Rowan MCP Server

MCP server for making it easy to run Rowan's molecular design and simulation tools.

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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:

{
  "mcpServers": {
    "rowan": {
      "type": "http",
      "url": "http://127.0.0.1:6276/sse"
    }
  }
}

Then start the server:

# 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:

uv add rowan-mcp

Using pip:

pip install rowan-mcp

Then configure and start:

{
  "mcpServers": {
    "rowan": {
      "type": "http", 
      "url": "http://127.0.0.1:6276/sse"
    }
  }
}

# Set API key and start server
export ROWAN_API_KEY="your_api_key_here"
rowan-mcp

Get API Key

Visit labs.rowansci.com → Create account → Generate API key

Start Using

Ask your AI: "Calculate the pKa of aspirin" or "Optimize the geometry of caffeine"

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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 (recommended) or pip
• Rowan API key (free at labs.rowansci.com)
• MCP-compatible client (Claude Desktop, etc.)

Development commands (if you cloned the repo):

# Run from source
export ROWAN_API_KEY="your_api_key_here"
uv run python -m rowan_mcp

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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

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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

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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.)

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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.

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Getting Help

• Documentation: docs.rowansci.com
• or ping me!

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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.

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Publishing (Maintainer Notes)

To publish a new version to PyPI:

# 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

# 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