Jennifer Wei
74e903e5db
Update OpenFold.ipynb
2024-05-17 11:38:48 +02:00
Jennifer Wei
935f51559e
Update OpenFold.ipynb
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Adds button for colab notebook.
2024-05-17 11:35:25 +02:00
Jennifer Wei
3c1fd31ac4
Merge pull request #443 from jnwei/main
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Fix formatting in installation.md
2024-05-17 09:50:16 +02:00
jnwei
775b57e226
Fix formatting in installation.md
2024-05-17 09:49:48 +02:00
Jennifer Wei
6af8158138
hotfix: Fix installation documentation
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Rename installation.md to Installation.md to fix typo in index file.
2024-05-15 23:11:13 +02:00
Jennifer Wei
feb45a521e
Merge pull request #440 from vaclavhanzl/patch-1
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Link OpenFold repo from the docs
2024-05-15 03:15:52 +07:00
Vaclav Hanzl
d2ffb8d09c
Link OpenFold repo from the docs
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The intro part taken from the main README (which makes a title on GitHub) obviously did not link to itself but now the repo is hard to find when reading the (great!) docs :)
2024-05-14 21:44:09 +02:00
Jennifer Wei
f434a2786b
Merge pull request #439 from aqlaboratory/setup-improvements
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Adds Documentation and minor quality of life fixes
2024-05-13 17:02:28 +07:00
Jennifer Wei
d8117ce373
in scripts/utils.py account for case where no conda environment is specified.
2024-05-13 16:37:11 +07:00
jnwei
97dae6c68a
Updates biopython version to 1.83 in colab notebook, which seems to work better
2024-05-13 16:33:50 +07:00
jnwei
ffc9b3f65a
updates biopython version to 1.80 in colab notebook
2024-05-13 16:22:15 +07:00
jnwei
6384d793e0
Removes mpi4py from environment.yml -- not supported for Docker builds
2024-05-13 16:06:47 +07:00
jnwei
49804a599a
small fix to docker-image ci workflow
2024-05-13 15:39:40 +07:00
Jennifer Wei
6706864754
Merge branch 'main' into setup-improvements
2024-05-13 15:35:03 +07:00
Jennifer Wei
3eef7caab3
Merge pull request #432 from vaclavhanzl/fix-colab-change-used-commit
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Fix Colab by using OF commit from pl_upgrades
2024-05-13 15:34:03 +07:00
Jennifer Wei
a3c131904b
Update OpenFold.ipynb to newest pl_upgrades commit
2024-05-13 15:13:55 +07:00
Jennifer Wei
29b5823e8b
Merge pull request #419 from aqlaboratory/setup-improvements_additional-scripts
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Duplicate expansion support
2024-05-13 14:57:36 +07:00
jnwei
6cba403b77
fix typo in environment.yml
2024-05-13 14:14:06 +07:00
Jennifer Wei
fcb7796710
edits to inference documentation and script for parameters
2024-05-13 04:50:25 +00:00
Jennifer Wei
f561cec0e5
Merge branch 'docs' into setup-improvements
2024-05-11 10:54:56 +00:00
Jennifer Wei
32765d20a1
Update test_permutation.py
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Fixed a small typo in permutation unit test docstring
2024-05-11 10:45:13 +00:00
Dingquan Yu
d9680984db
fixed typing error of anchor_gt_residue
2024-05-11 10:45:13 +00:00
Dingquan Yu
6f1329ef7c
Update tests and comments
2024-05-11 10:45:13 +00:00
Dingquan Yu
9a6eb64983
update comments;fixed typos
2024-05-11 10:45:13 +00:00
Geoffrey Yu
bc24032693
added comments
2024-05-11 10:45:13 +00:00
Geoffrey Yu
04d637828f
fixed typing errors; added more comments
2024-05-11 10:45:13 +00:00
Geoffrey Yu
6d41838460
make sure no padded features are going to be selected as anchors
2024-05-11 10:45:13 +00:00
Geoffrey Yu
f7571e25ed
added typing hints and fixed some comments
2024-05-11 10:45:13 +00:00
Geoffrey Yu
77cb41359f
restore to the verison on main
2024-05-11 10:45:12 +00:00
Geoffrey Yu
d1a32aa3b1
remove unnecessary lines
2024-05-11 10:45:12 +00:00
Geoffrey Yu
0df04f33b3
fixed bugs in unittests for multi-chain permutation. now working on extra subtests
2024-05-11 10:45:12 +00:00
Geoffrey Yu
17b8c142d4
make sure padded asym_id won't affect permutation steps
2024-05-11 10:45:12 +00:00
Jennifer Wei
9d88b8ebc6
Merge pull request #406 from dingquanyu/update-permutation-unittest
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Update multi-chain permutation and permutation unittest
2024-05-11 16:02:21 +07:00
Jennifer Wei
55c293ca0b
Update test_permutation.py
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Fixed a small typo in permutation unit test docstring
2024-05-11 15:37:12 +07:00
Dingquan Yu
15113dcb25
fixed typing error of anchor_gt_residue
2024-05-10 17:18:49 +02:00
Dingquan Yu
5f782370fc
Update tests and comments
2024-05-10 17:06:05 +02:00
Dingquan Yu
61191bff81
update comments;fixed typos
2024-05-10 16:00:30 +02:00
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
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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
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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
