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fetch_pdb

Download an experimental protein structure from RCSB PDB using its 4-character ID. Returns the file path for subsequent preparation in docking workflows.

Instructions

Download an experimental structure from the RCSB PDB by its 4-character ID (e.g. '1HSG'). Returns the path to the downloaded .pdb file. Use protein_prepwizard afterward to prepare it for docking.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes
output_dirNo
Behavior3/5

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 states the download source and return value but does not disclose potential side effects like file overwriting or internet dependency. It is adequate but not comprehensive.

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. Every sentence provides essential information: what the tool does, an example, the return type, and a recommended next step.

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?

For a simple download tool, the description covers the core functionality and next steps. It lacks details on error handling or output behavior, but given the low complexity, it is reasonably complete.

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 tool description does not explicitly explain the parameters. The pdb_id parameter is clear from the example, but output_dir is only hinted at by its name and default value. The description adds minimal value beyond the parameter names.

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 specifies the action: download an experimental structure from RCSB PDB by its 4-character ID. It provides an example ('1HSG') and distinguishes the tool from siblings by mentioning the next step (use protein_prepwizard).

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

Usage Guidelines4/5

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

The description gives clear context by suggesting to use protein_prepwizard afterward, implying a workflow. However, it does not explicitly exclude alternatives or state when not to use the tool.

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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