Pushed Revisions

branch: RFdiffusion:commits 「№44」
Commited by: Sergey Lyskov
GitHub Pull Request link: 「№358」
Merge: 「b44206a2a」← 「903bcadc2」 code diff
Scheduled at: 2025-06-22 17:27:15.076589

Pull Request №358 RosettaCommons/RFdiffusion/main ← lyskov/RFdiffusion/main Merge: b44206a2a79f219bb1a649ea50603a284c225050←903bcadc28391694c59050d5a3d13ae82efdb69b add GitHub CI workflow for running ppi-scaffolds tests ---------------- Merge commit message: add GitHub CI workflow for running ppi-scaffolds tests (#1)

branch: RFdiffusion:commits 「№43」
Commited by: David Juergens
GitHub Pull Request link: 「№357」
Merge: 「b44206a2a」← 「3ecb01f24」 code diff
Scheduled at: 2025-06-20 16:43:55.148099

Pull Request №357 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/rfpeptides Merge: b44206a2a79f219bb1a649ea50603a284c225050←3ecb01f2423e90ed524a70a1bcf02a2a249a64ac RFpeptides macrocyclic peptide design ---------------- Merge commit message: Update README.md

branch: RFdiffusion:commits 「№42」
Commited by: David Juergens
GitHub Pull Request link: 「№357」
Merge: 「b44206a2a」← 「140909edf」 code diff
Scheduled at: 2025-06-20 12:27:03.596583

Pull Request №357 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/rfpeptides Merge: b44206a2a79f219bb1a649ea50603a284c225050←140909edf2ba34a7edba4eb57a35f6d49b360d3f RFpeptides macrocyclic peptide design ---------------- Merge commit message: add .sh examples, gabarap pdb, import numpy

branch: RFdiffusion:commits 「№41」
Commited by: David Juergens
GitHub Pull Request link: 「№357」
Merge: 「b44206a2a」← 「5939d4c4b」 code diff
Scheduled at: 2025-06-20 03:44:48.602216

Pull Request №357 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/rfpeptides Merge: b44206a2a79f219bb1a649ea50603a284c225050←5939d4c4b008a27285297990cc766971b65be340 RFpeptides macrocyclic peptide design ---------------- Merge commit message: bugfix readme

branch: RFdiffusion:commits 「№40」
Commited by: kierannp
GitHub Pull Request link: 「№354」
Merge: 「b44206a2a」← 「0bdab9e89」 code diff
Scheduled at: 2025-06-17 20:20:14.011995

Pull Request №354 RosettaCommons/RFdiffusion/main ← kierannp/RFdiffusion/main Merge: b44206a2a79f219bb1a649ea50603a284c225050←0bdab9e897e28245d853a4ebcc5b73a3a3d5e2f2 Oligomer generation for translational symmetry ---------------- Merge commit message: Oligomer generation for translational symmetry

branch: RFdiffusion:commits 「№39」
Commited by: Brahm Yachnin
GitHub Pull Request link: 「№348」
Merge: 「b44206a2a」← 「d32205a17」 code diff
Scheduled at: 2025-06-17 13:34:29.696277

Pull Request №348 RosettaCommons/RFdiffusion/main ← BYachnin/RFdiffusion/BYachnin/main_chain_and_res_numbering Merge: b44206a2a79f219bb1a649ea50603a284c225050←d32205a17f244757fcbe94f4658329ef9cb0459c Retain chain and residue numbering in RFdiffusion ---------------- Merge commit message: Extend available new chains to include lowercase letters Also print a warning if the user exceeds 52 chains (using up all upper- and lower-case chain ids).

branch: RFdiffusion:commits 「№38」
Commited by: Brahm Yachnin
GitHub Pull Request link: 「№346」
Merge: 「b44206a2a」← 「63e270f71」 code diff
Scheduled at: 2025-05-21 14:16:48.993789

Pull Request №346 RosettaCommons/RFdiffusion/main ← BYachnin/RFdiffusion/BYachnin/enable_symmetry Merge: b44206a2a79f219bb1a649ea50603a284c225050←63e270f715104896a5684108f582046b1d551b1e Retain chain and residue numbering in RFdiffusion ---------------- Merge commit message: For fixed chains, retain residue numbering For chains that are completely fixed, retain the residue numbering from the input rather than renumbering. For chains that are partially or fully designed by RFdiffusion, it isn't clear to me what the 'correct' behaviour should be, so these chains will be re-numbered starting at residue 1.

branch: RFdiffusion:commits 「№37」
Commited by: Sergey Lyskov
GitHub Pull Request link: 「№309」
Merge: 「b44206a2a」← 「681693c34」 code diff
Scheduled at: 2025-04-24 11:33:47.875018

Pull Request №309 RosettaCommons/RFdiffusion/main ← arikat/RFdiffusion/main Merge: b44206a2a79f219bb1a649ea50603a284c225050←681693c346036cd1a5da61eb211c7898bd8bb13c Update Dockerfile to include numpy1.24.3 ---------------- Merge commit message: dummy commit to trigger test run

branch: RFdiffusion:commits 「№36」
Commited by: Aarya Venkat
GitHub Pull Request link: 「№309」
Merge: 「b44206a2a」← 「bdcd913c8」 code diff
Scheduled at: 2025-01-07 14:07:03.162420

