Skip to main content
Glama

h_add

Add hydrogens to a molecular selection to prepare for hydrogen bonding analysis and realistic rendering.

Instructions

Adds hydrogens to a selection

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?

With no annotations, the description carries the full burden. It merely states the action without disclosing any behavioral traits such as whether the operation is destructive, reversible, or requires specific molecular structures. The brevity leaves ambiguity about side effects.

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

Conciseness3/5

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

The description is concise at one sentence, but it is underspecified. While every word earns its place, the lack of additional sentences to clarify usage or parameters reduces its effectiveness. It could be expanded without losing conciseness.

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 low complexity (one optional parameter) and presence of an output schema, the description should still explain the tool's effect on the scene (e.g., modifies in place) and what the output represents. It fails to provide this context, leaving the agent unsure of the tool's complete behavior.

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

Parameters2/5

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

Schema description coverage is 0%, and the description adds little value beyond the schema. It mentions 'selection' but does not explain the parameter's meaning, accepted values, or how to specify it (e.g., by ID, by expression).

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 'Adds' and the resource 'hydrogens', specifying the scope 'to a selection'. It distinguishes the tool from siblings like 'alter' or 'delete', though it doesn't explicitly contrast with similar tools like 'h_fill'.

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 (e.g., 'h_fill'). The description lacks any context about prerequisites or typical use cases, leaving the agent without direction on tool selection.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/chemrich/MCPymol'

If you have feedback or need assistance with the MCP directory API, please join our Discord server