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0.6.0 #12

Merged
merged 247 commits into from
Feb 9, 2025
Merged

0.6.0 #12

merged 247 commits into from
Feb 9, 2025

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amorehead
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What does this PR do?

Introduces version 0.6.0 of the PoseBench codebase, data, and manuscript.

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  • Did you make sure title is self-explanatory and the description concisely explains the PR?
  • 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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@amorehead
Increase size of and font in figures
c4398d7
@amorehead
Upgrade PoseBusters, and update FASTA preparation script
51a0be1
@amorehead
Parse all cofactor inputs for all datasets
46f06b8
@amorehead
Add Dockgen support
37ceb24
@amorehead
Finalize one copy extraction of primary ligands
81397f2
@amorehead
Model ions by default
353c8cf
@amorehead
Support parsing CASP15 sequences
0833abe
@amorehead
Switch to PyMOL-based binding site-superimposed complex alignment rou…
5eef6cb 
…tine
@amorehead
Score primary (e.g., single) ligand(s) during inference analysis
e07a312
@amorehead
Make minor fixes
53b431c
@amorehead
Catch ValueErrors raised potentially during relaxation
f58353b
@amorehead
Update mmCIF to PDB conversion script to be compatible with AF3 local…
a695036 
… source code
@amorehead
Update apo-to-holo alignment based on PyMOL algorithm
455a34a
@amorehead
Support biomolecule FASTA creation
97d6225
@amorehead
Set default number of poses to sample per method to 5
0695201
@amorehead
Standardize multi-ligand delimiter for model inputs
97701a1
@amorehead
Make small fixes
b78b1e7
@amorehead
Update RFAA database paths
3e12cbf
@amorehead
Update protein sequence extraction function
5ba8ab8
@amorehead
Update import
3c2800a
@amorehead
Fix some inference edge cases for DiffDock
4b295a7
@amorehead
Handle for edge case in DynamicBind having missing protein outputs
5ec0705
@amorehead
Handle an edge case in relaxation
9f28b34
@amorehead
Fix DiffDock inference bug
0692595
@amorehead
Update chai-lab copy
48b28a3
@amorehead
Finish updating Chai-1's inference code
33cbdf8
@amorehead
Update conversion and alignment scripts
f8a8b85
@amorehead
Reenable function for ensembling only
0ff2ae1
@amorehead
Simplify
a37d46e
@amorehead
Revert
2d44890
@amorehead amorehead merged commit 60fde3b into main Feb 9, 2025
1 of 4 checks passed
@amorehead amorehead deleted the 0.6.0 branch February 9, 2025 21:20
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@amorehead