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glebo309
by glebo309

chemdraw_edit_document

Create an edited copy of a ChemDraw document by modifying atoms, bonds, and captions, then export the before/after versions and chemical diff.

Instructions

Make an edited COPY of one molecule with native before/after exports and chemical diff. Analyze first: use editing atom/bond IDs and source_token. Atom op: {kind:atom,id,element:S,hydrogens:1}; element optional, H count required. Bond op: {kind:bond,id,order:2}. Captions must explicitly replace, retain or null-remove every page text ID. Supports neutral main-group atom/H changes and plain nonaromatic bond orders; no insertions/deletions, charged/isotopic target edits, radicals, stereocentre edits or new alkene stereo. Coordinates preserved, no cleanup. Existing source untouched; final mapped chemistry, labels and coordinates verified after ChemDraw export. Visual review required.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pixelsNo
captionsYes
operationsYes
output_dirYes
document_idYes
expected_source_tokenYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.9.0

TDQS

A4.5/5.0
Behavior5/5

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

Annotations only signal a non-read-only, non-destructive operation. The description adds material behavioral context: it operates on a copy, leaves the existing source untouched, preserves coordinates, performs no cleanup, verifies chemistry/labels/coordinates after export, and requires visual review.

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

Conciseness4/5

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

The description is dense but front-loaded with the core purpose and contains no filler. All sentences add necessary detail, though a slightly more structured layout would improve scannability.

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 tool with no output schema, it explains outputs (before/after exports, chemical diff), verification behavior, and operational constraints. It relies on 'Analyze first' and source token naming, but does not state how to obtain document_id/source_token or what the exact return payload is; still, it is largely complete for calling the tool.

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?

With 0% schema description coverage, the description carries the burden. It documents the operations object structure (atom/bond kinds, required fields like hydrogens and order) and the caption rule (explicit replace/retain/null-remove). It does not spell out document_id/output_dir/pixels, but those are inferable from 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?

States a specific verb ('Make an edited COPY'), resource ('one molecule'), and outputs ('native before/after exports and chemical diff'). The copy semantics and diff output clearly distinguish it from sibling editing tools, even without naming them.

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?

Gives an explicit prerequisite ('Analyze first') and enumerates supported vs unsupported operations ('Supports neutral main-group atom/H changes... no insertions/deletions...'), which tells an agent when to use this tool and when not. It does not name alternative tools, but the exclusions are actionable.

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