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Full multimer merge #405

Merged
merged 281 commits into from Feb 8, 2024
Merged

Full multimer merge #405

merged 281 commits into from Feb 8, 2024

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christinaflo
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dingquanyu and others added 30 commits June 22, 2023 18:07
@dingquanyu
update test codes
ab659c3
@dingquanyu
revert data_utils and remove all the changes in this file
85cd91f
@dingquanyu
added multi-chain permutation to AlphaFoldMultimerLoss
a49e489
@dingquanyu
Merge pull request #2 from dingquanyu/cleanup-permutation
697ac82 
added multi-chain permutation to AlphaFoldMultimerLoss
@dingquanyu
remove unnecessary extra file
50abc1a
@dingquanyu
added example label files
a741b42
@dingquanyu
Update README.md
938782e
@dingquanyu
update codes
4666e15
@dingquanyu
update the test input to be A2B3
5621ac0
@dingquanyu
swtich to scipy's kabsch algorithm
82895ec
@dingquanyu
switch optimal alignment method to procustes package
458a62f
@dingquanyu
handel NaN and Inf in test output to avoid crashes
2a70e08
@dingquanyu
remove shuffling
24e470b
@dingquanyu
start working on loss part
eeb035c
@dingquanyu
Merge pull request #3 from dingquanyu/modify-assignment-stage
3d87ef2 
Modify assignment stage
@dingquanyu
Update README.md
a3ea7c6
@dingquanyu
added batch_size dimesion to compute_tm
1510507
@dingquanyu
added batch_size dimension
c69053e
@dingquanyu
update the compue_tm function
5e1af36
@dingquanyu
now check the batch_size in compute_tm function
a420160
@dingquanyu
update compute_tm so that it accomodates batch_size dimension in the …
8569353 
…input data
@dingquanyu
move some tensors back to gpu
3ab9da6
@dingquanyu
solved cuda error just for now by moving the 2 tensors to cpu
80f0d61
@dingquanyu
update greedy_align just in case there are nan in rmsd calculation
80b32a3
@dingquanyu
fix the aatype indexing error. now move all tensors to cpu and run ca…
beccaa4 
…lculations first
@dingquanyu
update config so that it will update multimer loss otherwise fape los…
b22bd4e 
…s calculation crashes
@dingquanyu
fixed the fape and backbone loss errors
bbf42cc
@dingquanyu
update test code
c8a3f35
@dingquanyu
Update README.md
76e5525
@dingquanyu
Merge branch 'permutation' of github.com:henrywotton/openfold into pe…
edb4858 
…rmutation
christinaflo and others added 27 commits January 23, 2024 12:17
@christinaflo
Additional fix for multimer deepspeed test
40d9e7d
@jnwei
Update README.md
81ca652 
fixed a typo in the readme for soloseq params path
@jnwei
np type update in openfold.np.relax
2120ce3
@jnwei
update deprecated jax.numpy.DeviceArray to jax.Array
8f8b537
@jnwei
Adds absolute error comparison function with better messaging.
30195c4
@jnwei
readme and small updates for soloseq support on multimer
26d555d
@jnwei
remove nested definition of local_alignmnet_dir in run_pretrained_ope…
0cf8b92 
…nfold.py
@jnwei
Change parse_fasta to split on whitespace or '|' character
790267e
@jnwei
Updates to setup.py and README
e94c97e
@dependabot @jnwei
Bump actions/setup-python from 4 to 5
51d6a41 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
@jnwei
suporting newer numpy
15b1bbd
@controny @jnwei
Fix Miniforge3 download link in Dockerfile
de12c0e
@jnwei
debugging for permutation test
bf8788c
@jnwei
create separate test configs for multimer and monomer
204ed19
@jnwei
fix deepspeed_evo_attention to work in both monomer and multimer sett…
0aa6947 
…ings.
@jnwei
Add fixes to permutation test after refactor
0fe5ea3
@jnwei
adds cutlass directory to .gitignore
396fd44
@jnwei
update setup.py file for version number
3c5233b
@jnwei
Adding multimer support to OpenFold notebook
94a3b18
@jnwei
edit starting sequence in notebook
5e0616b
@jnwei
Update README.md
81d817f 
fixed a typo in the readme for soloseq params path
@jnwei
Adding multimer support to OpenFold notebook
d4acbe6
@jnwei
edit starting sequence in notebook
1165d9e
@jnwei
Merge branch 'multimer' into multimer-small-edits
a2adb14
@jnwei
Merge pull request #404 from jnwei/multimer-small-edits
bc07500 
Type fixes and README changes for multimer branch
@christinaflo
Fixed learning rate scheduler issue, returned to original msa file pa…
6275091 
…rsing
@christinaflo
Merge branch 'main' into multimer
c33a0bd
@christinaflo christinaflo merged commit bb3f51e into main Feb 8, 2024
3 checks passed
@christinaflo christinaflo deleted the multimer branch February 8, 2024 04:06
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4 participants
@christinaflo @dingquanyu @jnwei @controny