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Analyze a prepared protein structure to detect and score potential ligand-binding sites. Returns a job ID; results include site maps and scores in output files.

Instructions

Detect and score potential ligand-binding sites on a protein with SiteMap. Accepts a prepared protein structure (.mae). Long-running — returns a job_id; site maps and SiteScore/Dscore are written to _out.maegz and per-site files.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
input_pathYes
num_sitesNo
jobnameNositemap
Behavior4/5

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

With no annotations, the description carries full burden for behavioral disclosure. It clearly states the tool is long-running, returns a job_id, and writes output files (site maps, SiteScore/Dscore). This adds significant value beyond the basic schema.

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?

Two sentences, no filler. The first sentence states purpose, the second provides key usage context. Every word earns its place.

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

Completeness3/5

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

The tool has 3 parameters, no output schema, and no annotations. The description covers input format, async nature, and output files, but neglects parameter details. Given the complexity, it is minimally complete but has clear gaps.

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 coverage is 0%, so the description must elaborate on parameters. It only indirectly mentions that 'input_path' is a prepared structure, but fails to explain 'num_sites' or 'jobname'. This leaves gaps for effective tool invocation.

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 tool detects and scores potential ligand-binding sites using SiteMap, a specific verb+resource. It distinguishes from siblings by specifying a unique function, but does not explicitly contrast with similar tools like 'analyze_interactions' or 'glide_dock'.

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?

The description provides context on input requirements (prepared .mae structure) and behavior (long-running, returns job_id). However, it lacks explicit guidance on when not to use this tool or mention of alternative tools for similar tasks.

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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