BioPython MCP Server

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calculate_structure_stats

Calculate key statistics for a PDB structure file, including atom counts, residue composition, and chain information. Returns a dictionary with structure metrics.

Instructions

Calculate statistics for a PDB structure file.

Args: pdb_file: Path to PDB file

Returns: Dictionary containing structure statistics

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": {
      "pdb_file": "<pdb_file>"
    },
    "name": "calculate_structure_stats"
  }
}

Input Schema

Name	Required	Description	Default
`pdb_file`	Yes

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.8Feb 5, 2026

TDQS

C2.8/5.0

Behavior2/5

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

No annotations provided, and the description lacks any behavioral traits: no mention of side effects, permissions, rate limits, or computational cost. The tool performs a calculation but gives no insight into execution behavior.

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?

The description is very short and front-loaded with the core purpose. Every sentence is functional, though the docstring-style 'Args' and 'Returns' are somewhat redundant given the schema but acceptable.

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?

For a one-parameter tool with an output schema (as noted in context signals), the description adequately summarizes the return type as a dictionary. However, lacking examples or typical keys, it is minimally complete.

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

Parameters2/5

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

Schema description coverage is 0%. The description weakly adds 'Path to PDB file' which is already implied by the parameter name pdb_file and type string. No additional context (e.g., file format, location restrictions) is provided.

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

Purpose4/5

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

The description clearly states the verb 'Calculate' and resource 'statistics for a PDB structure file', distinguishing it from fetching or other operations. However, it does not specify what statistics are computed, limiting clarity.

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

Usage Guidelines2/5

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

No guidance on when to use this tool vs siblings (e.g., fetch_pdb_structure). It does not mention prerequisites or typical use cases, leaving the agent to infer.

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