# Rowan MCP Server
MCP server for making it easy to run Rowan's molecular design and simulation tools.
---
## **Installation**
### **Option 1: Auto-Install (No manual installation needed!)**
Just add this to your MCP configuration and it will automatically install and run:
**HTTP/SSE configuration:**
```json
{
"mcpServers": {
"rowan": {
"type": "http",
"url": "http://127.0.0.1:6276/sse"
}
}
}
```
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**
If you prefer to install the package first:
**Using uv:**
```bash
uv add rowan-mcp
```
**Using pip:**
```bash
pip install rowan-mcp
```
Then configure and start:
```json
{
"mcpServers": {
"rowan": {
"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
### **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"*
- **Predict chemical behavior**: *"What's the pKa of acetic acid?"*
- **Run calculations**: *"Calculate the HOMO and LUMO of benzene"*
## **System Requirements**
- **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.)
**Development commands** (if you cloned the repo):
```bash
# Run from source
export ROWAN_API_KEY="your_api_key_here"
uv run python -m rowan_mcp
```
---
## **Available Tools**
**Total: 45 MCP Tools**
- 28 Dedicated Workflow Functions (all workflows from Rowan v2.1.9)
- 1 Batch Workflow Function
- 3 Molecule Lookup Tools
- 7 Workflow Management Tools
- 6 Protein Management Tools
---
### Chemistry Calculations
- `submit_basic_calculation_workflow` - Energy, optimization, frequencies with multiple engines (omol25, xtb, psi4)
- `submit_conformer_search_workflow` - Conformational search with multiple search modes (rapid/careful/meticulous)
- `submit_conformers_workflow` - Conformer generation and enumeration (different from conformer_search)
- `submit_multistage_opt_workflow` - Multi-stage geometry optimization with sequential accuracy levels
- `submit_scan_workflow` - Molecular scans (dihedral, bond, angle) with wavefront propagation
- `submit_irc_workflow` - Intrinsic reaction coordinate calculations for transition states
### Molecular Properties
- `submit_pka_workflow` - Microscopic pKa calculations with customizable pH ranges and elements
- `submit_macropka_workflow` - Macroscopic pKa calculations across pH and charge ranges
- `submit_solubility_workflow` - Solubility predictions across multiple solvents and temperatures
- `submit_redox_potential_workflow` - Electrochemical reduction/oxidation potentials
- `submit_descriptors_workflow` - ML-ready molecular descriptors and features
- `submit_tautomer_search_workflow` - Tautomer enumeration
- `submit_admet_workflow` - ADME/Tox property predictions for drug discovery
- `submit_hydrogen_bond_basicity_workflow` - Hydrogen bond basicity (pKBHX) predictions
### Reactivity Analysis
- `submit_fukui_workflow` - Fukui indices for electrophilic/nucleophilic reactivity sites
### Electronic Structure
- `submit_spin_states_workflow` - Spin state energy calculations for different multiplicities
### Spectroscopy & Analysis
- `submit_ion_mobility_workflow` - Ion mobility mass spectrometry collision cross-section (CCS) predictions
- `submit_strain_workflow` - Molecular strain energy calculations for rings and cages
### Transition States & Reactions
- `submit_double_ended_ts_search_workflow` - Transition state search from reactant and product structures
- `submit_pose_analysis_md_workflow` - Molecular dynamics simulations on docked protein-ligand complexes
### Protein & Drug Discovery
- `submit_docking_workflow` - Protein-ligand docking with multiple executables (Vina, QVina2, Smina)
- `submit_batch_docking_workflow` - High-throughput docking for virtual screening campaigns
- `submit_protein_cofolding_workflow` - Multi-protein and protein-ligand cofolding predictions
- `submit_msa_workflow` - Multiple sequence alignment for protein structure prediction
### Batch Processing
- `batch_submit_workflow` - Submit multiple molecules through any workflow type for high-throughput processing
---
### Molecule Management
- `molecule_lookup` - Convert molecule names, CAS numbers, IUPAC names to SMILES
- `batch_molecule_lookup` - Bulk molecule name to SMILES conversion
- `validate_smiles` - Validate and standardize SMILES strings
### Protein Management
- `create_protein_from_pdb_id` - Create protein from PDB ID (e.g., '1HCK')
- `retrieve_protein` - Get protein data by UUID
- `list_proteins` - List all available proteins
- `upload_protein` - Upload custom protein structures
- `delete_protein` - Remove protein from workspace
- `sanitize_protein` - Clean and validate protein structures
### Workflow Management
- `retrieve_workflow` - Get complete workflow data, status, and results (single source of truth)
- `workflow_stop` - Stop running workflows
- `workflow_delete` - Remove workflows from workspace
- `retrieve_calculation_molecules` - Extract molecular structures from calculations
- `list_workflows` - List all workflows with filtering options
- `workflow_update` - Modify workflow parameters
- `workflow_delete_data` - Remove workflow data while keeping metadata
## **Requirements**
- Python 3.11+
- Rowan API key
- MCP-compatible AI assistant (Claude Desktop, etc.)
---
## **Experimental: Desktop Extension (Work in Progress)**
Working on a one-click desktop extension (.dxt) for Claude Desktop that eliminates command-line setup! This feature is currently being refined for compatibility with the MCP extension system.
For now, use the standard Package Installation method above, which is fully tested and reliable.
---
## **Getting Help**
- **Documentation**: [docs.rowansci.com](https://docs.rowansci.com/)
- or ping me!
---
## **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/
```
### 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
```
