Fix: make visualization/collaborative imports optional

- These modules require extra deps (py3Dmol, fastapi) not needed for main UI
- Wrap imports in try/except to avoid startup failures
- Updated requirements.txt with all core dependencies

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

protein_conformal/backend/__init__.py

@@ -3,9 +3,9 @@ Backend module for Protein Conformal Prediction.
 Contains the server-side implementation components.
 """
 
-# Main interface components
+# Main interface components (always available)
 from .gradio_interface import (
-    create_interface, 
+    create_interface,
     process_input,
     validate_sequence,
     highlight_sequence,
@@ -15,17 +15,33 @@ from .gradio_interface import (
     export_current_results
 )
 
-# Visualization and collaborative modules
-from .visualization import (
-    create_structure_with_heatmap,
-    create_similarity_network,
-    create_statistical_summary,
-    format_html_report
-)
+# Optional: Visualization module (requires py3Dmol, networkx, seaborn)
+# These are not used by the main Gradio interface
+try:
+    from .visualization import (
+        create_structure_with_heatmap,
+        create_similarity_network,
+        create_statistical_summary,
+        format_html_report
+    )
+except ImportError:
+    # Visualization not available - missing optional dependencies
+    create_structure_with_heatmap = None
+    create_similarity_network = None
+    create_statistical_summary = None
+    format_html_report = None
 
-from .collaborative import (
-    save_session,
-    load_session,
-    export_report,
-    create_api_app
-) 
+# Optional: Collaborative API module (requires fastapi, uvicorn)
+try:
+    from .collaborative import (
+        save_session,
+        load_session,
+        export_report,
+        create_api_app
+    )
+except ImportError:
+    # Collaborative features not available - missing optional dependencies
+    save_session = None
+    load_session = None
+    export_report = None
+    create_api_app = None 

requirements.txt

@@ -8,14 +8,23 @@ biopython>=1.81
 # ML/Embeddings
 torch>=2.0.0
 faiss-cpu>=1.7.4
+transformers>=4.30.0
 
 # Gradio UI
 gradio>=4.0.0
 
-# Visualization
+# Visualization (required by gradio_interface)
 matplotlib>=3.5.0
 plotly>=5.9.0
 
-# HuggingFace integration
+# HuggingFace integration (for downloading assets)
 huggingface_hub>=0.20.0
-transformers>=4.30.0
+
+# Optional visualization dependencies (for visualization.py if used)
+# py3Dmol>=1.8.0
+# networkx>=2.8.0
+# seaborn>=0.12.0
+
+# Optional API dependencies (for collaborative.py if used)
+# fastapi>=0.90.0
+# uvicorn>=0.18.0