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Alierkn
by Alierkn

hbond

Calculate hydrogen bonds between two groups from a trajectory and topology file.

Instructions

Calculate hydrogen bonds with gmx hbond.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
tprYes
outputNohbond.xvg
group_aNoProtein
group_bNoWater
workdirYes
extra_argsNo
trajectoryYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior2/5

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

Annotations are present (readOnlyHint=false, openWorldHint=true) but the description adds no behavioral context beyond 'calculate'. It does not mention file outputs, potential side effects, or required permissions, leaving the agent without critical operational details.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness2/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single short sentence, but it is under-specified for a tool with 7 parameters. It lacks structure or front-loaded key info, resulting in poor conciseness for the tool's complexity.

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

Completeness1/5

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

Given the tool's complexity (7 parameters, no schema descriptions, output schema exists but not referenced) and zero guidance on return values, the description is severely incomplete. It fails to equip an agent with sufficient context for correct invocation.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters1/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, and the description provides no parameter meaning. Essential parameters like trajectory, tpr, group_a, group_b, extra_args are completely unexplained, forcing the agent to infer from parameter names alone.

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?

The description clearly states the verb 'calculate' and the resource 'hydrogen bonds', making the primary purpose clear. The tool name 'hbond' also aligns well. However, it does not differentiate from similar analysis tools among siblings, but the specificity of 'hydrogen bonds' is distinct enough.

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 guidance is provided on when to use this tool versus alternatives. There are no prerequisites, exclusions, or context hints for effective selection.

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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