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fix_rfpeptides_ci

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updated_scaffoldguided_fix

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v1.0.0

v1.1.0

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• 2d0c003df4 Adding files for the soon-to-be-released RFdiffusion video tutorial (#452) main Rachel Clune 2026-04-24 11:47:30 -07:00
• d1e7386992 Changed video_tutorials directory to just tutorials Rachel Clune 2026-04-24 11:46:58 -07:00
• 529b756796 feat: add inference.empty_cache_per_design flag to reduce CUDA allocator fragmentation (#451) Leonardo Marino-Ramirez 2026-04-24 11:41:07 -05:00
• 92f3c4ca27 Updated README Rachel Clune 2026-04-23 14:39:47 -07:00
• 2f2a301575 Update README.md Rachel Clune 2026-04-22 12:14:14 -07:00
• 122a2157c1 Adding files for the soon-to-be-released RFdiffusion video tutorial Rachel Clune 2026-04-22 11:30:54 -07:00
• 9535f19382 Updated "Fixed issues with designing in scaffoldguided mode" original PR 386 (#426) Hope Woods 2025-11-20 10:02:33 -06:00
• ecf161b4e2 Move cyclic_reses initialization to a helper function and call it for Sampler and ScaffoldedSampler updated_scaffoldguided_fix woodsh17 2025-11-18 15:43:09 -06:00
• 723a66408c Reverting changes to flag name, so you still use scaffoldguided.scaffoldguided=True instead of scaffoldguided_enabled woodsh17 2025-11-18 12:26:26 -06:00
• 1ba79929d3 Merge remote-tracking branch 'origin/main' into fix_scaffoldguided_design woodsh17 2025-11-18 10:46:28 -06:00
• ff20fbafef Fix workflow tests that are failing (#410) Hope Woods 2025-11-13 15:33:05 -06:00
• dd7643d640 Revert "Remove try block with except FileExistsError that isn't needed" After running the test, I found that this was needed This reverts commit ead721f326. woodsh17 2025-11-12 13:45:07 -06:00
• ead721f326 Remove try block with except FileExistsError that isn't needed woodsh17 2025-10-24 09:48:03 -05:00
• 4aea4fd65a Change design_nickel.sh num_designs back to 15 woodsh17 2025-10-23 12:26:00 -05:00
• 681874e6ea Reduce length for design_tetrahedral_oligos to 600 to reduce run time woodsh17 2025-10-22 15:16:41 -05:00
• be5b7b6b89 Preseed DGL so avoid examples that are ran at the same time failing woodsh17 2025-10-22 15:13:35 -05:00
• 4d870c07da In setUpClass check that directory doesn't already exists, so tests do not fail before running examples woodsh17 2025-10-22 10:03:07 -05:00
• dc1867dadf Edit main.yml so workflow runs woodsh17 2025-10-21 16:29:06 -05:00
• 56feb3bb4a Remove set pipefail woodsh17 2025-10-21 10:09:12 -05:00
• 4dd3a5f8c0 Remove -o option from pipefail woodsh17 2025-10-21 10:02:56 -05:00
• a570b2b8bd Edit main.yml workflow so if an example fails, the test doesn't pass woodsh17 2025-10-21 09:57:15 -05:00
• 260692d6c2 Edits to test_diffusion to make change setUp to setUpClass to make this a class method so examples run only once woodsh17 2025-10-20 08:48:02 -05:00
• 17f315b2de Add index of chunk to test directory name woodsh17 2025-10-17 12:45:28 -05:00
• a629d43e92 Add step to cd into tests directory in main.yml woodsh17 2025-10-17 11:04:32 -05:00
• 6d0036b480 Fix typo in main.yml in test_diffusion options woodsh17 2025-10-17 10:57:53 -05:00
• e2378c7358 Change num_designs in examples back to 10, since this is reset in test_diffusion.py woodsh17 2025-10-17 10:51:44 -05:00
• 5dff3eb188 These changes split the examples up in chunks and runs the different chunks to speed up the workflow. woodsh17 2025-10-17 10:39:26 -05:00
