Boltz v2.2.0: Contact conditioning fixes, new potentials

Highlight

• Fixes for contact and pocket conditioning which was not fully functional for Boltz2
• New potentials
• Kernels are now optional to avoid installation issues on non-linux platforms
• New security features for use of the MSA server (thanks @papagala!)

And many others!

What's Changed

• Generalize dropping leaving atoms for covalent modifications and noncanonical modifications. by @benf549 in #349
• Respect existing CUEQ envvars for tuning by @pechersky in #348
• Typos by @CurtisColwell in #351
• Fixes for training and Torch compatibility by @simonlevine in #364
• Fix Typo: Correct "neighboorhood" to "neighborhood" in Comments by @zeevick10 in #369
• Fix typo: "explicitly" instead of "explicitely" in prediction.md documentation by @maximevtush in #371
• Minor Documentation and Code Comments Improvements by @leopardracer in #386
• Fix for use_kernels for later torch versions for PairformerNoSeqModule by @simonlevine in #380
• Update mols.tar download logic by @brianloyal in #379
• fixed typo in prediction.md documentation by @fisand08 in #375
• Fix flag by @JohnKirwan in #440
• Docs: Update README and Prediction Documentation by @kilavvy in #410
• Optimize images by @paulpham157 in #376
• Fix --output_format pdb with --model boltz1 by @benf549 in #365
• Fix template matched by @Dawincy134 in #445
• Add support for dumping embeddings during prediction by @ribesstefano in #457
• Update prediction.md by @jansteinkuehler in #423
• Contacts and Template Potentials by @Noahb930 in #462
• Fix over-eager skip logic in filter_inputs_structure by @mohiuddin-khan-shiam in #426
• Fixes issue when training Boltz-1x with steering by @darianyang in #255
• Improve TrainingDataset __getitem__ performance by @gcroci2 in #441
• fix: pass full BoltzSteeringParams to affinity prediction by @tobiasploetz in #468
• Adding MSA server security by @papagala in #466
• Fix typo in schema for contact constraint by @glukhove in #472
• fix issue with non-linux installation by @gcorso in #479

New Contributors

• @pechersky made their first contribution in #348
• @CurtisColwell made their first contribution in #351
• @zeevick10 made their first contribution in #369
• @maximevtush made their first contribution in #371
• @leopardracer made their first contribution in #386
• @brianloyal made their first contribution in #379
• @fisand08 made their first contribution in #375
• @JohnKirwan made their first contribution in #440
• @kilavvy made their first contribution in #410
• @paulpham157 made their first contribution in #376
• @Dawincy134 made their first contribution in #445
• @ribesstefano made their first contribution in #457
• @jansteinkuehler made their first contribution in #423
• @mohiuddin-khan-shiam made their first contribution in #426
• @gcroci2 made their first contribution in #441
• @tobiasploetz made their first contribution in #468
• @papagala made their first contribution in #466
• @glukhove made their first contribution in #472
• @gcorso made their first contribution in #479

Full Changelog: v2.1.1...v2.2.0