rowan-mcp 0.1.0__tar.gz → 1.0.1__tar.gz

{rowan_mcp-0.1.0 → rowan_mcp-1.0.1}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: rowan-mcp
-Version: 0.1.0
+Version: 1.0.1
 Summary: Model Context Protocol server for Rowan computational chemistry platform
 Project-URL: Homepage, https://github.com/k-yenko/rowan-mcp
-Author-email: Katherine Yenko <katherineyenko@example.com>
+Author-email: Katherine Yenko <katherineayenko@gmail.com>
 License: MIT
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
@@ -32,7 +32,7 @@ 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 submit complex quantum chemistry calculations in natural everyday language. 
+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. 
 
 ---
 
@@ -50,31 +50,34 @@ That's it - no command line setup needed!
 
 ---
 
-## **Manual Installation**
+## **Package Installation**
 
-**For developers or users who prefer command-line setup:**
+### **Option 1: Auto-Install (No manual installation needed!)**
 
-### **1. Clone and Setup**
-```bash
-git clone https://github.com/k-yenko/rowan-mcp.git
-cd rowan-mcp
-uv sync
-```
-
-### **2. Get API Key**
-- Visit [labs.rowansci.com](https://labs.rowansci.com)
-- Create free account → Generate API key
+Just add this to your MCP configuration and it will automatically install and run:
 
-### **3. Configure Your MCP Client**
+**Using uvx (simplest):**
+```json
+{
+  "mcpServers": {
+    "rowan": {
+      "command": "uvx",
+      "args": ["--from", "rowan-mcp", "rowan-mcp"],
+      "env": {
+        "ROWAN_API_KEY": "your_api_key_here"
+      }
+    }
+  }
+}
+```
 
-**Claude Desktop Example:**
+**Using uv run (alternative):**
 ```json
 {
   "mcpServers": {
     "rowan": {
       "command": "uv",
-      "args": ["run", "python", "-m", "rowan_mcp"],
-      "cwd": "/path/to/rowan-mcp",
+      "args": ["run", "--with", "rowan-mcp", "-m", "rowan_mcp"],
       "env": {
         "ROWAN_API_KEY": "your_api_key_here"
       }
@@ -83,77 +86,68 @@ uv sync
 }
 ```
 
-*Replace `/path/to/rowan-mcp` with the actual path where you cloned the repository*
+### **Option 2: Manual Installation**
 
-**To find your path:**
+If you prefer to install the package first:
+
+**Using uv:**
 ```bash
-# After cloning, run this in the rowan-mcp directory:
-pwd
-# Copy the output and use it as your "cwd" value
+uv add rowan-mcp
 ```
 
-### **4. Start Using**
-Ask your AI: *"Calculate the pKa of aspirin"* or *"Optimize the geometry of caffeine"*
-
-### **Alternative: Use .env file**
-Instead of putting your API key in the MCP config, create a `.env` file:
+**Using pip:**
 ```bash
-# In the rowan-mcp directory:
-echo "ROWAN_API_KEY=your_actual_api_key_here" > .env
+pip install rowan-mcp
 ```
 
