rowan-mcp 0.1.0__tar.gz

rowan_mcp-0.1.0/.gitignore

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+/.venv
+/rowan-dxt
+.env
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.DS_Store
+
+.claude
+CLAUDE.md

rowan_mcp-0.1.0/MANIFEST.in

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+include README.md
+include ROWAN_MCP_TOOLS.md
+include ROWAN_MCP_TEST_QUERIES.md
+include rowan-dxt.dxt
+recursive-include rowan_mcp *.db
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude * .DS_Store 

rowan_mcp-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: rowan-mcp
+Version: 0.1.0
+Summary: Model Context Protocol server for Rowan computational chemistry platform
+Project-URL: Homepage, https://github.com/k-yenko/rowan-mcp
+Author-email: Katherine Yenko <katherineyenko@example.com>
+License: MIT
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+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-Dist: fastapi>=0.104.0
+Requires-Dist: fastmcp>=0.2.0
+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: typing-extensions>=4.0.0
+Requires-Dist: uvicorn>=0.24.0
+Provides-Extra: dev
+Requires-Dist: black>=23.0.0; extra == 'dev'
+Requires-Dist: isort>=5.0.0; extra == 'dev'
+Requires-Dist: mypy>=1.0.0; extra == 'dev'
+Requires-Dist: pytest>=7.0.0; extra == 'dev'
+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. 
+
+---
+
+## **Quick Install - Desktop Extension**
+
+**For Claude Desktop users - this is the easiest way:**
+
+1. **Download** the extension: [`rowan-dxt.dxt`](./rowan-dxt.dxt) 
+2. **Drag and drop** the file into **Claude Desktop > Settings > Extensions**
+3. **Enter your API key** from [labs.rowansci.com](https://labs.rowansci.com) 
+4. **Enable** the MCP tool in the extension settings
+5. **Start chatting** Try: *"Using the Rowan MCP tool, calculate the pKa of aspirin"*
+
+That's it - no command line setup needed!
+
+---
+
+## **Manual Installation**
+
+**For developers or users who prefer command-line setup:**
+
+### **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
+
+### **3. Configure Your MCP Client**
+
+**Claude Desktop Example:**
+```json
+{
+  "mcpServers": {
+    "rowan": {
+      "command": "uv",
+      "args": ["run", "python", "-m", "rowan_mcp"],
+      "cwd": "/path/to/rowan-mcp",
+      "env": {
+        "ROWAN_API_KEY": "your_api_key_here"
+      }
+    }
+  }
+}
+```
+
+*Replace `/path/to/rowan-mcp` with the actual path where you cloned the repository*
+
+**To find your path:**
+```bash
+# After cloning, run this in the rowan-mcp directory:
+pwd
+# Copy the output and use it as your "cwd" value
+```
+
+### **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:
+```bash
+# In the rowan-mcp directory:
+echo "ROWAN_API_KEY=your_actual_api_key_here" > .env
+```
+
+Then use this simpler config (no env section needed):
+```json
+{
+  "mcpServers": {
+    "rowan": {
+      "command": "uv",
+      "args": ["run", "python", "-m", "rowan_mcp"],
+      "cwd": "/path/to/rowan-mcp"
+    }
+  }
+}
+```
+
+---
+
+## **What You Can Do** 
+
+Ask the LLM to:
+- **Calculate drug properties**: *"Predict drug-likeness 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** 
+- **Rowan API key** (free at [labs.rowansci.com](https://labs.rowansci.com))
+- **MCP-compatible client** (Claude Desktop, Continue, etc.)
+
+## **Testing Your Setup**
+
+You can test the server directly:
+```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  
+uv run python -m rowan_mcp --http
+
+# Run server in STDIO mode (default)
+uv run python -m rowan_mcp
+```
+
+---
+
+## Available Tools
+
+### Chemistry Calculations
+- `rowan_basic_calculation` - Energy, optimization, frequencies
+- `rowan_multistage_opt` - geometry optimization  
+- `rowan_electronic_properties` - HOMO/LUMO, orbitals
+- `rowan_molecular_dynamics` - MD simulations
+
+### Molecular Properties
+- `rowan_pka` - Acid/base strength
+- `rowan_conformers` - Conformational search
+- `rowan_tautomers` - Tautomer enumeration
+- `rowan_descriptors` - ML-ready molecular features
+- `rowan_solubility` - Aqueous solubility
+- `rowan_redox_potential` - Electrochemical potentials
+
+### Drug Discovery
+- `rowan_admet` - ADME-Tox properties
+
+
+### Reactivity Analysis  
+- `rowan_fukui` - Reactivity sites
+- `rowan_spin_states` - Spin multiplicities
+
+### Project Management
+- `rowan_folder_create/list/update/delete` - Organize calculations
+- `rowan_workflow_create/list/status/stop` - Manage workflows
+
+## Requirements
+
+- Python 3.10+
+- Rowan API key
+- MCP-compatible AI assistant (Claude Desktop, etc.)
+
+## Getting Help
+
+- **Documentation**: [docs.rowansci.com](https://docs.rowansci.com/)
+- or ping me! 
+
+---
+
+## **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:
+
+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).

