Rosetta Context

★ 16

from Arielbs

Rosetta protein design & modeling for agents

🔥🔥🔥✓ VerifiedFreeQuick setup

#automation #database #security #translation

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

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:

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

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