rowan-mcp 1.0.2__tar.gz → 2.0.1__tar.gz

rowan_mcp-2.0.1/.gitignore

@@ -0,0 +1,21 @@
+/.venv
+/rowan-dxt
+.env
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.DS_Store
+
+.claude
+CLAUDE.md
+/dist
+
+# MCP configuration (may contain tokens)
+.mcp.json
+
+# Personal compatibility notes
+GEMINI_MCP_COMPATIBILITY.md
+MCP_CHATGPT_GEMINI_COMPATIBILITY_ANALYSIS.md
+ROWAN_MCP_TEST_QUERIES.md
+ROWAN_MCP_TOOLS.md

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-mcp
-Version: 1.0.2
+Version: 2.0.1
 Summary: Model Context Protocol server for Rowan computational chemistry platform
 Project-URL: Homepage, https://github.com/k-yenko/rowan-mcp
 Author-email: Katherine Yenko <katherineayenko@gmail.com>
@@ -13,14 +13,15 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.10
+Requires-Python: >=3.11
+Requires-Dist: aiohttp>=3.12.15
 Requires-Dist: fastapi>=0.104.0
-Requires-Dist: fastmcp>=0.2.0
+Requires-Dist: fastmcp>=2.11.3
 Requires-Dist: pubchempy>=1.0.4
 Requires-Dist: pydantic>=2.0.0
 Requires-Dist: python-dotenv>=1.0.0
 Requires-Dist: rdkit>=2025.3.2
-Requires-Dist: rowan-python>=0.1.0
+Requires-Dist: rowan-python>=2.1.1
 Requires-Dist: typing-extensions>=4.0.0
 Requires-Dist: uvicorn>=0.24.0
 Provides-Extra: dev
@@ -32,7 +33,7 @@ Description-Content-Type: text/markdown
 
 # Rowan MCP Server
 
-This project wraps an MCP (Model Context Protocol) around Rowan's tools, making it easy for users to design molecuels and run simulations in natural everyday language. 
+MCP server for making it easy to run Rowan's molecular design and simulation tools.
 
 ---
 
@@ -56,34 +57,25 @@ That's it - no command line setup needed!
 
 Just add this to your MCP configuration and it will automatically install and run:
 
-**Using uvx (simplest):**
+**HTTP/SSE configuration:**
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "uvx",
-      "args": ["--from", "rowan-mcp", "rowan-mcp"],
-      "env": {
-        "ROWAN_API_KEY": "your_api_key_here"
-      }
+      "type": "http",
+      "url": "http://127.0.0.1:6276/sse"
     }
   }
 }
 ```
 
-**Using uv run (alternative):**
-```json
-{
-  "mcpServers": {
-    "rowan": {
-      "command": "uv",
-      "args": ["run", "--with", "rowan-mcp", "-m", "rowan_mcp"],
-      "env": {
-        "ROWAN_API_KEY": "your_api_key_here"
-      }
-    }
-  }
-}
+Then start the server:
+```bash
+# Set your API key
+export ROWAN_API_KEY="your_api_key_here"
+
+# Start the HTTP server
+uvx --from rowan-mcp rowan-mcp
 ```
 
 ### **Option 2: Manual Installation**
@@ -100,20 +92,24 @@ uv add rowan-mcp
 pip install rowan-mcp
 ```
 
-Then use this configuration:
+Then configure and start:
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "rowan-mcp",
-      "env": {
-        "ROWAN_API_KEY": "your_api_key_here"
-      }
+      "type": "http", 
+      "url": "http://127.0.0.1:6276/sse"
     }
   }
 }
 ```
 
+```bash
+# Set API key and start server
+export ROWAN_API_KEY="your_api_key_here"
+rowan-mcp
+```
+
 ### **Get API Key**
 
 Visit [labs.rowansci.com](https://labs.rowansci.com) → Create account → Generate API key
@@ -134,7 +130,7 @@ Ask the LLM to:
 
 ## **System Requirements**
 
-- **Python 3.10+** (Python 3.11+ recommended)
+- **Python 3.11+** 
 - **Package manager**: [uv](https://docs.astral.sh/uv/) (recommended) or pip
 - **Rowan API key** (free at [labs.rowansci.com](https://labs.rowansci.com))
 - **MCP-compatible client** (Claude Desktop, etc.)
@@ -142,7 +138,8 @@ Ask the LLM to:
 **Development commands** (if you cloned the repo):
 ```bash
 # Run from source
-uv run python -m rowan_mcp --http
+export ROWAN_API_KEY="your_api_key_here"
+uv run python -m rowan_mcp
 ```
 
 ---
@@ -176,7 +173,7 @@ uv run python -m rowan_mcp --http
 
 ## **Requirements**
 
-- Python 3.10+
+- Python 3.11+
 - Rowan API key
 - MCP-compatible AI assistant (Claude Desktop, etc.)
 
