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:

Then start the server:

Option 2: Manual Installation

If you prefer to install the package first:

Using uv:

Using pip:

Then configure and start:

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"

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):

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

• 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.

Publishing (Maintainer Notes)

To publish a new version to PyPI:

MCP inspector