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Rosetta MCP Server

Rosetta MCP Server

by Arielbs
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xml_to_pyrosetta

Read-only

Translate RosettaScripts XML protocols into PyRosetta Python code for computational protein design and analysis.

Instructions

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.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "xml_content": "<xml_content>"
    },
    "name": "xml_to_pyrosetta"
  }
}

Input Schema

NameRequiredDescriptionDefault
xml_contentYesRosettaScripts XML content to translate
include_commentsNoInclude detailed comments in output (default: true)
output_formatNoOutput format (default: python)

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv1.3.1

TDQS

A4.2/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations provide readOnlyHint=true, so description adds value by specifying the scope (37 element types) and confirming it is a non-destructive translation. No contradiction.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences: first states core purpose, second adds supported element count and usage hint. No unnecessary information, highly efficient.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With no output schema, the description implies output is equivalent Python code. It covers supported types and usage context. Minor gap: lacks details on output format variations or error handling, but sufficient for a straightforward translation tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, with all three parameters described. The description does not add additional meaning beyond the schema's definitions, so the baseline score of 3 is appropriate.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Description specifies verb 'Translate' with clear resource: RosettaScripts XML to PyRosetta Python code. It also mentions support for 37 element types, distinguishing it from sibling translation tools like translate_rosetta_script_to_biotite.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Description includes explicit usage instruction 'Use when converting XML protocols to Python.' However, it does not mention when not to use or provide direct comparison to alternative tools among the siblings.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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