App restructure

apptainer/quantui-local.def

@@ -53,7 +53,8 @@ FROM: continuumio/miniconda3:latest
     scipy \
     matplotlib \
     plotly \
-    h5py
+    h5py \
+    rdkit
 
   echo "Installing pip packages..."
   pip install --no-cache-dir \
@@ -69,10 +70,12 @@ FROM: continuumio/miniconda3:latest
   echo "Verifying installation..."
   python -c "import quantui; print('QuantUI OK')"
   python -c "import pyscf; print('PySCF OK')"
+  python -c "import rdkit; print('RDKit OK')"
   python -c "import py3Dmol; print('py3Dmol OK')"
   python -c "import ase; print('ASE OK')"
   python -c "from quantui import optimize_geometry; print('optimize_geometry OK')"
   python -c "from quantui import run_freq_calc, run_tddft_calc; print('freq/tddft OK')"
+  python -c "from quantui.app import QuantUIApp; print('QuantUIApp OK')"
 
   echo "Cleaning up unnecessary files..."
   # Version control and caches
@@ -125,4 +128,5 @@ EOF
   python -c "import py3Dmol" || exit 1
   python -c "import ase" || exit 1
   python -c "from quantui import Molecule; print('Molecule OK')" || exit 1
+  python -c "from quantui.app import QuantUIApp; print('QuantUIApp OK')" || exit 1
   echo "All tests passed!"

local-setup/environment.yml

@@ -16,6 +16,7 @@ dependencies:
   # Scientific computing
   - numpy>=1.24.0
   - ase>=3.22.0          # Structure I/O, molecule library, geometry optimisation
+  - rdkit>=2022.03.1     # PubChem SDF→XYZ conversion, SMILES input
 
   # Visualization
   - py3dmol>=2.0.0       # Primary 3D molecular viewer

notebooks/_inspect_nb.py

@@ -0,0 +1,19 @@
+import json
+from pathlib import Path
+
+
+def main():
+    notebook_path = Path(__file__).resolve().parent / "molecule_computations.ipynb"
+    with notebook_path.open(encoding='utf-8') as f:
+        nb = json.load(f)
+    print("nbformat: {}.{}".format(nb["nbformat"], nb["nbformat_minor"]))
+    print("Total cells: {}".format(len(nb["cells"])))
+    for i, cell in enumerate(nb["cells"]):
+        cid = cell.get("id", "N/A")
+        src_preview = "".join(cell["source"])[:70].replace("\n", " ")
+        tags = cell.get("metadata", {}).get("tags", [])
+        print("  Cell {}: {} id={}  tags={}  src={}".format(i, cell["cell_type"], cid, tags, repr(src_preview)))
+
+
+if __name__ == "__main__":
+    main()