pub_soft/AlphaPulldown
3
0
Fork 0
mirror of https://github.com/KosinskiLab/AlphaPulldown.git synced 2026-06-04 14:14:24 +08:00
Code Issues Packages Projects Releases Wiki Activity

Commit Graph

  • 1d940d0b6a docs: point Snakemake install docs at 2.5.0 main Dima Molodenskiy 2026-05-26 16:22:27 +02:00
  • 4577f56b2f docs: point Snakemake deploy tag and env file to release 2.4.0 Dima Molodenskiy 2026-05-21 10:30:53 +02:00
  • 4c3e83ce78 docs: sync structure-inference SLURM options with AlphaPulldownSnakemake Dima Molodenskiy 2026-05-21 10:27:15 +02:00
  • 716c061230 Fix mocked precomputed MMseq A3M in integration test Dima Molodenskiy 2026-04-23 10:23:44 +02:00
  • cdd5fb57bf Align AF2 cluster tests with safer GPU defaults Dima Molodenskiy 2026-04-23 10:00:39 +02:00
  • fb09717cf3 Harden precomputed MSA identifier enrichment Dima Molodenskiy 2026-04-23 09:52:54 +02:00
  • ce4be4866b Handle tuple-shaped AF2 prediction results Dima Molodenskiy 2026-04-23 09:52:48 +02:00
  • ba2f6f09f5 Bump 2.4.0 2.4.0 Dima Molodenskiy 2026-04-15 12:24:30 +02:00
  • 3e74e3551c Make sure random seed is integer Dima Molodenskiy 2026-04-13 16:17:01 +02:00
  • 3d51beb2ec Default threshold, better colors, flag to show best n complexesk Dima Molodenskiy 2026-04-13 13:43:49 +02:00
  • 99a806fd31 Trim release-only AF3 trimer test scaffolding Dima 2026-04-10 20:01:45 +02:00
  • 7d18ea8ab2 Compare AF2 trimer translation with native AF3 pairing Dima 2026-04-10 19:45:49 +02:00
  • 7a8afc7c7a Handle grouped identical chains in AF3 trimer test Dima 2026-04-10 17:48:33 +02:00
  • f7176e87af Force cluster AF3 tests to use checkout code Dima 2026-04-10 17:12:35 +02:00
  • 609fecb3cd Add AF3 trimer cluster smoke test Dima 2026-04-10 16:45:25 +02:00
  • 0f081a4b02 Tighten AF3 trimer pairing summary Dima 2026-04-10 16:40:48 +02:00
  • 2c715001a9 fix(#42): add RF annotation to skip-MSA stockholm Dima 2026-04-10 12:14:14 +02:00
  • 392d3f7ec2 fix(#42): avoid AF2 bulk-db checks in skip-MSA mode Dima 2026-04-10 12:06:54 +02:00
  • 0f1f0c2cab fix: address skip-MSA review edge cases Dima 2026-04-10 11:52:59 +02:00
  • 49db627f23 docs(#42): document the skip-MSA flag Dima 2026-04-10 11:39:24 +02:00
  • 3dfd6d8aad fix(#42): add skip-MSA feature generation mode Dima 2026-04-10 11:35:27 +02:00
  • 098792fa21 [codex] Reuse existing monomer features in default TrueMultimer mode (#609) Dima 2026-04-09 16:48:15 +02:00
  • 0b09aa1cca fix(#332): support custom templates with mmseqs2 Dima 2026-04-09 16:16:10 +02:00
  • 39409d9387 fix: add distogram fallback for older af2plots Dima 2026-04-09 15:51:05 +02:00
  • d668a3342b fix: handle compressed diagnostics inputs and AP-style homo jobs Dima 2026-04-09 15:40:28 +02:00
  • 4e91d4e7bc feat(#141): add interaction network plotting Dima 2026-04-09 14:59:57 +02:00
  • 0bd4d4771e feat(#256,#258): add diagnostics plotting script Dima 2026-04-09 14:55:42 +02:00
  • 40c68b5738 feat(#336): add AlphaFold Server JSON exporter Dima 2026-04-09 14:52:44 +02:00
  • fc9c93860f fix(#463): match quick templates to chopped objects Dima 2026-04-09 14:25:31 +02:00
  • 1aaa473d67 fix(#471): preserve duplicate quick-template entries Dima 2026-04-09 14:24:35 +02:00