• a9b748be37 Add print statement to list failed examples woodsh17 2025-10-14 11:44:50 -05:00
• 778f8d4b28 Fix input_pdb path in design_macrocyclic_binder and fix incorrect call to res in test_diffusion.py woodsh17 2025-10-10 15:21:04 -05:00
• f43a81d59d Changing number of designs for examples from 10 to 2 to speed up tests woodsh17 2025-10-10 13:53:59 -05:00
• a45c3f9da7 Fail tests when example scripts exit non-zero woodsh17 2025-10-10 13:41:05 -05:00
• 2d157302d3 Adjusting command format for design_macrocyclic_binder.sh and design_macrocyclic_monomer.sh woodsh17 2025-10-10 09:36:45 -05:00
• a18f99614a Address 'command' referenced before assignment error in tests woodsh17 2025-10-10 09:35:57 -05:00
• caa732e2e1 Add conditional statement for including sampler.idx_pdb for writepdb since ScaffoldedSampler.sample_init() doesn't set idx_pdb. idx_pdb_scaffoldedsampler woodsh17 2025-09-29 13:03:27 -05:00
• e220924202 Retain chain and residue numbering in RFdiffusion (#348) Hope Woods 2025-09-24 09:28:03 -05:00
• 735de5edb1 Update README.md (#365) Hope Woods 2025-09-23 11:38:58 -05:00
• 7c30fee0ab Fixed issues with designing in scaffoldguided mode, for example: design_ppi_scaffold.sh. The solutions to issues 272 and 273 did not fully address the issue. Orange 2025-08-11 09:24:52 +00:00
• 637a6b7379 add python in front of macrocycle example execution fix_rfpeptides_ci David Juergens 2025-08-02 11:28:14 -07:00
• 25b908256a Update README.md Rachel Clune 2025-07-16 09:37:32 -07:00
• 35c3af8a0a Update README.md Rachel Clune 2025-07-14 15:58:06 -07:00
• fa340147b9 add GitHub CI workflow for running ppi-scaffolds tests (#1) Sergey Lyskov 2025-06-22 12:12:52 -06:00
• b254828f07 Update README.md David Juergens 2025-06-20 13:36:31 -07:00
• b1ba556871 add .sh examples, gabarap pdb, import numpy David Juergens 2025-06-20 09:17:16 -07:00
• cd64c5ae72 bugfix readme David Juergens 2025-06-20 00:34:04 -07:00
• 37e1d4da61 add rfpeptides img David Juergens 2025-06-20 00:31:29 -07:00
• ae036e30c6 Add RFpeptides code David Juergens 2025-06-20 00:29:58 -07:00
• 3ecb01f242 Update README.md rfpeptides David Juergens 2025-06-20 13:36:31 -07:00
• 140909edf2 add .sh examples, gabarap pdb, import numpy David Juergens 2025-06-20 09:17:16 -07:00
• 5939d4c4b0 bugfix readme David Juergens 2025-06-20 00:34:04 -07:00
• 7b97281289 add rfpeptides img David Juergens 2025-06-20 00:31:29 -07:00
• 2d6d57c3a3 Add RFpeptides code David Juergens 2025-06-20 00:29:58 -07:00
• d32205a17f Extend available new chains to include lowercase letters Brahm Yachnin 2025-06-17 13:24:16 -04:00
• 63e270f715 For fixed chains, retain residue numbering Brahm Yachnin 2025-05-20 10:38:19 -04:00
• 909fc01c03 Maintains the input chain ids in RFdiffusion output Brahm Yachnin 2025-05-16 10:31:01 -04:00
• b44206a2a7 correct example Joseph Watson 2024-08-25 06:58:26 -07:00
• 31f8091be2 Update README.md Joseph Watson/Watchwell 2024-08-25 14:57:58 +01:00
• f6ac51ee84 Added example Joseph Watson 2024-08-25 06:35:39 -07:00
• b819fd5aa0 Added secondary structure specification Joseph Watson 2024-08-25 05:42:55 -07:00
• 820bfdfade Update LICENSE Joseph Watson/Watchwell 2023-10-03 14:26:36 -07:00
• c68e28db22 Updated README JW_PR2 Joseph Watson 2023-09-13 17:15:03 -07:00
• 46c0ef6803 Implemented inpaint_str and added example Joseph Watson 2023-09-13 16:25:35 -07:00
• 7bdc90c9b7 Implemented inpaint_str and added example Joseph Watson 2023-09-13 16:25:35 -07:00