@@ -187,19 +184,6 @@ uv run python -m rowan_mcp --http
 
 ---
 
-## **Todo**
-
-- [ ] Remove unnecessary AI spaghetti formatting 🙃
-- [ ] Some complex conformer searches hang on "running"
-- [ ] Edit MCP one-liner context
-- [ ] Transition state finding and IRC
-- [X] `rowan_scan` - Potential energy surfaces
-- [ ] `rowan_docking` - Protein-ligand docking
-- [X] add in h-bond, BDE and macroscopic pka, logD, BBB
-- [ ] Folder listing API bug (returns 500 error) - Rowan side?
-- [ ] Multistage optimization sometimes shows unexpected imaginary frequencies
-- [ ] Some calculations show as finished in logs but not in Rowan UI
-
 ## **Citation**
 
 If you use this MCP tool in your research, please cite the underlying Rowan platform:
@@ -233,3 +217,12 @@ To update the dxt file:
 # Then update the desktop extension
 dxt pack rowan-dxt
 ```
+### MCP inspector
+```bash
+# Start the server first
+export ROWAN_API_KEY="your_api_key_here" 
+uv run python -m rowan_mcp &
+
+# Then inspect
+npx @modelcontextprotocol/inspector http://127.0.0.1:6276/sse
+```        

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/README.md

@@ -1,6 +1,6 @@
 # Rowan MCP Server
 
-This project wraps an MCP (Model Context Protocol) around Rowan's tools, making it easy for users to design molecuels and run simulations in natural everyday language. 
+MCP server for making it easy to run Rowan's molecular design and simulation tools.
 
 ---
 
@@ -24,34 +24,25 @@ That's it - no command line setup needed!
 
 Just add this to your MCP configuration and it will automatically install and run:
 
-**Using uvx (simplest):**
+**HTTP/SSE configuration:**
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "uvx",
-      "args": ["--from", "rowan-mcp", "rowan-mcp"],
-      "env": {
-        "ROWAN_API_KEY": "your_api_key_here"
-      }
+      "type": "http",
+      "url": "http://127.0.0.1:6276/sse"
     }
   }
 }
 ```
 
-**Using uv run (alternative):**
-```json
-{
-  "mcpServers": {
-    "rowan": {
-      "command": "uv",
-      "args": ["run", "--with", "rowan-mcp", "-m", "rowan_mcp"],
-      "env": {
-        "ROWAN_API_KEY": "your_api_key_here"
-      }
-    }
-  }
-}
+Then start the server:
+```bash
+# Set your API key
+export ROWAN_API_KEY="your_api_key_here"
+
+# Start the HTTP server
+uvx --from rowan-mcp rowan-mcp
 ```
 
 ### **Option 2: Manual Installation**
@@ -68,20 +59,24 @@ uv add rowan-mcp
 pip install rowan-mcp
 ```
 
