v0.2.0 — Miyazawa-Jernigan structural matrix

Highlights

structural is now a Miyazawa-Jernigan interaction-strength matrix. Each residue's interaction strength q(a) = mean_b e(a,b) is read off the MJ contact potential, and sim(a,b) = 10·(1 − |q̂(a) − q̂(b)|). Substitutions between residues of like interaction strength are cheap, so the matrix separates strong hydrophobic interactors (F W C L Y M I V) from weak polar/charged ones (S Q D E K) — the strong/weak-interactor axis of TCR-recognition models (Košmrlj et al., PNAS 2008, doi:10.1073/pnas.0808081105; MJ energies from Miyazawa & Jernigan, J Mol Biol 1996). This lets seqtrie align dissimilar-but-chemically-equivalent loops.

Other

• bench/gen_matrices.py is now self-contained (embeds the MJ contact matrix; drops the texshade.sty/kpsewhich build dependency).
• Docs, header comments, and test anchors updated.

Full diff: v0.1.0...v0.2.0