Commits · c07075cf7208ee97afcdc095438e2cafb8af3620 · OpenDAS / OpenFold

13 May, 2024 1 commit
- in scripts/utils.py account for case where no conda environment is specified. · c07075cf
  Jennifer Wei authored May 13, 2024
  
  c07075cf
02 May, 2024 9 commits
- Removes OF copy of zero_to_fp32.py favoring deepspeed.util version · 3a4ed753
  Jennifer authored Apr 02, 2024
  
  3a4ed753
- fix path error in scripts/utils.py and logging fix · 2dd481e1
  Jennifer authored Apr 29, 2024
  
  2dd481e1
- run_pretrained_openfold.py: Change default paths of binary to be conda environment bin · cfb4c19c
  jnwei authored Apr 23, 2024
  
  cfb4c19c
- Add log statement to weight conversion script · 711ba0ab
  Jennifer authored Feb 13, 2024
  
  711ba0ab
- bugfixes and adds a section to convert optim files · dd1dd641
  Jennifer authored Feb 12, 2024
  
  dd1dd641
- Adjust weight conversion and add a script for converting checkpoints. · 0a0dbb39
  Jennifer authored Feb 09, 2024
  
  0a0dbb39
- updates zero_to_fp32.py for new deepspeed version and import_weight bugfix · d9d4bf14
  Jennifer authored Feb 08, 2024
  
  d9d4bf14
- Add improved alignment-db creation script · eb4d1e57
  Lukas Jarosch authored Oct 06, 2023
```
- much faster due to the use of threading and mp
- also supports sharding
```
  eb4d1e57
- Scripts from Lukas to be used in improved setup process · 76b1ec98
  Christina Floristean authored Sep 08, 2023
  
  76b1ec98
29 Apr, 2024 1 commit
- fix path error in scripts/utils.py and logging fix · 09e74c76
  Jennifer authored Apr 29, 2024
  
  09e74c76
23 Apr, 2024 1 commit
- run_pretrained_openfold.py: Change default paths of binary to be conda environment bin · cb3ff410
  jnwei authored Apr 23, 2024
  
  cb3ff410
02 Apr, 2024 1 commit
- Removes OF copy of zero_to_fp32.py favoring deepspeed.util version · 577219c1
  Jennifer authored Apr 02, 2024
  
  577219c1
26 Mar, 2024 2 commits
- Add script to download embeddings for training SoloSeq · df8a002d
  Sachin Kadyan authored Mar 26, 2024
  
  df8a002d
- Fix usage example in `download_openfold_soloseq_params.sh` · 06eac9ea
  Sachin Kadyan authored Mar 26, 2024
  
  06eac9ea
20 Feb, 2024 2 commits
- Add improved alignment-db creation script · 70918209
  Lukas Jarosch authored Oct 06, 2023
```
- much faster due to the use of threading and mp
- also supports sharding
```
  70918209
- Scripts from Lukas to be used in improved setup process · 50949b9a
  Christina Floristean authored Sep 08, 2023
  
  50949b9a
14 Feb, 2024 1 commit
- Add log statement to weight conversion script · e31e0378
  Jennifer authored Feb 13, 2024
  
  e31e0378
12 Feb, 2024 1 commit
- bugfixes and adds a section to convert optim files · 775f77dd
  Jennifer authored Feb 12, 2024
  
  775f77dd
09 Feb, 2024 1 commit
- Adjust weight conversion and add a script for converting checkpoints. · 260592e0
  Jennifer authored Feb 09, 2024
  
  260592e0
08 Feb, 2024 1 commit
- updates zero_to_fp32.py for new deepspeed version and import_weight bugfix · 1df591b0
  Jennifer authored Feb 08, 2024
  
  1df591b0
08 Dec, 2023 1 commit
- Remove env restart from setup script · 67a00a6c
  Christina Floristean authored Dec 08, 2023
  
  67a00a6c
29 Nov, 2023 1 commit
- Adds Soloseq parameter download script. · 4a50c9c4
  jnwei authored Nov 29, 2023
  
  4a50c9c4
13 Nov, 2023 1 commit
- Update setup script and refactor qkv prep · 7fb12cf5
  Christina Floristean authored Nov 13, 2023
  
  7fb12cf5
03 Nov, 2023 1 commit
- Fix for loading old OF weights into refactored model · f65b75fe
  Christina Floristean authored Nov 03, 2023
  
  f65b75fe
30 Oct, 2023 1 commit
- Added multimer inference to README · 15850092
  Christina Floristean authored Oct 30, 2023
  
  15850092
27 Oct, 2023 1 commit
- Adds KMP_AFFINITY to conda environment. · e3716118
  Jennifer Wei authored Oct 27, 2023
  
  e3716118
24 Oct, 2023 2 commits
- 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
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
20 Oct, 2023 2 commits
- Remove conda env config setting and update to README · d6ae9f58
  jnwei authored Oct 20, 2023
  
  d6ae9f58
- - Moves python packages to conda installation · fcba3358
  Jennifer Wei authored Oct 20, 2023
```
  instead of pip
- Adds helper line to automatically prepend conda library to
  $LD_LIBRARY_PATH
```
  fcba3358
17 Oct, 2023 2 commits
- Updating $LD_LIBRARY_PATH to include conda environment library. · 705c2677
  Jennifer Wei authored Oct 17, 2023
  
  705c2677
- update installation scripts. · 4fde713c
  Jennifer Wei authored Oct 17, 2023
  
  4fde713c
16 Oct, 2023 2 commits
- Refactoring multimer data pipeline and permutation alignment. · 0cf1541c
  Christina Floristean authored Oct 16, 2023
  
  0cf1541c
- Removes conda installation from installation script. · 7922bd57
  Jennifer Wei authored Oct 16, 2023
  
  7922bd57
06 Oct, 2023 1 commit
- Add improved alignment-db creation script · a3bb3c40
  Lukas Jarosch authored Oct 06, 2023
```
- much faster due to the use of threading and mp
- also supports sharding
```
  a3bb3c40
20 Sep, 2023 1 commit
- Preserves one copy of `tests/test_data/sample_feats.pickle.gz` for unit · 73ff40b6
  Jennifer Wei authored Sep 20, 2023
```
tests in test_data_transforms.py
```
  73ff40b6