-Then use this simpler config (no env section needed):
+Then use this configuration:
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "uv",
-      "args": ["run", "python", "-m", "rowan_mcp"],
-      "cwd": "/path/to/rowan-mcp"
+      "command": "rowan-mcp",
+      "env": {
+        "ROWAN_API_KEY": "your_api_key_here"
+      }
     }
   }
 }
 ```
 
+### **Get API Key**
+
+Visit [labs.rowansci.com](https://labs.rowansci.com) → Create account → Generate API key
+
+### **Start Using**
+
+Ask your AI: *"Calculate the pKa of aspirin"* or *"Optimize the geometry of caffeine"*
+
 ---
 
 ## **What You Can Do** 
 
 Ask the LLM to:
 - **Calculate drug properties**: *"Predict drug-likeness of aspirin"*
-- **Optimize molecular structures**: *"Optimize the geometry of aspirin"*  
+- **Optimize molecular structures**: *"Optimize the geometry of aspirin"* 
 - **Predict chemical behavior**: *"What's the pKa of acetic acid?"*
 - **Run calculations**: *"Calculate the HOMO and LUMO of benzene"*
 
 ## **System Requirements**
 
 - **Python 3.10+** (Python 3.11+ recommended)
-- **[uv](https://docs.astral.sh/uv/) package manager** 
+- **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, Continue, etc.)
-
-## **Testing Your Setup**
+- **MCP-compatible client** (Claude Desktop, etc.)
 
-You can test the server directly:
+**Development commands** (if you cloned the repo):
 ```bash
-# In the rowan-mcp directory:
-uv run python -m rowan_mcp --help
-```
-
-## **Development**
-
-The installation above is the same for development! Additional commands:
-```bash
-# Run server in HTTP/SSE mode  
+# Run from source
 uv run python -m rowan_mcp --http
-
-# Run server in STDIO mode (default)
-uv run python -m rowan_mcp
 ```
 
 ---
 
-## Available Tools
+## **Available Tools**
 
 ### Chemistry Calculations
 - `rowan_basic_calculation` - Energy, optimization, frequencies
@@ -172,7 +166,6 @@ uv run python -m rowan_mcp
 ### Drug Discovery
 - `rowan_admet` - ADME-Tox properties
 
-
 ### Reactivity Analysis  
 - `rowan_fukui` - Reactivity sites
 - `rowan_spin_states` - Spin multiplicities
@@ -181,13 +174,13 @@ uv run python -m rowan_mcp
 - `rowan_folder_create/list/update/delete` - Organize calculations
 - `rowan_workflow_create/list/status/stop` - Manage workflows
 
-## Requirements
+## **Requirements**
 
 - Python 3.10+
 - Rowan API key
 - MCP-compatible AI assistant (Claude Desktop, etc.)
 
-## Getting Help
+## **Getting Help**
 
 - **Documentation**: [docs.rowansci.com](https://docs.rowansci.com/)
 - or ping me! 
@@ -207,10 +200,28 @@ uv run python -m rowan_mcp
 - [ ] Multistage optimization sometimes shows unexpected imaginary frequencies
 - [ ] Some calculations show as finished in logs but not in Rowan UI
 
-## Citation
+## **Citation**
 
 If you use this MCP tool in your research, please cite the underlying Rowan platform:
 
 Rowan Scientific. https://www.rowansci.com (accessed 2025-07-01).
 
 For complete citation information including specific computational engines, methods, and workflows used in your calculations, please refer to [Rowan's citation guidelines](https://docs.rowansci.com/citations).
+
+---
+
+## **Publishing (Maintainer Notes)**
+
+To publish a new version to PyPI:
+
+```bash
+# Update version in pyproject.toml and rowan_mcp/__init__.py
+# Build the package
+uv build
+
+# Publish to PyPI (requires API token)
+uv publish
+
+# Or publish to TestPyPI first
+uv publish --index-url https://test.pypi.org/simple/
+```

{rowan_mcp-0.1.0 → rowan_mcp-1.0.1}/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 submit complex quantum chemistry calculations in natural everyday language. 
+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. 
 
 ---
 
@@ -18,31 +18,34 @@ That's it - no command line setup needed!
 
 ---
 
-## **Manual Installation**
+## **Package Installation**
 
-**For developers or users who prefer command-line setup:**
+### **Option 1: Auto-Install (No manual installation needed!)**
 
-### **1. Clone and Setup**
-```bash
-git clone https://github.com/k-yenko/rowan-mcp.git
-cd rowan-mcp
-uv sync
-```
-
-### **2. Get API Key**
-- Visit [labs.rowansci.com](https://labs.rowansci.com)
-- Create free account → Generate API key
+Just add this to your MCP configuration and it will automatically install and run:
 
-### **3. Configure Your MCP Client**
+**Using uvx (simplest):**
+```json
+{
+  "mcpServers": {
+    "rowan": {
+      "command": "uvx",
+      "args": ["--from", "rowan-mcp", "rowan-mcp"],
+      "env": {
+        "ROWAN_API_KEY": "your_api_key_here"
+      }
+    }
+  }
+}
+```
 
-**Claude Desktop Example:**
+**Using uv run (alternative):**
 ```json
 {
   "mcpServers": {
     "rowan": {
       "command": "uv",
-      "args": ["run", "python", "-m", "rowan_mcp"],
-      "cwd": "/path/to/rowan-mcp",
+      "args": ["run", "--with", "rowan-mcp", "-m", "rowan_mcp"],
       "env": {
         "ROWAN_API_KEY": "your_api_key_here"
       }
@@ -51,77 +54,68 @@ uv sync
 }
 ```
 
-*Replace `/path/to/rowan-mcp` with the actual path where you cloned the repository*
+### **Option 2: Manual Installation**
 
-**To find your path:**
+If you prefer to install the package first:
+
+**Using uv:**
 ```bash
-# After cloning, run this in the rowan-mcp directory:
-pwd
-# Copy the output and use it as your "cwd" value
+uv add rowan-mcp
 ```
 
-### **4. Start Using**
-Ask your AI: *"Calculate the pKa of aspirin"* or *"Optimize the geometry of caffeine"*
-
-### **Alternative: Use .env file**
-Instead of putting your API key in the MCP config, create a `.env` file:
+**Using pip:**
 ```bash
-# In the rowan-mcp directory:
-echo "ROWAN_API_KEY=your_actual_api_key_here" > .env
+pip install rowan-mcp
 ```
 
-Then use this simpler config (no env section needed):
+Then use this configuration:
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "uv",
-      "args": ["run", "python", "-m", "rowan_mcp"],
-      "cwd": "/path/to/rowan-mcp"
+      "command": "rowan-mcp",
+      "env": {
+        "ROWAN_API_KEY": "your_api_key_here"
+      }
     }
   }
 }
 ```
 
