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Merged
amorehead merged 31 commits into from
Aug 11, 2025
Merged

0.7.0 #15

amorehead merged 31 commits into from
Aug 11, 2025

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@amorehead
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@amorehead amorehead commented Aug 11, 2025 •
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What does this PR do?

Introduces version 0.7.0 of the PoseBench codebase, data, and manuscript.

Before submitting

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  • Did you make sure your PR does only one thing, instead of bundling different changes together?
  • Did you list all the breaking changes introduced by this pull request?
  • Did you run pre-commit hooks with pre-commit run -a command?

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Make sure you had fun coding 🙃

amorehead and others added 30 commits July 29, 2025 12:25
@amorehead
Upgrade PoseBusters to canonical version of 0.4.5
ed84fb5
@amorehead
Add Boltz-2, commit ac33fe07eb8336c5046b740ffeedf1345fcb00af
a2ddac0
@amorehead
Begin integrating and documenting Boltz-2
43c1db1
@amorehead
Set up Boltz-2 inference format and MSAs
cf282c3
@amorehead
Prepare all Boltz-2 inputs
46317d6
@amorehead
Test correctness of Boltz-2 input, MSA, inference, and output extraction
0808efd
@amorehead
Add remaining code support for Boltz-2
d95cca0
@amorehead
Update all notebooks en masse
4cc4b0e
@amorehead
Add missing command
e3a210c
@amorehead
Differentiate CASP15 from PoseBusters rescoring
e2e7500
@amorehead
Update Boltz env
870ebbb
@amorehead
Ensure first MSA sequence for Boltz is the input protein sequence whe…
38f79d8 
…re possible
@amorehead
Rescue several Boltz MSAs with right-padding
502803f
@amorehead
Simplify checks
0606678
@amorehead
Fix up DockGen MSAs for Boltz
8d3fbf2
@amorehead
Identify and fix bug related to protein sequence count mismatch for C…
aaa18e8 
…hai-1 and Boltz-2's DockGen-E predictions
@amorehead
Fix RFAA scoring runtime error
eb86b21
@amorehead
Correct package version in Chai-1 env
2a96c16
@amorehead
Install custom fork of PLINDER, and update RDKit via PyPi
cc1ff0f
@amorehead
Sync up PoseBench env, and fix error logging issue in Boltz-2 inference
cb05a2b
@amorehead
Use Boltz-1 by default for sake of time-split validity
bc37125
@amorehead
Standardize name of Boltz to Boltz-1
a423ed0
@amorehead
Begin documenting PLINDER usage
74e42fa
@amorehead
Unpack PLINDER systems
1130e40
@amorehead
Document default and custom PLINDER-based similarity analyses
ed63ff2
@amorehead
Update PLINDER-based analysis
2513f6f
@amorehead
Clean up PLINDER-based plot
c1457db
@amorehead
Update notebook
ad89505
@amorehead
Add all new plots
844c0d9
@amorehead
Update Zenodo link
3d114b4
@amorehead amorehead merged commit 9cd4ccd into main Aug 11, 2025
4 checks passed
@amorehead amorehead deleted the 0.7.0 branch August 11, 2025 17:51
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@amorehead