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hbond_network

Build water hydrogen-bond networks and report coordination statistics, enabling assessment of clathrate-hydrate cage quality via tetrahedral H-bond counts.

Instructions

Build the water hydrogen-bond network and report coordination statistics.

A well-formed clathrate framework has ~4 H-bonds per water (tetrahedral).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
boxNoPeriodic box in nm (3/6/9 values). If omitted, read from get_symmetry.
rcut_nmNoO-O distance cutoff in nm.
angle_degNoDonor H-O...O angle cutoff in degrees.
selectionNoSelection of the water system.all
object_nameNoObject whose box to use.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior2/5

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

No annotations are provided, so the description carries the full burden. It does not disclose whether the tool is read-only, whether it creates or modifies session objects, or what the exact output shape is. The word 'Build' is ambiguous—it could mean constructing a network object or merely computing statistics.

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?

The description is two sentences with no fluff. The first sentence states the primary purpose, and the second provides an interpretative benchmark (~4 H-bonds per water), which is useful and earns its place.

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?

With a fully detailed input schema and an output schema present, the description is mostly sufficient. It lacks explicit note about water-system requirements or side effects of 'build,' but the core functionality is captured. The clathrate reference adds domain context, making it adequate for the intended use case.

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?

The schema covers all 5 parameters with detailed descriptions (100% coverage), so the baseline is 3. The description adds no parameter-specific information; it does not clarify relationships between parameters, typical ranges, or how they affect results beyond what the schema already states.

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 identifies the tool's action ('Build') and resource ('water hydrogen-bond network'), and specifies that it 'report[s] coordination statistics.' This distinguishes it from siblings like measure_distance or identify_cages, which focus on different structural analyses.

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?

Usage context is implied by 'water hydrogen-bond network' and the tetrahedral heuristic, but there is no explicit statement of when to use this tool vs. alternatives, nor any comparison with sibling tools. The description does not mention exclusions or prerequisites.

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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