protein-tools-mcp

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index_stats

Get corpus-level stats for the PDB-wide metal-site index: entry/site counts, per-metal and per-geometry distributions, artifact volume.

Instructions

Corpus-level stats for the PDB-wide metal-site index (premium: requires the hosted relay): entry/site counts, per-metal and per-geometry distributions, artifact volume.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "index_stats"
  }
}

Input Schema

Name	Required	Description	Default
`db_path`	No

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

B3.3/5.0

Behavior3/5

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

With no annotations, the description carries the full behavioral burden. It does disclose the premium/hosted-relay prerequisite and the returned metrics, which is genuine value. But it never states that this is a read-only operation, whether it has side effects, or any rate/scope limits, so it falls short of full disclosure.

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?

One tight sentence, front-loaded with the resource and immediately followed by the metric list and prerequisite. Every clause carries information with no filler.

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?

An output schema exists, so the return-value enumeration is somewhat redundant but harmless. The prerequisite is covered, yet the sole parameter is left undocumented and there are no annotations to carry safety/scope information, leaving a gap for an agent deciding how to call it.

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?

There is a single parameter (db_path) with 0% schema description coverage, and the description says nothing about it — no default behavior, no format, no interaction with the hosted relay. With low coverage the description should compensate, and it does not.

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 resource (corpus-level stats for the PDB-wide metal-site index) and enumerates the content: entry/site counts, per-metal and per-geometry distributions, artifact volume. It implies differentiation from per-structure tools like structure_stats or metal_geometry via 'corpus-level'/'PDB-wide', but does not name a sibling explicitly.

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?

The 'premium: requires the hosted relay' note gives a prerequisite, which is useful usage context. However, there is no explicit when-to-use guidance versus the many sibling stats tools, and no stated conditions under which it should be avoided. Usage is implied by 'corpus-level' but not spelled out.

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