rowan-mcp 2.3.2__tar.gz

rowan_mcp-2.3.2/.gitignore

@@ -0,0 +1,44 @@
+/.venv
+/rowan-dxt
+.env
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.DS_Store
+
+.claude
+CLAUDE.md
+/dist
+
+# MCP configuration (may contain tokens)
+.mcp.json
+
+# Test and example files
+/tests/
+/example_docs/
+test_*.py
+*_test.py
+test_*.txt
+debug_*.py
+*_debug.py
+
+# Log files
+*.log
+logs/
+
+# Personal compatibility notes
+GEMINI_MCP_COMPATIBILITY.md
+MCP_CHATGPT_GEMINI_COMPATIBILITY_ANALYSIS.md
+ROWAN_MCP_TEST_QUERIES.md
+ROWAN_MCP_TOOLS.md
+TOOLS_DOCUMENTATION.md
+
+# Large archive/data files
+*.dxt
+*.dxz
+
+# OpenRouter experimental clients (not part of core MCP server)
+openrouter_client.py
+openrouter_stdio_client.py
+setup_openrouter.py

rowan_mcp-2.3.2/PKG-INFO

@@ -0,0 +1,272 @@
+Metadata-Version: 2.4
+Name: rowan-mcp
+Version: 2.3.2
+Summary: Model Context Protocol server for Rowan computational chemistry platform
+Project-URL: Homepage, https://github.com/k-yenko/rowan-mcp
+Author-email: Katherine Yenko <katherineayenko@gmail.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: >=3.11
+Requires-Dist: aiohttp>=3.12.15
+Requires-Dist: fastapi>=0.104.0
+Requires-Dist: fastmcp>=2.11.3
+Requires-Dist: httpx>=0.25.0
+Requires-Dist: mcp>=1.0.0
+Requires-Dist: openai>=1.107.2
+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>=2.1.9
+Requires-Dist: stjames>=0.0.125
+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
+
+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: 48 MCP Tools**
+- 28 Dedicated Workflow Functions (all workflows from Rowan v2.1.9)
+- 1 Batch Workflow Function
+- 3 Molecule Lookup Tools
+- 10 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
+- `workflow_get_status` - Check workflow status with detailed progress information
+- `workflow_stop` - Stop running workflows
+- `workflow_delete` - Remove workflows from workspace
+- `retrieve_workflow` - Get complete workflow data and results
+- `retrieve_calculation_molecules` - Extract molecular structures from calculations
+- `list_workflows` - List all workflows with filtering options
+- `workflow_update` - Modify workflow parameters
+- `workflow_is_finished` - Check if workflow is complete
+- `workflow_delete_data` - Remove workflow data while keeping metadata
+- `workflow_fetch_latest` - Get most recent workflow results
+
+## **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
+```        

rowan_mcp-2.3.2/Procfile

@@ -0,0 +1 @@
+web: python railway_start.py

rowan_mcp-2.3.2/README.md

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+# 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: 48 MCP Tools**
+- 28 Dedicated Workflow Functions (all workflows from Rowan v2.1.9)
+- 1 Batch Workflow Function
+- 3 Molecule Lookup Tools
+- 10 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
+- `workflow_get_status` - Check workflow status with detailed progress information
+- `workflow_stop` - Stop running workflows
+- `workflow_delete` - Remove workflows from workspace
+- `retrieve_workflow` - Get complete workflow data and results
+- `retrieve_calculation_molecules` - Extract molecular structures from calculations
+- `list_workflows` - List all workflows with filtering options
+- `workflow_update` - Modify workflow parameters
+- `workflow_is_finished` - Check if workflow is complete
+- `workflow_delete_data` - Remove workflow data while keeping metadata
+- `workflow_fetch_latest` - Get most recent workflow results
+
+## **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
+```        

rowan_mcp-2.3.2/nixpacks.toml

@@ -0,0 +1,10 @@
+# Railway Nixpacks configuration for Rowan MCP
+# Python-based MCP server
+
+[phases.install]
+cmds = [
+  "pip install -e ."
+]
+
+[start]
+cmd = "python railway_start.py"

rowan_mcp-2.3.2/pyproject.toml

@@ -0,0 +1,79 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "rowan-mcp"
+version = "2.3.2"
+description = "Model Context Protocol server for Rowan computational chemistry platform"
+authors = [
+    {name = "Katherine Yenko", email = "katherineayenko@gmail.com"}
+]
+license = {text = "MIT"}
+readme = "README.md"
+requires-python = ">=3.11"
+urls = {Homepage = "https://github.com/k-yenko/rowan-mcp"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+dependencies = [
+    "fastmcp>=2.11.3",
+    "rowan-python>=2.1.9",
+    "stjames>=0.0.125",
+    "pydantic>=2.0.0",
+    "typing-extensions>=4.0.0",
+    "uvicorn>=0.24.0",
+    "fastapi>=0.104.0",
+    "python-dotenv>=1.0.0",
+    "pubchempy>=1.0.4",
+    "rdkit>=2025.3.2",
+    "aiohttp>=3.12.15",
+    "openai>=1.107.2",
+    "httpx>=0.25.0",
+    "mcp>=1.0.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0.0",
+    "black>=23.0.0",
+    "isort>=5.0.0",
+    "mypy>=1.0.0",
+]
+
+[project.scripts]
+rowan-mcp = "rowan_mcp.server:main"
+
+[tool.hatch.build.targets.wheel]
+packages = ["rowan_mcp"]
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+  "rowan-dxt/",
+  "dxt/", 
+  "*.log",
+  "test_*.py",
+  ".venv/",
+  "*.dxt"
+]
+
+[tool.black]
+line-length = 88
+target-version = ['py38']
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+
+[tool.mypy]
+python_version = "3.8"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = true 

rowan_mcp-2.3.2/railway_start.py

@@ -0,0 +1,18 @@
+#!/usr/bin/env python3
+"""Railway startup script for Rowan MCP server"""
+import os
+import sys
+
+# Add current directory to path to ensure rowan_mcp can be imported
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+
+from rowan_mcp.server import mcp
+
+if __name__ == "__main__":
+    # Get port from Railway's PORT environment variable
+    port = int(os.getenv("PORT", 6276))
+
+    print(f"Starting Rowan MCP Server on 0.0.0.0:{port}", file=sys.stderr)
+
+    # Start server with 0.0.0.0 binding (required for Railway)
+    mcp.run(transport="http", host="0.0.0.0", port=port)

rowan_mcp-2.3.2/rowan_mcp/__init__.py

@@ -0,0 +1,14 @@
+"""
+Rowan MCP Server - Computational Chemistry Platform Integration
+
+This package provides MCP (Model Context Protocol) server functionality
+for integrating with Rowan's computational chemistry platform.
+"""
+
+__version__ = "2.3.2"
+__author__ = "Kat Yenko"
+__description__ = "MCP server for Rowan computational chemistry platform"
+
+from .server import main
+
+__all__ = ["main"] 

rowan_mcp-2.3.2/rowan_mcp/__main__.py

@@ -0,0 +1,12 @@
+"""
+Main entry point for Rowan MCP Server when run as a module.
+
+Usage:
+    python -m rowan_mcp          # STDIO mode
+    python -m rowan_mcp --help   # Show help
+"""
+
+if __name__ == "__main__":
+    # STDIO transport
+    from .server import main
+    main()