# Foldnano Documentation

> Foldnano is a browser-based DNA nanostructure editor for designing DNA origami and staple routing structures.

Each link below is the page as plain markdown. Human-readable pages live at the same URL without `.md`.

## User Guide

- [Getting Started](https://fold.xinshilab.com/docs/guide/getting-started.md): Create your first DNA nanostructure in Foldnano and understand the editor workspace
- [Using The Docs With AI](https://fold.xinshilab.com/docs/guide/ai-assistants.md): Give ChatGPT, Claude, or a coding agent the Foldnano docs and ask it questions
- [Mental Model](https://fold.xinshilab.com/docs/guide/mental-model.md): Documents, Parts, DesignRegions, planes, virtual helices, oligos, segments, and ends
- [Creating A Design](https://fold.xinshilab.com/docs/guide/creating-a-design.md): New documents, regions, lattice/freeform virtual helices, routing, auto-staple, and scaffold setup
- [Editing Tools](https://fold.xinshilab.com/docs/guide/editing-tools.md): Draw, Break, Skip, Insert, Paint, Modification, Sequence, and Split Region tools in the strand viewer, with their panels
- [Views And Regions](https://fold.xinshilab.com/docs/guide/views.md): Plane, helix/freeform, strand, and 3D views, including multi-region workflows
- [Selection and Highlighting](https://fold.xinshilab.com/docs/guide/selection.md): End-based selection, lattice and freeform selection, selection filters, and highlight/hide controls
- [Duplicates And Repeat Groups](https://fold.xinshilab.com/docs/guide/duplicates-repeat-groups.md): Duplicate selected oligos, place linked mirror copies, and manage repeat groups
- [Simulation And Export](https://fold.xinshilab.com/docs/guide/simulation-export.md): Rigid-body simulation, NT model, inserts/skips, oxDNA, mrDNA, and file exports
- [3D Overlays](https://fold.xinshilab.com/docs/guide/3d-overlays.md): Load mrDNA results or PDB structures into the 3D view as movable reference overlays
- [Oligo Report And Diff](https://fold.xinshilab.com/docs/guide/oligo-report.md): Review every oligo of a design in a sortable table, download the CSV, and compare two saved designs
- [Saving And GitHub](https://fold.xinshilab.com/docs/guide/saving-github.md): IndexedDB, autosave, saved documents, GitHub connection, files, branches, staging, commits, conflicts, and backups
- [Plugins For Users](https://fold.xinshilab.com/docs/guide/plugins-for-users.md): Core plugins, Plugin Hub, manifest installs, ZIP installs, preview/apply strategies, and safety expectations
- [Script Lab](https://fold.xinshilab.com/docs/guide/script-lab.md): Write and run your own Python scripts against the open design, and apply their edits as one undoable step
- [Interface Reference](https://fold.xinshilab.com/docs/guide/interface-reference.md): Every toolbar button, menu, panel, and status indicator in the Foldnano editor, area by area
- [Keyboard Shortcuts](https://fold.xinshilab.com/docs/guide/keyboard-shortcuts.md): Complete keyboard shortcut reference for the Foldnano editor
- [Design Checks Reference](https://fold.xinshilab.com/docs/guide/design-checks.md): Every check Foldnano runs on import, while editing, and before simulation or cadnano export, and what to do about each
- [Wireframe Designs (Developer Preview)](https://fold.xinshilab.com/docs/guide/wireframe.md): Wireframe routing will be supported through plugins. What exists today, our current plan, what's still needed, and the early plugin API for developers

