rowan-mcp 1.0.0__tar.gz → 1.0.2__tar.gz

{rowan_mcp-1.0.0 → rowan_mcp-1.0.2}/.gitignore

@@ -9,3 +9,4 @@ __pycache__/
 
 .claude
 CLAUDE.md
+/dist

{rowan_mcp-1.0.0 → rowan_mcp-1.0.2}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: rowan-mcp
-Version: 1.0.0
+Version: 1.0.2
 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. 
 
 ---
 
@@ -52,36 +52,17 @@ That's it - no command line setup needed!
 
 ## **Package Installation**
 
-### **Using uv (recommended):**
-```bash
-# Install the package
-uv add rowan-mcp
-```
-
-### **Using pip:**
-```bash
-# Install the package
-pip install rowan-mcp
-
-# Or in a virtual environment
-python -m venv venv
-source venv/bin/activate  # On Windows: venv\Scripts\activate
-pip install rowan-mcp
-```
+### **Option 1: Auto-Install (No manual installation needed!)**
 
-### **Get API Key & Configure**
+Just add this to your MCP configuration and it will automatically install and run:
 
-1. **Get your API key**: Visit [labs.rowansci.com](https://labs.rowansci.com) → Create account → Generate API key
-
-2. **Configure your MCP client** (e.g., Claude Code, VSCode, Cursor, etc.):
-
-**With uv:**
+**Using uvx (simplest):**
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "uv",
-      "args": ["run", "rowan-mcp"],
+      "command": "uvx",
+      "args": ["--from", "rowan-mcp", "rowan-mcp"],
       "env": {
         "ROWAN_API_KEY": "your_api_key_here"
       }
@@ -90,12 +71,13 @@ pip install rowan-mcp
 }
 ```
 
-**With pip/system Python:**
+**Using uv run (alternative):**
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "rowan-mcp",
+      "command": "uv",
+      "args": ["run", "--with", "rowan-mcp", "-m", "rowan_mcp"],
       "env": {
         "ROWAN_API_KEY": "your_api_key_here"
       }
@@ -104,30 +86,26 @@ pip install rowan-mcp
 }
 ```
 
-### **Start Using**
-Ask your AI: *"Calculate the pKa of aspirin"* or *"Optimize the geometry of caffeine"*
-
----
+### **Option 2: Manual Installation**
 
-## **Development Installation**
+If you prefer to install the package first:
 
-**For developers or contributors:**
+**Using uv:**
+```bash
+uv add rowan-mcp
+```
 
-### **1. Clone and Setup**
+**Using pip:**
 ```bash
-git clone https://github.com/k-yenko/rowan-mcp.git
-cd rowan-mcp
-uv sync
+pip install rowan-mcp
 ```
 
-### **2. Configure for Development**
+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"
       }
@@ -136,7 +114,13 @@ uv sync
 }
 ```
 
-*Replace `/path/to/rowan-mcp` with your actual clone path. Find it with `pwd` in the project directory.*
+### **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"*
 
 ---
 
@@ -155,7 +139,6 @@ Ask the LLM to:
 - **Rowan API key** (free at [labs.rowansci.com](https://labs.rowansci.com))
 - **MCP-compatible client** (Claude Desktop, etc.)
 
-
 **Development commands** (if you cloned the repo):
 ```bash
 # Run from source
@@ -164,7 +147,7 @@ uv run python -m rowan_mcp --http
 
 ---
 
-## Available Tools
+## **Available Tools**
 
 ### Chemistry Calculations
 - `rowan_basic_calculation` - Energy, optimization, frequencies
@@ -183,7 +166,6 @@ uv run python -m rowan_mcp --http
 ### Drug Discovery
 - `rowan_admet` - ADME-Tox properties
 
-
 ### Reactivity Analysis  
 - `rowan_fukui` - Reactivity sites
 - `rowan_spin_states` - Spin multiplicities
@@ -192,13 +174,13 @@ uv run python -m rowan_mcp --http
 - `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! 
@@ -218,7 +200,7 @@ uv run python -m rowan_mcp --http
 - [ ] 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:
 
