ``formula`` is currently routed - like ``name`` (PubChem's async fastformula search is deferred to STRUCT.4). + like ``name`` (PubChem's async fastformula search is not used here). """ q = query.strip() if not q: diff --git a/quantui/structure_providers.py b/quantui/structure_providers.py index 907b70c..6c7aad8 100644 --- a/quantui/structure_providers.py +++ b/quantui/structure_providers.py @@ -1,24 +1,24 @@ -"""Unified structure-resolver chain with offline fallback (M-STRUCT STRUCT.4). +"""Unified structure-resolver chain with offline fallback. Resolution order (first hit wins): 1. **Local RDKit** for SMILES / InChI input — offline, no network. 2. **Bundled library** exact hit (formula key) — offline, instant. -3. **PubChem** (hardened client, STRUCT.2). -4. **NCI CACTUS** resolver (STRUCT.3). +3. **PubChem** (hardened client). +4. **NCI CACTUS** resolver. 5. **Bundled-library fuzzy fallback** (name/description substring) — the last-resort offline answer so the search box is never a dead end, even with no network. Every resolver returns a normalized :class:`ResolvedStructure` so callers -(and the future disambiguation UI, STRUCT.5) treat all sources uniformly. The +(and the disambiguation UI) treat all sources uniformly. The ``source`` field records which resolver answered, so the UI can be honest about provenance. The bundled-library steps currently search ``config.MOLECULE_LIBRARY`` (the 20 -presets). When STRUCT.6/.7/.8 move the library into an indexed package-data -store, only :func:`_library_exact` / :func:`_library_fuzzy` change — the chain -is unaffected. +presets). The library lives in an indexed package-data store, reached only +through :func:`_library_exact` / :func:`_library_fuzzy`, so the chain is +unaffected by how it is stored. """ import logging diff --git a/tests/test_orbital_visualization.py b/tests/test_orbital_visualization.py index bad6d3a..697fd16 100644 --- a/tests/test_orbital_visualization.py +++ b/tests/test_orbital_visualization.py @@ -291,9 +291,37 @@ def test_returns_figure(self, minimal_cube_file): fig = plot_cube_isosurface(minimal_cube_file) assert isinstance(fig, go.Figure) - def test_has_two_traces(self, minimal_cube_file): + def test_has_single_isosurface_trace(self, minimal_cube_file): + # Both lobes are drawn by one go.Isosurface trace (surface_count=2) to + # halve the figure payload (BUG-ISO-OOM). fig = plot_cube_isosurface(minimal_cube_file) - assert len(fig.data) == 2 + iso = [t for t in fig.data if t.type == "isosurface"] + assert len(iso) == 1 + assert iso[0].surface.count == 2 # both lobes via one trace + + def test_large_grid_is_downsampled(self): + # The cube is written at a fixed resolution regardless of molecule size; + # a full 60^3 = 216k-point grid flattened into the figure could exhaust + # browser memory. The render path must stride it under the cap. + from unittest.mock import patch + + from quantui import orbital_visualization as ov + + n = 60 + fake_cube = { + "nx": n, + "ny": n, + "nz": n, + "data": np.zeros((n, n, n)), + "origin": np.zeros(3), + "axes": np.eye(3) * 0.3, + "atoms": [], + } + with patch.object(ov, "parse_cube_file", return_value=fake_cube): + fig = ov.plot_cube_isosurface("dummy.cube", isovalue=0.02) + iso = [t for t in fig.data if t.type == "isosurface"][0] + assert len(iso.x) <= ov._MAX_ISOSURFACE_POINTS + assert len(iso.x) < n * n * n # actually downsampled def test_custom_title(self, minimal_cube_file): fig = plot_cube_isosurface(minimal_cube_file, title="HOMO Isosurface") @@ -304,8 +332,11 @@ def test_scene_has_axis_labels(self, minimal_cube_file): assert "Bohr" in fig.layout.scene.xaxis.title.text def test_show_molecule_adds_overlay_traces(self, minimal_cube_file): + # The isosurface