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

  • a181956cf2 ignore SSL certificate validation Dima 2026-03-19 15:28:28 +01:00
  • a9b28945eb Fix AF3 shared-root output isolation and sanitize job paths Dima 2026-03-19 14:37:32 +01:00
  • b3377be5da Prevent AF3 shared-root outputs from escaping via dot-only job names Dima 2026-03-19 14:14:31 +01:00
  • e7782196a8 invalid regression Dima 2026-03-19 13:54:57 +01:00
  • 7433d0cd44 fix stale af3 schema in json Dima 2026-03-19 13:45:14 +01:00
  • 3aa1e5bb59 use tiny monomers Dima 2026-03-19 13:25:14 +01:00
  • 630fd6028c xla flash attention env Dima 2026-03-19 13:14:05 +01:00
  • 24faf843bb Fix AF3 output directory handling for shared roots Dima 2026-03-19 13:05:53 +01:00
  • fb8ae2da2a debug msas and templates for alphafold2 backend too. clean dumps to save only end files for msas Dima 2026-03-18 12:08:51 +01:00
  • 390ad89794 Use AF2 all-seq species metadata to pair with AF3 Dima 2026-03-18 11:34:21 +01:00
  • db61c701d5 refactor AF2 multimer MSA translation for AlphaFold3 input Dima 2026-03-18 10:55:36 +01:00
  • 1357181d2b Fix AF3 backend MSA chain ordering (preserve paired signal) Dima 2026-03-17 16:45:36 +01:00
  • 48771fec06 Bump 2.1.9 2.1.9 Dima Molodenskiy 2026-02-27 11:00:31 +01:00
  • e1043163c4 Always return normalized asym_id feature copy Dima 2026-02-27 09:53:59 +01:00
  • 0c70eed149 Always init backend Dima 2026-02-25 16:51:38 +01:00
  • 31b7612b87 setuptools<82 Dima 2026-02-25 13:28:41 +01:00
  • e58fa46c9d setuptools<82 for pdbfixer at relaxation Dima 2026-02-25 13:05:32 +01:00
  • 1605443014 Update README.md amrismil 2026-02-11 17:15:15 +01:00
  • fdedfd0b2f Make folding backend manager lazy to avoid import-time AF2 deps Dima Molodenskiy 2026-02-18 10:41:18 +01:00
  • a6a5cd9eaa Do not import any backend bypassing backend manager Dima Molodenskiy 2026-02-18 09:59:33 +01:00
  • 0c71900d89 Exclude tests from af2 af3 al2 cf Dima Molodenskiy 2026-02-18 09:58:40 +01:00
  • 73f1cedba9 Do not install heavy jax that can't be used on cpu anyway Dima Molodenskiy 2026-02-18 09:58:02 +01:00
  • 846198edd3 Update setuptools version in pyproject.toml Dima 2026-02-18 08:42:06 +01:00
  • 794ef72658 Update README with new version numbers and SLURM setup 2.1.8 Dima 2026-02-10 12:43:22 +01:00
  • 6b6cbaccd9 Disable alphalink container build job Dima 2026-02-10 12:32:35 +01:00
  • ceaa4d38fa Use ap-parser 0.3.0 Dima 2026-02-10 11:37:16 +01:00
  • 986367e50c Bump 2.1.8 Dima 2026-02-10 11:33:37 +01:00
  • 4dfa6613cf Resolve issue with hash mismatches Dima 2026-02-10 11:32:54 +01:00
  • 370596ebb6 Fix #575 Dima Molodenskiy 2026-02-10 10:28:37 +01:00
  • 9fca958047 Delete old setup.py and setup.cfg Dima 2026-02-03 20:19:41 +01:00
  • 240e0764de Bump 2.1.6 Dima Molodenskiy 2026-02-03 20:12:52 +01:00
  • 8274eb0ad9 New Dima Molodenskiy 2026-02-03 20:08:42 +01:00
  • f216936439 Update example_2.md amrismil 2026-02-02 20:44:53 +01:00
  • af8c162f5a Update example_3.md amrismil 2026-02-02 20:44:31 +01:00
  • 3512bbdc61 Update example_1.md amrismil 2026-02-02 20:40:19 +01:00
