Replace Psi4/psikit with PySCF for molecular orbital calculations on HF Spaces

app.py

@@ -112,27 +112,12 @@ def smiles_to_molecular_orbitals(smiles_input: str, name_input: str) -> str:
         raise gr.Error("Please provide a molecule with 30 atoms or fewer for orbital visualization.")
 
     try:
-        from psikit import Psikit  # type: ignore[import]
+        import pyscf  # type: ignore[import]
     except ImportError:
         return (
-            "<p><strong>Molecular orbital rendering requires Psikit + Psi4.</strong> "
-            "Install them locally with <code>pip install psikit psi4 py3Dmol</code> "
-            "and run this app on your machine.</p>"
-            "<p><strong>Alternative online tools:</strong></p>"
-            "<ul>"
-            "<li><a href='https://www.webmo.net/' target='_blank'>WebMO</a> - Web-based molecular modeling</li>"
-            "<li><a href='https://gaussian.com/' target='_blank'>Gaussian</a> - Quantum chemistry software</li>"
-            "<li><a href='https://www.chemcraftprog.com/' target='_blank'>ChemCraft</a> - Molecular visualization</li>"
-            "</ul>"
-            f"<p>You can copy this SMILES to these tools: <code>{canonical_smiles}</code></p>"
-        )
-
-    try:
-        import psi4  # Check if psi4 is available
-    except ImportError:
-        return (
-            "<p><strong>Psi4 is not available on this platform.</strong> "
-            "Molecular orbital calculations require Psi4, which is not supported on Hugging Face Spaces.</p>"
+            "<p><strong>PySCF is not available.</strong> "
+            "Install it with <code>pip install pyscf</code> "
+            "for molecular orbital calculations.</p>"
             "<p><strong>Alternative online tools:</strong></p>"
             "<ul>"
             "<li><a href='https://www.webmo.net/' target='_blank'>WebMO</a> - Web-based molecular modeling</li>"
@@ -154,18 +139,43 @@ def smiles_to_molecular_orbitals(smiles_input: str, name_input: str) -> str:
         original_cwd = os.getcwd()
         os.chdir(tmpdir)
         try:
-            pk = Psikit()
-            pk.read_from_smiles(smiles)
-            pk.optimize()
-            pk.getMOview()
-
-            cube_candidates = sorted(Path(tmpdir).glob("Psi_a_*A.cube"))
-            if not cube_candidates:
-                return (
-                    "<p>Psikit did not produce cube files. Try a smaller molecule or different conformer.</p>"
-                )
-
-            mol_block = Chem.MolToMolBlock(pk.mol)
+            # Generate 3D coordinates with RDKit
+            mol_3d = Chem.AddHs(mol)
+            AllChem.EmbedMolecule(mol_3d, randomSeed=42)
+            AllChem.MMFFOptimizeMolecule(mol_3d)
+
+            # Extract coordinates and atomic numbers
+            coords = []
+            atoms = []
+            for atom in mol_3d.GetAtoms():
+                pos = mol_3d.GetConformer().GetAtomPosition(atom.GetIdx())
+                coords.append([pos.x, pos.y, pos.z])
+                atoms.append(atom.GetSymbol())
+
+            # Set up PySCF molecule
+            mol_pyscf = pyscf.gto.Mole()
+            mol_pyscf.atom = list(zip(atoms, coords))
+            mol_pyscf.basis = 'sto-3g'  # Small basis set for speed
+            mol_pyscf.build()
+
+            # Run Hartree-Fock calculation
+            mf = pyscf.scf.RHF(mol_pyscf)
+            mf.kernel()
+
+            # Get HOMO and LUMO indices
+            nocc = mol_pyscf.nelectron // 2
+            homo_idx = nocc - 1
+            lumo_idx = nocc
+
+            # Generate cube files for HOMO and LUMO
+            from pyscf.tools import cubegen
+            cube_files = []
+            for idx, label in [(homo_idx, 'HOMO'), (lumo_idx, 'LUMO')]:
+                cube_file = f'{label.lower()}.cube'
+                cubegen.orbital(mol_pyscf, cube_file, mf.mo_coeff[:, idx])
+                cube_files.append((cube_file, label))
+
+            mol_block = Chem.MolToMolBlock(mol_3d)
 
             html_sections: list[str] = []
             if name_input.strip():
@@ -173,9 +183,10 @@ def smiles_to_molecular_orbitals(smiles_input: str, name_input: str) -> str:
                     f"<p><strong>Resolved '{name_input.strip()}' to SMILES:</strong> {canonical_smiles}</p>"
                 )
 
-            labels = ["HOMO", "LUMO"]
-            for cube_file, label in zip(cube_candidates[:2], labels):
-                cube_data = cube_file.read_text()
+            for cube_file, label in cube_files:
+                if not Path(cube_file).exists():
+                    continue
+                cube_data = Path(cube_file).read_text()
                 view = py3Dmol.view(width=500, height=400)
                 view.addModel(mol_block, "mol")
                 view.setStyle({"stick": {}})
@@ -197,9 +208,6 @@ def smiles_to_molecular_orbitals(smiles_input: str, name_input: str) -> str:
             if not html_sections:
                 return "<p>Could not prepare HOMO/LUMO visualizations.</p>"
 
-            if not html_sections:
-                return "<p>Could not prepare HOMO/LUMO visualizations.</p>"
-
             return "".join(html_sections)
         except Exception as exc:  # pragma: no cover - runtime heavy
             return f"<p>Unable to compute molecular orbitals: {exc}</p>"

force_rebuild.txt

@@ -1,2 +1,2 @@
 # Force rebuild
-2025-11-08 v2
+2025-11-08 v3

requirements.txt

@@ -5,4 +5,5 @@ huggingface_hub==0.19.4
 cirpy
 pubchempy
 psikit
-py3Dmol
+py3Dmol
+pyscf