Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Rebase update-truemultimer #283

Closed
wants to merge 66 commits into from
Closed

Rebase update-truemultimer #283

wants to merge 66 commits into from

Conversation

dingquanyu
Copy link
Collaborator

No description provided.

jkosinski and others added 30 commits January 28, 2024 14:05
@jkosinski
Update example_3.md
331cc20 
Remove the space characters again.
@jkosinski
Delete test/test_data/true_multimer/cage_BC_AF.pdb
0bdbc32
@jkosinski
Delete test/test_data/true_multimer/cage_BC_AF.cif
d9f0113
@jkosinski
Delete test/test_data/true_multimer/templates/cage_AB_overlap.cif
729bbbe
@DimaMolod
Merge pull request #246 from KosinskiLab/jkosinski-patch-1
3153087 
Update example_3.md
@DimaMolod
Disable test_from_af_output_pdb
722a725
@DimaMolod
Use another template as AF input file
231863a
@DimaMolod
Calculate RMSD between mmt and each ranked_?.pdb
4df350c
@DimaMolod
Report RMSD between the predictions and the first template for TrueMu…
3756bda 
…ltimer
@DimaMolod
Update github_actions.yml
30a63fe 
disable pytorch installation (no space left on device)
@DimaMolod
Remove 4 letters long code. New rmsd interface. Use temp dir
36e56fa
@DimaMolod
Generate deterministic pdb code. Use all backbone atoms for RMSD
60e0ba7
@DimaMolod
Remove template alingments from multimeric features, can't store b-st…
d3a1920 
…ring in feature dict
@DimaMolod
Merge pull request #254 from KosinskiLab/autormsd
6490e91 
Autormsd
@DimaMolod
First working implementation
3c6a773
@jkosinski
Update Developing.md
9e28269
@jkosinski
Update example_1.md
93bf83a
@jkosinski
Update example_1.md
5cd6724
@DimaMolod
Merge pull request #263 from KosinskiLab/jkosinski-patch-3
0656f89 
Fix versions in example 1
@DimaMolod
Merge pull request #260 from KosinskiLab/jkosinski-patch-2
dc7701c 
Update Developing.md
@DimaMolod
save superposed structures to the temp_dir
df29661
@DimaMolod
Count only dirs to ignore new meta.json
0676faa
@DimaMolod
ignore meta.json in several other places. Save superposed structures …
3b2b474 
…to temp dir
@DimaMolod
Remove Bio.SeqIO as used AP parse_fasta instead
c3c2a30
@DimaMolod
Take fasta_paths from FLAGS, not from feature_dict
4c749d4
@DimaMolod
Mock uniref30_2023_02
ea1319d
@DimaMolod
create_and_save_monomer_objects made readable. Some functions moved t…
d3198d9 
…o utils
@DimaMolod
Deleted __pycache__ dir
b945b34
@DimaMolod
Deleted __pycache__ dir
313392f
@DimaMolod
Code linting. More explanaitations of threshol_clashes param
3b9c6c4
DimaMolod and others added 29 commits February 27, 2024 14:54
@DimaMolod
run 4 jobs in parallel
2443672
@dingquanyu
add warning not to overload the remote server. fixed #60
2b3fd2d
@dingquanyu
fixed the first point of issue 177
2d5a7b6
@DimaMolod
Update example_1.md
fcfbcfb 
fixes #15
@dingquanyu
update ColabFold submodule
47396b9
@DimaMolod
Update objects.py
724e485 
fix mmseqs2 features_all bug
@DimaMolod
remove create_individual_featrues(_with_templates).py for the merged …
4cb45c4 
…version
@DimaMolod
Update example_1.md
8c80d3b
@dingquanyu
Update setup.cfg
78c7fcf
@dingquanyu
Update github_actions.yml
15b8e13 
For now the unittests will not run if the develop-type if user
@DimaMolod
Call create_ind_feats, not create_ind_feats_with_template
6822570
@DimaMolod
Provide fastas twice to run all tests in one go
f25cd08
@DimaMolod
Update example_1.md
e612920
@DimaMolod
Update example_2.md
c0ffc1c
@DimaMolod
Update example_3.md
3355d98
@DimaMolod
Update example_2.md
b86dd43
@DimaMolod
Merge pull request #271 from KosinskiLab/DimaMolod-patch-1
4f61a96 
Update example 1,2,3
@dingquanyu
fixed the sorting and now it sorts numerically
f0b94c6
@dingquanyu
now uses regex to sort files numerically
0be420d
@dingquanyu
Merge pull request #273 from KosinskiLab/fix-185
9147a2f 
fixed the sorting and now it sorts numerically
@dingquanyu
Merge pull request #270 from KosinskiLab/fix-mmseqs-issue60-issue176-…
7cf4efb 
…issue177

Fix mmseqs ifixed #60 #176  #177
@dingquanyu
now allows monomeric model to run with num_recycles higher than 3 fixed
c32d1e2 
#272
@dingquanyu
add options to zip msa files
0615e2e
@DimaMolod
Use 1 fasta with 4 seqs
fabc41c
@DimaMolod
Bug fix: --use_mmseqs=False doesn't trigger mmseqs2 now
cee4f42
@dingquanyu
update zipping and unzipping codes
655fc3c
@dingquanyu
Merge pull request #277 from KosinskiLab/fix-9
2e88c42 
Fix 9
@DimaMolod
New.
c450325 
script for truncating pickles written by @gilep 
use absl flags and run in parallel
@DimaMolod
Merge pull request #280 from KosinskiLab/truncate_pickles
593e30b 
New.
@dingquanyu dingquanyu closed this Mar 7, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@dingquanyu @jkosinski @DimaMolod