io.github.Arielbs/rosetta-mcp-server
NPM · ROSETTA-MCP-SERVER · SCANNED AUG 3
Rosetta/PyRosetta protein modeling and Biotite translation for computational biology
Available components
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency45
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Provenance check failed: no build-provenance attestation is published. See how to fix → View diagnostics → Fail
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 121 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability77
- AI-judged instruction clarity (excellent).Pass
- Tool/resource definitions use about 1512 tokens (~84/item across 18 items; 18 tools + 0 resources), lean.Pass
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management27
- Stability observed for 8 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage98
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 94% of tool parameters carry a description.Partial
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
Add this component to your MCP client. Where a client-specific snippet is available, pick your client below and copy it straight into your config; otherwise use the connection detail shown.
npm · rosetta-mcp-server
claude mcp add arielbs-rosetta-mcp-server -- npx -y rosetta-mcp-server
codex mcp add arielbs-rosetta-mcp-server -- npx -y rosetta-mcp-server
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"arielbs-rosetta-mcp-server": {
"type": "local",
"command": [
"npx",
"-y",
"rosetta-mcp-server"
],
"enabled": true
}
}
} openclaw mcp add arielbs-rosetta-mcp-server --command npx --arg -y --arg rosetta-mcp-server
mcp_servers:
arielbs-rosetta-mcp-server:
command: "npx"
args: ["-y", "rosetta-mcp-server"] {
"mcpServers": {
"arielbs-rosetta-mcp-server": {
"command": "npx",
"args": [
"-y",
"rosetta-mcp-server"
]
}
}
} Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 2 Aug 26 +19
- Malware scan: unverified → pass ▲ security
- Stability: unverified → 0.23 ▲ functional
- 1 Aug 26 −9
- We updated how we score, so this day's move reflects our rubric, not a change to the server See what changed → functional
- 31 Jul 26 −18
- Malware scan: pass → unverified ▼ security
- 27 Jul 26 0
- We updated how we score, so this day's move reflects our rubric, not a change to the server See what changed → functional
- 26 Jul 26 81
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 3 Aug 2026 · Analysed npm/[email protected]
Provenance none
Ecosystem: npm · Outcome: none
Dependencies 0 packages
0 packages in the resolved dependency tree.
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability.
biotite_to_rosetta ~132
ALWAYS use this tool when asked about Biotite vs Rosetta equivalents. Returns the Rosetta/PyRosetta equivalent of a Biotite function with working example code. Covers: structure I/O, SASA, RMSD, superimposition, secondary structure, distances, angles, contacts, hydrogen bonds, B-factors, and residue selection.
| Name | Type | Req | Description |
|---|---|---|---|
| category | string | — | Optional category filter |
| query | string | yes | Biotite function or concept name (e.g., "sasa", "superimpose", "PDBFile.read", "annotate_sse") |
No output schema declared.
No examples provided.
check_pyrosetta ~35
Check if PyRosetta is importable in the current environment. Use before PyRosetta-dependent tools to verify availability.
Input schema present but exposes no named parameters.
No output schema declared.
No examples provided.
find_rosetta_scripts ~52
Resolve the rosetta_scripts executable path by checking exe_path, ROSETTA_BIN env, common directories, and PATH. Use to verify Rosetta is installed.
| Name | Type | Req | Description |
|---|---|---|---|
| exe_path | string | — | — |
No output schema declared.
No examples provided.
get_cached_docs ~78
Search locally cached Rosetta CLI docs for a keyword. Auto-caches on first use. Use to look up command-line flags or parser info.
| Name | Type | Req | Description |
|---|---|---|---|
| cache_dir | string | — | Directory where docs are cached |
| max_lines | number | — | Max number of lines to return (default 200) |
| query | string | — | Search string |
No output schema declared.
No examples provided.
get_rosetta_help ~75
Get help for any Rosetta topic, mover, filter, or concept. Accepts general topics (score_functions, movers, filters, xml, parameters) or specific names (FastRelax, Ddg, ChainSelector). Auto-fetches live documentation when available.
| Name | Type | Req | Description |
|---|---|---|---|
| topic | string | — | Topic to get help for |
No output schema declared.
No examples provided.
get_rosetta_info ~66
Get comprehensive Rosetta installation info including available score functions, movers, filters, selectors, task operations, parameters, and command-line options. Use this first to understand what Rosetta components are available. For live PyRosetta API details, use pyrosetta_introspect.
Input schema present but exposes no named parameters.
No output schema declared.
No examples provided.
get_rosetta_web_doc ~73
Fetch and extract text from a specific Rosetta docs URL. Use after search_rosetta_web_docs to read a documentation page.
| Name | Type | Req | Description |
|---|---|---|---|
| max_chars | number | — | Max characters of cleaned text to return (default 4000) |
| url | string | yes | Full URL to a Rosetta docs page |
No output schema declared.
