Jennifer Wei
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6f63267114
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Merge pull request #470 from rkosai/main
Remove unnecessary double-load of config_json.
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2024-07-18 15:29:51 +07:00 |
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Jannik Gut
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7d227395d6
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Merge branch 'main' into main
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2024-07-18 03:17:55 +02:00 |
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Ryan Kosai
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8b5212da72
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Remove unnecessary double-load of config_json.
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2024-07-16 20:48:43 -07:00 |
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Jennifer Wei
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fcb7796710
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edits to inference documentation and script for parameters
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2024-05-13 04:50:25 +00:00 |
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Jennifer
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e4f9af23e7
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Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold into setup-improvements
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2024-05-02 03:11:15 -04:00 |
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Jennifer
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c4cccb6b0e
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adds deepspeed_evoformer flag to inference script.
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2024-05-02 02:55:21 -04:00 |
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Jennifer
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0f2b292913
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Adds `experiment_config_json` for setting custom configurations with a json.
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2024-05-02 02:36:12 -04:00 |
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Jennifer
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d1fe024b20
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Adds `experiment_config_json` for setting custom configurations with a json.
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2024-03-13 01:22:46 -04:00 |
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rostro36
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10b6838817
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Fix always is_custom_template.
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2024-03-01 10:08:04 +01:00 |
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Christina Floristean
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ed40380c76
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Hotfix to switch order of feature dict generation
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2024-02-23 14:18:27 -05:00 |
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rostro36
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17f24bd7d2
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Added custom template folder
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2024-02-20 09:57:12 +01:00 |
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Christina Floristean
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6275091c96
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Fixed learning rate scheduler issue, returned to original msa file parsing
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2024-02-07 15:47:24 -05:00 |
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Jennifer
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0cf8b928e1
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remove nested definition of local_alignmnet_dir in run_pretrained_openfold.py
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2024-02-02 01:29:21 -05:00 |
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Christina Floristean
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f94ee668e5
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Fixes for inference alignment generation
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2023-11-02 13:43:48 -04:00 |
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Christina Floristean
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15850092d3
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Added multimer inference to README
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2023-10-30 16:15:05 -04:00 |
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Christina Floristean
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d7c115371e
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Merge branch 'main' into multimer
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2023-10-27 12:09:39 -04:00 |
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Sachin Kadyan
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86b990d6ed
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Separate out input parsing code in `EmbeddingGenerator`
Bugfix: Corrected paths for just-in-time embedding generation
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2023-10-24 12:30:25 -05:00 |
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Sachin Kadyan
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8185c30775
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Just-in-time embedding generation for the SoloSeq model
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2023-10-24 01:03:20 -05:00 |
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Sachin Kadyan
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e8de822e9b
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Improved UX: Automatically set the single seq mode flag
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2023-10-10 16:33:07 -04:00 |
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Sachin Kadyan
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299629903b
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Added documentation for some sequence embedding model changes.
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2023-10-10 16:33:07 -04:00 |
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Sachin Kadyan
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8c94482aa0
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Added a separate AlignmentRunner for handling seq_emb mode.
- In `seq_emb` mode, the AlignmentRunner works only on generating templates.
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2023-10-10 16:33:07 -04:00 |
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Sachin Kadyan
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aacf1b6fb2
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Added single seq mode in inference script and forwarded to the FASTA processors.
- Added `use_single_seq_mode` flag in inference script arguments.
- Passed on the flag to the FASTA file `data_processor`.
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2023-10-10 16:33:07 -04:00 |
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Dingquan Yu
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7f12c2a7fc
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Update run_pretrained_openfold.py
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2023-09-19 18:00:39 +02:00 |
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Geoffrey Yu
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9a679b3186
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fixed problem with multimer inference
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2023-09-19 11:21:49 +02:00 |
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Christina Floristean
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fdcb72e846
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Bug fixes for multimer inference and monomer training
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2023-08-02 15:15:06 -04:00 |
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Christina Floristean
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425bdb5e21
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Added UniRef30 to data pipeline
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2023-04-18 13:37:36 -04:00 |
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Christina Floristean
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736f27fdc8
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Merge main again
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2023-04-11 12:28:09 -04:00 |
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Christina Floristean
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39a6d0e64a
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Merging in main branch
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2023-04-09 11:07:04 -04:00 |
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Jose Duarte
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8a76cc153e
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WIP towards writing relaxed structure as modelcif
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2023-03-06 15:48:23 -08:00 |
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Jose Duarte
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9db8dc369b
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Adding output_cif as CLI argument
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2023-02-20 14:08:05 -08:00 |
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Sam DeLuca
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ef222a31cb
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add long_sequence_inference option to command line
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2022-12-13 19:46:07 +00:00 |
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mhrmsn
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b41a9c83a2
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Add subtract_plddt argument to prep_output call
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2022-09-21 14:33:45 -04:00 |
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Sam DeLuca
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71a274d89b
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adding a script for threading a sequence onto a structure
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2022-08-24 14:11:45 +00:00 |
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Brian Loyal
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450f523631
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Added more error handling
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2022-08-12 11:33:23 -05:00 |
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Brian Loyal
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95c83ae1df
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Bug fix
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2022-08-12 11:21:07 -05:00 |
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Brian Loyal
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32dd89bb1c
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Write the inference and relax times to file
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2022-08-12 10:52:13 -05:00 |
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Gustaf Ahdritz
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ecd5a7ed50
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Fix config setting bug in inference script
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2022-07-29 13:06:37 -04:00 |
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Santi Villalba
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88450a6798
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fix tag-sequence missmatch when predicting for multiple fastas
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2022-07-16 19:18:58 +02:00 |
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Gustaf Ahdritz
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4b3a102ffa
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Fix timing in inference script
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2022-07-15 16:07:12 -04:00 |
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Gustaf Ahdritz
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9617306a75
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Add option to subtract pLDDT from 100
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2022-07-08 16:49:48 -04:00 |
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Gustaf Ahdritz
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4f53624d92
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Add tracing, TensorFloat32 utilization, and FlashAttention
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2022-07-08 11:37:41 -04:00 |
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Sam DeLuca
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7d23b6543f
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improving file naming in run_pretrained_openfold
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2022-06-29 12:53:28 +00:00 |
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Brian Loyal
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294c04add3
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Updated code to and fix bad fasta inputs
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2022-06-23 13:53:59 -05:00 |
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Brian Loyal
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435c164dd4
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Only use .fa files, not subfolders or other files
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2022-06-23 08:42:10 -05:00 |
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Brian Loyal
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148afc98da
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Update fasta code to account for multi-line seqs
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2022-06-23 08:41:06 -05:00 |
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Gustaf Ahdritz
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3654b7f307
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Fix inference script again
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2022-06-22 23:41:01 -04:00 |
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Gustaf Ahdritz
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04d1f005f9
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Fix undefined reference
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2022-06-22 23:34:55 -04:00 |
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Gustaf Ahdritz
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1fa6ffab77
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Refactor run_pretrained_openfold.py a little
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2022-06-22 23:30:43 -04:00 |
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Sam DeLuca
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a2ab7ab7f5
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more fixes
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2022-06-22 18:58:39 +00:00 |
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Sam DeLuca
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ce04296201
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bugfix
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2022-06-22 18:28:20 +00:00 |