Custom template fix, IPSAE, and Protenix#47

Merged

hlasimpk merged 40 commits into

mainfrom

custom_template_fix

Jan 8, 2026

Commits on Nov 5, 2025

Refactor input JSON handling and update sequence processing in add_msa_to_json. I need to update output_json logic to be a flag instead of a pathway
hllelli2
committed

Commits on Dec 11, 2025

Inclusion of ipsae scoring
hlasimpk
committed

Commits on Dec 15, 2025

small bug fix
hlasimpk
committed
Updated how ipsae was called to fix some run time errors
hlasimpk
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Commits on Dec 18, 2025

Commits on Dec 19, 2025

Commits on Dec 22, 2025

Refactored boltz/chai to have their own micromamba envs. Changed sif_path to af3_sif_path and added the option to the config ini, this permits other programs to be included in the future
hlasimpk
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Fixed missed sif commands, and remembered to commit backend envs
hlasimpk
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Fixed bug
hlasimpk
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bug fix, and updates to readme
hlasimpk
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Fixed issue in af3_to_chai that required chai libs and removed py10 specific syntax
hlasimpk
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Small bug fix
hlasimpk
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Caught some missed bugs
hlasimpk
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Further attempt to mute annoying future warning from Chai
hlasimpk
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hard set panderas version to stop Chai complaining
hlasimpk
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Add in mute env option
hlasimpk
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Fixed ipsae tooltip and af3_sif config
hlasimpk
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Commits on Jan 2, 2026

Initial implementation of protenix within abcfold framework
hlasimpk
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Added missed files
hlasimpk
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Update the toml to include protenix
hlasimpk
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Fixed a few minor bugs and updated the css
hlasimpk
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Added in tests for ipsae and protenix
hlasimpk
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Commits on Jan 3, 2026

Ipsae tests were affecting downstream tests, therefore made the inputs deepcopies
hlasimpk
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Fixed bugs found in protenix testing
hlasimpk
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Commits on Jan 5, 2026

Add ccd_ prefix to ptms too
hlasimpk
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Patched an issue with ipsae score calculation with ptms, need to work on ptm handling generally
hlasimpk
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Bug fix
hlasimpk
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Updated docs and toml
hlasimpk
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Commits on Jan 6, 2026

Commits on Jan 8, 2026