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glebo309
by glebo309

chemdraw_draw_structures

Convert 1–24 SMILES records into a native ChemDraw figure with aligned scaffolds, cleanup, and editable vector/PNG output in a new directory.

Instructions

Create a native ChemDraw figure from 1..24 explicit {compound_id,label,smiles} records. Labels are caller supplied, not verified names. Connected supported nonradical structures only. RDKit supplies MOL coordinate seeds; actual ChemDraw imports, runs native Clean Up Structure and renders. Optional scaffold_smiles explicitly selects a common core, rigidly aligned to the first native structure without reflection; poor fits fail, no inferred core. Checks identity after import/cleanup and measured grid after native save. New absolute output directory, editable/vector/PNG preview and audit. Final document stays open, originals untouched. No name lookup or yields. Review stereo and intramolecular collisions visually. Native uncertainty stops without retry/close.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
layoutNo
pixelsNo
presetNohouse
columnsNo
output_dirYes
structuresYes
charge_styleNoplain
scaffold_smilesNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.9.0

TDQS

A3.9/5.0
Behavior5/5

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

The description discloses many behavioral traits beyond the minimal annotations: RDKit coordinate seeding, native ChemDraw import and Clean Up Structure, identity checks after import/cleanup, grid measurement after native save, new absolute output directory, editable/vector/PNG preview and audit, final document staying open, originals untouched, and stopping without retry on native uncertainty. No contradiction with annotations exists.

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 every sentence contributes operational or constraint information. It is front-loaded with the primary purpose, followed by relevant processing details and caveats. While not brief, the length is justified by the complexity of the tool and there is no obvious filler.

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 complex tool with no output schema, the description covers the main workflow, constraints, output artifacts, failure behavior, and review caveats. It does not explicitly describe the return value or audit contents, but it provides enough operational detail for an agent to invoke the tool and interpret a successful result.

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?

With 0% schema description coverage, the description must carry parameter meaning. It clearly explains structures (explicit 1..24 compound_id,label,smiles records), scaffold_smiles (explicit common core, rigid alignment, no inference), and output_dir (new absolute output directory). However, layout, pixels, preset, columns, and charge_style are not described, leaving several parameters without semantic context beyond their names and defaults.

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 opens with a specific verb and resource: 'Create a native ChemDraw figure from 1..24 explicit {compound_id,label,smiles} records,' making the tool's core action clear. It does not explicitly contrast itself with siblings such as chemdraw_create_document or chemdraw_build_reaction, though the stated focus on explicit SMILES records implicitly differentiates it.

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 several situational constraints: connected nonradical structures only, no name lookup, no yields, and scaffold_smiles behavior. It does not explicitly say when to use this tool instead of a sibling or mention alternatives for name lookup or yields, so the usage guidance is implied rather than explicit.

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