Commits · 86b990d6edfe577e905e8610f4c47633af95011a · OpenDAS / OpenFold

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
10 Oct, 2023 4 commits
- Improved UX: Automatically set the single seq mode flag · e8de822e
  Sachin Kadyan authored Oct 05, 2023
  
  e8de822e
- Added documentation for some sequence embedding model changes. · 29962990
  Sachin Kadyan authored Oct 28, 2022
  
  29962990
- 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 single seq mode in inference script and forwarded to the FASTA processors. · aacf1b6f
  Sachin Kadyan authored Oct 14, 2022
```
- Added `use_single_seq_mode` flag in inference script arguments.
- Passed on the flag to the FASTA file `data_processor`.
```
  aacf1b6f
06 Mar, 2023 1 commit
- WIP towards writing relaxed structure as modelcif · 8a76cc15
  Jose Duarte authored Mar 06, 2023
  
  8a76cc15
20 Feb, 2023 1 commit
- Adding output_cif as CLI argument · 9db8dc36
  Jose Duarte authored Feb 20, 2023
  
  9db8dc36
13 Dec, 2022 1 commit
- add long_sequence_inference option to command line · ef222a31
  Sam DeLuca authored Dec 13, 2022
  
  ef222a31
21 Sep, 2022 1 commit
- Add subtract_plddt argument to prep_output call · b41a9c83
  mhrmsn authored Sep 21, 2022
  
  b41a9c83
24 Aug, 2022 1 commit
- adding a script for threading a sequence onto a structure · 71a274d8
  Sam DeLuca authored Aug 24, 2022
  
  71a274d8
12 Aug, 2022 3 commits
- Added more error handling · 450f5236
  Brian Loyal authored Aug 12, 2022
  
  450f5236
- Bug fix · 95c83ae1
  Brian Loyal authored Aug 12, 2022
  
  95c83ae1
- Write the inference and relax times to file · 32dd89bb
  Brian Loyal authored Aug 12, 2022
  
  32dd89bb
29 Jul, 2022 1 commit
- Fix config setting bug in inference script · ecd5a7ed
  Gustaf Ahdritz authored Jul 29, 2022
  
  ecd5a7ed
16 Jul, 2022 1 commit
- fix tag-sequence missmatch when predicting for multiple fastas · 88450a67
  Santi Villalba authored Jul 16, 2022
  
  88450a67
15 Jul, 2022 1 commit
- Fix timing in inference script · 4b3a102f
  Gustaf Ahdritz authored Jul 15, 2022
  
  4b3a102f
08 Jul, 2022 2 commits
- Add option to subtract pLDDT from 100 · 9617306a
  Gustaf Ahdritz authored Jul 08, 2022
  
  9617306a
- Add tracing, TensorFloat32 utilization, and FlashAttention · 4f53624d
  Gustaf Ahdritz authored Jul 08, 2022
  
  4f53624d
29 Jun, 2022 1 commit
- improving file naming in run_pretrained_openfold · 7d23b654
  Sam DeLuca authored Jun 29, 2022
  
  7d23b654
23 Jun, 2022 7 commits
- Updated code to and fix bad fasta inputs · 294c04ad
  Brian Loyal authored Jun 23, 2022
  
  294c04ad
- fixing bug in jax handling · 07b522b7
  Sam DeLuca authored Jun 23, 2022
  
  07b522b7
- Only use .fa files, not subfolders or other files · 435c164d
  Brian Loyal authored Jun 17, 2022
  
  435c164d
- Update fasta code to account for multi-line seqs · 148afc98
  Brian Loyal authored Jun 13, 2022
  
  148afc98
- Fix inference script again · 3654b7f3
  Gustaf Ahdritz authored Jun 22, 2022
  
  3654b7f3
- Fix undefined reference · 04d1f005
  Gustaf Ahdritz authored Jun 22, 2022
  
  04d1f005
- Refactor run_pretrained_openfold.py a little · 1fa6ffab
  Gustaf Ahdritz authored Jun 22, 2022
  
  1fa6ffab
22 Jun, 2022 4 commits
- more fixes · a2ab7ab7
  Sam DeLuca authored Jun 22, 2022
  
  a2ab7ab7
- bugfix · ce042962
  Sam DeLuca authored Jun 22, 2022
  
  ce042962
- Fix even more undefined references · 99cdb062
  Gustaf Ahdritz authored Jun 22, 2022
  
  99cdb062
- Add logging to inference script · ce27a6ca
  Gustaf Ahdritz authored Jun 21, 2022
  
  ce27a6ca
21 Jun, 2022 3 commits
- Fixing model generation · 43b8c6f9
  Sam DeLuca authored Jun 21, 2022
  
  43b8c6f9
- wip · fcee03aa
  Sam DeLuca authored Jun 21, 2022
  
  fcee03aa
- Update inference script · 9dee6caa
  Gustaf Ahdritz authored Jun 21, 2022
  
  9dee6caa
17 Jun, 2022 1 commit
- Add support for public checkpoints · 1921ac99
  Gustaf Ahdritz authored Jun 16, 2022
  
  1921ac99
16 Jun, 2022 1 commit
- refactor to allow multiple models to run · 15a8c321
  Sam DeLuca authored Jun 16, 2022
  
  15a8c321
10 Jun, 2022 1 commit
- Vastly lower peak inference memory usage · 6e66b218
  Gustaf Ahdritz authored Jun 10, 2022
  
  6e66b218
25 May, 2022 3 commits
- Fix another undefined reference · a1cf7454
  Gustaf Ahdritz authored May 25, 2022
  
  a1cf7454
- Fix undefined reference · be87500a
  Gustaf Ahdritz authored May 25, 2022
  
  be87500a
- Add AlphaFold-Gap inference · f4043e1c
  Gustaf Ahdritz authored May 25, 2022
  
  f4043e1c