Cage Types Reference
Clavis detects and color-codes hydrate cage polyhedra by their face signature. This page provides a complete reference.Face Signature Notation
Cages are described by their polyhedral face composition. For example:- 5^12 means 12 pentagonal faces (dodecahedron)
- 5^12·6^2 means 12 pentagons + 2 hexagons (tetrakaidecahedron)
- 4^1·5^10·6^2 means 1 square + 10 pentagons + 2 hexagons
SEC Cage Types (Standard Edge-saturated Cages)
These are complete cages satisfying the Euler relation F - E + V = 2.| Face Signature | Common Name | Structure | Color |
|---|---|---|---|
| 5^12 | Dodecahedron | sI/sII small | Cyan #06b6d4 |
| 5^12·6^2 | Tetrakaidecahedron | sI large | Purple #8b5cf6 |
| 5^12·6^3 | - | - | Amber #f59e0b |
| 5^12·6^4 | Hexakaidecahedron | sII large | Red #ef4444 |
| 5^12·6^5 | - | - | Green #22c55e |
| 5^12·6^6 | - | - | Pink #ec4899 |
| 5^12·6^8 | Icosahedron | sH large | Blue #3b82f6 |
| 4^1·5^10·6^2 | - | - | Teal #14b8a6 |
| 4^1·5^10·6^3 | - | - | Sky #0ea5e9 |
| 4^1·5^10·6^4 | - | - | Indigo #6366f1 |
| 4^1·5^10·6^5 | - | - | Violet #a78bfa |
| 4^2·5^8·6^1 | - | - | Orange #f97316 |
| 4^2·5^8·6^2 | - | - | Light Orange #fb923c |
| 4^2·5^8·6^3 | - | - | Fuchsia #d946ef |
| 4^2·5^8·6^4 | - | - | Rose #f43f5e |
| 4^3·5^6·6^3 | - | sH medium | Lime #84cc16 |
| 4^3·5^6·6^4 | - | - | Dark Lime #65a30d |
| Other | Unclassified | - | Gray #9ca3af |
Incomplete Cages (IC)
Incomplete cages are partially formed structures missing some faces. They are rendered with pastel colors.| Label | Description | Color |
|---|---|---|
| IC:5^12 | Incomplete dodecahedron | Light Steel Blue #b0c4de |
| IC:5^12·6^2 | Incomplete tetrakaidecahedron | Lavender #c9b8d1 |
| IC:5^12·6^4 | Incomplete hexakaidecahedron | Mint #b8d4c9 |
| IC:unknown | Unidentified incomplete cage | Light Gray #d4d4d4 |
Non-SEC Cages (nSEC)
Non-standard cages that form closed polyhedra but have unusual topology (e.g., odd ring sizes, non-planar faces).| Label | Description | Color |
|---|---|---|
| nSEC:5^12 | Non-standard dodecahedron | Sky Blue #87ceeb |
| nSEC:5^12·6^2 | Non-standard tetrakaidecahedron | Plum #dda0dd |
| nSEC:5^12·6^4 | Non-standard hexakaidecahedron | Aqua #98d8c8 |
| nSEC:unknown | Unidentified non-standard cage | Silver #c0c0c0 |
HTR Ring Types
When using the HTR algorithm, individual primitive rings are also visualized:| Ring Type | Color |
|---|---|
| 4-ring | Yellow #fbbf24 |
| 5-ring | Cyan #06b6d4 |
| 6-ring | Purple #a855f7 |
Quality Levels
Each detected cage is assigned a quality level:| Quality | Code | Meaning |
|---|---|---|
| SEC | 2 | Standard edge-saturated cage with valid Euler topology |
| nSEC | 1 | Closed polyhedron with non-standard topology |
| IC | 0 | Incomplete cage, missing faces or edges |