Commits · a90da39554ca10f2f43d61727f4dd9e8c8aa30c5 · OpenDAS / OpenFold

24 Oct, 2023 1 commit
- Test flash-attention v0.2.1 on docker CI · a90da395
  jnwei authored Oct 24, 2023
  
  a90da395
23 Oct, 2023 7 commits
- Merge remote-tracking branch 'mattwthompson/ci' into installation-updates · 5f5c8f2a
  jnwei authored Oct 23, 2023
  
  5f5c8f2a
- Use conventional "short hash" style · 7666c802
  Matthew W. Thompson authored Oct 23, 2023
  
  7666c802
- Update name to `pytorch-lightning` · 58210350
  Matthew W. Thompson authored Oct 23, 2023
  
  58210350
- Add Dependabot for Actions · 736d6687
  Matthew W. Thompson authored Oct 23, 2023
  
  736d6687
- Update checkout action · 32c11376
  Matthew W. Thompson authored Oct 23, 2023
  
  32c11376
- Switch to Miniforge3 · f86d42f4
  Matthew W. Thompson authored Oct 23, 2023
  
  f86d42f4
- Update environment YAML · 6bf5c8ce
  Matthew W. Thompson authored Oct 23, 2023
  
  6bf5c8ce
20 Oct, 2023 6 commits
- Update BibTex · 0c20e3c9
  Gustaf Ahdritz authored Oct 19, 2023
  
  0c20e3c9
- Remove conda env config setting and update to README · d6ae9f58
  jnwei authored Oct 20, 2023
  
  d6ae9f58
- Updates Dockerfile to not use OpenMM patches. · b3a118fc
  Jennifer Wei authored Oct 20, 2023
  
  b3a118fc
- Merge branch 'installation-updates' of... · 2893fd93
  Jennifer Wei authored Oct 20, 2023
```
Merge branch 'installation-updates' of https://github.com/aqlaboratory/openfold into installation-updates

Merging changes from different systems
```
  2893fd93
- Updates installation instructions in the README. · 3e3f07c7
  Jennifer Wei authored Oct 20, 2023
  
  3e3f07c7
- - 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
19 Oct, 2023 1 commit
- Update BibTex · 2300f672
  Gustaf Ahdritz authored Oct 19, 2023
  
  2300f672
17 Oct, 2023 4 commits
- Merge branch 'installation-updates' of... · d77a8dab
  Jennifer authored Oct 17, 2023
```
Merge branch 'installation-updates' of https://github.com/aqlaboratory/openfold into installation-updates
```
  d77a8dab
- Remove openmm patches · fb34a0cb
  Jennifer authored Oct 17, 2023
  
  fb34a0cb
- 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 1 commit
- Removes conda installation from installation script. · 7922bd57
  Jennifer Wei authored Oct 16, 2023
  
  7922bd57
11 Oct, 2023 1 commit
- README fixes for single sequence model · 6381ddd6
  Sachin Kadyan authored Oct 11, 2023
  
  6381ddd6
10 Oct, 2023 19 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