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biotite_to_rosetta

Read-only

Finds the Rosetta/PyRosetta equivalent of any Biotite function and provides working example code for protein structure tasks like SASA, RMSD, superimposition, and residue selection.

Instructions

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.

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": {
      "query": "<query>"
    },
    "name": "biotite_to_rosetta"
  }
}

Input Schema

Name	Required	Description	Default
`query`	Yes	Biotite function or concept name (e.g., "sasa", "superimpose", "PDBFile.read")
`category`	No	Optional category filter

Schema Changelog

Changes observed during successful MCP inspections.

First observedv1.3.1May 29, 2026

TDQS

A4.5/5.0

Behavior5/5

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

Description discloses that the tool returns equivalents and example code, which aligns with the readOnlyHint annotation. It lists many covered categories (SASA, RMSD, etc.), providing transparency beyond annotations without contradiction.

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

Conciseness4/5

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

Description is a single paragraph that efficiently conveys usage, purpose, and coverage. It could be more structured (e.g., bullet points for categories) but is not verbose.

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?

For a lookup tool with no output schema, the description adequately covers purpose, parameters, and usage. It lacks explicit return format details, but the context (example code) implies a string. Sibling differentiation is clear.

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

Parameters4/5

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

Schema coverage is 100%, and the description adds meaningful context: the query parameter is described as a 'Biotite function or concept name', and the optional category is clarified. The list of covered topics helps the agent formulate appropriate queries.

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 clearly states the tool returns Rosetta/PyRosetta equivalents of Biotite functions with example code. It directly specifies the action and resource, and the 'ALWAYS use this tool' directive distinguishes it from siblings like rosetta_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?

Explicitly says 'ALWAYS use this tool when asked about Biotite vs Rosetta equivalents', providing clear when-to-use guidance. It does not explicitly state when not to use, but the sibling list and context imply alternatives exist for other queries.

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