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192 Commits

Author SHA1 Message Date
Gustaf Ahdritz
1c279f90ff Restore missing shebang 2022-07-14 07:26:57 -04:00
Gustaf Ahdritz
db43f4ec0e Add CAMEO download script 2022-07-07 19:29:39 -04:00
Gustaf Ahdritz
728f99fc2d Add alignment DB scripts 2022-06-27 18:23:31 -04:00
Gustaf Ahdritz
4e73026983 Fix bug in prep_mmseqs_dbs.sh 2022-06-27 17:32:23 -04:00
Gustaf Ahdritz
abc1ceb097 Fix bug in download_data.sh 2022-06-27 17:31:32 -04:00
Gustaf Ahdritz
d7367f9aee Touch up OF/AF conversion script 2022-06-24 02:13:22 -04:00
Gustaf Ahdritz
76599b12ab Come full circle 2022-06-24 01:58:10 -04:00
Gustaf Ahdritz
a35c44f52a Fix formatting of install_hh_suite.sh 2022-06-23 23:17:05 -04:00
Gustaf Ahdritz
c871ccf339 Fix install script 2022-06-23 13:08:00 -04:00
Gustaf Ahdritz
a48860cba2 Switch source of OF parameters to HuggingFace 2022-06-22 15:48:28 -04:00
Gustaf Ahdritz
07f988116b Fix parameter download script 2022-06-22 02:52:08 -04:00
Gustaf Ahdritz
4e934f7462 Add SLURM script acknowledgement 2022-06-21 01:29:42 -04:00
Gustaf Ahdritz
4a3c392446 Add SLURM alignment script 2022-06-21 01:27:18 -04:00
Gustaf Ahdritz
5fbb0d0d23 Update file ID in OpenFold parameter download script 2022-06-21 01:18:52 -04:00
Gustaf Ahdritz
f8f74006b0 Move parameter downloads 2022-06-17 01:19:26 -04:00
Gustaf Ahdritz
9d09bdb894 Update link in OpenFold parameter download script 2022-06-17 01:14:54 -04:00
Gustaf Ahdritz
233704c573 Add OpenFold parameter download script 2022-06-17 00:41:18 -04:00
Gustaf Ahdritz
6e66b21810 Vastly lower peak inference memory usage 2022-06-10 02:19:32 -04:00
Gustaf Ahdritz
dba4461221 Resolve merge conflicts 2022-04-28 18:51:57 -04:00
Gustaf Ahdritz
4bd1b4d548 Work on multimer continues 2022-04-28 18:45:54 -04:00
Gustaf Ahdritz
f362ebffa7 Undo DeepSpeed config change 2022-03-29 20:38:31 -04:00
Gustaf Ahdritz
9f5581781e Fix DeepSpeed config builder 2022-03-29 15:19:30 -04:00
Gustaf Ahdritz
c83c42e81c Fix bug in mmCIF cache script 2022-03-14 16:31:02 -04:00
Gustaf Ahdritz
950b02f040 One last adjustment to generate_chain_data_cache.py 2022-02-22 17:46:20 -05:00
Gustaf Ahdritz
39860f936c Adjust default behavior of generate_chain_data_cache.py 2022-02-22 17:42:22 -05:00
Gustaf Ahdritz
4c7c30b1d7 Fix chain data cache script bug, improve logging 2022-02-22 17:37:52 -05:00
Gustaf Ahdritz
70362e4b1f Fix bugs in chain data cache script 2022-02-05 00:17:17 -05:00
Gustaf Ahdritz
3b82ddb793 Add chain data cache generator 2022-02-04 23:55:45 -05:00
Gustaf Ahdritz
a46f1b1218 Revert changes to mmcif cache gen script 2022-02-04 15:59:37 -05:00
Gustaf Ahdritz
7f3a48ee80 Un-comment lines in alignment script 2022-02-04 15:17:48 -05:00
Gustaf Ahdritz
84f45ee1bf Fix bug in cache script 2022-02-04 15:10:16 -05:00
Gustaf Ahdritz
54deee17c6 Restore cache generation script 2022-02-04 15:07:12 -05:00
Gustaf Ahdritz
721e43be8d Add GPU relaxation 2022-02-03 22:50:34 -05:00
Gustaf Ahdritz
998155e9b6 Merge branch 'main' of github.com:aqlaboratory/openfold into chunking_experiment 2022-02-03 17:09:26 -05:00
Gustaf Ahdritz
fb341b174c Merge 2022-02-03 17:09:18 -05:00
Gustaf Ahdritz
f30d77b7d7 Prep for training 2022-02-03 17:07:10 -05:00
Gustaf Ahdritz
6ce8cfe31e Fixes 2022-02-03 17:06:45 -05:00
Gustaf Ahdritz
02fc43762b Beef up alignment script 2022-02-03 17:06:30 -05:00
Gustaf Ahdritz
81ebd4a8d3 Fix NVIDIA loggier issue in install script 2022-02-01 16:20:58 -05:00
Gustaf Ahdritz
52a8b8f313 Update AlphaFold parameter download link 2022-02-01 12:36:55 -05:00
Karl Leswing
ffd154146b Source the environment because it is reccomended that this is called via source 2022-01-20 10:57:37 -05:00
Karl Leswing
74675b7358 Ready For PR 2022-01-20 10:50:59 -05:00
Gustaf Ahdritz
36b9a8ea9c Add script for generating sample feature dict 2021-12-30 19:51:50 -05:00
Gustaf Ahdritz
f4701ffa91 Rename prepare_proteinnet_msas.py to prep_proteinnet_msas.py 2021-12-20 00:50:20 -05:00
Gustaf Ahdritz
edffead3c4 Make AlignmentRunner more flexible 2021-12-19 22:08:04 -05:00
Gustaf Ahdritz
f4316dc084 Fix AlphaFold DB download script 2021-12-19 15:44:13 -05:00
Gustaf Ahdritz
96709588dd Add low-memory attention (still needs to be incorporated) 2021-12-17 18:00:06 -05:00
Gustaf Ahdritz
71fabe1e3b Fix mmseqs script bug 2021-12-10 18:33:23 -05:00
Sachin Kadyan
ddf922df6f Made initialization consistent for template_featurizer in all modules. 
Added obsolete_pdbs_file and release_dates_path in all initialization points.
 2021-12-10 18:58:56 -04:00
Gustaf Ahdritz
57720ec78e Merge pull request #24 from yuzhiguo07/patch-1 
Update precompute_alignments_mmseqs.py
 2021-11-29 22:02:34 -05:00