+### **Get API Key**
+
+Visit [labs.rowansci.com](https://labs.rowansci.com) → Create account → Generate API key
+
+### **Start Using**
+
+Ask your AI: *"Calculate the pKa of aspirin"* or *"Optimize the geometry of caffeine"*
+
 ---
 
 ## **What You Can Do** 
 
 Ask the LLM to:
 - **Calculate drug properties**: *"Predict drug-likeness of aspirin"*
-- **Optimize molecular structures**: *"Optimize the geometry of aspirin"*  
+- **Optimize molecular structures**: *"Optimize the geometry of aspirin"* 
 - **Predict chemical behavior**: *"What's the pKa of acetic acid?"*
 - **Run calculations**: *"Calculate the HOMO and LUMO of benzene"*
 
 ## **System Requirements**
 
 - **Python 3.10+** (Python 3.11+ recommended)
-- **[uv](https://docs.astral.sh/uv/) package manager** 
+- **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, Continue, etc.)
-
-## **Testing Your Setup**
+- **MCP-compatible client** (Claude Desktop, etc.)
 
-You can test the server directly:
+**Development commands** (if you cloned the repo):
 ```bash
-# In the rowan-mcp directory:
-uv run python -m rowan_mcp --help
-```
-
-## **Development**
-
-The installation above is the same for development! Additional commands:
-```bash
-# Run server in HTTP/SSE mode  
+# Run from source
 uv run python -m rowan_mcp --http
-
-# Run server in STDIO mode (default)
-uv run python -m rowan_mcp
 ```
 
 ---
 
-## Available Tools
+## **Available Tools**
 
 ### Chemistry Calculations
 - `rowan_basic_calculation` - Energy, optimization, frequencies
@@ -140,7 +134,6 @@ uv run python -m rowan_mcp
 ### Drug Discovery
 - `rowan_admet` - ADME-Tox properties
 
-
 ### Reactivity Analysis  
 - `rowan_fukui` - Reactivity sites
 - `rowan_spin_states` - Spin multiplicities
@@ -149,13 +142,13 @@ uv run python -m rowan_mcp
 - `rowan_folder_create/list/update/delete` - Organize calculations
 - `rowan_workflow_create/list/status/stop` - Manage workflows
 
-## Requirements
+## **Requirements**
 
 - Python 3.10+
 - Rowan API key
 - MCP-compatible AI assistant (Claude Desktop, etc.)
 