  • 12476a55c2 fix(#456): gate best-model relaxation by score Dima 2026-04-09 14:20:00 +02:00
  • 4f173d9aec fix(#464): support template filters in quick multimer mode Dima 2026-04-09 14:15:57 +02:00
  • 34c04d1ade fix(#293): skip full-db paths for reduced_dbs Dima 2026-04-09 14:09:37 +02:00
  • 894c4aa355 fix(#459): explain TrueMultimer template code logs Dima 2026-04-09 14:08:02 +02:00
  • 39309b2c67 i)AF3 rejects --use_mmseqs2 ii)more deterministic identification of a molecule type from FASTA iii)AF3 failures raises RuntimeError instead of Exception Dima 2026-04-09 13:45:39 +02:00
  • 6120be9500 Fix #602 Dima 2026-04-09 13:29:32 +02:00
  • 74f2df62a7 cache species ids when using mmseqs2 features with precomputed MSAs Dima 2026-04-08 18:09:16 +02:00
  • 0de121ea5e Bump 2.3.0 2.3.0 Dima Molodenskiy 2026-04-08 10:05:42 +02:00
  • fff63051b4 Tests (#600) Dima 2026-04-01 14:13:35 +02:00
  • 9bd18ce9b2 Keep testing instructions only in wiki Dima 2026-03-27 16:24:08 +01:00
  • 00aec3456f Add CPU unit coverage for AlphaFold3 backend helpers Dima 2026-03-27 15:55:48 +01:00
  • a941becec3 Publish HTML coverage reports via GitHub Pages Dima 2026-03-27 15:49:31 +01:00
  • db61670129 Expand unit coverage for objects.py edge cases Dima 2026-03-27 15:47:27 +01:00
  • 090fb0b026 Expand unit coverage for template and post-processing helpers Dima 2026-03-27 15:33:59 +01:00
  • 3e6fc368cd New. Dima 2026-03-27 15:29:48 +01:00
  • cbfaf51b0e New. Dima 2026-03-27 15:25:22 +01:00
  • 74d0e1cfaf Expand unit coverage for helper and backend manager utilities Dima 2026-03-27 15:19:15 +01:00
  • d78a93ff37 Fix function coverage checker def-line false positives Dima 2026-03-27 15:15:32 +01:00
  • 407764479b New Dima 2026-03-27 15:12:16 +01:00
  • 7fd121f842 Reorganize tests for CPU coverage CI Dima 2026-03-27 15:00:46 +01:00
  • f6af91a8ff Harden MMseqs species ID resolution fallback Dima 2026-03-27 14:59:14 +01:00
  • 84ccc6846b Add AF3 regression for precomputed MMseq MSAs Dima 2026-03-27 13:57:20 +01:00
  • 0444f8f2d0 Fix AF2 MMseqs pairing sanity check Dima 2026-03-27 13:39:57 +01:00
  • fe9b0c840a Tighten MMseqs AF2/AF3 inference ipTM regressions Dima 2026-03-27 13:19:00 +01:00
  • 6cd6511a77 Add MMseqs regression coverage for pairing and template reuse Dima 2026-03-27 13:07:47 +01:00
  • 53a75e14c8 Recover mmseqs species identifiers for AF2 pairing Dima 2026-03-27 12:13:19 +01:00
  • 269c15b215 Relax issue #588 translation mode expectations Dima 2026-03-27 09:34:06 +01:00
  • 6896775a8f Relax issue #588 metadata boolean assertions Dima 2026-03-27 09:30:54 +01:00
  • 2223191a05 Add issue #588 AF3 regression fixtures and tests Dima 2026-03-27 09:25:30 +01:00
  • f387696724 New implementation for splicing seqs with AF3 Dima 2026-03-26 12:10:38 +01:00
  • 865c336e84 Guard shared-root GPU wrapper runs Dima 2026-03-26 11:17:53 +01:00
  • fcafd0630c Isolate GPU functional test wrapper runs Dima 2026-03-26 10:46:19 +01:00
  • e3b09b296d Ignore test_logs from slurm Dima 2026-03-26 06:51:14 +01:00
  • 9713f35132 Fallback to module introspection in Slurm test wrappers Dima 2026-03-26 06:43:17 +01:00
  • c3cf197fec Skip GPU functional suites on CI without override Dima 2026-03-26 06:35:09 +01:00
