protein-tools-mcp

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md_preflight

Validates PDB/mmCIF structures, detects metal sites, and checks force-field metal parameters to return GO or NO-GO before MD simulations.

Instructions

MD pre-flight gate for a structure: PDB/mmCIF validation + metal-site detection + force-field metal parameter check. Returns GO or NO-GO with blocking issues. Treat NO-GO as a hard stop before any GPU/MD launch.

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": "md_preflight"
  }
}

Input Schema

Name	Required	Description	Default
`ff_dir`	No
`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

A3.8/5.0

Behavior3/5

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

With no annotations at all, the description carries the full disclosure burden. It usefully reveals the composite nature of the checks, the GO/NO-GO verdict, and the blocking-issue semantics, but says nothing about compute cost, whether it touches the filesystem beyond reading, or any side effects of a pre-flight run.

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?

Three tight sentences, front-loaded with the tool's role, followed by the return contract and the required action. Every clause carries information; nothing is redundant 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 return values need no elaboration, and the gate semantics are conveyed. But for a two-parameter tool with zero schema coverage, the absence of any explanation of ff_dir and of what a NO-GO blocks leaves a real gap in call correctness.

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% and the description does not name or explain either parameter. pdb_path is at least inferrable from "for a structure," but ff_dir is entirely opaque — its purpose (forcing a force-field directory) and the effect of its empty default are documented nowhere.

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?

States a specific verb+resource (an MD pre-flight gate for a structure) and enumerates the three checks it composes: PDB/mmCIF validation, metal-site detection, and force-field metal parameter check. This clearly differentiates it from siblings like validate_pdb and check_metal_params, which perform only one of those constituent steps.

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?

"Treat NO-GO as a hard stop before any GPU/MD launch" gives a clear usage context and prescribed reaction. However, it never explicitly contrasts itself with validate_pdb, metal_geometry, or check_metal_params, so the agent must infer that this tool supersedes those for a gate decision.

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