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vmd-hydrate-mcp

vmd-hydrate-mcp

by wjgoarxiv
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

clear_representations

Clear all representations of a molecule to start with a fresh view. Resets the visualization for a clean slate.

Instructions

Remove all representations from a molecule (start a fresh view).

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": {
      "molid": "<molid>"
    },
    "name": "clear_representations"
  }
}

Input Schema

NameRequiredDescriptionDefault
molidYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.0

TDQS

A3.5/5.0
Behavior3/5

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

Description states it removes all representations, which is the key behavior. No annotations exist, so no contradiction. However, it does not mention side effects (e.g., does it reset view properties?) or return value. Adequate but not rich.

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?

Single sentence, no wasted words, front-loaded with action and scope.

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?

For a simple tool with 1 param and no output schema, the description covers the main purpose. It could mention that it doesn't affect other data or require prerequisites, but it is largely 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 coverage is 0%, so description must add meaning. It mentions 'from a molecule' but does not explicitly explain that 'molid' is the molecule ID. Parameter semantics are only implied.

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 verb 'Remove' and resource 'representations from a molecule' are specific. The parenthetical 'start a fresh view' adds context. Clearly distinguishes from sibling tools like add_representation and set_representation.

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 explicit guidance on when to use vs alternatives. The phrase 'start a fresh view' implies a use case, but there is no direct comparison to siblings or exclusion criteria.

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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