rowan-mcp 1.0.2__tar.gz → 2.0.0__tar.gz

rowan_mcp-2.0.0/.gitignore

@@ -0,0 +1,19 @@
+/.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-1.0.2 → rowan_mcp-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-mcp
-Version: 1.0.2
+Version: 2.0.0
 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
@@ -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
 ```
 
 ---
@@ -189,16 +186,18 @@ uv run python -m rowan_mcp --http
 
 ## **Todo**
 
-- [ ] Remove unnecessary AI spaghetti formatting 🙃
+- [X] Remove unnecessary AI spaghetti formatting
+- [X] Remove no longer necessary API config lines
 - [ ] Some complex conformer searches hang on "running"
-- [ ] Edit MCP one-liner context
+- [X] 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
+- [X] Some calculations show as finished in logs but not in Rowan UI
+- [ ] Can you hook up Rowan's visual capabilites? 
 
 ## **Citation**
 
@@ -233,3 +232,12 @@ 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-2.0.0}/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
@@ -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
 ```
 
 ---
@@ -157,16 +153,18 @@ uv run python -m rowan_mcp --http
 
 ## **Todo**
 
-- [ ] Remove unnecessary AI spaghetti formatting 🙃
+- [X] Remove unnecessary AI spaghetti formatting
+- [X] Remove no longer necessary API config lines
 - [ ] Some complex conformer searches hang on "running"
-- [ ] Edit MCP one-liner context
+- [X] 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
+- [X] Some calculations show as finished in logs but not in Rowan UI
+- [ ] Can you hook up Rowan's visual capabilites? 
 
 ## **Citation**
 
@@ -201,3 +199,12 @@ 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-2.0.0}/ROWAN_MCP_TEST_QUERIES.md

@@ -28,7 +28,7 @@ An unexpected large imaginary frequency was encountered, meaning that the calcul
 - What are the molecular orbitals of methanol? ✅
 
 ### conformational analysis
-- Find the stable conformers of glucose ❌ - stuck on "running"
+- can you test a ❌ - stuck on "running"
 - Generate 5 conformers of butane ✅
 - What are the different shapes ethanol can adopt? ✅
 

{rowan_mcp-1.0.2 → rowan_mcp-2.0.0}/pyproject.toml

@@ -4,14 +4,14 @@ build-backend = "hatchling.build"
 
 [project]
 name = "rowan-mcp"
-version = "1.0.2"
+version = "2.0.0"
 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]

{rowan_mcp-1.0.2 → rowan_mcp-2.0.0}/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-2.0.0/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-2.0.0/rowan_mcp/functions_v2/BENCHMARK.md

@@ -0,0 +1,86 @@
+# Rowan MCP Benchmark Suite
+
+## Overview
+Systematic evaluation of the Rowan MCP server's ability to handle chemistry workflows through natural language queries.
+
+## Evaluation Tiers
+
+### Tier 1: Single Tool Calls
+**Tests**: Basic tool invocation and parameter passing  
+**Characteristics**:
+- Single workflow submission
+- Explicit parameters
+- No dependencies
+- Direct SMILES or common molecule names
+
+**Example Queries**:
+- "Calculate the pKa of phenol"
+- "Optimize water geometry with GFN2-xTB"
+- "Find conformers of ethanol"
+
+### Tier 2: Parameter Interpretation
+**Tests**: Natural language to parameter mapping, molecule name resolution  
+**Characteristics**:
+- Requires interpreting descriptive terms into API parameters
+- Mode selection (rapid/careful/meticulous)
+- Element specification by name vs atomic number
+- Common name to SMILES conversion
+
+**Example Queries**:
+- "Calculate the oxidation potential of caffeine using careful mode"
+- "Find the pKa of aspirin, only considering oxygen atoms"
+- "Dock ibuprofen to CDK2 without optimization"
+
+### Tier 3: Batch Operations
+**Tests**: Multiple independent calculations, result organization  
+**Characteristics**:
+- Multiple molecules or methods
+- Parallel workflow submission
+- Result comparison/aggregation
+- Folder organization
+
+**Example Queries**:
+- "Calculate pKa for phenol, p-nitrophenol, and p-chlorophenol"
+- "Optimize butane with GFN2-xTB, UMA, and R2SCAN-3c methods"
+- "Screen 5 molecules for docking against CDK2"
+
+### Tier 4: Workflow Chaining
+**Tests**: Sequential dependent calculations, data extraction from results  
+**Characteristics**:
+- Output from one workflow feeds into next
+- Requires waiting for completion
+- UUID and result extraction
+- Proper async handling
+
+**Example Queries**:
+- "Find conformers of benzophenone, then calculate redox potential for top 3"
+- "Optimize this transition state, then run IRC from the result"
+- "Calculate pKa, then run conformer search at the predicted pKa value"
+
+### Tier 5: Conditional Logic
+**Tests**: Decision-making based on results, complex multi-step analysis  
+**Characteristics**:
+- Conditional branching based on results
+- Threshold-based decisions
+- Error handling and retries
+- Statistical analysis of results
+
+**Example Queries**:
+- "Screen molecules for docking, only run detailed analysis if score < -8.0"
+- "Calculate conformer energies, identify outliers (>2 kcal/mol from lowest), recalculate outliers with meticulous mode"
+- "Find pKa sites, if any are between 6-8, run pH-dependent calculations at those values"
+
+## Scoring Criteria
+
+### Per Query
+- **Success**: Workflow submitted correctly (1 point)
+- **Parameters**: All parameters correctly mapped (1 point)
+- **Completion**: Workflow completes without error (1 point)
+- **Chaining**: Dependencies handled correctly (1 point, Tier 4-5 only)
+- **Logic**: Conditional logic executed correctly (1 point, Tier 5 only)
+
+### Overall Metrics
+- Success rate per tier
+- Average time to completion
+- Error recovery rate
+- Parameter accuracy rate