is one trace now; show_molecule adds ≥1 scatter3d + # overlay (atoms, plus bonds when there are ≥2 atoms). fig = plot_cube_isosurface(minimal_cube_file, show_molecule=True) - assert len(fig.data) >= 3 + scatter = [t for t in fig.data if t.type == "scatter3d"] + assert len(scatter) >= 1 def test_show_grid_false_hides_scene_grid(self, minimal_cube_file): fig = plot_cube_isosurface(minimal_cube_file, show_grid=False) From 5d6b0a78aa575fa68b422a4e95d4b55b54caf8ee Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Thu, 11 Jun 2026 13:49:56 -0400 Subject: [PATCH 15/16] Add correlation breakdown and geom-opt labels MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Persist MP2/CCSD/(T) correlation values and render a post-HF breakdown in saved-result cards, including HF reference + correlation rows. Prefix geometry-optimization seed options with a ⚙ "Geom-opt" label so users can distinguish optimized geometries from raw inputs. Update tests to use substring matching for labels (more resilient than startswith) and add unit tests verifying MP2/CCSD breakdown rendering. --- quantui/app_formatters.py | 32 ++++++++++++++++++- quantui/app_runflow.py | 7 ++++- quantui/results_storage.py | 5 +++ tests/test_app.py | 28 ++++++++--------- tests/test_app_formatters.py | 60 ++++++++++++++++++++++++++++++++++++ 5 files changed, 116 insertions(+), 16 deletions(-) diff --git a/quantui/app_formatters.py b/quantui/app_formatters.py index 3c53c06..292cda8 100644 --- a/quantui/app_formatters.py +++ b/quantui/app_formatters.py @@ -401,6 +401,36 @@ def format_past_result(data: dict[str, Any], result_dir: Optional[Path] = None) ) ts = data.get("timestamp", "") + # Post-HF correlation breakdown rows (MP2 / CCSD / CCSD(T)). ``energy_hartree`` + # already includes every correlation contribution, so the HF reference is + # the total minus those contributions. + _extra = "" + _mp2_corr = data.get("mp2_correlation_hartree") + if _mp2_corr is not None: + _hf_e = data["energy_hartree"] - _mp2_corr + _extra += ( + f'HF reference' + f'{_hf_e:.8f} Ha' + f'MP2 correlation' + f'{_mp2_corr:.8f} Ha' + ) + _ccsd_corr = data.get("ccsd_correlation_hartree") + _ccsd_t_corr = data.get("ccsd_t_correction_hartree") + if _ccsd_corr is not None: + _hf_e = data["energy_hartree"] - _ccsd_corr - (_ccsd_t_corr or 0.0) + _extra += ( + f'HF reference' + f'{_hf_e:.8f} Ha' + f'CCSD correlation' + f'{_ccsd_corr:.8f} Ha' + ) + if _ccsd_t_corr is not None: + _extra += ( + f'' + f"(T) triples correction" + f'{_ccsd_t_corr:.8f} Ha' + ) + # Embed thumbnail if saved _thumb_html = "" if result_dir is not None: @@ -421,5 +451,5 @@ def format_past_result(data: dict[str, Any], result_dir: Optional[Path] = None) f'{data["formula"]} — {data["method"]}/{data["basis"]}' f' {ts}' f'' - f"{_rows}
    " + f"{_rows}{_extra}" ) diff --git a/quantui/app_runflow.py b/quantui/app_runflow.py index 46fb3b3..40f9b19 100644 --- a/quantui/app_runflow.py +++ b/quantui/app_runflow.py @@ -303,7 +303,12 @@ def _refresh_seed_options(app: Any, dropdown: Any) -> None: # formula-only match (don't punish the user for a malformed # trajectory.json on an otherwise-matching result). ts = data.get("timestamp", d.name[:19]) - label = f"{data['formula']} {data['method']}/{data['basis']}" f" — {ts}" + # Every entry here is a geometry_opt result; prefix the label so the + # user can see the seed is an optimized geometry, not a raw input. + label = ( + f"⚙ Geom-opt · {data['formula']} " + f"{data['method']}/{data['basis']} — {ts}" + ) options.append((label, str(d))) except Exception: continue diff --git a/quantui/results_storage.py b/quantui/results_storage.py index 55cbcbb..d25c03a 100644 --- a/quantui/results_storage.py +++ b/quantui/results_storage.py @@ -130,6 +130,11 @@ def save_result( "homo_lumo_gap_ev": getattr(result, "homo_lumo_gap_ev", None), "converged": getattr(result, "converged", None), "n_iterations": getattr(result, "n_iterations", -1), + # Post-HF correlation breakdown — None for HF/DFT. Persisted so the + # saved-result card can show the HF reference + correlation rows. + "mp2_correlation_hartree": getattr(result, "mp2_correlation_hartree", None), + "ccsd_correlation_hartree": getattr(result, "ccsd_correlation_hartree", None), + "ccsd_t_correction_hartree": getattr(result, "ccsd_t_correction_hartree", None), "spectra": spectra if spectra is not None else {}, } if extras: diff --git a/tests/test_app.py b/tests/test_app.py index 1b89a03..2a770df 100644 --- a/tests/test_app.py +++ b/tests/test_app.py @@ -1251,8 +1251,8 @@ def test_unfiltered_when_no_molecule_loaded(self, tmp_path, monkeypatch): assert app._molecule is None app._refresh_freq_seed_options() labels = [lbl for lbl, _ in app._freq_seed_dd.options] - assert any(lbl.startswith("H2O") for lbl in labels) - assert any(lbl.startswith("CH4") for lbl in labels) + assert any("H2O" in lbl for lbl in labels) + assert any("CH4" in lbl for lbl in labels) def test_filtered_to_current_molecule_formula(self, tmp_path, monkeypatch): monkeypatch.setenv("QUANTUI_RESULTS_DIR", str(tmp_path)) @@ -1263,8 +1263,8 @@ def test_filtered_to_current_molecule_formula(self, tmp_path, monkeypatch): app._refresh_freq_seed_options() labels = [lbl for lbl, _ in app._freq_seed_dd.options] assert labels[0] == "(use current molecule)" - assert any(lbl.startswith("H2O") for lbl in labels) - assert not any(lbl.startswith("CH4") for lbl in labels) + assert any("H2O" in lbl for lbl in labels) + assert not any("CH4" in lbl for lbl in labels) def test_set_molecule_triggers_filter(self, tmp_path, monkeypatch): # Loading a new molecule should auto-refresh the dropdown so stale @@ -1275,8 +1275,8 @@ def test_set_molecule_triggers_filter(self, tmp_path, monkeypatch): app = QuantUIApp() app._set_molecule(self._water(), label="test") labels = [lbl for lbl, _ in app._freq_seed_dd.options] - assert any(lbl.startswith("H2O") for lbl in labels) - assert not any(lbl.startswith("CH4") for lbl in labels) + assert any("H2O" in lbl for lbl in labels) + assert not any("CH4" in lbl for lbl in labels) class TestPopIsosurfaceBug8: @@ -1435,8 +1435,8 @@ def test_seed_options_filtered_by_formula(self, tmp_path, monkeypatch): app._molecule = self._water() app._refresh_tddft_seed_options() labels = [lbl for lbl, _ in app._tddft_seed_dd.options] - assert any(lbl.startswith("H2O") for lbl in labels) - assert not any(lbl.startswith("CH4") for lbl in labels) + assert any("H2O" in lbl for lbl in labels) + assert not any("CH4" in lbl for lbl in labels) def test_set_molecule_triggers_tddft_seed_filter(self, tmp_path, monkeypatch): monkeypatch.setenv("QUANTUI_RESULTS_DIR", str(tmp_path)) @@ -1445,8 +1445,8 @@ def test_set_molecule_triggers_tddft_seed_filter(self, tmp_path, monkeypatch): app = QuantUIApp() app._set_molecule(self._water(), label="test") labels = [lbl for lbl, _ in app._tddft_seed_dd.options] - assert any(lbl.startswith("H2O") for lbl in labels) - assert not any(lbl.startswith("CH4") for lbl in labels) + assert any("H2O" in lbl for lbl in labels) + assert not any("CH4" in lbl for lbl in labels) def test_picking_seed_disables_preopt_and_shows_note(self, tmp_path, monkeypatch): monkeypatch.setenv("QUANTUI_RESULTS_DIR", str(tmp_path)) @@ -1831,7 +1831,7 @@ def test_same_formula_different_geometry_excluded(self, tmp_path, monkeypatch): labels = [lbl for lbl, _ in app._freq_seed_dd.options] assert len(labels) == 2, labels assert labels[0] == "(use current molecule)" - assert labels[1].startswith("H2O") + assert "H2O" in labels[1] def test_same_formula_within_tolerance_included(self, tmp_path, monkeypatch): monkeypatch.setenv("QUANTUI_RESULTS_DIR", str(tmp_path)) @@ -1847,7 +1847,7 @@ def test_same_formula_within_tolerance_included(self, tmp_path, monkeypatch): app._refresh_freq_seed_options() labels = [lbl for lbl, _ in app._freq_seed_dd.options] assert len(labels) == 3, labels - assert sum(1 for lbl in labels if lbl.startswith("H2O")) == 2 + assert sum(1 for lbl in labels if "H2O" in lbl) == 2 def test_atom_order_mismatch_excluded(self, tmp_path, monkeypatch): # Strict atom-order policy: ["H","O","H"] is not the same as @@ -1864,7 +1864,7 @@ def test_atom_order_mismatch_excluded(self, tmp_path, monkeypatch): app._refresh_freq_seed_options() labels = [lbl for lbl, _ in app._freq_seed_dd.options] assert len(labels) == 2 - assert labels[1].startswith("H2O") + assert "H2O" in labels[1] def test_malformed_trajectory_falls_back_to_formula_match( self, tmp_path, monkeypatch @@ -1892,7 +1892,7 @@ def test_malformed_trajectory_falls_back_to_formula_match( app._molecule = self._water_molecule() app._refresh_freq_seed_options() labels = [lbl for lbl, _ in app._freq_seed_dd.options] - assert any(lbl.startswith("H2O") for lbl in labels) + assert any("H2O" in lbl for lbl in labels) def test_starting_geometry_cache_hit_avoids_reread(self, tmp_path): # _load_starting_geometry must cache per-result so back-to-back diff --git a/tests/test_app_formatters.py b/tests/test_app_formatters.py index 3a47871..2ed2596 100644 --- a/tests/test_app_formatters.py +++ b/tests/test_app_formatters.py @@ -161,3 +161,63 @@ def test_format_past_result_contains_calc_type_badge(): html = format_past_result(data) assert "Single Point" in html assert "H2O" in html + + +def test_format_past_result_renders_ccsd_breakdown(): + # The saved-result card (Results tab) must show the HF reference + CCSD + # correlation + (T) triples rows when those fields were persisted. + data = { + "calc_type": "single_point", + "converged": True, + "homo_lumo_gap_ev": 27.0, + "energy_hartree": -75.0139, + "energy_ev": -2041.23, + "n_iterations": 5, + "timestamp": "2026-06-10_15-48-02-285574", + "formula": "H2O", + "method": "CCSD(T)", + "basis": "STO-3G", + "ccsd_correlation_hartree": -0.0497, + "ccsd_t_correction_hartree": -0.0008, + } + html = format_past_result(data) + assert "HF reference" in html + assert "CCSD correlation" in html + assert "(T) triples correction" in html + + +def test_format_past_result_renders_mp2_breakdown(): + data = { + "calc_type": "single_point", + "converged": True, + "homo_lumo_gap_ev": 20.0, + "energy_hartree": -75.01, + "energy_ev": -2041.0, + "n_iterations": 8, + "timestamp": "2026-06-10_15-48-02-285574", + "formula": "H2O", + "method": "MP2", + "basis": "STO-3G", + "mp2_correlation_hartree": -0.035, + } + html = format_past_result(data) + assert "HF reference" in html + assert "MP2 correlation" in html + + +def test_format_past_result_hf_dft_has_no_breakdown(): + data = { + "calc_type": "single_point", + "converged": True, + "homo_lumo_gap_ev": 10.0, + "energy_hartree": -75.0, + "energy_ev": -2040.0, + "n_iterations": 10, + "timestamp": "2026-05-02_12-00-00-000001", + "formula": "H2O", + "method": "RHF", + "basis": "STO-3G", + } + html = format_past_result(data) + assert "correlation" not in html + assert "HF reference" not in html From 117593cfc6f932287de47f31569f75e30be58817 Mon Sep 17 00:00:00 2001 From: NCCU-Schultz-Lab Date: Thu, 11 Jun 2026 18:57:41 -0400 Subject: [PATCH 16/16] Release 0.3.0: bump version and update changelog Bump package version to 0.3.0 in pyproject.toml and quantui/__init__.py and add the 0.3.0 changelog entry. The changelog documents the 'structure-sourcing' release: