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Polish Reaction Scheme

polish_reaction_scheme

Refine and standardize CDXML reaction schemes with deterministic polishing, including alignment, condition merging, and preview rendering for publication-ready output.

Instructions

Run the audited deterministic polishing pipeline on a CDXML scheme.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
eln_csvNo
approachNochemdraw_mimic
align_modeNordkit
input_pathYes
output_pathNo
render_previewNo
reference_cdxmlNo
merge_conditionsNo
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It adds the terms 'audited' and 'deterministic', hinting at reproducibility and review, but does not explain side effects, whether files are modified in place, or what the pipeline actually does to the scheme. This is insufficient for a mutation-like tool.

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 a single sentence with no waste, which is concise. However, it is under-specified for the tool's complexity, providing only a minimal phrase that does not earn its place by adding needed information. It is better than a pure tautology but still lacks substance.

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

Completeness1/5

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

With 8 parameters, no annotations, and no output schema, this description is drastically incomplete. It fails to explain what 'polishing' entails, how inputs/outputs are specified, or what the pipeline returns. An agent would have to guess at most aspects of usage.

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

Parameters1/5

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

Schema description coverage is 0% and the description mentions no parameters at all. It does not clarify input_path, output_path, approach, align_mode, or any other of the 8 parameters. The description offers zero help in understanding how to invoke the tool with correct arguments.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose3/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a verb ('run') and a resource ('polishing pipeline on a CDXML scheme'), but 'polishing' is vague and undefined. It does not distinguish the tool from siblings like clean_scheme_layout or merge_reaction_schemes, leaving an agent unsure what specific transformation is performed.

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 given about when to use this tool versus alternatives. The phrase 'audited deterministic polishing pipeline' implies some context but does not specify conditions, prerequisites, or exclusions, so an agent cannot route to it correctly.

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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