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ModelAngelo 1.0 #43

Merged
merged 181 commits into from
May 16, 2023
Merged

ModelAngelo 1.0 #43

merged 181 commits into from
May 16, 2023

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jamaliki
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jamaliki added 30 commits October 18, 2022 16:29
@jamaliki
Lukas HMM
1817b02
@jamaliki
Lukas HMM, output HMM files instead of HHM
f6b24b7
@jamaliki
Lukas HMM, output HMM files instead of HHM
3318b64
@jamaliki
Fix sigmoid bugs
d031b17
@jamaliki
Merge pull request #4 from jamaliki/lukas-hmm
81141bb 
Lukas hmm
@jamaliki
Update README.md
d821ca1
@jamaliki
Update README.md
f6ccb16
@jamaliki
Add rigid_group_atom_positions for nucleotides
eaa5b1a
@jamaliki
Add atom type names, migrate to atom23
60d26c1
@jamaliki
Fix naming issue
80d43cd
@jamaliki
Always do aggressive pruning
f6b38db
@jamaliki
Merge branch 'main' into minimize-memory-usage
553e62e
@jamaliki
Merge pull request #5 from jamaliki/minimize-memory-usage
fa761fd 
Minimize memory usage
@jamaliki
Prune chains based on length
cc6093f
@jamaliki
Update success statement
4f8c4e2
@jamaliki
Working on torsion angles for nucleotides
0674045
@jamaliki
Working on torsion angles for nucleotides
008ae75
@jamaliki
Finished atomf_to_frames
fe1303a
@jamaliki
In the middle of atomf to torsions
2f0198a
@jamaliki
Untested: atomf_to_torsion_angles
c451468
@jamaliki
Untested: torsion_angles_to_frames
fab88bb
@jamaliki
Things run, now to see if reverse works correctly
370f269
@jamaliki
Everything works!!!! 🥳🥳🥳
4a2e2f9
@jamaliki
Everything works!!!! 🥳🥳🥳
15bc82e
@jamaliki
Nucleotides should not show up in unified_seq
138a6e8
@jamaliki
Fix bug
a3976a2
@jamaliki
Fix bug
e1a052f
@jamaliki
Merge pull request #8 from jamaliki/main
2a1e6af 
Bring updated post processing to nucleotides
@jamaliki
IPR: Postprocessing with nucleotides
7903e1b
@jamaliki
IPR: Run scripts with nucleotides
1f9abd4
jamaliki added 28 commits March 24, 2023 20:32
@jamaliki
Changes in evaluate for very large complexes
4875e39
@jamaliki
Eval updates
eb6841e
@jamaliki
Fix back params of HMM
e54e695
@jamaliki
Try speeding up hmmsearch
1deaf2c
@jamaliki
Update README.md
5d7d773
@jamaliki
Update README.md
0b092e8
@jamaliki
Update README.md
393ee4e
@jamaliki
Update README.md
89a8de4
@jamaliki
Update README.md
e7cc213
@jamaliki
Update README.md
98b1ec8
@jamaliki
Update README.md
5ecac73
@jamaliki
Update README.md
435bbad
@jamaliki
Update README.md
0ce55c4
@jamaliki
Update README.md
a564c2f
@jamaliki
Update README.md
32abfb5
@jamaliki
Add compile_if_possible function
36999b1
@jamaliki
Compile module if possible
9f235b6
@jamaliki
Try to speed up inference
43ba721
@jamaliki
Merge remote-tracking branch 'origin/main' into main
774f8c4
@jamaliki
Remove compile
b2905c4
@jamaliki
Debug timing
ef2e4f1
@jamaliki
Debug timing
ea39498
@jamaliki
Debug timing
7ea3930
@jamaliki
Debug timing
e763059
@jamaliki
Much faster now
8b09e6c
@jamaliki
Make Protein able to parse only nucleotide structures
fc128fc
@jamaliki
Merge branch 'main' into nucleotide
03d2ddc
@jamaliki
Merge pull request #1 from jamaliki/nucleotide
bfb4ca3 
Nucleotide
scheres
scheres approved these changes May 16, 2023
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ModelAngelo 1.0 allows nucleotide building and improved protein identification

@scheres scheres merged commit 55f599b into main May 16, 2023
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@scheres scheres scheres approved these changes

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@jamaliki @scheres