Create molecule_viewer.py

genesis/molecule_viewer.py

@@ -0,0 +1,45 @@
+# genesis/molecule_viewer.py
+import requests
+from typing import Optional
+
+def fetch_pdb(pdb_id: str) -> Optional[str]:
+    """Fetch PDB file from RCSB."""
+    url = f"https://files.rcsb.org/download/{pdb_id.upper()}.pdb"
+    r = requests.get(url)
+    if r.status_code == 200:
+        return r.text
+    return None
+
+def fetch_alphafold(uniprot_id: str) -> Optional[str]:
+    """Fetch PDB model from AlphaFold."""
+    url = f"https://alphafold.ebi.ac.uk/files/AF-{uniprot_id}-F1-model_v4.pdb"
+    r = requests.get(url)
+    if r.status_code == 200:
+        return r.text
+    return None
+
+def render_3dmol(pdb_data: str) -> str:
+    """Generate HTML for 3Dmol.js viewer with biotech neon styling."""
+    return f"""
+    <div id="viewer" style="width: 100%; height: 600px; background-color: black; border: 2px solid #00ff99; box-shadow: 0 0 20px #ff6600;"></div>
+    <script src="https://3dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
+    <script>
+      let viewer = $3Dmol.createViewer('viewer', {{ backgroundColor: 'black' }});
+      let pdbData = `{pdb_data}`;
+      viewer.addModel(pdbData, "pdb");
+      viewer.setStyle({{}}, {{cartoon: {{color: 'spectrum'}}}});
+      viewer.zoomTo();
+      viewer.render();
+    </script>
+    """
+
+def get_molecule_view(pdb_or_gene: str) -> str:
+    """Fetch molecule structure and return 3D viewer HTML."""
+    # Try PDB ID first
+    pdb_data = fetch_pdb(pdb_or_gene)
+    if not pdb_data:
+        # Try AlphaFold with UniProt ID or gene name
+        pdb_data = fetch_alphafold(pdb_or_gene)
+    if pdb_data:
+        return render_3dmol(pdb_data)
+    return f"<p style='color:red;'>No structure found for {pdb_or_gene}</p>"