io.github.Arielbs/rosetta-mcp-server MCP Server

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Rosetta MCP Server

Author: Ariel J. Ben-Sasson

A Model Context Protocol (MCP) server that lets Cursor (or any MCP client) work with Rosetta, PyRosetta, and Biotite: run RosettaScripts, validate XML protocols, translate between Rosetta and Biotite, score structures, and query documentation -- all from your AI coding assistant.

What's new in v1.3.0 (vs v1.1.8 on npm)

New: Biotite integration

• rosetta_to_biotite -- Find the Biotite equivalent of any Rosetta function with working example code (21 mappings covering structure I/O, SASA, RMSD, superimposition, secondary structure, contacts, hydrogen bonds, B-factors, angles, and more)
• biotite_to_rosetta -- Reverse lookup: find the Rosetta equivalent of a Biotite function
• translate_rosetta_script_to_biotite -- Translate entire RosettaScripts XML or PyRosetta code to Biotite Python. Design/optimization operations are flagged as Rosetta-only.
• Fuzzy search with keyword aliases ("contacts", "binding energy", "surface area", "align", etc.)

Improved: XML to PyRosetta translator

• 37 element types supported (was 6): 11 movers, 9 filters, 10 selectors, 7 task operations
• Full attribute handling: repeats, disable_design, cartesian, tolerance, threshold, distance, and more
• Child element support: MoveMap (with Span), Reweight, ScoreFunction
• Reports unrecognized elements so you know what needs manual work

Improved: Help and documentation

• get_rosetta_help now accepts any topic: movers by name ("FastRelax"), concepts ("constraints", "docking"), or score functions ("ref2015") -- auto-fetches live docs from rosettacommons.org
• search_rosetta_web_docs fallback: when DuckDuckGo is rate-limited, probes direct Rosetta docs URLs
• get_cached_docs auto-caches: no need to call cache_cli_docs first
• Expanded static help for score_functions, movers, filters, xml, and parameters

Improved: Scoring

• pyrosetta_score: new per_residue option returns per-residue energy breakdown
• scorefxn parameter now works (was ignored in v1.1.8)
• Proper error messages for missing files instead of silent {}

Improved: Validation

• validate_xml: new validate_against_schema option checks element names against the Rosetta XSD schema (catches typos like FastRleax)

MCP spec compliance fixes

• tools/call responses now use correct { content: [{ type: "text", text }] } format
• Tool errors return isError: true (not JSON-RPC errors)
• Standard JSON-RPC error codes (-32601, -32700, -32603)
• Removed false resources capability advertisement

Security fixes

• User input no longer interpolated into Python code (uses env vars / stdin)
• Temp files written to os.tmpdir() (not module directory)

Cleanup

• Removed 3 redundant tools: list_functions (merged into get_rosetta_info), search_pyrosetta_wheels, cache_cli_docs (auto-cache in get_cached_docs)
• Removed hardcoded personal paths
• Fixed shadowed variables, async anti-patterns, dead code
• 18 tools (was 21), all with improved agent-oriented descriptions

---

Example: asking a naive question

This is what makes the MCP server powerful -- an AI agent can answer domain questions by calling the right tools automatically:

User asks in Cursor: "How do I relax my protein and what's the Biotite equivalent?"

The agent calls two MCP tools behind the scenes:

1. get_rosetta_help("FastRelax") returns 6000+ chars of live documentation:

FastRelax performs all-atom relaxation using the FastRelax protocol. Parameters include scorefxn, repeats, cartesian, disable_design, MoveMap configuration...

2. rosetta_to_biotite("FastRelax") returns:

{
  "found": true,
  "results": [{
    "rosetta": { "name": "FastRelax", "example": ["relax = FastRelax()", "relax.set_scorefxn(get_score_function('ref2015'))", "relax.apply(pose)"] },
    "biotite": null,
    "equivalence": "none_from_biotite",
    "notes": "Biotite does NOT perform structure optimization. These are Rosetta-specific capabilities."
  }]
}

The agent synthesizes: "FastRelax is Rosetta's all-atom relaxation protocol. Here's how to use it... Note: Biotite is analysis-only and has no equivalent -- you need PyRosetta for structure optimization."