rowan_mcp-2.0.0/rowan_mcp/functions_v2/molecule_lookup.py

@@ -0,0 +1,232 @@
+"""
+Molecule name to SMILES converter using Chemical Identifier Resolver (CIR).
+Enables natural language molecule input for Rowan workflows.
+"""
+
+from typing import List, Dict, Annotated
+from urllib.request import urlopen
+from urllib.parse import quote
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+def molecule_lookup(
+    molecule_name: Annotated[str, "Common name, IUPAC name, or CAS number of molecule (e.g., 'aspirin', 'caffeine', '50-78-2')"],
+    fallback_to_input: Annotated[bool, "If lookup fails, return the input string assuming it might be SMILES"] = False
+) -> str:
+    """Convert molecule names to SMILES using Chemical Identifier Resolver (CIR).
+    
+    Args:
+        molecule_name: Common name, IUPAC name, or CAS number of molecule (e.g., 'aspirin', 'caffeine', '50-78-2')
+        fallback_to_input: If lookup fails, return the input string assuming it might be SMILES
+    
+    This tool enables natural language input for molecules by converting common names,
+    IUPAC names, CAS numbers, and other identifiers to SMILES strings that can be
+    used with Rowan workflows.
+    
+    Supported Input Types:
+    - Common names: 'aspirin', 'caffeine', 'benzene', 'glucose'
+    - IUPAC names: '2-acetoxybenzoic acid', '1,3,7-trimethylpurine-2,6-dione'
+    - CAS numbers: '50-78-2' (aspirin), '58-08-2' (caffeine)
+    - InChI strings
+    - Already valid SMILES (will be validated)
+    
+    Returns:
+        SMILES string if successful, error message if not found
+        
+    Examples:
+        # Common drug name
+        result = molecule_lookup("aspirin")
+        # Returns: "CC(=O)Oc1ccccc1C(=O)O"
+        
+        # IUPAC name
+        result = molecule_lookup("2-acetoxybenzoic acid")
+        # Returns: "CC(=O)Oc1ccccc1C(=O)O"
+        
+        # CAS number
+        result = molecule_lookup("50-78-2")
+        # Returns: "CC(=O)Oc1ccccc1C(=O)O"
+        
+        # Complex molecule
+        result = molecule_lookup("paracetamol")
+        # Returns: "CC(=O)Nc1ccc(O)cc1"
+    """
+    try:
+        # Clean input
+        molecule_name = molecule_name.strip()
+        
+        # Check if already SMILES-like (contains typical SMILES characters)
+        smiles_chars = {'=', '#', '(', ')', '[', ']', '@', '+', '-'}
+        if any(char in molecule_name for char in smiles_chars):
+            logger.info(f"Input '{molecule_name}' appears to be SMILES, returning as-is")
+            return molecule_name
+        
+        # Query CIR service
+        logger.info(f"Looking up molecule: {molecule_name}")
+        url = f'http://cactus.nci.nih.gov/chemical/structure/{quote(molecule_name)}/smiles'
+        
+        response = urlopen(url, timeout=10)
+        smiles = response.read().decode('utf8').strip()
+        
+        # CIR may return multiple SMILES for some queries, take the first one
+        if '\n' in smiles:
+            smiles = smiles.split('\n')[0]
+        
+        logger.info(f"Successfully converted '{molecule_name}' to SMILES: {smiles}")
+        return smiles
+        
+    except Exception as e:
+        logger.warning(f"Failed to lookup '{molecule_name}': {e}")
+        
+        if fallback_to_input:
+            logger.info(f"Returning original input as fallback: {molecule_name}")
+            return molecule_name
+        else:
+            return f"Could not find SMILES for '{molecule_name}'. Please check the name or provide a valid SMILES string."
+
+
+def batch_molecule_lookup(
+    molecule_names: Annotated[List[str], "List of molecule names to convert to SMILES"],
+    skip_failures: Annotated[bool, "Skip molecules that fail lookup instead of stopping"] = True
+) -> Dict[str, str]:
+    """Convert multiple molecule names to SMILES in batch.
+    
+    Args:
+        molecule_names: List of molecule names to convert to SMILES
+        skip_failures: Skip molecules that fail lookup instead of stopping
+    
+    Useful for preparing multiple molecules for workflows or screening.
