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h_fill

Add missing hydrogens to a molecular selection and correct atom valences for accurate structural modeling.

Instructions

Adds hydrogens and adjusts valences

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoall

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations provided, so description carries full burden. It states the action but does not disclose reversibility, required permissions, or side effects on existing hydrogens.

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?

Extremely concise, using a single sentence. However, it could be more informative without being verbose.

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 is a mutation operation with one parameter and an output schema, the description lacks details about which atoms are affected and the nature of valence adjustments. Sibling differentiation is missing.

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?

Input schema has one parameter 'selection' with no further description. Schema coverage is 0%, but the description does not explain how the selection affects the operation, adding no value beyond the parameter name.

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?

Description clearly states it adds hydrogens and adjusts valences, which is specific. However, it does not differentiate from sibling tool h_add, which likely has a similar purpose.

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 on when to use this tool versus alternatives like h_add. Usage is only implied, and no exclusions or prerequisites are mentioned.

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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