Without the MCP, the agent would guess from training data and likely get parameter names or API signatures wrong.

---

What you get (18 tools)

Discovery & Help

Tool	Description
get_rosetta_info	All available score functions, movers, filters, selectors, parameters
get_rosetta_help	Help for any topic -- accepts mover names, concepts, or score functions
pyrosetta_introspect	Live PyRosetta API search with docs and signatures

Documentation

Tool	Description
search_rosetta_web_docs	Search rosettacommons.org documentation
get_rosetta_web_doc	Fetch and read a specific docs page
get_cached_docs	Search cached CLI help (auto-caches on first use)

Execution & Scoring

Tool	Description
run_rosetta_scripts	Run a RosettaScripts XML protocol on a PDB
pyrosetta_score	Score a PDB with optional per-residue breakdown

Translation

Tool	Description
xml_to_pyrosetta	XML to PyRosetta Python (37 element types)
rosetta_to_biotite	Find Biotite equivalent of a Rosetta function
biotite_to_rosetta	Find Rosetta equivalent of a Biotite function
translate_rosetta_script_to_biotite	Translate full scripts from Rosetta to Biotite

Validation & Schema

Tool	Description
validate_xml	Check XML syntax + optional schema validation
rosetta_scripts_schema	Generate XSD schema and extract element names

Environment

Tool	Description
python_env_info	Python version and installed packages
check_pyrosetta	Verify PyRosetta is available
install_pyrosetta_installer	Auto-install PyRosetta (10-30 min)
find_rosetta_scripts	Locate the rosetta_scripts binary

---

Quick start

1. Install from npm

npm install -g rosetta-mcp-server

2. Set up Python environment

# Create a venv with PyRosetta and Biotite
uv venv ~/.venvs/rosetta-mcp
~/.venvs/rosetta-mcp/bin/pip install pyrosetta-installer biotite
~/.venvs/rosetta-mcp/bin/python -c "import pyrosetta_installer as I; I.install_pyrosetta()"

Or skip this step -- PyRosetta auto-installs on first use (takes 10-30 min).

3. Configure your MCP client

Cursor (~/.cursor/mcp.json):

{
  "mcpServers": {
    "rosetta": {
      "command": "rosetta-mcp-server",
      "args": [],
      "env": {
        "ROSETTA_BIN": "/path/to/rosetta_scripts.default.macosclangrelease",
        "PYTHON_BIN": "/path/to/.venvs/rosetta-mcp/bin/python"
      }
    }
  }
}

Claude Desktop (~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "rosetta": {
      "command": "rosetta-mcp-server",
      "env": {
        "ROSETTA_BIN": "/path/to/rosetta_scripts.default.macosclangrelease",
        "PYTHON_BIN": "/path/to/.venvs/rosetta-mcp/bin/python"
      }
    }
  }
}

Environment variables:

Variable	Required	Description
ROSETTA_BIN	No	Path to rosetta_scripts binary or its directory. If not set, searches common paths and PATH.
PYTHON_BIN	No	Python interpreter with PyRosetta/Biotite. Defaults to python3.
MCP_DEBUG	No	Set to 1 for debug logging to stderr.

4. Restart your editor

Open Settings -> MCP. The "rosetta" server should appear green with 18 tools.

---

XML to PyRosetta translation example

Input XML:

<ROSETTASCRIPTS>
  <SCOREFXNS>
    <ScoreFunction name="ref" weights="ref2015"/>
  </SCOREFXNS>
  <RESIDUE_SELECTORS>
    <Chain name="chainA" chains="A"/>
  </RESIDUE_SELECTORS>
  <MOVERS>
    <FastRelax name="relax" scorefxn="ref" repeats="5" cartesian="true"/>
  </MOVERS>
  <PROTOCOLS>
    <Add mover="relax"/>
  </PROTOCOLS>
</ROSETTASCRIPTS>

