chemdraw-mcp

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batch_generate

Draw multiple compounds at once as separate PNG/SVG/CDXML files and panels from names or SMILES, returning successful structures and reporting failed names.

Instructions

Draw several individual compounds as separate PNG/SVG files and panels.

Failed names are reported in failed while successful structures are returned. Pass English or IUPAC names, or SMILES.

Not this tool for: one compound (use generate_molecule), structural differences (use compare_molecules), or a reaction scheme (use generate_reaction).

Args: molecules: List of English/IUPAC compound names or SMILES strings. formats: Output file formats, any of "png", "svg", "cdxml" (default: ["png", "svg"]). Include "cdxml" ONLY when the user wants to edit the structures in ChemDraw. abbreviate_groups: Set True to draw common substituents as short labels (Ph, Bn, OAc, OMe, CO2H, tBu, Boc, Ts …) instead of full skeletons. Applies to every molecule in the batch, so a series of structures stays visually consistent. render_style: Named look applied to every molecule in the batch. Empty = standard style. "compact" for small printed figures, "presentation" for slides, "grayscale" for grayscale printing.

Input Schema

Name	Required	Description	Default
`formats`	No
`molecules`	Yes
`render_style`	No
`annotate_stereo`	No
`abbreviate_groups`	No

Output Schema

Name	Required	Default
`type`	No	batch
`failed`	No
`molecules`	No
`cdxml_paths`	No

Schema Changelog

Changes observed during successful MCP inspections.

Changed12 schema fields changedv0.6.0Oct 26, 2026

addedOutput schema / $defs / IsomerCandidate

Added value: +{
+  "description": "One structure a family name (\"xylene\", \"Glucose\") can mean.",
+  "properties": {
+    "label": {
+      "title": "Label",
+      "type": "string"
+    },
+    "name": {
+      "default": "",
+      "title": "Name",
+      "type": "string"
+    },
+    "smiles": {
+      "title": "Smiles",
+      "type": "string"
+    },
+    "svg": {
+      "default": "",
+      "title": "Svg",
+      "type": "string"
+    }
+  },
+  "required": [
+    "label",
+    "smiles"
+  ],
+  "title": "IsomerCandidate",
+  "type": "object"
+}

addedOutput schema / $defs / MoleculePayload / properties / candidates

Added value: +{
+  "default": [],
+  "items": {
+    "$ref": "#/$defs/IsomerCandidate"
+  },
+  "title": "Candidates",
+  "type": "array"
+}

addedOutput schema / $defs / MoleculePayload / properties / initialView

Added value: +{
+  "default": "",
+  "title": "Initialview",
+  "type": "string"
+}

addedOutput schema / $defs / MoleculePayload / properties / message

Added value: +{
+  "default": "",
+  "title": "Message",
+  "type": "string"
+}

addedOutput schema / $defs / MoleculePayload / properties / projectionNote

Added value: +{
+  "default": "",
+  "title": "Projectionnote",
+  "type": "string"
+}

addedOutput schema / $defs / MoleculePayload / properties / stereoNote

Added value: +{
+  "default": "",
+  "title": "Stereonote",
+  "type": "string"
+}

addedOutput schema / $defs / MoleculePayload / properties / stereoWarnings

Added value: +{
+  "default": [],
+  "items": {
+    "$ref": "#/$defs/StereoWarning"
+  },
+  "title": "Stereowarnings",
+  "type": "array"
+}

addedOutput schema / $defs / MoleculePayload / properties / viewAtoms

Added value: +{
+  "default": [],
+  "items": {
+    "$ref": "#/$defs/AtomData"
+  },
+  "title": "Viewatoms",
+  "type": "array"
+}

addedOutput schema / $defs / MoleculePayload / properties / viewRequest

Added value: +{
+  "additionalProperties": true,
+  "default": {},
+  "title": "Viewrequest",
+  "type": "object"
+}

addedOutput schema / $defs / MoleculePayload / properties / viewSvg

Added value: +{
+  "default": "",
+  "title": "Viewsvg",
+  "type": "string"
+}

addedOutput schema / $defs / MoleculePayload / properties / views

Added value: +{
+  "default": [],
+  "items": {
+    "type": "string"
+  },
+  "title": "Views",
+  "type": "array"
+}

addedOutput schema / $defs / StereoWarning

Added value: +{
+  "description": "Ein Stereoelement, dessen Konfiguration die Eingabe offen lässt.",
+  "properties": {
+    "atoms": {
+      "default": [],
+      "items": {
+        "type": "integer"
+      },
+      "title": "Atoms",
+      "type": "array"
+    },
+    "kind": {
+      "title": "Kind",
+      "type": "string"
+    },
+    "label": {
+      "default": "",
+      "title": "Label",
+      "type": "string"
+    }
+  },
+  "required": [
+    "kind"
+  ],
+  "title": "StereoWarning",
+  "type": "object"
+}

First observedv0.1.0Oct 26, 2026

TDQS

A4.8/5.0

Behavior4/5

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

Since no annotations are provided, the description carries the full burden and performs well. It explicitly details a key behavioral trait: failed names are reported while successful structures are returned. It also explains the conditional use of 'cdxml' for ChemDraw editing.

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

Conciseness5/5

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

The tool definition is structured logically, starting with the core function, then providing limitations, and finally detailing parameters. Every section is tightly written and efficiently organized.

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?

Given the complexity of handling batch processing, multiple formats, and custom rendering, the description is remarkably complete. It provides all the necessary context and constraints for an agent to invoke the tool correctly despite the sparse structured data.

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

Parameters5/5

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

Despite having 0% schema description coverage, the description provides high-value semantic context for every parameter. For instance, it explains the functional difference between 'abbreviate_groups' (consistency) and 'render_style' (use case for printing/slides), adding meaning far beyond the schema data.

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 purpose is highly specific: drawing multiple individual compounds as PNG/SVG files and panels. It clearly distinguishes itself from sibling tools by stating it is not suitable for single compounds (use generate_molecule), reaction schemes, or structural comparisons.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The tool explicitly forbids certain use cases, detailing that it should not be used for single molecules, structural differences, or reaction schemes. It provides direct redirection to the correct alternative sibling tool for each specific scenario.

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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