rowan_mcp-0.1.0/README.md

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+# 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. 
+
+---
+
+## **Quick Install - Desktop Extension**
+
+**For Claude Desktop users - this is the easiest way:**
+
+1. **Download** the extension: [`rowan-dxt.dxt`](./rowan-dxt.dxt) 
+2. **Drag and drop** the file into **Claude Desktop > Settings > Extensions**
+3. **Enter your API key** from [labs.rowansci.com](https://labs.rowansci.com) 
+4. **Enable** the MCP tool in the extension settings
+5. **Start chatting** Try: *"Using the Rowan MCP tool, calculate the pKa of aspirin"*
+
+That's it - no command line setup needed!
+
+---
+
+## **Manual Installation**
+
+**For developers or users who prefer command-line setup:**
+
+### **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
+
+### **3. Configure Your MCP Client**
+
+**Claude Desktop Example:**
+```json
+{
+  "mcpServers": {
+    "rowan": {
+      "command": "uv",
+      "args": ["run", "python", "-m", "rowan_mcp"],
+      "cwd": "/path/to/rowan-mcp",
+      "env": {
+        "ROWAN_API_KEY": "your_api_key_here"
+      }
+    }
+  }
+}
+```
+
+*Replace `/path/to/rowan-mcp` with the actual path where you cloned the repository*
+
+**To find your path:**
+```bash
+# After cloning, run this in the rowan-mcp directory:
+pwd
+# Copy the output and use it as your "cwd" value
+```
+
+### **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:
+```bash
+# In the rowan-mcp directory:
+echo "ROWAN_API_KEY=your_actual_api_key_here" > .env
+```
+
+Then use this simpler config (no env section needed):
+```json
+{
+  "mcpServers": {
+    "rowan": {
+      "command": "uv",
+      "args": ["run", "python", "-m", "rowan_mcp"],
+      "cwd": "/path/to/rowan-mcp"
+    }
+  }
+}
+```
+
+---
+
+## **What You Can Do** 
+
+Ask the LLM to:
+- **Calculate drug properties**: *"Predict drug-likeness 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** 
+- **Rowan API key** (free at [labs.rowansci.com](https://labs.rowansci.com))
+- **MCP-compatible client** (Claude Desktop, Continue, etc.)
+
+## **Testing Your Setup**
+
+You can test the server directly:
+```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  
+uv run python -m rowan_mcp --http
+
+# Run server in STDIO mode (default)
+uv run python -m rowan_mcp
+```
+
+---
+
+## Available Tools
+
+### Chemistry Calculations
+- `rowan_basic_calculation` - Energy, optimization, frequencies
+- `rowan_multistage_opt` - geometry optimization  
+- `rowan_electronic_properties` - HOMO/LUMO, orbitals
+- `rowan_molecular_dynamics` - MD simulations
+
+### Molecular Properties
+- `rowan_pka` - Acid/base strength
+- `rowan_conformers` - Conformational search
+- `rowan_tautomers` - Tautomer enumeration
+- `rowan_descriptors` - ML-ready molecular features
+- `rowan_solubility` - Aqueous solubility
+- `rowan_redox_potential` - Electrochemical potentials
+
+### Drug Discovery
+- `rowan_admet` - ADME-Tox properties
+
+
+### Reactivity Analysis  
+- `rowan_fukui` - Reactivity sites
+- `rowan_spin_states` - Spin multiplicities
+
+### Project Management
+- `rowan_folder_create/list/update/delete` - Organize calculations
+- `rowan_workflow_create/list/status/stop` - Manage workflows
+
+## Requirements
+
+- Python 3.10+
+- Rowan API key
+- MCP-compatible AI assistant (Claude Desktop, etc.)
+
+## Getting Help
+
+- **Documentation**: [docs.rowansci.com](https://docs.rowansci.com/)
+- or ping me! 
+
+---
+
+## **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:
+
+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).