Generated PyRosetta code:

import pyrosetta
from pyrosetta import pose_from_pdb
from pyrosetta.rosetta.core.scoring import get_score_function
from pyrosetta.rosetta.core.select.residue_selector import *
from pyrosetta.rosetta.protocols.relax import *

pyrosetta.init("-mute all")

pose = pose_from_pdb("your_protein.pdb")

# Residue Selectors
chainSelector = ChainSelector()
chainSelector.set_chain_strings("A")

# Movers
fastRelax = FastRelax()
fastRelax.set_scorefxn(get_score_function("ref"))
fastRelax.set_default_repeats(5)
fastRelax.cartesian(True)

sfxn = get_score_function("ref2015")

# Apply movers
fastRelax.apply(pose)

pose.dump_pdb("output.pdb")
score = pose.energies().total_energy()
print(f"Final score: {score}")

---

Rosetta <-> Biotite mapping coverage

Category	Rosetta	Biotite	Equivalence
Structure I/O	pose_from_pdb	PDBFile.read	Full
Structure I/O	pose.dump_pdb	PDBFile.write	Full
Structure I/O	pose_from_file (CIF)	CIFFile.read	Full
Surface Analysis	SasaMetric	biotite.structure.sasa	Full
Alignment	SuperimposeMover	biotite.structure.superimpose	Full
RMSD	all_atom_rmsd	biotite.structure.rmsd	Full
Secondary Structure	DsspMover	annotate_sse	Partial
Sequence	pose.sequence()	get_residues	Full
Distance	AtomPairConstraint	biotite.structure.distance	Full
Angles	pose.phi/psi/omega	biotite.structure.dihedral	Full
Interface	InterfaceAnalyzerMover	sasa + selection	Partial
Database	rcsb.pose_from_rcsb	rcsb.fetch	Full
Selection	ChainSelector etc.	numpy boolean indexing	Full
Contacts	distance matrices	CellList	Partial
Ramachandran	pose.phi/psi	dihedral_backbone	Partial
H-bonds	HBondSet	biotite.structure.hbond	Partial
B-factors	pdb_info().bfactor	AtomArray.b_factor	Full
Center of Mass	center_of_mass	mass_center	Full
Scoring	ScoreFunction	None	Rosetta only
Optimization	FastRelax	None	Rosetta only
Design	FastDesign	None	Rosetta only

---

Troubleshooting

• Server shows red in Cursor: Restart Cursor. Use absolute path in config (e.g., /opt/homebrew/bin/rosetta-mcp-server). Ensure Node 14+ and Python 3.8+.
• run_rosetta_scripts fails: Verify ROSETTA_BIN points to a valid binary. Try "$ROSETTA_BIN" -help.
• PyRosetta tools say "not available": Install via pip install pyrosetta-installer then run the installer, or let the MCP server auto-install on first use.
• Biotite tools return no results: Install Biotite in the same Python env: pip install biotite
• get_rosetta_help returns "No detailed help": Try the exact Rosetta class name (e.g., "FastRelax" not "relax"). The tool resolves common aliases but may miss unusual names.

Verify from the command line

# Check version
echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05"}}' | rosetta-mcp-server 2>/dev/null | python3 -c "import sys,json; print(json.loads(sys.stdin.readline())['result']['serverInfo'])"

# List all tools
echo '{"jsonrpc":"2.0","id":1,"method":"tools/list","params":{}}' | rosetta-mcp-server 2>/dev/null | python3 -c "import sys,json; [print(t['name']) for t in json.loads(sys.stdin.readline())['result']['tools']]"

Development

rosetta-mcp-server/
├── rosetta_mcp_wrapper.js   # Node MCP server (protocol + all 18 tools)
├── rosetta_mcp_server.py    # Python helper (static Rosetta data)
├── install_pyrosetta.js     # Standalone PyRosetta installer
├── package.json             # npm package config
└── README.md

License and attribution

• MIT for this repository
• Rosetta/PyRosetta: see RosettaCommons licenses; commercial use requires the appropriate license
• Biotite: BSD 3-Clause license