Burrete

A macOS molecular file workspace with Finder Quick Look previews, Mol* 3D, external xyzrender SVG rendering, RDKit molecule grids, and Ketcher sketching.

What Is Burrete?

Burrete is a macOS desktop app and Finder Quick Look extension for molecular structure files. It is built for the small daily loop of computational chemistry, structural biology, and cheminformatics work: open a structure, confirm what it is, switch renderer when needed, compare files in tabs, and recover quickly when Quick Look or renderer caches need maintenance.

Use it in two ways:

• Finder previews: select a molecular file in Finder and press Space.
• Desktop workspace: open Burrete directly to inspect files in tabs, browse project folders, search commands and structures, sketch molecules, review collections, and send files to external chemistry tools.

Burrete is intentionally a compact utility, not a full molecular modeling environment.

Download

You can install Burrete with the Homebrew tap:

brew tap SergeiNikolenko/burrete
brew install --cask burrete

Check the cask version when you need to confirm a specific release:

brew info --cask SergeiNikolenko/burrete/burrete

For the latest stable GitHub release, use the Burrete Bun CLI:

bunx burrete latest
bunx burrete install
bunx burrete doctor

The Bun installer places Burrete in ~/Applications by default. Use bunx burrete install --system only when you intentionally want the app in /Applications for all users. If Finder previews do not appear after install, run bunx burrete doctor to check the app bundle, Quick Look extension, qlmanage, and installed version.

You can also download Burrete from the GitHub Releases page:

Download the latest Burrete release

1. Open the latest release.
2. Download the Burrete-<version>.zip file.
3. Unzip it.
4. Move Burrete.app to your Applications folder.
5. Open Burrete once from Applications.

Quick Start

After installation:

1. Open Burrete.app once so macOS registers the app and Quick Look extension.
2. In Finder, select a supported molecular file and press Space.
3. Open Burrete directly for the full workspace:
   • Cmd+O opens molecular structure files.
   • Cmd+P or / opens the command palette.
   • Cmd+, opens settings.
   • The sidebar browses project folders, nested structures, and recent files.
4. If previews do not appear, run:

bunx burrete doctor

Supported Files

Burrete supports several preview paths. Some formats open directly in Mol*, some use the RDKit grid runtime, and some require the external xyzrender renderer.

Path	Formats	Notes
Mol* interactive 3D	PDB, ENT, PDBQT, PQR, CIF, MMCIF, MCIF, BCIF, SDF, SD, MOL, MOL2, XYZ, GRO	Default path for most structure files. XYZ can also use xyzrender.
RDKit molecule grids	SDF, SD, SMILES, SMI, CSV, TSV	Collection view with search, sorting, SMARTS filtering/highlighting, selection, append/merge, and export.
External xyzrender	XYZ, CUB, CUBE, ABI, COM, FDF, IN, INP, LOG, NW, OUT, PSI4, QCIN, VASP, MAE, MAE.GZ, MAEGZ, CMS	Requires a local xyzrender executable. Used by default for single-frame XYZ and required for external-renderer-only formats.
Molecular dynamics / topology	XTC, TRR, DCD, NCTRAJ, LAMMPSTRJ, TOP, PSF, PRMTOP	Registered as molecular files and routed to Mol* where supported by the runtime.
OpenMM coordinate artifacts	XML, INPCRD, RST7, CRD, RST, STATE	Render as structures when standalone coordinates are present, with the raw text available in the document surfaces. System XML without positions falls back to text.
OpenMM workflow artifacts	PAR, PRM, RTF, STR, KEY, CHK, CHECKPOINT	Open as text/workflow artifacts. Binary checkpoints show metadata because OpenMM checkpoint payloads are tied to the matching system, platform, version, and hardware context.
FEP network workspace	GraphML	Opens a ligand network preview workspace rather than a standard molecule preview.

Multi-frame XYZ files stay in Mol* when Burrete detects trajectory content so the native trajectory controls can show the available frames. When you rotate a molecule in Mol* and switch to xyzrender, Burrete can pass the current orientation through the renderer handoff. CUBE, CIF, MMCIF, MCIF, XYZ, and external-renderer input previews expose an optional VESTA handoff when VESTA is installed.

Desktop Workspace

Opening Burrete directly gives you a compact molecular workspace:

• tabbed previews that keep renderer state alive while you switch files
• a project sidebar for folders, nested structures, recent files, and search
• a command palette for opening files, switching renderers, maintenance actions, exports, project navigation, Ketcher, and FEP network previews
• right and bottom docks for comparing structures, text files, Ketcher, grids, and workflow panels
• "Open In" actions for Finder, the default app, or discovered chemistry editors
• text-file viewing for logs, scripts, configs, and related project files

Molecule Collections and Ketcher

Burrete includes an RDKit-powered collection grid for SDF, SMILES, CSV, and TSV files. The grid supports search, sorting, SMARTS filtering/highlighting, selection, infinite loading, append/merge workflows, and export.

The desktop app also includes a Ketcher small-molecule editor. You can sketch a molecule, import/export common small-molecule formats, send a sketch to Mol*, xyzrender, or a collection grid, and edit grid rows through Ketcher.

Macromolecule editing is not enabled in the current Ketcher integration.

Workspace Workflows

Beyond single-file previews, the desktop workspace includes focused workflows for structure triage:

• xyzrender sheets for comparing SVG-rendered structures and exported artwork
• docking and pose-review surfaces backed by the shared Mol* viewer runtime
• FEP network GraphML previews with ligand cards and grid handoff
• FEP setup panels for assembling ligand-network inputs

These workflows live in the desktop app. Finder Quick Look remains optimized for quick file previews.

Settings and Maintenance

Burrete settings cover:

• General workspace defaults and open documents
• Appearance, themes, and preview backgrounds
• Keyboard shortcuts and command-palette navigation
• Structure rendering, including Auto, Mol*, and external xyzrender
• Stable and beta update checks
• Files, recent structures, and project folders
• Burrete/Codex integration status
• Quick Look reset, preview cache cleanup, logs, diagnostics, and maintenance

Optional integrations include a local xyzrender executable, VESTA, and external chemistry editors discovered by macOS.

Build From Source

Most users should install Burrete with Homebrew, the Bun CLI, or GitHub Releases. If you want to build it yourself, clone the repository and run:

./scripts/doctor.sh
./scripts/build.sh
./scripts/install.sh

The local installer places the app here:

~/Applications/Burrete.app

Current project documentation starts at docs/README.md.

Development

Burrete follows the Writer Computer development convention of using Vite+ through the vp CLI. Use vp as the entrypoint for frontend work and JavaScript validation:

vp install
vp dev
vp check
vp test
vp build

Existing Burrete package scripts may still be run through vp run <script> for project-specific checks, but day-to-day development and JavaScript validation should use the Vite+ built-ins above. Rust validation runs from apps/desktop/src-tauri; native release scripts remain under scripts/. See docs/vite-plus.md and docs/releasing.md.

The Quick Look extension caches generated runtime files under the extension container. After replacing the app, refresh Quick Look with:

qlmanage -r
qlmanage -r cache
killall quicklookd 2>/dev/null || true

License

MIT