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Update truemultimer #268

Merged
merged 26 commits into from
Mar 7, 2024
Merged

Update truemultimer #268

merged 26 commits into from
Mar 7, 2024

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dingquanyu
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@dingquanyu
added the script that contains necessry utility functions for creatin…
d8d6199 
…g multimeric template features
@dingquanyu
update multimeric_template_utils
cb447ab
@dingquanyu
finished creating multimeric tempalte features for a single chain
d47b21e
@dingquanyu
update objects.py
47bde79
@dingquanyu
finished modifying objects.py to accomodate new way of creating multi…
530fa5a 
…meric template features
@dingquanyu
fixed error in _extract_template_features
7ba4ebe
@dingquanyu
update alphapulldown/multimeric_template_utils.py
0b29566
@dingquanyu
added the unittest for the other version of truemultimer
f81ae58
@dingquanyu
update objects.py and multimeric template utils accordingly
25eabc5
@dingquanyu
start working on inference script
1c74619
@dingquanyu
fixed bugs
fb8ebf5
@dingquanyu
update the test script for multimeric template features
dc63118
@dingquanyu
removed structural prediction part
ad38407
@dingquanyu
update multimeric object initialisation and run_multimer.py accordingly
0e63a63
@dingquanyu
added a script that tests imports after pip installation
a06996f
@dingquanyu
added testing python imports to github_actions
d8269aa
@dingquanyu
fixed the testing step in the user mode
d5f5b83
@dingquanyu
fixed bugs but template_atom_mask dimension is still wrong
8f1ec0f
@dingquanyu
fixed template_atom_mask error
39298cf
@dingquanyu
fixed the reproduction issue by forcing the template_sequence to be t…
c6c2221 
…he same as query_seq
@dingquanyu
update the utils so that it can parse pdb files as multimeric templates
2c672a6
@dingquanyu
restore the util file back to the previous commit
7a49c64
@dingquanyu
fixed dimension issue
9398f64
@dingquanyu
revert objects.py back to one commit before
e96d395
@dingquanyu
now import MmcifChainFiltered to handel parsing of PDB files when usi…
8f7fe44 
…ng multimeric templates
@DimaMolod
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Would be cool to put this part into a separate function, so I could re-use it for truemultimer e.g. here (after adding the check that exactly 1 template was provided)

@dingquanyu dingquanyu merged commit 473fbfa into main Mar 7, 2024
4 checks passed
@dingquanyu dingquanyu deleted the update-truemultimer branch March 7, 2024 16:21
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2 participants
@dingquanyu @DimaMolod