Pl upgrades#1

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harshagrawal13 wants to merge 128 commits intosoftnanolab:pl_upgradesfrom

aqlaboratory:pl_upgrades

Commits on Feb 16, 2024

added typing hints and fixed some comments
dingquanyu
committed

Commits on Feb 20, 2024

Commits on Mar 1, 2024

Fix always is_custom_template.
rostro36
committed

Commits on Mar 2, 2024

Commits on Mar 19, 2024

Commits on Mar 21, 2024

Commits on Mar 25, 2024

Added alignment method.
rostro36
committed

Commits on Apr 27, 2024

Fix Colab by using OF commit from pl_upgrades
vaclavhanzl
committed

Commits on May 8, 2024

Commits on May 9, 2024

Hotfix to switch order of feature dict generation

christinaflo
authored and
jnwei
committed
Added script for running decoy ranking experiments

sachinkadyan7
authored and
jnwei
committed
Fix distributed seeding behavior

ljarosch
authored and
jnwei
committed
Add LICENSE information to decoy ranking script

sachinkadyan7
authored and
jnwei
committed
Update README to include details for SoloSeq Embeddings

sachinkadyan7
authored and
jnwei
committed
Fix usage example in `download_openfold_soloseq_params.sh`

sachinkadyan7
authored and
jnwei
committed
Add script to download embeddings for training SoloSeq

sachinkadyan7
authored and
jnwei
committed
Fix resolution field in mmcif_parsing

ljarosch
authored and
jnwei
committed
Adds mkl version to environment.yml
jnwei
committed
make space for docker CI
jnwei
committed
Shorten README.md main page.
jnwei
committed
adds mmseqs2 to environment.yml for clustering
jnwei
committed

Commits on May 11, 2024

Update test_permutation.py
jnwei
authored
Merge pull request #406 from dingquanyu/update-permutation-unittest
jnwei
authored
make sure padded asym_id won't affect permutation steps

dingquanyu
authored and
jnwei
committed
fixed bugs in unittests for multi-chain permutation. now working on extra subtests

dingquanyu
authored and
jnwei
committed
remove unnecessary lines

dingquanyu
authored and
jnwei
committed
restore to the verison on main

dingquanyu
authored and
jnwei
committed
added typing hints and fixed some comments

dingquanyu
authored and
jnwei
committed
make sure no padded features are going to be selected as anchors

dingquanyu
authored and
jnwei
committed
fixed typing errors; added more comments

dingquanyu
authored and
jnwei
committed
added comments

dingquanyu
authored and
jnwei
committed
update comments;fixed typos

dingquanyu
authored and
jnwei
committed
Update tests and comments

dingquanyu
authored and
jnwei
committed
fixed typing error of anchor_gt_residue

dingquanyu
authored and
jnwei
committed
Update test_permutation.py
jnwei
committed
Merge branch 'docs' into setup-improvements
jnwei
committed

Commits on May 13, 2024

Commits on May 14, 2024

Commits on May 15, 2024

hotfix: Fix installation documentation
jnwei
authored

Commits on May 17, 2024

Commits on May 23, 2024

Commits on Jul 6, 2024

Fix 3-to-1 letter conversion to use extended mapping
ljarosch
committed

Commits on Jul 8, 2024

Merge pull request #464 from ljarosch/main
jnwei
authored

Commits on Jul 17, 2024

Remove unnecessary double-load of config_json.
ryan-attunely
committed

Commits on Aug 24, 2024

Update Installation.md - fix pl_upgrades clone instructions
vaclavhanzl
authored

Commits on Nov 7, 2024

Merge pull request #479 from vaclavhanzl/patch-3
jnwei
authored

Commits on Nov 13, 2024

add environment variables
etowahadams
committed

Commits on Dec 4, 2024

Merge pull request #505 from etowahadams/update-install
jnwei
authored

Commits on Dec 26, 2024

Minor typo fix in Installation.md
nenuadrian
authored

Commits on Feb 23, 2025

updated script
etowahadams
committed

Commits on Feb 24, 2025

Commits on Apr 23, 2025

Commits on Apr 26, 2025