Add reaction visualizer API endpoint and improve error handling

.gitignore

@@ -0,0 +1,84 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Temporary files
+*.tmp
+*.temp
+.cache/

app.py

@@ -92,6 +92,7 @@ def parse_cube_file(cube_file):
 import gradio as gr
 from rdkit import Chem
 from rdkit.Chem import Descriptors, Draw, AllChem
+from rdkit.Chem import rdChemReactions
 import cirpy
 import pubchempy as pcp
 from urllib.error import HTTPError, URLError
@@ -149,6 +150,8 @@ def name_to_smiles(name: str) -> str:
         if smiles is None:
             raise gr.Error(f"Could not find SMILES for chemical name: {name}")
         return smiles
+    except (HTTPError, URLError) as e:
+        raise gr.Error(f"Unable to connect to chemical database service. Please try again later. Error: {str(e)}")
     except Exception as e:
         raise gr.Error(f"Error converting name to SMILES: {str(e)}")
 
@@ -184,6 +187,23 @@ def smiles_to_name(smiles: str) -> str:
     return f"No name available. Canonical SMILES: {canonical_smiles}"
 
 
+def reaction_smiles_to_svg(reaction_smiles: str) -> str:
+    """Convert reaction SMILES to SVG image"""
+    try:
+        # Parse the reaction SMILES
+        reaction = rdChemReactions.ReactionFromSmarts(reaction_smiles)
+        if reaction is None:
+            raise gr.Error(f"Invalid reaction SMILES: {reaction_smiles}")
+
+        # Draw the reaction as SVG
+        svg = Draw.ReactionToImage(reaction, subImgSize=(300, 300), useSVG=True)
+        
+        return svg
+
+    except Exception as e:
+        raise gr.Error(f"Error generating reaction image: {str(e)}")
+
+
 CHEMISCOPE_TEMPLATE_URL = "https://chemiscope.org/chemiscope_standalone.html"
 CHEMISCOPE_TEMPLATE_CACHE = Path(tempfile.gettempdir()) / "chemiscope_standalone.html"
 CHEMISCOPE_ASSET_DIR = Path("chemiscope_artifacts")
@@ -686,10 +706,15 @@ def smiles_to_molecular_orbitals(smiles_input: str, name_input: str) -> str:
 def name_to_3d_molecule(name: str) -> str:
     """Convert chemical name to 3D molecule visualization"""
     try:
-        # Convert name to SMILES
-        smiles = cirpy.resolve(name, 'smiles')
-        if smiles is None:
-            raise gr.Error(f"Could not find SMILES for chemical name: {name}")
+        # Convert name to SMILES with better error handling
+        try:
+            smiles = cirpy.resolve(name, 'smiles')
+            if smiles is None:
+                raise gr.Error(f"Could not find SMILES for chemical name: {name}")
+        except (HTTPError, URLError) as e:
+            raise gr.Error(f"Unable to connect to chemical database service. Please try again later or use SMILES directly. Error: {str(e)}")
+        except Exception as e:
+            raise gr.Error(f"Error resolving chemical name '{name}': {str(e)}")
 
         # Create molecule from SMILES
         mol = Chem.MolFromSmiles(smiles)
@@ -733,6 +758,9 @@ def name_to_3d_molecule(name: str) -> str:
 
         return html_content
 
+    except gr.Error:
+        # Re-raise Gradio errors as-is
+        raise
     except Exception as e:
         raise gr.Error(f"Error creating 3D molecule: {str(e)}")
 
@@ -1268,6 +1296,25 @@ scaffold_interface = gr.Interface(
     examples=[["c1ccc(CCN)cc1\nc1ccc(CCO)cc1\nc1ccc(CCC)cc1\nCCOc1ccc(CCN)cc1\nCCc1ccc(O)cc1"]],
 )
 
+# Reaction visualization interface
+reaction_interface = gr.Interface(
+    fn=reaction_smiles_to_svg,
+    inputs=gr.Textbox(
+        label="Reaction SMILES",
+        placeholder="CCO.O=C=O>>CC(=O)O.CO2 (Esterification reaction)",
+        info="Use '>>' to separate reactants from products"
+    ),
+    outputs=gr.HTML(label="Reaction Visualization"),
+    title="Reaction Visualizer",
+    description="Visualize chemical reactions from SMILES notation.",
+    api_name="reaction_visualizer",
+    examples=[
+        ["CCO.O=C=O>>CC(=O)O.CO2"],
+        ["c1ccccc1.ClC(Cl)Cl>>c1ccccc1Cl.HCl"],
+        ["CC(=O)O.[Na]>>CC(=O)O[Na]"]
+    ],
+)
+
 
 demo = gr.TabbedInterface(
     [
@@ -1276,6 +1323,7 @@ demo = gr.TabbedInterface(
         properties_interface,
         clustering_interface,
         scaffold_interface,
+        reaction_interface,
         name_interface,
         molecule_3d_interface,
         chemiscope_interface,
@@ -1291,6 +1339,7 @@ demo = gr.TabbedInterface(
         "Property Calculator",
         "Molecular Clustering",
         "Scaffold Analysis",
+        "Reaction Visualizer",
         "Name to SMILES",
         "3D Molecule Viewer",
         "Chemiscope Explorer",