-Then use this configuration:
+Then configure and start:
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "rowan-mcp",
-      "env": {
-        "ROWAN_API_KEY": "your_api_key_here"
-      }
+      "type": "http", 
+      "url": "http://127.0.0.1:6276/sse"
     }
   }
 }
 ```
 
+```bash
+# Set API key and start server
+export ROWAN_API_KEY="your_api_key_here"
+rowan-mcp
+```
+
 ### **Get API Key**
 
 Visit [labs.rowansci.com](https://labs.rowansci.com) → Create account → Generate API key
@@ -102,7 +97,7 @@ Ask the LLM to:
 
 ## **System Requirements**
 
-- **Python 3.10+** (Python 3.11+ recommended)
+- **Python 3.11+** 
 - **Package manager**: [uv](https://docs.astral.sh/uv/) (recommended) or pip
 - **Rowan API key** (free at [labs.rowansci.com](https://labs.rowansci.com))
 - **MCP-compatible client** (Claude Desktop, etc.)
@@ -110,7 +105,8 @@ Ask the LLM to:
 **Development commands** (if you cloned the repo):
 ```bash
 # Run from source
-uv run python -m rowan_mcp --http
+export ROWAN_API_KEY="your_api_key_here"
+uv run python -m rowan_mcp
 ```
 
 ---
@@ -144,7 +140,7 @@ uv run python -m rowan_mcp --http
 
 ## **Requirements**
 
-- Python 3.10+
+- Python 3.11+
 - Rowan API key
 - MCP-compatible AI assistant (Claude Desktop, etc.)
 
@@ -155,19 +151,6 @@ uv run python -m rowan_mcp --http
 
 ---
 
-## **Todo**
-
-- [ ] Remove unnecessary AI spaghetti formatting 🙃
-- [ ] Some complex conformer searches hang on "running"
-- [ ] Edit MCP one-liner context
-- [ ] Transition state finding and IRC
-- [X] `rowan_scan` - Potential energy surfaces
-- [ ] `rowan_docking` - Protein-ligand docking
-- [X] add in h-bond, BDE and macroscopic pka, logD, BBB
-- [ ] Folder listing API bug (returns 500 error) - Rowan side?
-- [ ] Multistage optimization sometimes shows unexpected imaginary frequencies
-- [ ] Some calculations show as finished in logs but not in Rowan UI
-
 ## **Citation**
 
 If you use this MCP tool in your research, please cite the underlying Rowan platform:
@@ -201,3 +184,12 @@ To update the dxt file:
 # Then update the desktop extension
 dxt pack rowan-dxt
 ```
+### MCP inspector
+```bash
+# Start the server first
+export ROWAN_API_KEY="your_api_key_here" 
+uv run python -m rowan_mcp &
+
+# Then inspect
+npx @modelcontextprotocol/inspector http://127.0.0.1:6276/sse
+```        

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/pyproject.toml

@@ -4,14 +4,14 @@ build-backend = "hatchling.build"
 
 [project]
 name = "rowan-mcp"
-version = "1.0.2"
+version = "2.0.1"
 description = "Model Context Protocol server for Rowan computational chemistry platform"
 authors = [
     {name = "Katherine Yenko", email = "katherineayenko@gmail.com"}
 ]
 license = {text = "MIT"}
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 urls = {Homepage = "https://github.com/k-yenko/rowan-mcp"}
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -24,8 +24,8 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Chemistry",
 ]
 dependencies = [
-    "fastmcp>=0.2.0",
-    "rowan-python>=0.1.0",
+    "fastmcp>=2.11.3",
+    "rowan-python>=2.1.1",
     "pydantic>=2.0.0",
     "typing-extensions>=4.0.0",
     "uvicorn>=0.24.0",
@@ -33,6 +33,7 @@ dependencies = [
     "python-dotenv>=1.0.0",
     "pubchempy>=1.0.4",
     "rdkit>=2025.3.2",
+    "aiohttp>=3.12.15",
 ]
 
 [project.optional-dependencies]
@@ -49,6 +50,16 @@ rowan-mcp = "rowan_mcp.server:main"
 [tool.hatch.build.targets.wheel]
 packages = ["rowan_mcp"]
 
+[tool.hatch.build.targets.sdist]
+exclude = [
+  "rowan-dxt/",
+  "dxt/", 
+  "*.log",
+  "test_*.py",
+  ".venv/",
+  "*.dxt"
+]
+
 [tool.black]
 line-length = 88
 target-version = ['py38']

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/__init__.py

@@ -5,7 +5,7 @@ This package provides MCP (Model Context Protocol) server functionality
 for integrating with Rowan's computational chemistry platform.
 """
 
-__version__ = "1.0.0"
+__version__ = "1.0.2"
 __author__ = "Kat Yenko"
 __description__ = "MCP server for Rowan computational chemistry platform"
 

rowan_mcp-2.0.1/rowan_mcp/__main__.py

@@ -0,0 +1,12 @@
+"""
+Main entry point for Rowan MCP Server when run as a module.
+
+Usage:
+    python -m rowan_mcp          # HTTP/SSE mode
+    python -m rowan_mcp --help   # Show help
+"""
+
+if __name__ == "__main__":
+    # HTTP transport only
+    from .server import main
+    main() 

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/admet.py

@@ -16,11 +16,6 @@ except ImportError:
 # Setup logging
 logger = logging.getLogger(__name__)
 
-# Setup API key
-api_key = os.getenv("ROWAN_API_KEY")
-if rowan and api_key:
-    rowan.api_key = api_key
-
 
 def log_rowan_api_call(workflow_type: str, **kwargs):
     """Log Rowan API calls with detailed parameters."""