Pull Request №309 RosettaCommons/RFdiffusion/main ← arikat/RFdiffusion/main Merge: b44206a2a79f219bb1a649ea50603a284c225050←bdcd913c897ad5fccadbd967676f093206d0043a Update Dockerfile to include numpy1.24.3 ---------------- Merge commit message: Update Dockerfile to include numpy1.24.3 Numpy2 does not work w/ current RFDiffusion, but the dockerfile automatically installs numpy2 (breaking RFDiffusion when running via docker). This just hardcodes numpy==1.24.3 to allow RFDiffusion to continue working properly.

branch: RFdiffusion:commits 「№35」
Commited by: Brian Loyal
GitHub Pull Request link: 「№286」
Merge: 「b44206a2a」← 「142930960」 code diff
Scheduled at: 2024-10-21 15:44:17.430288

Pull Request №286 RosettaCommons/RFdiffusion/main ← brianloyal/RFdiffusion/main Merge: b44206a2a79f219bb1a649ea50603a284c225050←142930960dd5905403b0d6fd90696fe40650a128 Update model_runners.py ---------------- Merge commit message: Update model_runners.py Fixes https://github.com/RosettaCommons/RFdiffusion/issues/273

branch: RFdiffusion:commits 「№34」
Commited by: David Prihoda
GitHub Pull Request link: 「№278」
Merge: 「b44206a2a」← 「94c952534」 code diff
Scheduled at: 2024-10-15 08:32:51.375378

Pull Request №278 RosettaCommons/RFdiffusion/main ← prihoda/RFdiffusion-fork/prihoda-patch1 Merge: b44206a2a79f219bb1a649ea50603a284c225050←94c952534d41743ad6e6ce47e22a4abb07ce1d68 Enable running with T < 15 ---------------- Merge commit message: Enable running with T < 15

branch: RFdiffusion:commits 「№33」
Commited by: David Prihoda
GitHub Pull Request link: 「№278」
Merge: 「b44206a2a」← 「b866ad44d」 code diff
Scheduled at: 2024-09-06 11:25:57.253909

Pull Request №278 RosettaCommons/RFdiffusion/main ← prihoda/RFdiffusion-fork/prihoda-patch1 Merge: b44206a2a79f219bb1a649ea50603a284c225050←b866ad44d0f524f7246ca226d9cd77a87334334c Enable running with T < 15 ---------------- Merge commit message: Enable running with T < 15

branch: RFdiffusion:commits 「№32」
Commited by: David Prihoda
GitHub Pull Request link: 「№277」
Merge: 「b44206a2a」← 「a7a04730e」 code diff
Scheduled at: 2024-09-06 11:15:02.914512

Pull Request №277 RosettaCommons/RFdiffusion/main ← prihoda/RFdiffusion-fork/main Merge: b44206a2a79f219bb1a649ea50603a284c225050←a7a04730e8037b2c954825b6d0d484ddac861209 Fix Torch CPU support in SE3Transformer ---------------- Merge commit message: Fix Torch CPU support in SE3Transformer

branch: RFdiffusion:commits 「№31」
Commited by: Joseph Watson
GitHub Pull Request link: 「№269」
Merge: 「820bfdfad」← 「521a488d0」 code diff
Scheduled at: 2024-08-25 10:10:10.568090

Pull Request №269 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/liuetal Merge: 820bfdfaded8c260b962dc40a3171eae316b6ce0←521a488d0c0a39b9f08da4d2a1486ff0700a23ff Merge in code for Caixuan's paper ---------------- Merge commit message: correct example

branch: RFdiffusion:commits 「№30」
Commited by: Junior Martins
GitHub Pull Request link: 「№229」
Merge: 「820bfdfad」← 「abc3b005d」 code diff
Scheduled at: 2024-07-11 16:07:33.133923

Pull Request №229 RosettaCommons/RFdiffusion/main ← jrom99/RFdiffusion/main Merge: 820bfdfaded8c260b962dc40a3171eae316b6ce0←abc3b005dc82ed0925807e83861e8cd611b57c64 Allow manually setting device name (CUDA/CPU) ---------------- Merge commit message: Use prefix_05d format

branch: RFdiffusion:commits 「№29」
Commited by: Eric DEVEAUD
GitHub Pull Request link: 「№253」
Merge: 「820bfdfad」← 「d3496a85f」 code diff
Scheduled at: 2024-06-21 11:02:21.255695

Pull Request №253 RosettaCommons/RFdiffusion/main ← EricDeveaud/RFdiffusion/main Merge: 820bfdfaded8c260b962dc40a3171eae316b6ce0←d3496a85ffa4d2c421ac382b84d969d522c23cf0 use user HOME dir for cache, config, models ---------------- Merge commit message: hydra config searched under HOME/rfdissusion/config/inference hydra config location may be overwitten by RFD_HYDRA_CFG env var

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