sae notebook sync

[imathur1]

Changes

Binder design

• adds epitope loss to steer binder contacts toward specified target hotspot residues
• reworks critic scoring into a shared score_critic helper that lazy-loads scaling critics on GPU instead of keeping them CPU-resident
• adds deterministic mode + Triton/CUEQ kernel backend selection

Forge SDK

• new to_float32 helper to upcast ESMC logits/embeddings/hidden states
• adds a default request_timeout (120s SequenceStructure/ESM3, 60s ESMC) and per-request timeout override
• switch retry to use jitter and exponential backoff. Added 503 retry code

Other

• MolecularComplex.from_atomarray is a new classmethod to build a complex from a biotite AtomArray keeping all atoms (inverse of to_mmcif).
• Adding Protein Characterization with SAE Features, a Retrospective Analysis Case study to SAE notebook
• Changing ESMFold2 notebook to replace the synthetic antibody–antigen case in favor of a real vaccinia G3/L5 complex (PDB 7YTU) with per-chain MSAs
• login widget links point to the new Biohub developer console
• README Slack link
• Pins DockQ as an explicit dependency (a numpy-2-compatible fork) so DockQ scoring keeps working after the env moves to numpy>=2.0.

[github-actions]

Tests	Skipped	Failures	Errors	Time
43	1 💤	0 ❌	0 🔥	16.182s ⏱️