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Add ruff, run ruff and black
a71a737
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Allow selecting individual chains
Defaults to all chains selected.58b87e3 -
Plot avg attention not sum
3de389d -
Remove Prot-T5 and ProtGPT2
The attention visualization was not implemented since these models don't tokenize single residues, and the models are too large to be loaded with the current infrastructure. Could be added back in the future if needed.386fb31 -
Changet test structure in get_structure
d1b48a1 -
Add PROT BERT
1c423ed
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Split attention.py into attention.py and models.py
eb9ae1f
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Add ZymCTRL model
Needs some tweaking. Massive attention to the same residue makes weird disks in the attention bars. It is also noticeably slow on a CPU only instance.cfba77f
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Rename project protention -> hexviz
GPT4 says is best HexViz: In the Discworld series, Hex is a magical computer-like machine created by the wizards of the Unseen University. HexViz combines the name Hex with "viz," short for visualization. This name suggests that the tool has a magical ability to decipher and visualize the attention patterns within protein structures, much like Hex's ability to solve complex problems in the Discworld universe.28d4b1e -
Visualize attention pairs on structure
58c7b8d
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Add ModelType enum and Model class to hold layers and head count
ebbe380 -
Implement get_attention for tape BERT
466a8f2
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Add get_sequence
b7ab123 -
Add get_protT5
Sentencepiece is needed for the T5 tokenizer87c0dbc -
Add get_structure
f8402f9