# Clavis

## Docs

- [Cage Types Reference](https://docs.claviscage.app/analysis/cage-types.md): Color-coded reference for all detected cage types
- [F3/F4 Order Parameters](https://docs.claviscage.app/analysis/f3f4.md): Order parameters for hydrate structure characterization
- [GRADE Classification](https://docs.claviscage.app/analysis/grade.md): Automatic hydrate structure type classification
- [HTR Algorithm](https://docs.claviscage.app/analysis/htr.md): H-bond Topology Ring analysis for hydrate structures
- [Guest Occupancy](https://docs.claviscage.app/analysis/occupancy.md): Calculate cage occupancy ratios (θ_S, θ_L, overall occupancy) for guest molecules in clathrate hydrate structures.
- [TRACE Algorithm](https://docs.claviscage.app/analysis/trace.md): Topological ring and cage detection for hydrate structures
- [FAQ](https://docs.claviscage.app/faq.md): Frequently asked questions about Clavis
- [Exporting Data](https://docs.claviscage.app/getting-started/export.md): Export analysis results, images, render frames, and videos from Clavis
- [Layer Management](https://docs.claviscage.app/getting-started/layers.md): Use multiple structure layers for waters, guests, comparison structures, and per-layer styling
- [Keyboard Shortcuts](https://docs.claviscage.app/getting-started/shortcuts.md): Complete keyboard shortcut reference for Clavis
- [Uploading Files](https://docs.claviscage.app/getting-started/upload.md): How to prepare and upload structure files for analysis
- [Visualization Controls](https://docs.claviscage.app/getting-started/visualization.md): Customize how atoms, cages, guests, and bonds are displayed
- [Introduction](https://docs.claviscage.app/introduction.md): Clavis - Hydrate Cage Structure Visualization
- [Path-Traced Rendering](https://docs.claviscage.app/pro/path-tracer.md): Create photorealistic renders of your hydrate structures
- [Video Export](https://docs.claviscage.app/pro/video-export.md): Export trajectory animations as MP4 videos

## OpenAPI Specs

- [openapi](https://docs.claviscage.app/api-reference/openapi.json)