rowan_mcp-0.1.0/ROWAN_MCP_TEST_QUERIES.md

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+# ROWAN MCP TEST QUERIES
+
+Natural language test queries for all Rowan MCP tools.
+
+✅: passed with expected results
+
+⚠️: passed-ish (submitted/ran, but maybe unexpected results or needs some tweaking)
+
+❌: failed
+
+---
+
+# simple queries
+
+## core calculations
+
+### geometry optimizations
+- Optimize the geometry of aspirin ✅
+- Run a multistage optimization on caffeine ⚠️ (Unexpected Imaginary Frequency
+
+An unexpected large imaginary frequency was encountered, meaning that the calculation is far from a critical point on the PES. It's likely this structure has not been successfully optimized! Thermochemical results will be unreliable.)
+
+- Get the best structure for benzene ✅
+
+### electronic props
+- Calculate the HOMO and LUMO of benzene ✅
+- Get the electronic properties of nicotine ✅
+- What are the molecular orbitals of methanol? ✅
+
+### conformational analysis
+- Find the stable conformers of glucose ❌ - stuck on "running"
+- Generate 5 conformers of butane ✅
+- What are the different shapes ethanol can adopt? ✅
+
+### scans
+- Scan the C-C bond in ethane from 1.3 to 1.8 Angstroms ✅
+
+### spin states
+- What spin states are possible for iron(III) complex? ✅
+- Calculate different spin multiplicities for NO radical ✅ - calculated doublet and quartet states (?)
+- Check if iron porphyrin prefers singlet or triplet state ⚠️ log files indicate that this run finished, but doesn't say "finished" on rowan UI. stopped
+
+## cheimcal properties
+
+### redox
+- What's the reduction potential of benzoquinone? ✅ (Large Oxidation Potential Predicted. The predicted oxidation potential is very large. The workflow not been thoroughly tested on values in this range—results may be less accurate!)
+- Can vitamin E be easily oxidized? ⚠️ log files indicate that this run finished, but doesn't say "finished" on rowan UI. stopped
+- Predict the redox behavior of phenol ✅
+
+### solubility
+- How soluble is aspirin in water?✅
+- How soluble is caffeine in different solvents? Pick 5, and run them at 5 different temps in ascending order. ✅
+
+### descriptors
+- Generate descriptors for benzene ✅
+- Get QSAR features for ethanol ✅
+
+### pka
+- What's the pKa of acetic acid? ✅
+- What's the pKa of caffeine? ✅
+- What are the pKa values of citric acid? ✅
+
+### bond dissociation energy (no access)
+
+### hydrogen bond basicity (no access)
+
+## reactions / dynamics 
+
+### reactivity (fukui)
+- Where will electrophiles attack benzene? ✅
+- Find the most reactive sites in phenol ✅
+
+### rxn coordinate/irc ❌ 
+- Find the transition state for hydrogen migration in formic acid, then trace the reaction path to confirm it connects HCOOH and HOCOH isomers ❌
+
+### molecular dynamics
+- Run a short MD simulation of water ✅ (use molecule='water', not 'O')
+- Simulate the flexibility of ethanol for 500 steps ✅
+- Run molecular dynamics on butanol for 1000 steps ✅
+
+## drug discovery
+
+### admet
+- Predict drug-likeness of aspirin (follow-up: is it orally bioavailable?) ✅
+- Calculate ADMET for KarXT from Karuna Therapeutics ✅
+
+### docking (couldn't resolve) ❌
+- Dock aspirin to COX-2 enzyme
+- Find binding pose of this ligand
+- Predict protein-drug interaction
+
+### tautomers
+- What tautomers does acetylacetone have? ✅
+- Find tautomers of barbituric acid ✅
+- What keto-enol tautomers does phenol have? ✅
+
+## workflow management
+
+### data retrieval
+- Get results from this calculation UUID ✅
+- List 5 most recent workflows ✅
+- Update name of most recent workflow to "x" ✅
+
+### project organization
+- Create a new project folder for drug discovery (and delete) ✅
+- List all folders in my account ✅
+- "Move KarXT-related calculations into the folder" ✅
+- fix list folders ❌ 
+
+### server administration
+- Check server status ✅
+
+# more comprehensive queries tbd...
+
+### to do 
+- reaction coordinates, irc, docking 
+- rowan folder list - i think there's a bug
+    - tried paramter filtering (non-None params to avoid sending empty strings)
+    - direct API calls with rowan.Folder.list() with no params
+    - string, None, type checks
+    - used the example directly from Rowan's API docs (after adding redox folder), still getting 500 error
+- edit descriptions for one-liners to feed into the mcp tool
+- break up the folder and workflow mega tools