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generate_2d_report

Generate a 2D report of structures from a file, each drawn with labeled properties like docking scores. Share screening results as PDF or HTML.

Instructions

Build a 2D structure report (PDF or HTML) of every structure in a file, each drawn in 2D and labeled with properties (e.g. docking scores from a pose-viewer). Great for sharing docking/screening results. properties is 'all' or a comma-separated list of property names. Returns the path to the report.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
input_pathYes
propertiesNoall
output_formatNopdf
output_pathNo
Behavior3/5

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

No annotations provided, so the description must disclose behavior. It explains the properties parameter format, output format options, and that it returns a file path. However, it omits side effects (e.g., whether it modifies input), permissions, or error conditions, leaving gaps.

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 sentences, front-loaded with the core purpose, and contains no fluff. Every sentence adds essential information.

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?

Given the complexity (4 parameters, no enums, no output schema), the description covers input, parameters, and return value. It distinguishes from siblings by noting 'every structure in a file.' It lacks details on supported file types or error handling but is mostly complete for typical use.

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

Parameters4/5

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

Schema description coverage is 0%, so the description compensates well by explaining the 'properties' format ('all' or comma-separated), implying output_format options (PDF/HTML from context), and that output_path is the report location. It adds meaning beyond the bare schema.

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 tool builds a 2D structure report for all structures in a file, with labeled properties (e.g., docking scores). It mentions PDF or HTML output, distinguishing it from sibling tools like render_2d_structure that likely handle single structures.

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?

It states the tool is 'Great for sharing docking/screening results,' implying suitable use cases but does not explicitly exclude alternatives or provide when-not-to-use guidance, despite siblings like summarize_docking and render_2d_structure existing.

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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