@@ -243,3 +225,11 @@ uv publish
 # Or publish to TestPyPI first
 uv publish --index-url https://test.pypi.org/simple/
 ```
+
+To update the dxt file:
+```bash
+# After updating the PyPI package, update all changed tools/functions
+
+# Then update the desktop extension
+dxt pack rowan-dxt
+```

{rowan_mcp-1.0.0 → rowan_mcp-1.0.2}/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. 
 
 ---
 
@@ -20,36 +20,17 @@ That's it - no command line setup needed!
 
 ## **Package Installation**
 
-### **Using uv (recommended):**
-```bash
-# Install the package
-uv add rowan-mcp
-```
-
-### **Using pip:**
-```bash
-# Install the package
-pip install rowan-mcp
-
-# Or in a virtual environment
-python -m venv venv
-source venv/bin/activate  # On Windows: venv\Scripts\activate
-pip install rowan-mcp
-```
+### **Option 1: Auto-Install (No manual installation needed!)**
 
-### **Get API Key & Configure**
+Just add this to your MCP configuration and it will automatically install and run:
 
-1. **Get your API key**: Visit [labs.rowansci.com](https://labs.rowansci.com) → Create account → Generate API key
-
-2. **Configure your MCP client** (e.g., Claude Code, VSCode, Cursor, etc.):
-
-**With uv:**
+**Using uvx (simplest):**
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "uv",
-      "args": ["run", "rowan-mcp"],
+      "command": "uvx",
+      "args": ["--from", "rowan-mcp", "rowan-mcp"],
       "env": {
         "ROWAN_API_KEY": "your_api_key_here"
       }
@@ -58,12 +39,13 @@ pip install rowan-mcp
 }
 ```
 
-**With pip/system Python:**
+**Using uv run (alternative):**
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "rowan-mcp",
+      "command": "uv",
+      "args": ["run", "--with", "rowan-mcp", "-m", "rowan_mcp"],
       "env": {
         "ROWAN_API_KEY": "your_api_key_here"
       }
@@ -72,30 +54,26 @@ pip install rowan-mcp
 }
 ```
 
-### **Start Using**
-Ask your AI: *"Calculate the pKa of aspirin"* or *"Optimize the geometry of caffeine"*
-
----
+### **Option 2: Manual Installation**
 
-## **Development Installation**
+If you prefer to install the package first:
 
-**For developers or contributors:**
+**Using uv:**
+```bash
+uv add rowan-mcp
+```
 
-### **1. Clone and Setup**
+**Using pip:**
 ```bash
-git clone https://github.com/k-yenko/rowan-mcp.git
-cd rowan-mcp
-uv sync
+pip install rowan-mcp
 ```
 
-### **2. Configure for Development**
+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"
       }
@@ -104,7 +82,13 @@ uv sync
 }
 ```
 
-*Replace `/path/to/rowan-mcp` with your actual clone path. Find it with `pwd` in the project directory.*
+### **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"*
 
 ---
 
@@ -123,7 +107,6 @@ Ask the LLM to:
 - **Rowan API key** (free at [labs.rowansci.com](https://labs.rowansci.com))
 - **MCP-compatible client** (Claude Desktop, etc.)
 
-
 **Development commands** (if you cloned the repo):
 ```bash
 # Run from source
@@ -132,7 +115,7 @@ uv run python -m rowan_mcp --http
 
 ---
 
-## Available Tools
+## **Available Tools**
 
 ### Chemistry Calculations
 - `rowan_basic_calculation` - Energy, optimization, frequencies
@@ -151,7 +134,6 @@ uv run python -m rowan_mcp --http
 ### Drug Discovery
 - `rowan_admet` - ADME-Tox properties
 
-
 ### Reactivity Analysis  
 - `rowan_fukui` - Reactivity sites
 - `rowan_spin_states` - Spin multiplicities
@@ -160,13 +142,13 @@ uv run python -m rowan_mcp --http
 - `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! 
@@ -186,7 +168,7 @@ uv run python -m rowan_mcp --http
 - [ ] 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:
 
@@ -211,3 +193,11 @@ uv publish
 # Or publish to TestPyPI first
 uv publish --index-url https://test.pypi.org/simple/
 ```
+
+To update the dxt file:
+```bash
+# After updating the PyPI package, update all changed tools/functions
+
+# Then update the desktop extension
+dxt pack rowan-dxt
+```

{rowan_mcp-1.0.0 → rowan_mcp-1.0.2}/pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "hatchling.build"
 
 [project]
 name = "rowan-mcp"
-version = "1.0.0"
+version = "1.0.2"
 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-1.0.0 → rowan_mcp-1.0.2}/rowan_mcp/__init__.py

@@ -6,7 +6,7 @@ for integrating with Rowan's computational chemistry platform.
 """
 
 __version__ = "1.0.0"
-__author__ = "Rowan MCP Team"
+__author__ = "Kat Yenko"
 __description__ = "MCP server for Rowan computational chemistry platform"
 
 from .server import main

rowan_mcp-1.0.2/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-1.0.0 → rowan_mcp-1.0.2}/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."""