-## Getting Help
+## **Getting Help**
 
 - **Documentation**: [docs.rowansci.com](https://docs.rowansci.com/)
 - or ping me! 
@@ -175,10 +168,28 @@ uv run python -m rowan_mcp
 - [ ] Multistage optimization sometimes shows unexpected imaginary frequencies
 - [ ] Some calculations show as finished in logs but not in Rowan UI
 
-## Citation
+## **Citation**
 
 If you use this MCP tool in your research, please cite the underlying Rowan platform:
 
 Rowan Scientific. https://www.rowansci.com (accessed 2025-07-01).
 
 For complete citation information including specific computational engines, methods, and workflows used in your calculations, please refer to [Rowan's citation guidelines](https://docs.rowansci.com/citations).
+
+---
+
+## **Publishing (Maintainer Notes)**
+
+To publish a new version to PyPI:
+
+```bash
+# Update version in pyproject.toml and rowan_mcp/__init__.py
+# Build the package
+uv build
+
+# Publish to PyPI (requires API token)
+uv publish
+
+# Or publish to TestPyPI first
+uv publish --index-url https://test.pypi.org/simple/
+```

{rowan_mcp-0.1.0 → rowan_mcp-1.0.1}/pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "hatchling.build"
 
 [project]
 name = "rowan-mcp"
-version = "0.1.0"
+version = "1.0.1"
 description = "Model Context Protocol server for Rowan computational chemistry platform"
 authors = [
-    {name = "Katherine Yenko", email = "katherineyenko@example.com"}
+    {name = "Katherine Yenko", email = "katherineayenko@gmail.com"}
 ]
 license = {text = "MIT"}
 readme = "README.md"

{rowan_mcp-0.1.0 → rowan_mcp-1.0.1}/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__ = "0.1.0"
+__version__ = "1.0.0"
 __author__ = "Rowan MCP Team"
 __description__ = "MCP server for Rowan computational chemistry platform"
 

rowan_mcp-1.0.1/rowan_mcp/functions/conformers.py

@@ -0,0 +1,80 @@
+"""
+Rowan conformers function for conformational analysis.
+"""
+
+import os
+import logging
+import time
+from typing import Optional
+
+try:
+    import rowan
+except ImportError:
+    rowan = None
+
+# 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."""
+    
+    # Simple logging for long-running calculations
+    if workflow_type in ["multistage_opt", "conformer_search"]:
+        blocking = kwargs.get('blocking', True)
+        if blocking:
+            logger.info(f" Starting {workflow_type.replace('_', ' ')}...")
+        else:
+            logger.info(f" Submitting {workflow_type.replace('_', ' ')} without waiting")
+    
+    # Let Rowan handle everything - no custom error handling
+    return rowan.compute(workflow_type=workflow_type, **kwargs)
+
+def rowan_conformers(
+    name: str,
+    molecule: str,
+    max_conformers: int = 50,
+    mode: str = "rapid",
+    folder_uuid: Optional[str] = None,
+    blocking: bool = True,
+    ping_interval: int = 5
+):
+    """Generate and optimize molecular conformers using Rowan's conformer_search workflow. Valid modes are "reckless", "rapid", "careful", and "meticulous", and default to using SMILES strings for the "molecule" parameter.
+    
+    Args:
+        name: Name for the calculation
+        molecule: Molecule SMILES string or common name
+        max_conformers: Maximum number of conformers to generate (default: 50)
+        mode: Conformer search mode - "reckless", "rapid", "careful", "meticulous" (default: "rapid")
+        folder_uuid: UUID of folder to organize calculation in
+        blocking: Whether to wait for completion (default: True)
+        ping_interval: How often to check status in seconds (default: 5)
+    
+    Returns:
+        Conformer search results (actual results if blocking=True)
+    """
+    
+    # Validate mode parameter
+    valid_modes = ["reckless", "rapid", "careful", "meticulous"]
+    if mode not in valid_modes:
+        raise ValueError(
+            f"Invalid mode '{mode}'. Valid modes are: {', '.join(valid_modes)}"
+        )
+    
+    return log_rowan_api_call(
+        workflow_type="conformer_search",
+        name=name,
+        molecule=molecule,
+        mode=mode,
+        max_conformers=max_conformers,
+        folder_uuid=folder_uuid,
+        blocking=blocking,
+        ping_interval=ping_interval
+    )
+
+if __name__ == "__main__":
+    pass 