## Plugin Development

- [Plugin Quick Start](https://fold.xinshilab.com/docs/plugin-development/plugin-quickstart.md): Write and install your first Foldnano plugin in under five minutes
- [Runtime Model](https://fold.xinshilab.com/docs/plugin-development/runtime-model.md): How Foldnano loads, runs, scopes, and applies Python plugins
- [Formats and Apply Strategies](https://fold.xinshilab.com/docs/plugin-development/plugin-formats.md): Choosing between cadnano_json, foldnano_json, and foldnano_edit; apply strategy matrix
- [Plugin Manifest](https://fold.xinshilab.com/docs/plugin-development/plugin-manifest.md): Complete plugin manifest schema, wheel URL restrictions, side panel options, icons and code-editor execution modes
- [Context API Reference](https://fold.xinshilab.com/docs/plugin-development/context-api.md): Every name on PluginContext, the ctx argument of run(ctx), with what it reads or stores
- [Parse API Reference](https://fold.xinshilab.com/docs/plugin-development/plugin-api.md): The read-only view of a Foldnano JSON design in the foldnano package, with PartData and its oligo, segment, helix, region and plane proxies
- [foldnano.edit API Reference](https://fold.xinshilab.com/docs/plugin-development/foldnano-edit-api.md): Every public name in foldnano.edit, what it does, and whether it reads or changes the design
- [Plugin Patterns](https://fold.xinshilab.com/docs/plugin-development/plugin-patterns.md): Round-trip mutation, foldnano.edit mutable API, user-configurable parameters, and patterns by use case
- [Testing Plugins](https://fold.xinshilab.com/docs/plugin-development/plugin-testing.md): Offline unit testing for foldnano.edit plugins using CPython, pytest fixtures and the self-consistency replay check, and testing in the app with Plugin Dev Mode
- [Plugin Dev Mode](https://fold.xinshilab.com/docs/plugin-development/plugin-dev-mode.md): Link a plugin folder on your computer and run it in Foldnano as you edit it, without zipping or reinstalling
- [Agent Runs (Experimental)](https://fold.xinshilab.com/docs/plugin-development/agent-runs.md): Let a coding agent such as Claude Code or Codex run Python on your open design through a linked plugin folder, and what that does and does not protect
- [Wireframe Plugin APIs (Developer Preview)](https://fold.xinshilab.com/docs/plugin-development/wireframe-plugins.md): The early API for writing routing plugins for wireframe regions. Creating a region, the referenceGeometry shape, reading and storing a mesh, placing helices along edges, and example plugins

## Contributors

- [Contributor Overview](https://fold.xinshilab.com/docs/contributors/contributor-overview.md): How the contributor docs relate to the internal repo docs and where to start
- [Coming From Python](https://fold.xinshilab.com/docs/contributors/coming-from-python.md): JS/TS/Svelte concepts, Node install, and coding-agent setup for contributors with a Python background
- [Local Setup](https://fold.xinshilab.com/docs/contributors/local-setup.md): Install dependencies, run the app, and execute checks for Foldnano development
- [Architecture Overview](https://fold.xinshilab.com/docs/contributors/architecture.md): Source tree orientation, process layers, routes, editor contexts, and viewer responsibilities
- [Model, Commands, And History](https://fold.xinshilab.com/docs/contributors/model-commands-history.md): Mutation ownership, command transactions, topology identity, reactivity, and undo/redo invariants
- [Storage, Autosave, And GitHub](https://fold.xinshilab.com/docs/contributors/storage-github.md): IndexedDB working copies, tab ownership, autosave rules, GitHub proxy routes, and sync boundaries
- [Plugin Runtime Architecture](https://fold.xinshilab.com/docs/contributors/plugin-runtime.md): Plugin formats, apply strategies, Pyodide worker ownership, mutation logs, and host-side replay
- [Code Style And Testing](https://fold.xinshilab.com/docs/contributors/code-style-testing.md): Naming, type rules, comments, formatting, and test expectations for contributors
- [File Format (.fn.json)](https://fold.xinshilab.com/docs/contributors/file-format.md): The contract for Foldnano design files, field by field, with versioning rules and a JSON Schema

## Full Content

- [All documentation in one file](https://fold.xinshilab.com/llms-full.txt)
- [User Guide in one file](https://fold.xinshilab.com/docs/guide/llms.txt): Using the Foldnano editor
- [Plugin Development in one file](https://fold.xinshilab.com/docs/plugin-development/llms.txt): Writing Python plugins and Script Lab scripts
- [Contributors in one file](https://fold.xinshilab.com/docs/contributors/llms.txt): Working on the Foldnano codebase