  • a281fe2a9f Update example_3.md amrismil 2026-02-02 20:32:00 +01:00
  • 650f8390c1 Update example_2.md amrismil 2026-02-02 20:31:47 +01:00
  • fb561a8e3c Update example_1.md amrismil 2026-02-02 20:31:33 +01:00
  • d3bed62af1 Update example_2.md amrismil 2026-02-02 20:28:58 +01:00
  • f11f5ea7ae Update example_2.md amrismil 2026-01-23 18:53:22 +01:00
  • a0c731690e Remove conda, build dev-requirements.txt on-the-fly Dima 2026-01-08 12:18:37 +01:00
  • 69af382af0 Force numpy<2 installation Dima 2026-01-08 12:17:07 +01:00
  • 0705a109c1 Don't build old analysis container on release - discontinued development Dima 2026-01-08 12:16:39 +01:00
  • be2c3710f3 Update to 2e3703e Dima 2026-01-08 12:15:29 +01:00
  • 41689871fe Make sure autogenerated pseudo pdb ID is parsable by AF2 parser Dima Molodenskiy 2025-12-16 10:52:32 +01:00
  • 6f8ac81647 Update installation instructions and version tags Dima 2025-12-09 12:16:55 +01:00
  • f7ace780d4 Re-establish link to APS Dima 2025-11-26 10:49:17 +01:00
  • 6250f6da80 SLURM defaults move from results Dima 2025-11-26 10:35:04 +01:00
  • 298e614641 Fix #564 Dima 2025-11-26 10:29:55 +01:00
  • db58bbc46a Change template flag to re_search_templates_mmseqs2 Quentin Rouger 2025-11-19 15:55:23 +01:00
  • 39d0c430f0 Change use_templates parameter to False Quentin Rouger 2025-11-18 16:58:25 +01:00
  • a4c44ca02f Add use_templates flag to make_mmseq_features call Quentin Rouger 2025-11-18 16:43:01 +01:00
  • 6b76dac43a Add use_templates option for MSA calculation Quentin Rouger 2025-11-18 16:25:05 +01:00
  • 9b90c1d850 Update README to mention APLit Dima 2025-11-19 14:34:33 +01:00
  • e717d8c773 Update supported backends in README Dima 2025-11-13 16:21:24 +01:00
  • 4c43d5eda3 Update installation instructions and workflow tag Dima 2025-11-13 16:20:00 +01:00
  • 7cd4a2e73f Fix formatting of alphapulldown_input_parser installation 2.1.5 Dima 2025-11-13 15:34:21 +01:00
  • 25c7ebcd07 Add alphapulldown_input_parser to AF3 Dockerfile Dima 2025-11-13 15:01:36 +01:00
  • 0c6f4abdf5 Rename alphafold backend to alphafold2 Dima Molodenskiy 2025-11-13 13:16:35 +01:00
  • 3cd11aa9e7 Bump 2.0.5 Dima Molodenskiy 2025-11-12 14:39:27 +01:00
  • 1d8ddbb822 Use parser from pip Dima Molodenskiy 2025-11-12 11:48:51 +01:00
  • f4f8415782 Refactor for clarity, deal with overlapping env vars Dima Molodenskiy 2025-11-10 14:50:04 +01:00
  • 6d21537c4b Build command as argv list: [python, script, ...] Dima 2025-11-10 14:34:26 +01:00
  • 40fa1cba4a Update cached_ccd to use Ccd for user_ccd Quentin Rouger 2025-11-05 14:53:09 +01:00
  • 3972c31081 Add 'use_ap_style' flag to af3_flags Quentin Rouger 2025-11-05 14:51:56 +01:00
  • d8e6d7b22b Simplify command arguments for alphafold3 Quentin Rouger 2025-11-05 14:48:21 +01:00
  • aebcf92fc3 Add tests for modeling with run_multimer_jobs.py wrapper Dima Molodenskiy 2025-11-10 14:29:58 +01:00
  • 8336829041 Fix typing_extensions=4.14.0 and reduce image size by 5GB Dima 2025-11-07 10:22:40 +01:00
  • c1bb9d5c5b Convert off-diagonal MSA to dense representation when using af3 backend with af2 features Dima Molodenskiy 2025-11-06 10:13:32 +01:00