external structure search (name/CID/InChI/SMILES/CAS) with PubChem/NCI fallbacks and an offline bundled library; disambiguation pick-list; a three-tier bundled molecule library and new browse/search UI; migration of presets into the indexed library store; labeling clarification for seed geometries. Also notes fixes for orbital isosurface memory use, CCSD/MP2 result-card fields, live-log scrolling, and 3D re-embedding/salt handling. --- CHANGELOG.md | 43 +++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 2 +- quantui/__init__.py | 2 +- 3 files changed, 45 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f2f8a7..68f34ec 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,49 @@ and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.ht ## [Unreleased] +## [0.3.0] - 2026-06-11 + +Structure-sourcing release. Repairs the external-database structure search and +replaces the 20-entry inline molecule list with an indexed, three-tier bundled +library, alongside visualization and result-card fixes. + +### Added + +- **External structure search** — resolve molecules by name, PubChem CID, InChI, + InChIKey, SMILES, or CAS number. Input is routed by type: SMILES/InChI resolve + locally via RDKit with no network, while names and identifiers query PubChem + through a hardened client (URL-encoding, request throttling, bounded retry on + server throttling). NCI CACTUS acts as a fallback resolver, and an offline + bundled-library fallback keeps the search usable without a network connection. +- **Disambiguation pick-list** — an ambiguous query (e.g. a name with several + PubChem matches) presents a selectable list instead of silently choosing the + first hit. +- **Three-tier bundled molecule library** — 20 presets, 156 curated named + molecules, and ~1,900 bulk QM9 structures (CC0), held in an indexed, + lazily-loaded package-data store. Bulk entries are reachable via search. +- **Library browse/search tab** — category filter plus name/formula search, + replacing the flat preset dropdown. + +### Changed + +- The molecule preset list moved from an inline `config.py` dictionary into the + indexed library store; `config.MOLECULE_LIBRARY` is preserved as a + backward-compatible accessor. +- Frequency / UV-Vis seed-geometry dropdown entries are now labeled as optimized + geometries so their source is explicit. + +### Fixed + +- **Orbital isosurface could exhaust browser memory** — the full volumetric grid + was serialized into the Plotly figure. The rendered surface is now downsampled + to a bounded point count (the saved cube file remains full-resolution). +- **CCSD / MP2 result cards** now show the HF reference and correlation-energy + breakdown (plus the (T) triples correction for CCSD(T)); these fields are also + persisted with saved results. +- The live calculation log no longer jumps to the top while streaming output. +- Structures fetched as 2D records are re-embedded in 3D, and salt/counterion + fragments are separated so bond perception does not misread them. + ## [0.2.0] - 2026-05-22 First substantial release after `v0.1.0`. The codebase moved from a single diff --git a/pyproject.toml b/pyproject.toml index 52ce47b..3ee417e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "quantui" -version = "0.2.0" +version = "0.3.0" description = "An open-source frontend for DFT and post-HF quantum chemistry with PySCF" readme = "README.md" requires-python = ">=3.9" diff --git a/quantui/__init__.py b/quantui/__init__.py index 2327305..f9648d2 100644 --- a/quantui/__init__.py +++ b/quantui/__init__.py @@ -7,7 +7,7 @@ PySCF requires Linux/macOS/WSL. Windows users should use the Apptainer container. """ -__version__ = "0.2.0" +__version__ = "0.3.0" import logging