Commits · d7c115371ef54c1660ea75d9608f3049ca242bb0 · OpenDAS / OpenFold

27 Oct, 2023 1 commit
- Merge branch 'main' into multimer · d7c11537
  Christina Floristean authored Oct 27, 2023
  
  d7c11537
25 Oct, 2023 1 commit
- README: Small improvements, info regarding templates · 9e32781f
  Sachin Kadyan authored Oct 25, 2023
  
  9e32781f
24 Oct, 2023 4 commits
- README: Update details about SoloSeq and inference-time embedding generation. · 2d4fe4f4
  Sachin Kadyan authored Oct 24, 2023
  
  2d4fe4f4
- Separate out input parsing code in `EmbeddingGenerator` · 86b990d6
  Sachin Kadyan authored Oct 24, 2023
```
Bugfix: Corrected paths for just-in-time embedding generation
```
  86b990d6
- Just-in-time embedding generation for the SoloSeq model · 8185c307
  Sachin Kadyan authored Oct 24, 2023
  
  8185c307
- README: Add details about using the bulk embedding generation script · 4c8e3764
  Sachin Kadyan authored Oct 23, 2023
  
  4c8e3764
23 Oct, 2023 2 commits
- More cleaning of bulk embedding generation script · 92835fd5
  Sachin Kadyan authored Oct 23, 2023
  
  92835fd5
- Cleaned up `precompute_embeddings.py`. · 0026173e
  Sachin Kadyan authored Oct 22, 2023
  
  0026173e
21 Oct, 2023 1 commit
- New script for generating ESM embeddings in bulk · bcc6d97b
  Sachin Kadyan authored Oct 09, 2023
  
  bcc6d97b
19 Oct, 2023 1 commit
- Update BibTex · 2300f672
  Gustaf Ahdritz authored Oct 19, 2023
  
  2300f672
17 Oct, 2023 1 commit
- Refactoring multimer perm alignment, temporary fixes before removing recycling dimension · 7c7dffd0
  Christina Floristean authored Oct 16, 2023
  
  7c7dffd0
16 Oct, 2023 5 commits
- Removed references to jax · def329b8
  Christina Floristean authored Oct 16, 2023
  
  def329b8
- Fix multimer sampling · 8470b803
  Christina Floristean authored Oct 16, 2023
  
  8470b803
- Merge branch 'multimer' of https://github.com/aqlaboratory/openfold into multimer · 14853379
  Christina Floristean authored Oct 16, 2023
  
  14853379
- Refactoring multimer data pipeline and permutation alignment. · 0cf1541c
  Christina Floristean authored Oct 16, 2023
  
  0cf1541c
- Merge pull request #359 from dingquanyu/update-kabsch_rotation · ec75fe22
  Christina Floristean authored Oct 16, 2023
```
move the kabsch rotation step to gpu
```
  ec75fe22
12 Oct, 2023 1 commit
- move the kabsch rotation step to gpu · cdfb0c75
  Geoffrey Yu authored Oct 12, 2023
  
  cdfb0c75
11 Oct, 2023 1 commit
- README fixes for single sequence model · 6381ddd6
  Sachin Kadyan authored Oct 11, 2023
  
  6381ddd6
10 Oct, 2023 22 commits
- Improved UX: Automatically set the single seq mode flag · e8de822e
  Sachin Kadyan authored Oct 05, 2023
  
  e8de822e
- Separate out the seq mode configs from vanilla OF config · c8c12397
  Sachin Kadyan authored Oct 02, 2023
  
  c8c12397
- Limit the MSA distillation clusters to 1 in seq mode · b45a91ba
  Sachin Kadyan authored Oct 02, 2023
  
  b45a91ba
- Reduce redundancy in seq embedding config presets · 3f592307
  Sachin Kadyan authored Oct 02, 2023
  
  3f592307
- Fix typos · 6aefa986
  Gustaf Ahdritz authored Sep 29, 2023
  
  6aefa986
- Updated README: Running seqemb model inference · 3c240cb3
  Sachin Kadyan authored Sep 27, 2023
  
  3c240cb3
- Added test for no column attention Evoformer · 28334db3
  Sachin Kadyan authored Sep 18, 2023
  
  28334db3
- Added sequence embedding mode test for `model`. · a7c0d0d1
  Sachin Kadyan authored Sep 18, 2023
  
  a7c0d0d1
- Added test for PreembeddingEmbedder · 777d738a
  Sachin Kadyan authored Sep 17, 2023
  
  777d738a
- Default value for --use_single_seq_mode arg · 6012b9e1
  Sachin Kadyan authored Sep 15, 2023
  
  6012b9e1
- Add sequence embedding mode option to .core file parser · 08ef6e9f
  Sachin Kadyan authored Sep 15, 2023
  
  08ef6e9f
- Added flag in training script for using sequence embeddings · 395a9f1b
  Sachin Kadyan authored Sep 14, 2023
  
  395a9f1b
- Bugfix for timings.json - now store timings per tag. · f85d67f4
  sachinkadyan7 authored Sep 13, 2023
  
  f85d67f4
- Renamed `preembedding_embedder` to `input_embedder` · 9b114f28
  sachinkadyan7 authored Sep 11, 2023
  
  9b114f28
- Properly reading the embedding file · 5a8d2b78
  sachinkadyan7 authored Sep 11, 2023
  
  5a8d2b78
- Added config presets for esm1b model inference · 36d5708c
  sachinkadyan7 authored Sep 11, 2023
  
  36d5708c
- Fix for a bug in data_transforms which wouldn't allow creation of MSA mask if... · 047e69af
  Sachin Kadyan authored Nov 01, 2022
```
Fix for a bug in data_transforms which wouldn't allow creation of MSA mask if there is only input sequence in MSA.
- Set `max_msa_clusters=1` in model presets for allowing the input sequence to be a MSA cluster centre.
```
  047e69af
- Added switch for sequence embedding mode to the PDB file pipeline. · 624b5aa6
  Sachin Kadyan authored Oct 29, 2022
```
- In `seqemb_mode`, `process_pdb` loads sequence embedding for the PDB's protein, and a dummy MSA
```
  624b5aa6
- Added documentation for some sequence embedding model changes. · 29962990
  Sachin Kadyan authored Oct 28, 2022
  
  29962990
- Added inference model preset for seqemb mode. · a83c6fcc
  Sachin Kadyan authored Oct 28, 2022
  
  a83c6fcc
- Added a separate AlignmentRunner for handling seq_emb mode. · 8c94482a
  Sachin Kadyan authored Oct 28, 2022
```
- In `seq_emb` mode, the AlignmentRunner works only on generating templates.
```
  8c94482a
- Added the seq_emb features to the list of features to be processed by feature... · 380947c4
  Sachin Kadyan authored Oct 28, 2022
```
Added the seq_emb features to the list of features to be processed by feature pipeline , if using seq_emb mode
- In `seq_emb` mode, add list of `seq_emb` features to `feature_names`
```
  380947c4