• ba8446eae0 Added input pdb for p53 case Joseph Watson 2023-07-25 10:35:27 -07:00
• 47b738f604 Added p53 scaffolding example Joseph Watson 2023-07-25 10:34:21 -07:00
• c9ba72d90f Added input pdb for p53 case JW_PR Joseph Watson 2023-07-25 10:35:27 -07:00
• e6def5b7b2 Added p53 scaffolding example Joseph Watson 2023-07-25 10:34:21 -07:00
• 9149e5395a Fixed incorrect variable name in contig parsing Javier Castellanos 2023-07-20 15:26:11 -07:00
• 5606075d45 updating rosetta-ci test script, adding unpacking ppi scaffolds Sergey Lyskov 2023-06-27 15:47:00 -04:00
• 9da13dc5b3 Update install instructions for model directory location. Rocco Moretti 2023-06-27 10:20:57 -05:00
• b4f4c264a7 Fixed model_only_neighbors typo Nick Randolph 2023-06-12 21:51:27 -04:00
• 8810bf28e5 Swapped SymGen arguments Nick Randolph 2023-06-12 21:45:39 -04:00
• 25e9cda154 adding pdb-diff prefix to comparison test names Sergey Lyskov 2023-05-31 19:29:55 -04:00
• 471b36ebe8 adding pdb-diff prefix to comparison test names Sergey Lyskov 2023-05-31 14:14:00 -04:00
• 3ae829475d adding .rosetta-ci dir to GitHub code-owners file Sergey Lyskov 2023-05-31 13:47:56 -04:00
• a191281e97 updating test config Sergey Lyskov 2023-05-25 17:05:29 -04:00
• 58c310a66a adding accounting of comparisons results Sergey Lyskov 2023-05-17 17:22:27 -04:00
• ba4a76af81 updating test-suite result calculation Sergey Lyskov 2023-05-16 16:41:09 -04:00
• 74bdf45cb5 updating test-sets Sergey Lyskov 2023-05-16 14:24:17 -04:00
• 9bb4c568d3 updating test files Sergey Lyskov 2023-05-11 19:31:44 -04:00
• 060347773f updating test_diffusion script Sergey Lyskov 2023-05-10 20:01:57 -04:00
• 711e0b7aff adding test_diffusion.py Sergey Lyskov 2023-05-10 19:58:22 -04:00
• db2997d237 updating test scripts Sergey Lyskov 2023-05-10 16:41:48 -04:00
• d9fd60c756 updating test files Sergey Lyskov 2023-05-09 20:25:12 -04:00
• 6cf803f5cb adding rosetta-ci Sergey Lyskov 2023-05-06 17:26:18 -04:00
• 06ae1cbcaf Finalize removing icecream as a dependency. Rocco Moretti 2023-05-12 11:02:28 -05:00
• e783762568 changed --parents to -p to be used by each OS tmsincomb 2023-05-17 12:19:48 -07:00
• 5f924fe2e3 Added examples, and updated README Joseph Watson 2023-05-04 17:34:11 -07:00
• 0d629aa672 Code cleaning suggestions from arogozhnikov Joseph Watson 2023-04-26 11:26:17 -07:00
• 5c6f2f1b14 Made necessary changes for integration tests based on example submissions Joseph Watson 2023-04-26 09:11:27 -07:00
• 49b9245204 Fixed 2 typos ISDementyev 2023-05-02 21:21:52 -04:00
• 10fdde9d25 fix output directory for multipleseq example Ryan Henderson 2023-04-26 11:44:35 -04:00
• bee4a9a5c7 cleanup readme Ryan Henderson 2023-04-24 10:55:29 -04:00
• 7b3cc0f682 add example of partial diffusion with multiple sequences Ryan Henderson 2023-04-24 10:52:08 -04:00
• 7d725cedcd Update README.md Ryan Henderson 2023-04-19 11:17:16 -04:00
• e0d10814d2 fix provide_seq contig processing to allow multiple sequences Ryan Henderson 2023-04-19 11:13:45 -04:00
• a9be807e06 Update README.md Jungsub Lim 2023-04-24 13:43:59 +09:00
• 3139977cdb Add instructions for running the Docker container Brian Loyal 2023-04-21 09:56:16 -05:00
• afcee27eed Add Dockerfile with usage instructions Brian Loyal 2023-04-04 12:52:40 -05:00
• 487c72068a Add script to download model files Brian Loyal 2023-04-04 12:52:25 -05:00
• 3e6eb96e35 Switch setup.py from distutils to setuptools Brian Loyal 2023-04-04 12:52:08 -05:00