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Rosetta MCP Server

Rosetta MCP Server

by Arielbs
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translate_rosetta_script_to_biotite

Read-only

Translates RosettaScripts XML or PyRosetta code into Biotite Python code for analysis operations, while flagging design and optimization tasks as Rosetta-only.

Instructions

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.

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": {
      "code": "<code>"
    },
    "name": "translate_rosetta_script_to_biotite"
  }
}

Input Schema

NameRequiredDescriptionDefault
codeYesRosettaScripts XML content or PyRosetta Python code to translate
input_formatNoInput format (default: "auto")
include_commentsNoInclude explanatory comments in output (default: true)

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv1.3.1

TDQS

A4.1/5.0
Behavior4/5

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

Annotations indicate readOnlyHint=true (no destructive side effects). The description adds behavioral context: it translates only analysis operations and flags design/optimization as Rosetta-only. This goes beyond annotations without contradicting them.

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 with no fluff. The critical instruction is front-loaded with 'ALWAYS use this tool.' Every sentence adds value without redundancy.

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

Completeness3/5

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

The description covers purpose, scope, and limitations. However, without an output schema, it could specify the return format (e.g., returns translated code as a string) or error handling. It is adequate but not comprehensive.

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 description coverage is 100%, so parameters are already documented. The description adds context about what types of code are accepted (analysis vs design/optimization), but does not add significant meaning beyond the schema. Baseline 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?

The description clearly states the tool's purpose: translating RosettaScripts XML or PyRosetta code to Biotite Python code. It explicitly says 'ALWAYS use this tool when asked to convert or translate Rosetta code to Biotite,' which strongly differentiates it from sibling tools like biotite_to_rosetta.

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?

The description gives explicit when-to-use guidance ('ALWAYS use this tool when asked to convert...') and notes limitations (analysis translated, design/optimization flagged). It does not explicitly list alternatives, but siblings imply the reverse direction.

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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