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Update truemultimer#268

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dingquanyu merged 26 commits intomainKosinskiLab/AlphaPulldown:mainfrom update-truemultimerKosinskiLab/AlphaPulldown:update-truemultimerCopy head branch name to clipboardMar 7, 2024

+302-8

Commits

Commits on Jan 26, 2024

• added the script that contains necessry utility functions for creating multimeric template features

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  d8d6199

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• update multimeric_template_utils

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  cb447ab

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• finished creating multimeric tempalte features for a single chain

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Commits on Jan 29, 2024

• update objects.py

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  47bde79

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• finished modifying objects.py to accomodate new way of creating multimeric template features

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  530fa5a

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• fixed error in _extract_template_features

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  7ba4ebe

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• update alphapulldown/multimeric_template_utils.py

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• added the unittest for the other version of truemultimer

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Commits on Jan 30, 2024

• update objects.py and multimeric template utils accordingly

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  25eabc5

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• start working on inference script

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  1c74619

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• fixed bugs

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  fb8ebf5

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• update the test script for multimeric template features

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Commits on Jan 31, 2024

• removed structural prediction part

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• update multimeric object initialisation and run_multimer.py accordingly

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  0e63a63

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• added a script that tests imports after pip installation

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• added testing python imports to github_actions

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• fixed the testing step in the user mode

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  d5f5b83

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• fixed bugs but template_atom_mask dimension is still wrong

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Commits on Feb 1, 2024

• fixed template_atom_mask error

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Commits on Feb 2, 2024

• fixed the reproduction issue by forcing the template_sequence to be the same as query_seq

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Commits on Feb 6, 2024

• update the utils so that it can parse pdb files as multimeric templates

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Commits on Feb 7, 2024

• restore the util file back to the previous commit

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  7a49c64

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• fixed dimension issue

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• revert objects.py back to one commit before

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Commits on Feb 23, 2024

• now import MmcifChainFiltered to handel parsing of PDB files when using multimeric templates

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Commits on Mar 7, 2024

• Merge branch 'main' into update-truemultimer

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