{rowan_mcp-0.1.0 → rowan_mcp-1.0.1}/rowan_mcp/functions/electronic_properties.py

@@ -186,68 +186,10 @@ def rowan_electronic_properties(
             **electronic_params
         )
         
-        # Enhanced result formatting for electronic properties
-        if blocking:
-            status = result.get('status', result.get('object_status', 'Unknown'))
-            
-            if status == 2:  # Completed successfully
-                formatted = f"Electronic properties calculation for '{name}' completed successfully!\n\n"
-            elif status == 3:  # Failed
-                formatted = f"Electronic properties calculation for '{name}' failed!\n\n"
-            else:
-                formatted = f"Electronic properties calculation for '{name}' submitted!\n\n"
-            
-            formatted += f"Molecule: {molecule}\n"
-            formatted += f"Canonical SMILES: {canonical_smiles}\n"
-            formatted += f"Job UUID: {result.get('uuid', 'N/A')}\n"
-            formatted += f"Status: {status}\n\n"
-            
-            formatted += f"Molecule Lookup: Advanced PubChemPy + SQLite + RDKit system\n\n"
-            formatted += f"Calculation Settings:\n"
-            formatted += f"• Method: {method.upper()}\n"
-            formatted += f"• Basis Set: {basis_set}\n"
-            formatted += f"• Engine: {engine.upper()}\n"
-            formatted += f"• Charge: {charge}, Multiplicity: {multiplicity}\n\n"
-            
-            formatted += f"Property Calculations:\n"
-            formatted += f"• Density Cube: {'Enabled' if compute_density_cube else 'Disabled'}\n"
-            formatted += f"• ESP Cube: {'Enabled' if compute_electrostatic_potential_cube else 'Disabled'}\n"
-            formatted += f"• Occupied MOs: {compute_num_occupied_orbitals}\n"
-            formatted += f"• Virtual MOs: {compute_num_virtual_orbitals}\n\n"
-            
-            if status == 2:
-                formatted += f"Additional Analysis:\n"
-                formatted += f"• Use rowan_calculation_retrieve('{result.get('uuid')}') for full calculation details\n"
-                formatted += f"• Use rowan_workflow_management(action='retrieve', workflow_uuid='{result.get('uuid')}') for workflow metadata\n"
-                
-            elif status == 3:
-                formatted += f"Troubleshooting:\n"
-                formatted += f"• Try simpler method/basis: method='hf', basis_set='sto-3g'\n"
-                formatted += f"• Check molecular charge and multiplicity\n"
-                formatted += f"• Disable cube generation for faster calculations\n"
-                formatted += f"• Use rowan_workflow_management(action='retrieve', workflow_uuid='{result.get('uuid')}') for error details\n"
-            else:
-                formatted += f"Next Steps:\n"
-                formatted += f"• Monitor status with rowan_workflow_management(action='retrieve', workflow_uuid='{result.get('uuid')}')\n"
-                formatted += f"• Electronic properties calculations may take several minutes\n"
-            
-            return formatted
-        else:
-            return str(result)
+        return result
             
     except Exception as e:
-        error_msg = f"Electronic properties calculation failed: {str(e)}\n\n"
-        error_msg += f"Molecule: {molecule}\n"
-        error_msg += f"Canonical SMILES: {canonical_smiles}\n"
-        error_msg += f"Settings: {method}/{basis_set}/{engine}\n\n"
-        error_msg += f"Molecule Lookup: Advanced PubChemPy + SQLite + RDKit system\n\n"
-        error_msg += f"Common Issues:\n"
-        error_msg += f"• Invalid method/basis set combination\n"
-        error_msg += f"• Incorrect charge/multiplicity for molecule\n"
-        error_msg += f"• Engine compatibility issues\n"
-        error_msg += f"• Molecule not found in PubChem database\n"
-        error_msg += f"• Try with default parameters first\n"
-        return error_msg
+        return f"Electronic properties calculation failed: {str(e)}"
 
 def test_electronic_properties():
     """Test the electronic properties function with advanced molecule lookup."""