Package Map

Package Map

This page maps every immediate package, app and tool directory to its responsibility and boundaries.

The workspace globs in pnpm-workspace.yaml include apps/*, packages/* and examples/plugins/*. The tools/ directories are repository tooling, not additional application workspaces. Directory presence alone does not mean a subsystem is a production implementation: some packages deliberately contain only types or scaffolding.

The ownership rules below follow AGENTS.md section 6, package READMEs and current entry points. A “must not” entry is a boundary to preserve when adding code, not a claim that a package has performed that forbidden action.

Shared packages

Paths in this table are relative to packages/.

Package	Owns	Must not
analysis-core	Pure analysis contracts: interpretations, classification flags, methods, results and provenance	Import engines, derive chemistry or branch on derivation/claim instead of flags
art-engine	Graphic plans, strokes, markers, arrow geometry and boolean operations	Own documents, change molecules or copy molecule rendering math
cdx-compat	CDXML read/write, best-effort CDX read and unknown-object preservation	Become the native model, depend on GPL code or promise perfect compatibility
chem-core	Native types, Zod schemas, pages, styles, validation, patches, serialization and migrations	Import UI, Tauri, filesystem, concrete engines or plugin loading
chemdraft-cli	Headless command modules, validated input and JSON Lines output	Import apps/, mix progress with stdout results or silently change chemistry
chemdraft-mcp	Local stdio MCP server calling CLI modules in-process	Create a second document implementation or bypass CLI validation and warning contracts
chemistry-adapter	Engine-neutral chemistry and conformer interfaces	Expose concrete engine internals, mutate documents or own UI state
clipboard-adapter	Format detection and conversion with compatibility warnings	Hide lossy conversions or own desktop native clipboard APIs
document-workflow-core	Pure native builders, label expansion, validation bookkeeping and SMILES writing shared by app and agents	Import React, Tauri, DOM, apps/, plugin runtime or engine loaders
editor-adapter	Abstract editor sessions and capability-gap reporting	Own the native document or implement a concrete editor
editor-shell	Reserved editor-shell types and coordination scaffold	Grow speculatively or become the native document owner
engine3d-api	Versioned app-to-sidecar protocol types and guards	Add native dependencies or change protocol shape without a version bump
export-engine	SVG, PDF and other export orchestration with warnings	Diverge from canvas geometry or claim an unimplemented format is complete
fixtures	Shared chemistry, compatibility and regression inputs	Supply production behavior or include assets without redistribution rights
isospec-adapter	Unpatched vendored IsoSpec WebAssembly, checked boundaries and binary-table lookups	Patch IsoSpec, retype abundance tables, skip array-length checks or build final envelope results
ketcher-adapter	Injected editor wrapper and supported molecule-session load/save	Expose editor internals, pretend to support page objects or own document state
layout-engine	Molecule geometry, labels, strokes, depth cues, valence/order resolution, growth and arrangement plans	Change chemical identity or leave copied rendering math in callers
mechanism-tools	Shared mechanism-annotation types	Treat editable annotations as opaque SVG; assume this types package contains the working desktop tool implementation
ocl-adapter	OpenChemLib depiction, stereochemistry and conformers behind the chemistry contract	Leak engine internals or collapse an unrepresentable bond order to single
plugin-api	Public manifests, permissions, capability contexts and contribution types	Contain app implementation or document mutation logic
plugin-host	Validation, shared commands, permission enforcement, storage, lifecycle and patch review	Grant undeclared access or run native code/download models without required permission and user action
rdkit-adapter	RDKit analysis, isotope-envelope result construction and ETKDGv3 conformers on the custom MinimalLib build	Load heavy resources at startup without need or substitute an unreviewed RDKit build
shortcut-engine	Command-bound shortcuts, conflicts and platform modifier handling	Hide important actions in click handlers
style-compat	.cds metadata conversion into native style presets	Parse style files in UI, change chemistry or claim partial imports are complete
template-library	Original fragments, abbreviation definitions and template data	Copy proprietary templates or commit user style-sheet files
test-utils	Generic testing helpers	Ship production behavior or bury chemistry assertions in unrelated helpers
toolset-registry	Toolbar/toolset schemas, layout overrides, menu models and command-ID validation	Own chemistry, permissions, native windows or document mutation
ui-kit	Reserved original UI components, theme tokens and icons	Grow speculatively, contain chemistry logic or copy proprietary artwork
viewport-engine	Coordinates, zoom, pan and ruler math	Render UI or mutate documents

rdkit-adapter depends on isospec-adapter, never the reverse. The envelope builder belongs to the former. IsoSpec's carbon-13 abundance convention must be disclosed wherever a derived number is shown; Analysis and Properties explains result conventions.

App and repository tools

These are complete immediate directory inventories under apps/ and tools/ for this checkout.

Path	Owns	Boundary
apps/desktop	React desktop orchestration, Tauri native integration, windows and platform adapters	Consume shared chemistry and geometry; do not create parallel implementations for agent tools
tools/agent-skill	Agent-skill/CLI/MCP consistency and styled-document regression tests	Keep automation documentation aligned with implemented capabilities
tools/cdxml-corpus	CDXML compatibility corpus checks	Assert fixture-backed behavior, not universal format compatibility
tools/codex-prompts	Historical implementation-task prompts	Do not treat an old prompt as current feature status or policy
tools/plugin-extract	Plugin extraction, import-boundary checks, licence gates and ZIP checks	Fail closed on invalid packages or missing data-licence declarations
tools/plugin-package	Packaging and committed-copy helpers	Preserve validated package boundaries rather than bypassing extraction gates
tools/rdkit-oracle	Independent Python RDKit test oracle and chemistry/flattening checks	Remain test tooling, not a production engine dependency
tools/release	Windows update manifest generation, signature verification and release tests	Do not fabricate signatures or publish feeds ahead of reachable assets
tools/structure-to-name-benchmark	Naming benchmarks, read-back checks and comparison scripts	Do not equate a generated name with a verified structural match

tools/bug-audit.test.ts is a standalone test at the tool root, not another package. Native 3D source lives separately in native/avogadro3d-sidecar; build and audit scripts live in scripts/.

Examples and SDK boundaries

The two SDK packages, plugin-api and plugin-host, are MIT-licensed. A plugin itself imports only @chemdraft/plugin-api among ChemDraft packages. Host internals are not a plugin API.

examples/plugins/mass-fragment-demo is the working example and intentionally contains no NMR functionality. advanced-style-pack and journal-style-pack are README-only placeholders. The official NMR and recognition plugins live in separate repositories; do not look for their implementations in the example folders.

See also

• Architecture Overview
• Document Model
• Writing a Plugin
• Licensing and Notices