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/bde.py

@@ -10,14 +10,7 @@ from typing import Optional, List, Union
 import logging
 logger = logging.getLogger(__name__)
 
-# Configure rowan API key
-if not hasattr(rowan, 'api_key') or not rowan.api_key:
-    api_key = os.getenv("ROWAN_API_KEY")
-    if api_key:
-        rowan.api_key = api_key
-        logger.info("🔑 Rowan API key configured")
-    else:
-        logger.error("No ROWAN_API_KEY found in environment")
+
 
 def log_rowan_api_call(workflow_type: str, **kwargs):
     """Log Rowan API calls and let Rowan handle its own errors."""

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/conformers.py

@@ -15,10 +15,7 @@ except ImportError:
 # Setup logging
 logger = logging.getLogger(__name__)
 
-# Setup API key
-api_key = os.getenv("ROWAN_API_KEY")
-if rowan and api_key:
-    rowan.api_key = api_key
+
 
 def log_rowan_api_call(workflow_type: str, **kwargs):
     """Log Rowan API calls and let Rowan handle its own errors."""

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/descriptors.py

@@ -15,10 +15,7 @@ except ImportError:
 # Setup logging
 logger = logging.getLogger(__name__)
 
-# Setup API key
-api_key = os.getenv("ROWAN_API_KEY")
-if rowan and api_key:
-    rowan.api_key = api_key
+
 
 def log_rowan_api_call(workflow_type: str, **kwargs):
     """Log Rowan API calls with detailed parameters."""

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/docking.py

@@ -192,63 +192,13 @@ def rowan_docking(
         if conformers is not None:
             compute_params["conformers"] = conformers
         
-        # Submit docking calculation
+        # Submit docking calculation and return raw result
         result = rowan.compute(**compute_params)
-        
-        # Format results
-        uuid = result.get('uuid', 'N/A')
-        status = result.get('status', 'unknown')
-        
-        if blocking:
-            # Blocking mode - check if successful
-            if status == "success":
-                formatted = f"✅ Docking calculation '{name}' completed successfully!\n"
-                formatted += f"🔖 Workflow UUID: {uuid}\n"
-                formatted += f"📊 Status: {status}\n\n"
-                
-                # Extract docking results if available
-                object_data = result.get("object_data", {})
-                scores = object_data.get("scores", [])
-                
-                if scores:
-                    formatted += f"🎯 Docking Results: {len(scores)} poses generated\n"
-                    formatted += f"📈 Best docking score: {scores[0] if scores else 'N/A'}\n"
-                    
-                    # Show top poses
-                    formatted += "\nTop poses:\n"
-                    for i, score in enumerate(scores[:5]):
-                        formatted += f"  {i+1}. Score: {score}\n"
-                        
-                    if len(scores) > 5:
-                        formatted += f"  ... and {len(scores) - 5} more poses\n"
-                else:
-                    formatted += "📈 Results: Check workflow details for docking data\n"
-                    
-                return formatted
-            else:
-                # Failed calculation
-                return f"❌ Docking calculation failed\n🔖 UUID: {uuid}\n📋 Status: {status}\n💬 Check workflow details for more information"
-        else:
-            # Non-blocking mode
-            formatted = f"📋 Docking calculation '{name}' submitted!\n"
-            formatted += f"🔖 Workflow UUID: {uuid}\n"
-            formatted += f"⏳ Status: Running...\n"
-            formatted += f"💡 Use rowan_workflow_management to check status\n\n"
-            
-            formatted += f"Docking Details:\n"
-            formatted += f"🧬 Ligand: {initial_molecule}\n"
-            formatted += f"🎯 Target: {target_uuid or target[:50] + '...' if target and len(target) > 50 else target}\n"
-            formatted += f"📍 Pocket: center={pocket[0]}, size={pocket[1]}\n"
-            formatted += f"⚙️  Settings: csearch={do_csearch}, optimize={do_optimization}, refine={do_pose_refinement}\n"
-            
-            if conformers:
-                formatted += f"🔬 Pre-optimized conformers: {len(conformers)}\n"
-                
-            return formatted
+        return result
             
     except Exception as e:
         logger.error(f"Error in rowan_docking: {str(e)}")
-        return f"❌ Docking calculation failed: {str(e)}"
+        return f"Docking calculation failed: {str(e)}"
 
 def rowan_docking_pdb_id(
     name: str,
@@ -297,7 +247,7 @@ def rowan_docking_pdb_id(
         else:
             ligand_param = f"    smiles={smiles},\n"
     
