Add interactive molecule explorer with visual property analysis and 3D viewer

app.py

@@ -869,6 +869,255 @@ def analyze_scaffolds(smiles_list: str) -> str:
     return "\n".join(results)
 
 
+def interactive_molecule_explorer(input_text: str, input_type: str):
+    """Interactive molecule explorer - input name or SMILES, get structure and properties"""
+    from rdkit.Chem import Lipinski, Crippen, Descriptors
+    import pandas as pd
+    
+    # Parse input
+    if input_type == "Name":
+        try:
+            smiles = cirpy.resolve(input_text, 'smiles')
+            if smiles is None:
+                return None, None, "Could not resolve chemical name. Please try a different name or use SMILES.", None
+            name = input_text
+        except:
+            return None, None, "Error resolving chemical name. Please try SMILES input.", None
+    else:  # SMILES
+        smiles = input_text
+        # Try to get name
+        try:
+            name = cirpy.resolve(smiles, 'name')
+            if name is None:
+                name = smiles
+        except:
+            name = smiles
+    
+    # Create molecule
+    try:
+        mol = Chem.MolFromSmiles(smiles)
+        if mol is None:
+            return None, None, "Invalid SMILES string", None
+    except:
+        return None, None, "Error parsing molecule", None
+    
+    # Generate 2D structure image
+    mol_2d = Draw.MolToImage(mol, size=(400, 400))
+    
+    # Calculate comprehensive properties
+    properties = {
+        "Molecular Formula": Chem.rdMolDescriptors.CalcMolFormula(mol),
+        "Molecular Weight": f"{Descriptors.MolWt(mol):.2f} g/mol",
+        "LogP (Lipophilicity)": f"{Descriptors.MolLogP(mol):.2f}",
+        "TPSA (Polar Surface Area)": f"{Descriptors.TPSA(mol):.2f} Ų",
+        "H-Bond Donors": Lipinski.NumHDonors(mol),
+        "H-Bond Acceptors": Lipinski.NumHAcceptors(mol),
+        "Rotatable Bonds": Lipinski.NumRotatableBonds(mol),
+        "Aromatic Rings": Lipinski.NumAromaticRings(mol),
+        "Fraction Csp3": f"{Lipinski.FractionCsp3(mol):.2f}",
+        "Molar Refractivity": f"{Crippen.MolMR(mol):.2f}",
+        "Heavy Atoms": Lipinski.HeavyAtomCount(mol),
+    }
+    
+    # Create properties visualization
+    fig = go.Figure()
+    
+    # Create a radar chart for key properties
+    categories = ['MW/100', 'LogP+5', 'TPSA/20', 'HBD*10', 'HBA*5', 'RotBonds*5']
+    values = [
+        Descriptors.MolWt(mol) / 100,
+        Descriptors.MolLogP(mol) + 5,
+        Descriptors.TPSA(mol) / 20,
+        Lipinski.NumHDonors(mol) * 10,
+        Lipinski.NumHAcceptors(mol) * 5,
+        Lipinski.NumRotatableBonds(mol) * 5
+    ]
+    
+    fig.add_trace(go.Scatterpolar(
+        r=values,
+        theta=categories,
+        fill='toself',
+        name='Properties',
+        line_color='rgb(30, 144, 255)'
+    ))
+    
+    fig.update_layout(
+        polar=dict(
+            radialaxis=dict(
+                visible=True,
+                range=[0, 15]
+            )
+        ),
+        showlegend=False,
+        title=f"Property Profile: {name}",
+        height=400
+    )
+    
+    # Create properties text
+    props_text = f"**Molecule:** {name}\n**SMILES:** {smiles}\n\n"
+    props_text += "**Properties:**\n"
+    for key, value in properties.items():
+        props_text += f"- {key}: {value}\n"
+    
+    # Check Lipinski's Rule of 5
+    lipinski_violations = 0
+    lipinski_text = "\n**Lipinski's Rule of 5:**\n"
+    
+    if Descriptors.MolWt(mol) > 500:
+        lipinski_violations += 1
+        lipinski_text += "❌ MW > 500\n"
+    else:
+        lipinski_text += "✅ MW ≤ 500\n"
+    
+    if Descriptors.MolLogP(mol) > 5:
+        lipinski_violations += 1
+        lipinski_text += "❌ LogP > 5\n"
+    else:
+        lipinski_text += "✅ LogP ≤ 5\n"
+    
+    if Lipinski.NumHDonors(mol) > 5:
+        lipinski_violations += 1
+        lipinski_text += "❌ HBD > 5\n"
+    else:
+        lipinski_text += "✅ HBD ≤ 5\n"
+    
+    if Lipinski.NumHAcceptors(mol) > 10:
+        lipinski_violations += 1
+        lipinski_text += "❌ HBA > 10\n"
+    else:
+        lipinski_text += "✅ HBA ≤ 10\n"
+    
+    if lipinski_violations <= 1:
+        lipinski_text += f"\n✅ **Drug-like** (Violations: {lipinski_violations})"
+    else:
+        lipinski_text += f"\n⚠️ **Not drug-like** (Violations: {lipinski_violations})"
+    
+    props_text += lipinski_text
+    
+    return mol_2d, fig, props_text, smiles
+
+
+def generate_3d_interactive(smiles: str):
+    """Generate interactive 3D molecule viewer"""
+    if not smiles or smiles == "None":
+        return "<p>Please enter a molecule first</p>"
+    
+    try:
+        mol = Chem.MolFromSmiles(smiles)
+        if mol is None:
+            return "<p>Invalid SMILES</p>"
+        
+        # Add hydrogens and generate 3D coordinates
+        mol_3d = Chem.AddHs(mol)
+        AllChem.EmbedMolecule(mol_3d, randomSeed=42)
+        AllChem.MMFFOptimizeMolecule(mol_3d)
+        
+        # Get molecular structure
+        mol_block = Chem.MolToMolBlock(mol_3d)
+        
+        # Escape for JavaScript
+        mol_block_escaped = mol_block.replace('`', '\\`').replace('${', '\\${')
+        
+        # Create standalone HTML with 3Dmol.js
+        html_content = f"""
+<!DOCTYPE html>
+<html>
+<head>
+    <script src="https://3dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
+    <style>
+        body {{ margin: 0; padding: 0; }}
+        #viewer {{ width: 100%; height: 500px; }}
+    </style>
+</head>
+<body>
+    <div id="viewer"></div>
+    <script>
+        var viewer = $3Dmol.createViewer("viewer", {{backgroundColor: 'white'}});
+        var molData = `{mol_block_escaped}`;
+        viewer.addModel(molData, "sdf");
+        viewer.setStyle({{}}, {{stick: {{radius: 0.15}}, sphere: {{scale: 0.3}}}});
+        viewer.zoomTo();
+        viewer.render();
+    </script>
+</body>
+</html>
+"""
+        
+        iframe_html = f"""
+        <iframe srcdoc="{html_content.replace('"', '&quot;')}" 
+                style="width: 100%; height: 520px; border: 2px solid #2196F3; border-radius: 8px;"
+                sandbox="allow-scripts allow-same-origin">
+        </iframe>
+        """
+        
+        return iframe_html
+    except Exception as e:
+        return f"<p>Error generating 3D structure: {str(e)}</p>"
+
+
+# Interactive Molecule Explorer - Main Feature
+with gr.Blocks(theme=gr.themes.Soft()) as interactive_explorer:
+    gr.Markdown("# 🔬 Interactive Molecule Explorer")
+    gr.Markdown("Enter a molecule name or SMILES to explore its structure and properties")
+    
+    with gr.Row():
+        with gr.Column(scale=1):
+            input_text = gr.Textbox(
+                label="Enter Molecule", 
+                placeholder="e.g., aspirin, caffeine, or CCO",
+                lines=1
+            )
+            input_type = gr.Radio(
+                choices=["Name", "SMILES"], 
+                value="Name", 
+                label="Input Type"
+            )
+            analyze_btn = gr.Button("🔍 Analyze Molecule", variant="primary", size="lg")
+            
+            gr.Markdown("### Quick Examples:")
+            gr.Examples(
+                examples=[
+                    ["aspirin", "Name"],
+                    ["caffeine", "Name"],
+                    ["glucose", "Name"],
+                    ["c1ccccc1", "SMILES"],
+                    ["CCO", "SMILES"],
+                ],
+                inputs=[input_text, input_type],
+            )
+        
+        with gr.Column(scale=1):
+            structure_2d = gr.Image(label="2D Structure", type="pil")
+    
+    with gr.Row():
+        properties_plot = gr.Plot(label="Property Radar Chart")
+    
+    with gr.Row():
+        properties_text = gr.Markdown(label="Detailed Properties")
+    
+    gr.Markdown("---")
+    gr.Markdown("## 🧊 Interactive 3D Viewer")
+    gr.Markdown("Click below to generate the interactive 3D molecular structure")
+    
+    smiles_state = gr.State(value=None)
+    generate_3d_btn = gr.Button("🎯 Generate 3D Structure", variant="secondary", size="lg")
+    viewer_3d = gr.HTML(label="3D Molecular Viewer")
+    
+    # Connect the analyze button
+    analyze_btn.click(
+        fn=interactive_molecule_explorer,
+        inputs=[input_text, input_type],
+        outputs=[structure_2d, properties_plot, properties_text, smiles_state]
+    )
+    
+    # Connect the 3D button
+    generate_3d_btn.click(
+        fn=generate_3d_interactive,
+        inputs=[smiles_state],
+        outputs=[viewer_3d]
+    )
+
+
 smiles_interface = gr.Interface(
     fn=smiles_to_canonical,
     inputs=gr.Textbox(label="SMILES"),
@@ -1006,13 +1255,14 @@ scaffold_interface = gr.Interface(
 
