Commits · 8b5212da72f26d804b0b01d86541c86708f63b80 · OpenDAS / OpenFold

17 Jul, 2024 1 commit
- Remove unnecessary double-load of config_json. · 8b5212da
  Ryan Kosai authored Jul 16, 2024
  
  8b5212da
13 May, 2024 1 commit
- edits to inference documentation and script for parameters · fcb77967
  Jennifer Wei authored May 13, 2024
  
  fcb77967
09 May, 2024 1 commit
- Hotfix to switch order of feature dict generation · 02493a8c
  Christina Floristean authored Feb 23, 2024
  
  02493a8c
02 May, 2024 2 commits
- adds deepspeed_evoformer flag to inference script. · c4cccb6b
  Jennifer authored Apr 30, 2024
  
  c4cccb6b
- Adds `experiment_config_json` for setting custom configurations with a json. · 0f2b2929
  Jennifer authored Mar 13, 2024
  
  0f2b2929
13 Mar, 2024 1 commit
- Adds `experiment_config_json` for setting custom configurations with a json. · d1fe024b
  Jennifer authored Mar 13, 2024
  
  d1fe024b
23 Feb, 2024 1 commit
- Hotfix to switch order of feature dict generation · ed40380c
  Christina Floristean authored Feb 23, 2024
  
  ed40380c
07 Feb, 2024 1 commit
- Fixed learning rate scheduler issue, returned to original msa file parsing · 6275091c
  Christina Floristean authored Feb 07, 2024
  
  6275091c
02 Feb, 2024 1 commit
- remove nested definition of local_alignmnet_dir in run_pretrained_openfold.py · 0cf8b928
  Jennifer authored Feb 02, 2024
  
  0cf8b928
06 Nov, 2023 1 commit
- Hotfix to correct seed type in inference · 099769d2
  Christina Floristean authored Nov 06, 2023
  
  099769d2
02 Nov, 2023 1 commit
- Fixes for inference alignment generation · f94ee668
  Christina Floristean authored Nov 02, 2023
  
  f94ee668
30 Oct, 2023 1 commit
- Added multimer inference to README · 15850092
  Christina Floristean authored Oct 30, 2023
  
  15850092
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
04 Oct, 2023 1 commit
- Remove scale when using ds kernel · a0985761
  Christina Floristean authored Oct 03, 2023
  
  a0985761
20 Sep, 2023 1 commit
- fixed inference script · 01ef215e
  Geoffrey Yu authored Sep 20, 2023
  
  01ef215e
19 Sep, 2023 2 commits
- Update run_pretrained_openfold.py · 7f12c2a7
  Dingquan Yu authored Sep 19, 2023
  
  7f12c2a7
- fixed problem with multimer inference · 9a679b31
  Geoffrey Yu authored Sep 19, 2023
  
  9a679b31
02 Aug, 2023 1 commit
- Bug fixes for multimer inference and monomer training · fdcb72e8
  Christina Floristean authored Aug 02, 2023
  
  fdcb72e8
18 Apr, 2023 1 commit
- Added UniRef30 to data pipeline · 425bdb5e
  Christina Floristean authored Apr 18, 2023
  
  425bdb5e
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 2 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