-    return (f"✅ PDB {pdb_id} found in RCSB database!\n\n"
+    return (f"PDB {pdb_id} found in RCSB database!\n\n"
             f"To perform docking with this protein:\n\n"
             f"1. Go to https://labs.rowansci.com\n"
             f"2. Upload the PDB file for {pdb_id}\n"
@@ -329,11 +279,11 @@ def test_rowan_docking():
             pocket=((0.0, 0.0, 0.0), (20.0, 20.0, 20.0)),
             blocking=False
         )
-        print("✅ Docking test result:")
+        print("Docking test result:")
         print(result)
         return True
     except Exception as e:
-        print(f"❌ Docking test failed: {e}")
+        print(f"Docking test failed: {e}")
         return False
 
 if __name__ == "__main__":

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/electronic_properties.py

@@ -22,10 +22,7 @@ except ImportError:
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-# Setup API key
-api_key = os.getenv("ROWAN_API_KEY")
-if api_key and rowan:
-    rowan.api_key = api_key
+
 
 def log_rowan_api_call(workflow_type: str, **kwargs):
     """Log Rowan API calls with detailed parameters."""

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/folder_management.py

@@ -10,14 +10,7 @@ from typing import Optional
 import logging
 logger = logging.getLogger(__name__)
 
-# Configure rowan API key
-if not hasattr(rowan, 'api_key') or not rowan.api_key:
-    api_key = os.getenv("ROWAN_API_KEY")
-    if api_key:
-        rowan.api_key = api_key
-        logger.info("Rowan API key configured")
-    else:
-        logger.error("No ROWAN_API_KEY found in environment")
+
 
 def rowan_folder_management(
     action: str,

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/fukui.py

@@ -22,10 +22,7 @@ except ImportError:
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-# Setup API key
-api_key = os.getenv("ROWAN_API_KEY")
-if api_key and rowan:
-    rowan.api_key = api_key
+
 
 def log_rowan_api_call(workflow_type: str, **kwargs):
     """Log Rowan API calls with detailed parameters."""

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/hydrogen_bond_basicity.py

@@ -10,14 +10,7 @@ from typing import Optional
 import logging
 logger = logging.getLogger(__name__)
 
-# Configure rowan API key
-if not hasattr(rowan, 'api_key') or not rowan.api_key:
-    api_key = os.getenv("ROWAN_API_KEY")
-    if api_key:
-        rowan.api_key = api_key
-        logger.info("🔑 Rowan API key configured")
-    else:
-        logger.error("No ROWAN_API_KEY found in environment")
+
 
 def log_rowan_api_call(workflow_type: str, **kwargs):
     """Log Rowan API calls and let Rowan handle its own errors."""

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/multistage_opt.py

@@ -15,10 +15,7 @@ except ImportError:
 # Setup logging
 logger = logging.getLogger(__name__)
 
-# Setup API key
-api_key = os.getenv("ROWAN_API_KEY")
-if rowan and api_key:
-    rowan.api_key = api_key
+
 
 def log_rowan_api_call(workflow_type: str, **kwargs):
     """Log Rowan API calls with detailed parameters."""

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/pka.py

@@ -10,14 +10,7 @@ from typing import Optional
 import logging
 logger = logging.getLogger(__name__)
 
-# Configure rowan API key
-if not hasattr(rowan, 'api_key') or not rowan.api_key:
-    api_key = os.getenv("ROWAN_API_KEY")
-    if api_key:
-        rowan.api_key = api_key
-        logger.info("Rowan API key configured")
-    else:
-        logger.error("No ROWAN_API_KEY found in environment")
+
 
 def log_rowan_api_call(workflow_type: str, **kwargs):
     """Log Rowan API calls and let Rowan handle its own errors."""

{rowan_mcp-1.0.2 → rowan_mcp-2.0.1}/rowan_mcp/functions/redox_potential.py

@@ -15,10 +15,7 @@ except ImportError:
 # Setup logging
 logger = logging.getLogger(__name__)
 
-# Setup API key
-api_key = os.getenv("ROWAN_API_KEY")
-if rowan and api_key:
-    rowan.api_key = api_key
+
 
 def lookup_molecule_smiles(molecule_name: str) -> str:
     """Look up canonical SMILES for common molecule names."""
@@ -287,7 +284,7 @@ def rowan_redox_potential(
         formatted += f" Job UUID: {result.get('uuid', 'N/A')}\n"
         formatted += f" Status: {status}\n"
         formatted += f"⚙ Mode: {mode_lower.title()}\n"
-        formatted += f"💧 Solvent: Acetonitrile\n"
+        formatted += f"Solvent: Acetonitrile\n"
         
         # Show which potentials were calculated
         calc_types = []