  • 4b9beb262f Update README.md amrismil 2025-11-03 08:23:18 +01:00
  • 489d33053b Add citation in README.md amrismil 2025-11-01 00:27:10 +01:00
  • 2d4a28549f Update link text in README for clarity Jan Kosinski 2025-10-29 12:32:34 +01:00
  • 0f31d956a0 Revise CCP4 section for clarity and detail Jan Kosinski 2025-10-29 12:59:47 +01:00
  • 8b465a33ec Snakemake README w/ flags (#538) 2.1.4 amrismil 2025-10-29 10:37:31 +01:00
  • 94f0e4ac35 Fix and trim to 11.7 GB Dima 2025-10-28 14:15:22 +01:00
  • d0216854d8 Remove redundant CUDA toolchain from alphalink.dockerfile and consolidate environment settings (#537) Copilot 2025-10-27 14:39:08 +01:00
  • ab215ca0b5 Add missing --models_to_relax to af2 flags Dima Molodenskiy 2025-10-27 13:58:34 +01:00
  • c76b9c2ea2 Bump to 2.1.4 Dima Molodenskiy 2025-10-27 13:08:44 +01:00
  • c95cb96560 Move postprocessing to postprocessing. Use new af3 flags: num_recycles, return_embeddings, return_distogram. Add tests Dima Molodenskiy 2025-10-27 13:08:06 +01:00
  • 55519801a7 Validate that flags belong to folding backend. Define new af3 flags: num_recycles, return_embeddings, return_distogram Dima Molodenskiy 2025-10-27 13:06:52 +01:00
  • 88a72b67bc New test for af3 homo-dimer Dima 2025-10-22 13:57:23 +02:00
  • d9b20fb3bf Update README to remove MSA features warning Dima 2025-10-15 19:47:57 +02:00
  • a9685df783 Rename build container from 'fold' to 'alphafold2' Dima 2025-10-09 12:56:12 +02:00
  • 215dedac6c Rename docker files; Make alphalink image smaller Dima 2025-10-09 12:33:24 +02:00
  • ff2d7d736c Rename pulldown to alphafold2 Dima 2025-10-08 14:42:15 +02:00
  • d94121488c Revise README for AlphaPulldown Snakemake usage Dima 2025-10-08 14:27:01 +02:00
  • 918cb7f309 Sync: flash attention, n cpus for MSA tools, etc Dima 2025-10-07 12:40:07 +02:00
  • 602c892754 Remove af3 tests so that CI/CD doesn't die Dima Molodenskiy 2025-09-25 15:52:47 +02:00
  • ab37a743f8 Fix #534 Dima Molodenskiy 2025-09-11 16:36:44 +02:00
  • a5f09846c1 Fix #512 2.1.2 Dima Molodenskiy 2025-09-04 10:43:01 +02:00
  • 916721666f Revert truncated README.md Dima 2025-09-01 15:40:29 +02:00
  • e7cb78a4c3 Use AF3 IDs->Chars mapping for MSA debug Dima Molodenskiy 2025-08-28 13:24:54 +02:00
  • 6435ceb6a4 Move utilities for converting MSA to AF IDs to a separate file Dima Molodenskiy 2025-08-28 11:19:54 +02:00
  • 69560fe3b9 Added --debug_msas for af3 backend. Pass MultimericObject.feature_dict['msa'] as is to af3 Dima Molodenskiy 2025-08-28 11:16:50 +02:00
  • d39fa8ca5f Fix #340 Dima Molodenskiy 2025-08-22 15:32:47 +02:00
  • 9638c4e6bf Added --dropout for af2 and tests. Use jax cache for tests Dima Molodenskiy 2025-08-22 14:01:04 +02:00
  • d693051731 Revert deleted file: used for CI/CD Dima 2025-08-12 15:13:15 +02:00
  • 75eb05cdbb remove .ipynb_checkpoints .vscode .coverage from repo and ignore them Dima 2025-08-12 15:06:47 +02:00
  • bc524f0157 remove temporary files and add tmp/ to .gitignore Dima 2025-08-12 15:02:38 +02:00
  • fc41c1a5eb AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues Dima 2025-08-12 14:04:33 +02:00