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glebo309
by glebo309

chemdraw_build_reaction

Build a native ChemDraw reaction scheme from reactants, products, and conditions, outputting editable CDXML, SVG, PNG, and HTML files.

Instructions

Create a native reaction with explicit 1..3 reactant and 1..3 product records {compound_id,label,smiles,coefficient?}, single-line above/below conditions and measured spacing. The expanded path supports water, hydroxide, halide/alkali ions, bounded charge-balanced salts and explicit positive coefficients. Connected-only input may use explicit shared-core alignment; expanded input with scaffold alignment is rejected. Actual ChemDraw cleanup and native identity/layout checks; no reaction prediction or balance certificate. New absolute output directory, editable CDXML/SVG/PNG and HTML review. Originals untouched, native uncertainty stops without retry/close.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
layoutNo
pixelsNo
presetNohouse
productsYes
reactantsYes
output_dirYes
scaffold_smilesNo
conditions_aboveNo
conditions_belowNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.9.0

TDQS

A3.6/5.0
Behavior4/5

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

Annotations are minimal (readOnlyHint=false, destructiveHint=false), so the description carries the burden. It discloses that originals are untouched (consistent with destructiveHint=false), performs cleanup and checks, and stops without retry on native uncertainty. It does not mention permissions or error details, but covers key behavior.

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 a single dense paragraph that front-loads the main purpose and packs many details efficiently. It is not overly verbose, though it could be more structured with separate sentences for distinct aspects. It earns its place without much redundancy.

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

Completeness3/5

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

Given the tool's complexity (9 parameters, no output schema, no param descriptions), the description covers many aspects but misses specifics on layout, pixels, preset, and exact output delivery. It also does not clarify the 'expanded path' vs 'connected-only' input distinction fully. It is adequate but not comprehensive.

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 explains the structure of reactants/products and conditions, but leaves layout, pixels, preset, and scaffold_smiles semantics vague. For instance, 'pixels' and 'preset' are not described beyond defaults, and the expanded/connected-only distinction is not fully defined.

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 clearly states the tool creates a native reaction with explicit reactant/product records and conditions, and mentions constraints (1..3 each). It distinguishes from siblings like chemdraw_build_reaction_series by focusing on a single reaction, though it does not name alternatives explicitly.

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 provides guidance on input types (expanded vs connected-only) and what it does not do (reaction prediction). However, it does not explicitly compare with sibling tools or state when to prefer this over others, leaving some usage decisions to inference.

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