updated to working molgallery3D but still need to fix bugs for H2 and H2O, app crashing now for unknown reasons

app.py

@@ -53,6 +53,15 @@ import sys
 import json
 import os
 
+def install_dependencies():
+    """Install required packages from requirements.txt."""
+    try:
+        subprocess.check_call([sys.executable, "-m", "pip", "install", "-r", "requirements.txt"])
+        print("Dependencies installed successfully")
+    except subprocess.CalledProcessError as e:
+        print(f"Error installing dependencies: {e}")
+        sys.exit(1)
+
 # Load molecule definitions
 def load_molecules():
     """Load molecule definitions from JSON file."""
@@ -77,6 +86,7 @@ import gradio as gr
 import numpy as np
 from quantum_utils import run_vqe_simulation
 from visualization import plot_convergence, create_molecule_viewer, format_molecule_params
+from gradio_molgallery3d import MolGallery3D
 import spaces
 
 # Add immediate logging
@@ -162,7 +172,9 @@ def create_interface():
                 molecule_choice = gr.Dropdown(
                     choices=list(molecules.keys()),
                     value=list(molecules.keys())[0],
-                    label="Select Molecule"
+                    label="Select Molecule",
+                    allow_custom_value=False,  # Prevent text input
+                    type="value"  # Ensure it stays as a dropdown
                 )
                 
                 # Get scale range from selected molecule
@@ -195,17 +207,20 @@ def create_interface():
         
         # Plots and visualization
         with gr.Row():
-            convergence_plot = gr.Plot(
-                label="VQE Convergence",
-                show_label=True
-            )
-            # Create MolGallery3D component
-            molecule_viz = MolGallery3D(
-                columns=1,
-                height=400,
-                label="3D Molecule Viewer",
-                automatic_rotation=True
-            )
+            with gr.Column(scale=1):
+                convergence_plot = gr.Plot(
+                    label="VQE Convergence",
+                    show_label=True
+                )
+            with gr.Column(scale=1):
+                # Create MolGallery3D component with more space
+                molecule_viz = MolGallery3D(
+                    columns=1,
+                    height=600,  # Increased height
+                    width=600,   # Added explicit width
+                    label="3D Molecule Viewer",
+                    automatic_rotation=True
+                )
         
         def update_molecule_info(molecule_choice):
             """Update description and scale range when molecule is selected."""
@@ -223,8 +238,9 @@ def create_interface():
                 
                 # Create molecule visualization
                 mol_list = create_molecule_viewer(molecule_choice, default_scale)
-                if mol_list is None:
-                    mol_list = []  # Empty list if molecule creation failed
+                if mol_list is None or not mol_list:
+                    print(f"No molecule visualization created for {molecule_choice}", file=sys.stderr)
+                    mol_list = []
                 
                 return [
                     params_html,  # Update params display

visualization.py

@@ -8,7 +8,7 @@ import numpy as np
 import logging
 from rdkit import Chem
 from rdkit.Chem import AllChem
-from gradio_molgallery import MolGallery3D
+from gradio_molgallery3d import MolGallery3D
 import json
 
 # Configure logging
@@ -154,14 +154,22 @@ def create_molecule_viewer(molecule_id: str, scale_factor: float) -> MolGallery3
         
         molecule_data = molecules[molecule_id]
         
-        # Create molecule using SMILES
-        mol = Chem.MolFromSmiles(molecule_data['smiles'])
-        if mol is None:
-            logger.error(f"Could not create molecule from SMILES: {molecule_data['smiles']}")
-            return None
+        # Special handling for H2 and H2O
+        if molecule_id == "H2":
+            mol = Chem.MolFromSmiles("[H][H]")
+        elif molecule_id == "H2O":
+            mol = Chem.MolFromSmiles("O")
+            mol = Chem.AddHs(mol)
+        else:
+            # Create molecule using SMILES
+            mol = Chem.MolFromSmiles(molecule_data['smiles'])
+            if mol is None:
+                logger.error(f"Could not create molecule from SMILES: {molecule_data['smiles']}")
+                return None
+            mol = Chem.AddHs(mol)
         
-        mol = AllChem.AddHs(mol)
-        AllChem.EmbedMolecule(mol, randomSeed=42)  # Use fixed seed for consistency
+        # Generate 3D coordinates with distance matrix
+        AllChem.EmbedMolecule(mol, randomSeed=42)
         
         # Scale the molecule coordinates
         conf = mol.GetConformer()
@@ -174,13 +182,6 @@ def create_molecule_viewer(molecule_id: str, scale_factor: float) -> MolGallery3
             conf.SetAtomPosition(i, scaled_pos)
         
         # Create the MolGallery3D component
-        gallery = MolGallery3D(
-            columns=1,
-            height=400,
-            label=f"{molecule_data.get('name', molecule_id)} (Scale: {scale_factor:.2f})",
-            automatic_rotation=True
-        )
-        
         logger.info("Created MolGallery3D component")
         return [mol]  # Return the molecule as a list as expected by MolGallery3D