+        
+    Returns:
+        Dictionary mapping input names to SMILES strings (or error messages)
+        
+    Examples:
+        # Drug screening set
+        result = batch_molecule_lookup([
+            "aspirin",
+            "ibuprofen", 
+            "paracetamol",
+            "caffeine"
+        ])
+        # Returns: {
+        #     "aspirin": "CC(=O)Oc1ccccc1C(=O)O",
+        #     "ibuprofen": "CC(C)Cc1ccc(C(C)C(=O)O)cc1",
+        #     "paracetamol": "CC(=O)Nc1ccc(O)cc1",
+        #     "caffeine": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
+        # }
+        
+        # Mixed input types
+        result = batch_molecule_lookup([
+            "benzene",           # Common name
+            "50-78-2",          # CAS number
+            "ethanoic acid"     # IUPAC name
+        ])
+    """
+    results = {}
+    
+    for name in molecule_names:
+        try:
+            smiles = molecule_lookup(name, fallback_to_input=False)
+            results[name] = smiles
+        except Exception as e:
+            error_msg = f"Lookup failed: {str(e)}"
+            if skip_failures:
+                logger.warning(f"Skipping {name}: {error_msg}")
+                results[name] = error_msg
+            else:
+                raise ValueError(f"Failed to lookup '{name}': {error_msg}")
+    
+    return results
+
+
+def validate_smiles(
+    smiles: Annotated[str, "SMILES string to validate"]
+) -> Dict[str, any]:
+    """Validate a SMILES string and return basic molecular properties.
+    
+    Args:
+        smiles: SMILES string to validate
+    
+    Uses RDKit to validate SMILES and extract basic properties.
+        
+    Returns:
+        Dictionary with validation status and properties if valid
+        
+    Examples:
+        result = validate_smiles("CC(=O)O")
+        # Returns: {
+        #     "valid": True,
+        #     "canonical_smiles": "CC(=O)O",
+        #     "molecular_formula": "C2H4O2",
+        #     "molecular_weight": 60.05
+        # }
+    """
+    try:
+        from rdkit import Chem
+        from rdkit.Chem import Descriptors
+        
+        mol = Chem.MolFromSmiles(smiles)
+        
+        if mol is None:
+            return {
+                "valid": False,
+                "error": "Invalid SMILES string"
+            }
+        
+        return {
+            "valid": True,
+            "canonical_smiles": Chem.MolToSmiles(mol),
+            "molecular_formula": Chem.rdMolDescriptors.CalcMolFormula(mol),
+            "molecular_weight": round(Descriptors.MolWt(mol), 2),
+            "num_atoms": mol.GetNumAtoms(),
+            "num_bonds": mol.GetNumBonds()
+        }
+        
+    except ImportError:
+        return {
+            "valid": "unknown",
+            "error": "RDKit not available for validation"
+        }
+    except Exception as e:
+        return {
+            "valid": False,
+            "error": str(e)
+        }
+
+
+# Common molecules reference (for documentation)
+COMMON_MOLECULES = {
+    # Drugs
+    "aspirin": "CC(=O)Oc1ccccc1C(=O)O",
+    "paracetamol": "CC(=O)Nc1ccc(O)cc1",
+    "acetaminophen": "CC(=O)Nc1ccc(O)cc1",  # Same as paracetamol
+    "ibuprofen": "CC(C)Cc1ccc(C(C)C(=O)O)cc1",
+    "caffeine": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C",
+    "penicillin": "CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O",
+    
+    # Solvents
+    "water": "O",
+    "ethanol": "CCO",
+    "methanol": "CO",
+    "acetone": "CC(=O)C",
+    "dmso": "CS(=O)C",
+    "chloroform": "C(Cl)(Cl)Cl",
+    "benzene": "c1ccccc1",
+    "toluene": "Cc1ccccc1",
+    
+    # Organic compounds
+    "glucose": "C(C1C(C(C(C(O1)O)O)O)O)O",
+    "acetic acid": "CC(=O)O",
+    "ethanoic acid": "CC(=O)O",  # IUPAC for acetic acid
+    "phenol": "Oc1ccccc1",
+    "aniline": "Nc1ccccc1",
+    "naphthalene": "c1ccc2c(c1)cccc2",
+    
+    # Amino acids
+    "glycine": "C(C(=O)O)N",
+    "alanine": "CC(C(=O)O)N",
+    "valine": "CC(C)C(C(=O)O)N",
+    "leucine": "CC(C)CC(C(=O)O)N",
+    "lysine": "C(CCN)CC(C(=O)O)N",
+}