Commits · eeda001cde0fd1e634a6b179d3a373c123f03a90 · OpenDAS / OpenFold · GitLab

12 Oct, 2021 7 commits
- Exclude tests and scripts from import · eeda001c
  Gustaf Ahdritz authored Oct 12, 2021
  
  eeda001c
- Add sample DeepSpeed config · 8bbe9e5a
  Gustaf Ahdritz authored Oct 12, 2021
  
  8bbe9e5a
- Reformat README, require run script option · 29315bdc
  Gustaf Ahdritz authored Oct 11, 2021
  
  29315bdc
- Rename runner, update command in README · 1b802b29
  Gustaf Ahdritz authored Oct 11, 2021
  
  1b802b29
- Merge branch 'main' of ssh://github.com/aqlaboratory/openfold into main · 911795ca
  Gustaf Ahdritz authored Oct 11, 2021
  
  911795ca
- Refactor run script (WIP) · 9b60d737
  Gustaf Ahdritz authored Oct 11, 2021
  
  9b60d737
- Fix TM calculation bugs · 71189e20
  Gustaf Ahdritz authored Oct 11, 2021
  
  71189e20
10 Oct, 2021 2 commits
- Rename run script parameter · 376c60c7
  Gustaf Ahdritz authored Oct 10, 2021
  
  376c60c7
- Add TM calculations, move testing wrappers · a3c2ae51
  Gustaf Ahdritz authored Oct 10, 2021
  
  a3c2ae51
09 Oct, 2021 6 commits
- Fix incorrect types in data pipeline · 9eda0b43
  Gustaf Ahdritz authored Oct 09, 2021
  
  9eda0b43
- Fix another typo · 05e08750
  Gustaf Ahdritz authored Oct 08, 2021
  
  05e08750
- Remove Python 3.9-only math function · fb785094
  Gustaf Ahdritz authored Oct 08, 2021
  
  fb785094
- Fix typo · 3bb47f89
  Gustaf Ahdritz authored Oct 08, 2021
  
  3bb47f89
- Move config script, reformat data_transforms · 651949b2
  Gustaf Ahdritz authored Oct 08, 2021
  
  651949b2
- Tweak run script args, roll back repo to Python 3.7 (for Colab) · f4150fa1
  Gustaf Ahdritz authored Oct 08, 2021
  
  f4150fa1
08 Oct, 2021 25 commits
- Merge branch 'main' of ssh://github.com/aqlaboratory/openfold into main · bec2292d
  Gustaf Ahdritz authored Oct 08, 2021
  
  bec2292d
- Fix setup.py for Colab · 82b24508
  Gustaf Ahdritz authored Oct 08, 2021
  
  82b24508
- Added a wrapper shell script to download all databases by executing each of the individual scripts. · 83fa3b90
  Sachin Kadyan authored Oct 08, 2021
  
  83fa3b90
- Added the shell script to download the uniref90 database. · e8ac4317
  Sachin Kadyan authored Oct 08, 2021
  
  e8ac4317
- Added the shell script to download the uniclust30 database. · a78c0445
  Sachin Kadyan authored Oct 08, 2021
  
  a78c0445
- Added the shell script to download the small BFD database. · ac8d5677
  Sachin Kadyan authored Oct 08, 2021
  
  ac8d5677
- Added the shell script to download the PDB mmCIF database. · 44e87083
  Sachin Kadyan authored Oct 08, 2021
  
  44e87083
- Added the shell script to download the PDB70 database. · e8226a58
  Sachin Kadyan authored Oct 08, 2021
  
  e8226a58
- Added the shell script to download the Mgnify database for JackHMMer MSA queries. · 48df5d18
  Sachin Kadyan authored Oct 08, 2021
  
  48df5d18
- Added the shell script to download the BFD database for HHBlits queries. · 365254a7
  Sachin Kadyan authored Oct 08, 2021
  
  365254a7
- Remove automatic import of OpenMM scripts · 7e923e72
  Gustaf Ahdritz authored Oct 08, 2021
  
  7e923e72
- Update requirements · 3dcc2bb5
  Gustaf Ahdritz authored Oct 08, 2021
  
  3dcc2bb5
- Merge branch 'features' into main · 961d86fc
  Gustaf Ahdritz authored Oct 08, 2021
  
  961d86fc
- Update README · 0f1b1968
  Gustaf Ahdritz authored Oct 08, 2021
  
  0f1b1968
- Fix FP precision issue in test · 8048efd6
  Gustaf Ahdritz authored Oct 08, 2021
  
  8048efd6
- Fix DRMSD bug · 4dd50722
  Gustaf Ahdritz authored Oct 08, 2021
  
  4dd50722
- Make minor formatting edits · e8e0b66f
  Gustaf Ahdritz authored Oct 08, 2021
  
  e8e0b66f
- Moved the DataPipeline class (which uses numpy) to a different directory. · f8c81df4
  Sachin Kadyan authored Oct 08, 2021
  
  f8c81df4
- Moved all external tool executor classes (which use np) to a different directory. · 822fda7d
  Sachin Kadyan authored Oct 08, 2021
  
  822fda7d
- Integrated the feature processing pipeline in the 'main' runner script. · 9337ed13
  Sachin Kadyan authored Oct 08, 2021
  
  9337ed13
- Fixes the import paths for the internal imports. · c8e54318
  Sachin Kadyan authored Oct 08, 2021
  
  c8e54318
- Implemented the feature_pipeline wrapper for taking in the raw features and... · 455731cc
  Sachin Kadyan authored Oct 08, 2021
```
Implemented the feature_pipeline wrapper for taking in the raw features and executing the feature transformations on the tensors.
```
  455731cc
- Implemented the main input_pipeline wrapper for executing all ensembled and... · 0b180437
  Sachin Kadyan authored Oct 08, 2021
```
Implemented the main input_pipeline wrapper for executing all ensembled and non-ensembled feature transformations and collecting them appropriately.
```
  0b180437
- Added feature transformations for making denser (14 atom) dimensions instead of 37 atom. · c16e400e
  Sachin Kadyan authored Oct 08, 2021
  
  c16e400e
- Added feature transformations for making MSA features. · bc43ccf0
  Sachin Kadyan authored Oct 08, 2021
  
  bc43ccf0