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Author SHA1 Message Date
Dima
f6af91a8ff Harden MMseqs species ID resolution fallback 2026-03-27 15:57:10 +01:00
Dima
84ccc6846b Add AF3 regression for precomputed MMseq MSAs 2026-03-27 14:10:54 +01:00
Dima
0444f8f2d0 Fix AF2 MMseqs pairing sanity check 2026-03-27 14:10:54 +01:00
Dima
fe9b0c840a Tighten MMseqs AF2/AF3 inference ipTM regressions 2026-03-27 14:10:54 +01:00
Dima
6cd6511a77 Add MMseqs regression coverage for pairing and template reuse 
Add opt-in AF2 and AF3 inference regressions that regenerate fresh MMseqs-derived AF2 features for the issue #588 A0ABD7FQG0/P18004 reproducer, verify recovered species identifiers, and exercise the existing wrapper entrypoints.\n\nAdd FASTA fixtures for that reproducer so the tests do not depend on a live UniProt download.\n\nAdd focused coverage for the MMseqs precomputed-MSA plus template re-search branch in make_mmseq_features(), and relax the outdated AF3 wrapper so it can submit Slurm jobs from login nodes without requiring a local GPU.
 2026-03-27 14:10:54 +01:00
Dima
53a75e14c8 Recover mmseqs species identifiers for AF2 pairing 2026-03-27 14:10:54 +01:00
Dima
269c15b215 Relax issue #588 translation mode expectations 2026-03-27 14:10:54 +01:00
Dima
6896775a8f Relax issue #588 metadata boolean assertions 2026-03-27 14:10:54 +01:00
Dima
2223191a05 Add issue #588 AF3 regression fixtures and tests 2026-03-27 14:10:54 +01:00
Dima
f387696724 New implementation for splicing seqs with AF3 2026-03-26 12:10:38 +01:00
Dima
865c336e84 Guard shared-root GPU wrapper runs 2026-03-26 11:48:24 +01:00
Dima
fcafd0630c Isolate GPU functional test wrapper runs 2026-03-26 11:48:24 +01:00
Dima
e3b09b296d Ignore test_logs from slurm 2026-03-26 11:48:24 +01:00
Dima
9713f35132 Fallback to module introspection in Slurm test wrappers 2026-03-26 11:48:24 +01:00
Dima
c3cf197fec Skip GPU functional suites on CI without override 2026-03-26 11:48:24 +01:00
Dima
0497f68310 Add Slurm wrapper for AF2 functional tests 2026-03-26 11:48:24 +01:00
Dima
a028f654d0 Add Slurm wrapper for AF3 functional tests 2026-03-26 11:48:24 +01:00
Dima
ab07675972 Gate AF3 runtime benchmark behind env var 2026-03-26 11:48:24 +01:00
Dima
82663085de Fix AF3 chopped-input residue ID expectations 2026-03-26 11:48:24 +01:00
Dima
022a5bd800 Fix AF3 PTM sequence serialization and expectations 2026-03-26 11:48:24 +01:00
Dima
cbdd1a0677 Preserve canonical AF3 polymer input sequences 2026-03-26 11:48:24 +01:00
Dima
51a028386f Repoint alphafold3 to pre-Tokamax main 2026-03-26 11:48:24 +01:00
Dima
69a5ccbd57 Normalize AF3 overlapping chopped MSA inputs 2026-03-26 11:48:24 +01:00
Dima
2f153aac50 Skip invalid AF3 JSON templates 2026-03-26 11:48:24 +01:00
Dima
7fb11ef554 Fix AF3 naming and ligand JSON handling 2026-03-26 11:48:24 +01:00
Dima
c9e9e8c381 Point alphafold3 submodule to public main 2026-03-26 11:48:24 +01:00
Dima
bb4f8474b7 Add AF3 inference test for copied gapped chains 2026-03-26 11:48:24 +01:00
Dima
da63ed78ca Fix AF3 homomer gapped-chain JSON expectation 2026-03-26 11:48:24 +01:00
Dima
89d2625120 Fix AF3 copied gapped-chain test input syntax 2026-03-26 11:48:24 +01:00
Dima
ca546102e5 Add AF3 test for copied out-of-order gapped chains 2026-03-26 11:48:24 +01:00
Dima
c0cff91d23 Fix AF3 viewer numbering and output names 2026-03-26 11:48:24 +01:00
Dima
f16189bcd8 Fix AF3 viewer annotation tables for duplicate residues 2026-03-26 11:48:24 +01:00
Dima
a9b9905e79 Use insertion codes for duplicate AF3 residue ids 2026-03-26 11:48:24 +01:00
Dima
8a6f4a1463 Write ChimeraX-safe AF3 outputs 2026-03-26 11:48:24 +01:00
Dima
e6016ac2a3 Parse AF3 chain sequences directly from mmCIF 2026-03-26 11:48:24 +01:00
Dima
941dba76b4 Read AF3 residue numbers directly from mmCIF 2026-03-26 11:48:24 +01:00
Dima
ab4b7fbf11 Fix AF3 duplicate-residue regression test 2026-03-26 11:48:24 +01:00
Dima
962bca9256 Handle duplicate AF3 residue IDs during inference 2026-03-26 11:48:24 +01:00
Dima
04e945a3b7 Preserve AF3 residue IDs when promoting MSAs 2026-03-26 11:48:24 +01:00
Dima
ae8bdbeaa8 Point AF3 gap branch to pre-Tokamax submodule 2026-03-26 11:48:24 +01:00
Dima
78398ee705 Update AF3 backend for Tokamax attention API 2026-03-26 11:48:24 +01:00
Dima
025af52c2f Implement gapped discontinuous chains for AF3 2026-03-26 11:48:24 +01:00
Dima
ec8f07f27a Point alphafold3 submodule to KosinskiLab gapped-chain branch 2026-03-26 11:48:24 +01:00
Dima Molodenskiy
5a4d17ef59 Bump 2.2.1 2026-03-24 14:56:43 +01:00
Dima
23b3160419 How to model discontinuous regions with AF3 2026-03-24 14:38:47 +01:00
Dima
c990ab6659 Support chopped AF3 JSON feature inputs 2026-03-24 12:06:44 +01:00
Dima
070c7f377e run actual inference too 2026-03-24 12:06:44 +01:00
Dima
f5770472e4 ProteinChain now don't have description kwarg 2026-03-24 12:06:44 +01:00
Dima
fee7779ed7 Support discontinuous chopped regions in AlphaFold3 backend 2026-03-24 12:06:44 +01:00
Dima Molodenskiy
22c1b08604 Bump 2.2.0 2.2.0 2026-03-23 10:25:16 +01:00