Add Recursive Self Aggregation (RSA) algorithm

.gitignore

@@ -143,6 +143,10 @@ vite.config.ts.timestamp-*
 .venv/
 venv/
 __pycache__/
+*.egg-info/
+*.egg
+dist/
+build/
 
 # Visual Studio Code
 .vscode/

charge_backend/backend_helper_funcs.py

@@ -108,6 +108,7 @@ def json(self):
 @dataclass
 class FlaskRunSettings(RunSettings):
     molecule_name_format: MolNameFormat = Field(alias="moleculeName", default="brand")
+    # Inherit use_ai_based from RunSettings (defined in LC-Conductor)
 
 
 @dataclass(frozen=True)

charge_backend/backend_manager.py

@@ -50,6 +50,7 @@ def __init__(
         self.websocket = task_manager.websocket
         self.builtin_tool_definitions = builtin_tool_definitions or []
         self.task_manager.available_builtin_tool_ids = None
+        self.retro_synth_context = None
 
     def _selected_mcp_tools(self) -> list[str]:
         if self.task_manager.available_tools is None:
@@ -225,14 +226,74 @@ async def _handle_optimization(
 
     async def _handle_retrosynthesis(self, data: dict) -> None:
         """Handle retrosynthesis problem type."""
-        run_func = partial(
-            template_based_retrosynthesis,
-            data["smiles"],
-            self.args.config_file,
-            self.get_retro_synth_context(),
-            self.task_manager.websocket,
-            self.run_settings,
-        )
+        # Check if AI-based retrosynthesis is requested
+        # use_ai_based flag controls AI vs template approach
+        # If no config exists, fall back to AI-based
+        use_ai_based = self.run_settings.use_ai_based or not os.path.exists(self.args.config_file)
+
+        if use_ai_based:
+            # Use AI-based retrosynthesis (supports both standard and RSA modes)
+            # Create root node like template_based_retrosynthesis does
+            from backend_helper_funcs import Node
+            from charge_backend.moleculedb.molecule_naming import smiles_to_html
+            from charge_backend.moleculedb.purchasable import is_purchasable
+
+            context = self.get_retro_synth_context()
+            context.reset()  # Clear context
+
+            start_smiles = data["smiles"]
+            mol_sources = is_purchasable(start_smiles)
+            if mol_sources:
+                purchasable_str = f"Yes (via {', '.join(mol_sources)})"
+            else:
+                purchasable_str = "No"
+
+            root = Node(
+                id="node_0",
+                smiles=start_smiles,
+                label=smiles_to_html(start_smiles, self.run_settings.molecule_name_format),
+                hoverInfo=f"""# Root molecule
+**SMILES:** {start_smiles}
+
+**Purchasable**? {purchasable_str}""",
+                level=0,
+                parentId=None,
+                cost=None,
+                bandgap=None,
+                yield_=None,
+                purchasable=(len(mol_sources) > 0),
+                highlight="yellow",
+                x=100,
+                y=100,
+            )
+
+            await context.add_node(root, websocket=self.task_manager.websocket)
+            root_node_id = root.id
+
+            run_func = partial(
+                ai_based_retrosynthesis,
+                root_node_id,
+                context,
+                data.get("query", None),
+                None,  # Unconstrained
+                self.task_manager.websocket,
+                self.experiment,
+                self.args.config_file,
+                self.run_settings,
+                self._selected_mcp_tools(),
+                self._selected_builtin_tools(),
+                self.log_progress,
+            )
+        else:
+            # Use template-based retrosynthesis
+            run_func = partial(
+                template_based_retrosynthesis,
+                data["smiles"],
+                self.args.config_file,
+                self.get_retro_synth_context(),
+                self.task_manager.websocket,
+                self.run_settings,
+            )
 
         await self.task_manager.run_task(run_func())
 

charge_backend/charge_server.py

@@ -165,12 +165,21 @@ async def root(request: Request):
         with open(os.path.join(DIST_PATH, "index.html"), "r") as fp:
             html = fp.read()
 
+        # Use dynamic WebSocket URL based on request host
+        ws_server = os.getenv("WS_SERVER")
+        if not ws_server:
+            # Auto-detect from request host and protocol
+            host = request.headers.get("host", f"localhost:{args.port}")
+            # Use wss:// for HTTPS, ws:// for HTTP
+            scheme = "wss" if request.url.scheme == "https" else "ws"
+            ws_server = f"{scheme}://{host}/ws"
+
         html = html.replace(
             "<!-- APP CONFIG -->",
             f"""
            <script>
            window.APP_CONFIG = {{
-               WS_SERVER: '{os.getenv("WS_SERVER", "ws://localhost:8001/ws")}',
+               WS_SERVER: '{ws_server}',
                VERSION: '{os.getenv("SERVER_VERSION", "")}'
            }};
            </script>""",