Allaun Silverfox
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35ad40cfae
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binding-site: 3 outlines, 1,300 lines, Hachimoji × protein structures
BindingSiteHachimoji.lean (589 lines):
- 50-token amino acid vocabulary (20 core + 30 modified)
- 8-state Hachimoji classification for residues
- Extended Fisher metric on 50-simplex (Chentsov unique)
- Chaos game basin discovery with Sidon addressing
- Typed BindingSiteReceipt compatible with PVGS-DQ
BindingSiteEntropy.lean (376 lines):
- Information entropy per residue site (Void-X Eq. 3)
- Entropy from B-factors (PDB) or cluster diversity
- Bindability score B* normalized to 0-100
- Sidon address generation from entropy profiles
- Fisher-Rao approximate distance between sites
BindingSiteCodec.lean (335 lines):
- pdbToReceipt : PDB ID → BindingSiteReceipt (one function)
- screenDruggable : filter library for bindable pockets
- rankByEnergy : sort by dual quaternion energy
- Test cases: EGFR (1YY9), Tautomerase (9MUA), KIR2DL1 (9HML)
Architecture: PDB → entropy profile → Hachimoji state → PVGS params
→ dual quaternion energy → typed receipt → PVGS-DQ system
All three files compile as outlines with sorry for future proofs.
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2026-06-21 04:16:34 -05:00 |
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