Skip to main content
Glama
glebo309
by glebo309

chemdraw_annotate_document

Add native electron-flow curves (full or fishhook) to a ChemDraw document copy, preserving the source file. Outputs before/after CDXML, SVG, and PNG for visual review.

Instructions

Add native full or fishhook electron-flow curves to a NEW copy. Inspect annotations first. Each arrow has unique key, electrons 2 or 1, source {kind:symbol,id} for a displayed CircleMinus/LonePair (2 electrons) or Electron dot (1 electron), OR source {kind:bond,id,offset:[dx,dy]} for a donating bond. Atom-label sources and positive-charge donors are rejected; add a symbol first if needed. Target {kind:atom|bond,id,offset:[dx,dy]}; controls:[[dx1,dy1],[dx2,dy2]] relative to start/end; optional fishhook_side left/right only for one electron. Symbol targets rejected. A negative charge may represent a donating lone pair, but this is caller-supplied chemical intent, not inferred for every anion. Existing molecules/symbols retained; no chemical/radical-state edits. New absolute output directory, native CDXML/SVG/PNG before/after, recipe and audit. Source untouched. Visual review required; no whole-path collision or native moving attachment promise. Native errors not retried.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
arrowsYes
pixelsNo
line_widthNo
output_dirYes
document_idYes
expected_source_tokenYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.9.0

TDQS

A4.4/5.0
Behavior5/5

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

Annotations only say readOnlyHint=false and destructiveHint=false, so the description carries the behavioral disclosure burden. It does so thoroughly: source document is untouched, a new copy is created, existing molecules/symbols are retained, native errors are not retried, visual review is required, and no collision-free or native moving-attachment guarantee is promised. This goes well beyond the annotations.

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 and front-loaded with the core purpose, followed by essential mechanics and caveats. It is long, and some parts could be clearer as structured bullets, but every sentence carries useful information and there is no filler. For a tool with six parameters and complex arrow semantics, this length is justified.

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

Completeness5/5

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

This is a complex tool with no output schema, yet the description adequately covers inputs, arrow construction rules, rejection cases, outputs (CDXML/SVG/PNG before/after, recipe, audit), safety behavior, and required follow-up review. The only notable gap is expected_source_token semantics, but overall an agent has enough to select and invoke the tool correctly.

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

Parameters3/5

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

Schema description coverage is 0%, so the description must compensate. It richly explains the arrows parameter structure, including source kinds, target kinds, offsets, controls, fishhook_side, and chemical-intent caveats. However, it does not explain expected_source_token at all, and pixels and line_width are entirely unmentioned. The description covers the hardest parameter well but leaves other parameters underexplained.

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 opens with a specific verb and resource: 'Add native full or fishhook electron-flow curves to a NEW copy.' This clearly distinguishes the tool from siblings like chemdraw_edit_document, chemdraw_add_symbols, or chemdraw_draw_structures by specifying the operation, the artifact being modified, and the non-destructive copy behavior.

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 provides clear usage context: inspect annotations first, add a symbol before annotating if needed, use atom/bond sources but not atom-label or positive-charge donors, and expect visual review afterward. It does not explicitly name alternative sibling tools or state when not to use it, but the preconditions and limitations are strong enough for an agent to decide when this tool applies.

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