 demo = gr.TabbedInterface(
     [
-        name_interface,
-        molecule_3d_interface,
-        chemiscope_interface,
+        interactive_explorer,
         orbital_interface,
         properties_interface,
         clustering_interface,
         scaffold_interface,
+        name_interface,
+        molecule_3d_interface,
+        chemiscope_interface,
         smiles_interface,
         smiles_to_name_interface,
         mw_interface,
@@ -1020,21 +1270,22 @@ demo = gr.TabbedInterface(
         tpsa_interface,
     ],
     [
-        "Name to SMILES",
-        "3D Molecule Viewer",
-        "Chemiscope Explorer",
+        "🔬 Interactive Explorer",
         "Molecular Orbitals",
         "Property Calculator",
         "Molecular Clustering",
         "Scaffold Analysis",
+        "Name to SMILES",
+        "3D Molecule Viewer",
+        "Chemiscope Explorer",
         "SMILES to Canonical",
         "SMILES to Name",
         "Molecular Weight",
         "LogP",
         "TPSA",
     ],
-    title="RDKit API",
-    css=".gradio-container {max-width: 800px; margin: auto;}",
+    title="RDKit API - Interactive Molecular Analysis",
+    css=".gradio-container {max-width: 1200px; margin: auto;}",
 )
 
 

force_rebuild.txt

@@ -1,2 +1,2 @@
 # Force rebuild
-2025-11-08 v16
+2025-11-08 v17