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wjgoarxiv

vmd-hydrate-mcp

by wjgoarxiv

hbond_network

Build the water-water hydrogen-bond network from a trajectory frame, reporting bond count and average coordination to identify clathrate-hydrate cages.

Instructions

Build the water-water hydrogen-bond network for a frame and report bond count and average coordination (the substrate for cage identification). rcut is the O-O cutoff (nm), theta the H-O...O angle cutoff (degrees).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pathYes
rcutNo
frameNo
thetaNo
topologyNo
Behavior3/5

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

No annotations provided, so the description carries the full burden. It describes what it computes, but does not disclose return format, side effects, or authentication needs. Some transparency about output (bond count, average coordination) but incomplete.

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 sentences, concise and front-loaded with main purpose. Every sentence adds value. No wasted words.

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?

Given 5 parameters, no output schema, and no annotations, the description is brief. It omits details on path, frame, topology, and return format. Adequate for basic understanding but incomplete for full usage.

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 description coverage is 0%, so description adds meaning for rcut and theta (cutoffs). However, path, frame, and topology are not explained. Helpful but incomplete for a 5-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 builds the water-water hydrogen-bond network for a frame and reports bond count and average coordination. It uses specific verbs and resources, and distinguishes from sibling tools like 'identify_cages' which uses this as input.

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 implies usage as a prerequisite for cage identification, but does not explicitly state when to use it vs alternatives or provide usage context. There is no 'when not to use' guidance.

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

Install Server

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