Cage Types Reference
Clavis detects and color-codes hydrate cage polyhedra by their face signature. The available labels depend on the selected algorithm: TRACE accepts arbitrary signatures, HTR reports generalizedn4-n5-n6 counts, and GRADE is restricted to 5^12, 5^12·6^2, and 5^12·6^4.
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 TRACE display types for complete cages satisfying the Euler relation F - E + V = 2. Their presence does not imply a GRADE structure verdict.Incomplete Cages (IC)
Incomplete cages are partially formed structures missing some faces. They are rendered with pastel colors.Non-SEC Cages (nSEC)
Non-standard cages that form closed polyhedra but have unusual topology (e.g., odd ring sizes, non-planar faces).HTR Ring Types
When using the HTR algorithm, individual primitive rings are also visualized:
HTR cage counts use
n4-n5-n6; for example, 0-12-0 corresponds to 5^12. GRADE uses only the three canonical machine labels 512, 51262, and 51264.