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h_fill

Fill open valences on the picked atom in PyMOL with hydrogens. Select an atom first, then call this tool to add missing hydrogen atoms.

Instructions

Fills open valences on the currently picked atom with hydrogens.

Takes no selection: cmd.h_fill operates on PyMOL's editor pick, so it needs an atom picked in the GUI and cannot be aimed from here. Passing it a selection used to land the string in its quiet argument and fail with an integer conversion error. For adding hydrogens to a selection over the bridge, use h_add.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

With no annotations, the description carries full responsibility for behavioral disclosure. It clearly states the tool operates on the editor pick rather than a selection and explains a common failure mode. However, it does not explicitly describe side effects (e.g., structure modification) or reversibility, though the operation is implied.

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 three concise sentences with no filler. The first sentence provides the core purpose, the second details usage constraints and a pitfall, and the third names the alternative tool. Every sentence earns its place.

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

Completeness5/5

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

The description fully explains the tool's unique requirement (editor pick), prerequisite (atom picked in GUI), a common error, and the alternative tool for selection-based additions. Since an output schema exists, return values need not be explained. This is complete for a simple utility.

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

Parameters5/5

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

The tool has zero parameters, and the schema is an empty object (100% coverage baseline is 4). The description adds valuable context by stating that it takes no selection and explaining that passing a selection would incorrectly land in the quiet argument and fail. This goes beyond the empty schema, earning a 5.

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 states the tool fills open valences on the currently picked atom with hydrogens, a specific verb+resource. It also explicitly distinguishes itself from the sibling h_add tool, which adds hydrogens to a selection.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly states when to use this tool (requires an atom picked in the GUI, takes no selection) and directs users to h_add for selection-based additions. It also warns about passing a selection causing a specific error, preventing misuse.

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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