Fix structure search and add 3-tier bundled molecule library

.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 ─────────────────────────────────

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

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"
@@ -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.

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
 
@@ -123,20 +123,33 @@
 
 # PubChem integration (optional — requires internet)
 try:
+    from .cactus import fetch_from_cactus
     from .pubchem import (
         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,
+        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,
+        search_candidates,
+    )
 
     PUBCHEM_AVAILABLE = True
 except ImportError:
@@ -238,7 +251,18 @@
     "optimize_geometry",
     # PubChem (optional)
     "fetch_molecule",
+    "fetch_structure",
+    "classify_query",
     "student_friendly_fetch",
+    "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",