  • 0497f68310 Add Slurm wrapper for AF2 functional tests Dima 2026-03-26 06:33:13 +01:00
  • a028f654d0 Add Slurm wrapper for AF3 functional tests Dima 2026-03-26 06:30:14 +01:00
  • ab07675972 Gate AF3 runtime benchmark behind env var Dima 2026-03-25 22:59:29 +01:00
  • 82663085de Fix AF3 chopped-input residue ID expectations Dima 2026-03-25 22:58:25 +01:00
  • 022a5bd800 Fix AF3 PTM sequence serialization and expectations Dima 2026-03-25 21:51:41 +01:00
  • cbdd1a0677 Preserve canonical AF3 polymer input sequences Dima 2026-03-25 21:09:38 +01:00
  • 51a028386f Repoint alphafold3 to pre-Tokamax main Dima 2026-03-25 20:59:52 +01:00
  • 69a5ccbd57 Normalize AF3 overlapping chopped MSA inputs Dima 2026-03-25 20:27:24 +01:00
  • 2f153aac50 Skip invalid AF3 JSON templates Dima 2026-03-25 20:19:17 +01:00
  • 7fb11ef554 Fix AF3 naming and ligand JSON handling Dima 2026-03-25 20:11:55 +01:00
  • c9e9e8c381 Point alphafold3 submodule to public main Dima 2026-03-25 20:02:30 +01:00
  • bb4f8474b7 Add AF3 inference test for copied gapped chains Dima 2026-03-25 19:43:25 +01:00
  • da63ed78ca Fix AF3 homomer gapped-chain JSON expectation Dima 2026-03-25 19:40:06 +01:00
  • 89d2625120 Fix AF3 copied gapped-chain test input syntax Dima 2026-03-25 19:36:01 +01:00
  • ca546102e5 Add AF3 test for copied out-of-order gapped chains Dima 2026-03-25 19:30:32 +01:00
  • c0cff91d23 Fix AF3 viewer numbering and output names Dima 2026-03-25 17:17:55 +01:00
  • f16189bcd8 Fix AF3 viewer annotation tables for duplicate residues Dima 2026-03-25 16:54:34 +01:00
  • a9b9905e79 Use insertion codes for duplicate AF3 residue ids Dima 2026-03-25 16:39:59 +01:00
  • 8a6f4a1463 Write ChimeraX-safe AF3 outputs Dima 2026-03-25 16:29:19 +01:00
  • e6016ac2a3 Parse AF3 chain sequences directly from mmCIF Dima 2026-03-25 16:21:34 +01:00
  • 941dba76b4 Read AF3 residue numbers directly from mmCIF Dima 2026-03-25 16:14:35 +01:00
  • ab4b7fbf11 Fix AF3 duplicate-residue regression test Dima 2026-03-25 15:50:19 +01:00
  • 962bca9256 Handle duplicate AF3 residue IDs during inference Dima 2026-03-25 15:48:06 +01:00
  • 04e945a3b7 Preserve AF3 residue IDs when promoting MSAs Dima 2026-03-25 15:41:19 +01:00
  • ae8bdbeaa8 Point AF3 gap branch to pre-Tokamax submodule Dima 2026-03-25 15:28:08 +01:00
  • 78398ee705 Update AF3 backend for Tokamax attention API Dima 2026-03-25 15:14:32 +01:00
  • 025af52c2f Implement gapped discontinuous chains for AF3 Dima 2026-03-25 15:05:33 +01:00
  • ec8f07f27a Point alphafold3 submodule to KosinskiLab gapped-chain branch Dima 2026-03-25 14:56:38 +01:00
  • 5a4d17ef59 Bump 2.2.1 Dima Molodenskiy 2026-03-24 14:56:43 +01:00
  • 23b3160419 How to model discontinuous regions with AF3 Dima 2026-03-24 14:29:56 +01:00
  • c990ab6659 Support chopped AF3 JSON feature inputs Dima 2026-03-24 10:33:47 +01:00
  • 070c7f377e run actual inference too Dima 2026-03-24 09:50:50 +01:00
  • f5770472e4 ProteinChain now don't have description kwarg Dima 2026-03-24 09:47:28 +01:00
  • fee7779ed7 Support discontinuous chopped regions in AlphaFold3 backend Dima 2026-03-24 09:38:57 +01:00
  • 22c1b08604 Bump 2.2.0 2.2.0 Dima Molodenskiy 2026-03-23 10:25:16 +01:00