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Author SHA1 Message Date
jnwei
d61f585e86 Adds example directory 2024-05-10 17:21:28 +07:00
jnwei
11d5fdf45d Update training OpenFold docs with correct paths. 2024-05-10 17:04:54 +07:00
jnwei
9a6deab736 adds mmseqs2 to environment.yml for clustering 2024-05-09 17:18:42 +07:00
jnwei
7f8d1246ae Shorten README.md main page. 2024-05-09 17:18:42 +07:00
jnwei
cf367df964 make space for docker CI 2024-05-09 17:18:42 +07:00
Jennifer
60eff6326f Adds mkl version to environment.yml 2024-05-09 17:18:42 +07:00
ljarosch
7e76be0622 Fix resolution field in mmcif_parsing 
Without the break statement this function will fall back to setting the resolution to _reflns.d_resolution_high for most structures, which reflects the resolution limit in the raw data and not the final structure (see https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.d_resolution_high.html and https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_d_res_high.html).
 2024-05-09 17:18:42 +07:00
Sachin Kadyan
453ae89bf4 Add script to download embeddings for training SoloSeq 2024-05-09 17:18:42 +07:00
Sachin Kadyan
6d1ca2637b Fix usage example in download_openfold_soloseq_params.sh 2024-05-09 17:18:42 +07:00
Sachin Kadyan
b5db6c3448 Update README to include details for SoloSeq Embeddings 2024-05-09 17:18:42 +07:00
Sachin Kadyan
5a7b024257 Add LICENSE information to decoy ranking script 2024-05-09 17:18:42 +07:00
Lukas Jarosch
9660a43d10 Fix distributed seeding behavior 
This adds workers=True to the Lightning seed_everything function which guarantees different random states across all processes in distributed training. Prior to that some processes on different GPUs with the same worker ID could share the same random state.

Note that this will break reproducibility between runs prior to and after this change.

Also removes the seed and supress_output modules that were not used anymore in OpenFold.
 2024-05-09 17:18:42 +07:00
Sachin Kadyan
cc6deaa882 Added script for running decoy ranking experiments 2024-05-09 17:18:42 +07:00
Christina Floristean
02493a8c85 Hotfix to switch order of feature dict generation 2024-05-09 17:18:42 +07:00
jnwei
945ecc0cc0 minor language edits 2024-05-08 23:40:57 +07:00
jnwei
d22a354b32 small edits to main page 2024-05-08 23:36:17 +07:00
jnwei
6c25555ada creates link to FAQ in documentation 2024-05-08 23:34:34 +07:00
jnwei
72bb51eca3 Adds FAQ section 2024-05-08 23:27:01 +07:00
jnwei
24dc3af010 add convert v1 weights instructions 2024-05-08 23:16:15 +07:00
jnwei
60cfbcc166 Add addtional inference pages 2024-05-08 22:48:26 +07:00
jnwei
087cf9f816 updates to Inference.md 2024-05-08 20:36:58 +07:00
jnwei
b87946a26f cleanup makefiles and original readme 2024-05-08 15:36:30 +07:00
jnwei
67668153e1 replace doc environment pip dependencies with conda builds 2024-05-08 15:16:25 +07:00
jnwei
fd294f86a1 fix typo in readthedocs.yaml 2024-05-08 15:12:28 +07:00
jnwei
a432a93664 Rough draft dump of docs and readthedocs build 2024-05-08 15:10:25 +07:00
jnwei
e41e6517f6 Initial commit for sphinx documentation. 2024-03-20 18:40:56 +07:00
jnwei
f1cd138152 removes outputs from OpenFold.ipynb 2024-02-21 14:39:11 +07:00
jnwei
9776b69634 Merge weight-loading changes into setup-improvements 2024-02-21 14:06:18 +07:00
jnwei
9f346d3598 Updates commit value for OpenFold notebook. 2024-02-21 14:03:49 +07:00
Christina Floristean
119529972e Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold into setup-improvements 2024-02-20 12:30:05 -05:00
Lukas Jarosch
70918209d4 Add improved alignment-db creation script 
- much faster due to the use of threading and mp
- also supports sharding
 2024-02-20 12:21:32 -05:00
Christina Floristean
50949b9a58 Scripts from Lukas to be used in improved setup process 2024-02-20 12:21:32 -05:00
Jennifer
ddfccd56d7 changes reloading weights to account for possible state_dict headers. 2024-02-20 04:40:40 -05:00
Jennifer
e31e03781f Add log statement to weight conversion script 2024-02-14 00:48:00 -05:00
Jennifer
775f77dd12 bugfixes and adds a section to convert optim files 2024-02-12 05:14:53 -05:00
Jennifer
260592e066 Adjust weight conversion and add a script for converting checkpoints. 2024-02-09 04:00:07 -05:00
Jennifer
1df591b06f updates zero_to_fp32.py for new deepspeed version and import_weight bugfix 2024-02-08 04:08:35 -05:00
Christina Floristean
bb3f51e5a2 Merge pull request #405 from aqlaboratory/multimer 
Full multimer merge
v2.0.0 		2024-02-07 23:06:08 -05:00
Christina Floristean
c33a0bd68e Merge branch 'main' into multimer 2024-02-07 15:47:58 -05:00
Christina Floristean
6275091c96 Fixed learning rate scheduler issue, returned to original msa file parsing 2024-02-07 15:47:24 -05:00
Jennifer Wei
bc07500422 Merge pull request #404 from jnwei/multimer-small-edits 
Type fixes and README changes for multimer branch
 2024-02-07 23:25:00 +07:00
jnwei
a2adb14748 Merge branch 'multimer' into multimer-small-edits 2024-02-07 23:19:27 +07:00
jnwei
1165d9ebef edit starting sequence in notebook 2024-02-07 23:02:23 +07:00
jnwei
d4acbe6ef8 Adding multimer support to OpenFold notebook 2024-02-07 23:02:23 +07:00
Jennifer Wei
81d817fe68 Update README.md 
fixed a typo in the readme for soloseq params path
 2024-02-07 23:02:19 +07:00
jnwei
5e0616b641 edit starting sequence in notebook 2024-02-07 22:57:37 +07:00
jnwei
94a3b18e23 Adding multimer support to OpenFold notebook 2024-02-07 22:57:37 +07:00
jnwei
3c5233bdaf update setup.py file for version number 2024-02-07 22:54:16 +07:00
Jennifer
396fd44afa adds cutlass directory to .gitignore 2024-02-07 01:04:12 -05:00
Jennifer
0fe5ea3168 Add fixes to permutation test after refactor 2024-02-07 01:03:40 -05:00