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vmd-hydrate-mcp

vmd-hydrate-mcp

by wjgoarxiv
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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resolve_selection

Check how many atoms match an MDAnalysis selection to avoid zero-atom errors in .gro files before running measurements.

Instructions

Report how many atoms an MDAnalysis selection matches — use this to catch the common 0-atom trap on bare .gro files before running measurements.

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": {
      "path": "<path>",
      "selection": "<selection>"
    },
    "name": "resolve_selection"
  }
}

Input Schema

NameRequiredDescriptionDefault
pathYes
topologyNo
selectionYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.0

TDQS

B3.4/5.0
Behavior3/5

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

With no annotations, the description carries full burden. It discloses the tool returns a count and warns about the 0-atom outcome, but does not mention read-only behavior, error handling, or parameter constraints beyond the schema. Adds some context but not comprehensive.

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 a single, front-loaded sentence that efficiently conveys purpose and a key use case. It is concise and well-structured, though it sacrifices parameter details.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's complexity (3 parameters, no output schema, no annotations), the description is incomplete. It lacks parameter descriptions, return format, error cases, and does not address the 'topology' parameter or edge conditions.

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%, so the description must compensate. It only explains the 'selection' parameter via the MDAnalysis context, while 'path' and 'topology' are left undefined. This is insufficient for a 3-parameter tool.

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?

The description clearly states the tool reports the count of atoms matched by an MDAnalysis selection, with a specific verb and resource. It distinguishes from siblings by focusing on selection validation.

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 description gives a concrete use case (catching the 0-atom trap before measurements) but does not explicitly state when not to use it or suggest alternative sibling tools. The guidance is implied but lacks explicit exclusions.

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

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