No examples provided.
install_pyrosetta_installer ~55
Install PyRosetta using the pyrosetta-installer package. Takes 10-30 minutes. Use when PyRosetta is not available and needed for scoring or design.
| Name | Type | Req | Description |
|---|---|---|---|
| silent | boolean | — | — |
No output schema declared.
No examples provided.
pyrosetta_introspect ~95
Search PyRosetta API classes (movers, filters, selectors, task operations) and return docs and signatures. Use to discover available PyRosetta classes or get constructor details.
| Name | Type | Req | Description |
|---|---|---|---|
| kind | string | — | Filter by kind: mover|filter|selector|task |
| max_results | number | — | Max number of results (default 50) |
| query | string | — | Substring to match class names |
No output schema declared.
No examples provided.
pyrosetta_score ~98
Score a PDB file using PyRosetta. Returns total energy in REU. Use to evaluate structure quality or compare designs. Optionally returns per-residue energy breakdown.
| Name | Type | Req | Description |
|---|---|---|---|
| pdb_path | string | yes | Path to input PDB |
| per_residue | boolean | — | If true, include per-residue energy breakdown (default: false) |
| scorefxn | string | — | Score function name (default: ref2015) |
No output schema declared.
No examples provided.
python_env_info ~31
Get Python executable path, version, and pip package list. Use to diagnose environment issues or verify package installations.
Input schema present but exposes no named parameters.
No output schema declared.
No examples provided.
rosetta_scripts_schema ~87
Generate and cache the RosettaScripts XML schema (XSD). Optionally extract element names. Use to get the authoritative list of valid XML elements.
| Name | Type | Req | Description |
|---|---|---|---|
| cache_dir | string | — | Directory to store schema |
| exe_path | string | — | Path to rosetta_scripts executable (optional) |
| extract_elements | boolean | — | If true, return a list of element names |
No output schema declared.
No examples provided.
rosetta_to_biotite ~156
ALWAYS use this tool when asked about Rosetta vs Biotite equivalents. Returns the Biotite equivalent of a Rosetta/PyRosetta function with working example code. Covers: structure I/O, SASA, RMSD, superimposition, secondary structure, distances, angles, contacts, hydrogen bonds, B-factors, interface analysis, database access, and residue selection.
| Name | Type | Req | Description |
|---|---|---|---|
| category | string | — | Optional category filter (e.g., "Structure I/O", "Geometry", "Surface Analysis") |
| query | string | yes | Rosetta method or concept name (e.g., "pose_from_pdb", "FastRelax", "SuperimposeMover", "SASA", "RMSD") |
No output schema declared.
No examples provided.
run_rosetta_scripts ~109
Run a RosettaScripts XML protocol on an input PDB file. Use when executing Rosetta protocols. Requires rosetta_scripts binary.
| Name | Type | Req | Description |
|---|---|---|---|
| exe_path | string | — | Path to rosetta_scripts executable (optional if on PATH) |
| extra_flags | array | — | Additional command-line flags |
| input_pdb | string | yes | Path to input PDB |
| out_dir | string | yes | Output directory |
| xml_path | string | yes | Path to Rosetta XML protocol |
No output schema declared.
No examples provided.
search_rosetta_web_docs ~72
Search online Rosetta documentation at rosettacommons.org. Use when you need docs for a specific Rosetta feature.
| Name | Type | Req | Description |
|---|---|---|---|
| max_results | number | — | Number of results to return (default 3) |
| query | string | yes | Search query (e.g., FastRelax, AtomPair constraint) |
No output schema declared.
No examples provided.
translate_rosetta_script_to_biotite ~118
ALWAYS use this tool when asked to convert or translate Rosetta code to Biotite. Translates RosettaScripts XML or PyRosetta code to Biotite Python code. Analysis operations are translated; design/optimization are flagged as Rosetta-only.
| Name | Type | Req | Description |
|---|---|---|---|
| code | string | yes | RosettaScripts XML content or PyRosetta Python code to translate |
| include_comments | boolean | — | Include explanatory comments in output (default: true) |
| input_format | string | — | Input format (default: "auto") |
No output schema declared.
No examples provided.
validate_xml ~85
Validate a RosettaScripts XML protocol. Checks XML syntax and optionally validates element names against the Rosetta XSD schema. Use before run_rosetta_scripts to catch errors early.
| Name | Type | Req | Description |
|---|---|---|---|
| validate_against_schema | boolean | — | If true, also check element names against the cached Rosetta XSD schema (default: false) |
| xml_content | string | yes | XML content to validate |
No output schema declared.
No examples provided.
xml_to_pyrosetta ~95
Translate RosettaScripts XML to equivalent PyRosetta Python code. Supports 37 element types including movers, filters, selectors, and task operations. Use when converting XML protocols to Python.
| Name | Type | Req | Description |
|---|---|---|---|
| include_comments | boolean | — | Include detailed comments in output (default: true) |
| output_format | string | — | Output format (default: python) |
| xml_content | string | yes | RosettaScripts XML content to translate |
No output schema declared.
No examples provided.