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f55f6fb
Fix AlphaLink backend issue #524
DimaMolod Aug 4, 2025
0894720
Update AlphaLink tests with correct weights path and crosslinks testing
DimaMolod Aug 4, 2025
77b64cb
Add final summary of AlphaLink issue #524 resolution
DimaMolod Aug 4, 2025
94de41f
Correct AlphaLink test structure and environment requirements
DimaMolod Aug 4, 2025
c3781e1
Fix AlphaLink backend predict method parameter handling
DimaMolod Aug 4, 2025
0f5f4fe
Add debugging to AlphaLink backend to understand parameter structure
DimaMolod Aug 4, 2025
c87807d
Fix AlphaLink test configuration and remove debug code
DimaMolod Aug 4, 2025
129059d
Update README.md with correct AlphaLink2 instructions
DimaMolod Aug 4, 2025
9c9224f
Fix AlphaLink test sequence extraction for homo-oligomer chopped prot…
DimaMolod Aug 4, 2025
bee4211
Remove invalid AlphaLink flags from run_multimer_jobs.py
DimaMolod Aug 4, 2025
90378f1
Fix subprocess Python executable in run_multimer_jobs.py
DimaMolod Aug 4, 2025
ebd39e2
Add threading control to AlphaLink tests to prevent SIGABRT
DimaMolod Aug 4, 2025
9fc9c06
Fix AlphaLink test to handle subdirectory output structure
DimaMolod Aug 4, 2025
7db2d27
Fix AlphaLink test sequence validation for generative model
DimaMolod Aug 4, 2025
a414273
Add comprehensive AlphaLink test validation
DimaMolod Aug 4, 2025
9200ac3
Fix AlphaLink model name and sequence validation
DimaMolod Aug 4, 2025
dd8a236
Fix AlphaLink to respect num_predictions_per_model flag
DimaMolod Aug 4, 2025
999572f
Add comprehensive AlphaLink test validation and threading controls
DimaMolod Aug 4, 2025
fd1247d
Fix AlphaLink output directory creation issue
DimaMolod Aug 4, 2025
04aae52
Fix AlphaLink chain_id_map compatibility issue
DimaMolod Aug 4, 2025
3e2ba0d
Fix PDB file detection in _check_chain_counts_and_sequences
DimaMolod Aug 4, 2025
23743e5
Fix sequence extraction logic for all test cases
DimaMolod Aug 4, 2025
cdc75bd
Add tests without crosslinks for comprehensive AlphaLink testing
DimaMolod Aug 4, 2025
ffc7975
Fix feature preprocessing for AlphaLink2 compatibility
DimaMolod Aug 4, 2025
8b795b1
Update AlphaLink2 submodule to latest main branch and commit all changes
DimaMolod Aug 5, 2025
aa346e9
Remove leftover test files: test_simple_alphalink.py, fix_test_templa…
DimaMolod Aug 5, 2025
8e55bda
Remove alphapulldown.egg-info directory and add *.egg-info/ to .gitig…
DimaMolod Aug 5, 2025
d62db61
All tests passed but chain id == '9' for all monomers
DimaMolod Aug 7, 2025
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,4 @@ __pycache__*
.idea*
test/test_data/predictions/af*
build/
*.egg-info/
2 changes: 1 addition & 1 deletion AlphaLink2
380 changes: 90 additions & 290 deletions README.md

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1,954 changes: 0 additions & 1,954 deletions alphapulldown.egg-info/PKG-INFO

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228 changes: 0 additions & 228 deletions alphapulldown.egg-info/SOURCES.txt

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1 change: 0 additions & 1 deletion alphapulldown.egg-info/dependency_links.txt

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24 changes: 0 additions & 24 deletions alphapulldown.egg-info/requires.txt

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7 changes: 0 additions & 7 deletions alphapulldown.egg-info/top_level.txt

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