protein-tools-mcp

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structure_stats

Summarize protein structure files by reporting atom, residue, and chain counts plus gaps and altLoc details from PDB or mmCIF input.

Instructions

General structure summary: atoms, residues, chains, gaps, altLocs.

Accepts PDB or mmCIF (auto-detected). Free; local compute.

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_path": "<pdb_path>"
    },
    "name": "structure_stats"
  }
}

Input Schema

Name	Required	Description	Default
`pdb_path`	Yes

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A3.6/5.0

Behavior3/5

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

No annotations exist, so the description carries the full burden. It does add real behavioral context — PDB and mmCIF are auto-detected, and the operation is free/local rather than a billed remote call — but says nothing about failure modes (malformed file, unsupported format) or whether it ever mutates or caches anything.

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 short lines, the output inventory front-loaded, followed by format and cost facts. No filler, no repetition of the title.

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?

This is a low-complexity, one-input, read-only summary tool and an output schema exists, so return values need not be described. The description covers purpose, accepted formats, and cost profile; only edge-case behavior for bad inputs is unstated.

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 0% for the single pdb_path parameter, so the schema contributes nothing. The description partially compensates by clarifying that the path may point to either a PDB or mmCIF file, but gives no guidance on relative vs absolute paths or expected file naming.

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?

States a specific verb+resource (structure summary) and enumerates the computed quantities (atoms, residues, chains, gaps, altLocs), so an agent knows exactly what comes back. It does not explicitly differentiate itself from near-neighbors like aa_composition or index_stats, which also report structural counts.

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

Usage Guidelines3/5

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

Usage is implied: you call it to get a top-level inventory of a structure file. There is no statement of when to prefer it over siblings such as validate_pdb or sequence_from_pdb, and no prerequisites or exclusions are given.

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