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BioinfoMachineLearning
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Address primary-ligand scoring bug
- #22
#22
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amorehead
merged 26 commits into
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BioinfoMachineLearning/PoseBench:main
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dev/20
BioinfoMachineLearning/PoseBench:dev/20
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Mar 21, 2026
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Address primary-ligand scoring bug
#22
amorehead
merged 26 commits into
main
BioinfoMachineLearning/PoseBench:main
from
dev/20
BioinfoMachineLearning/PoseBench:dev/20
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Commits on Mar 12, 2026
fix: Avoid potential side effects by breaking references to original molecule objects in select_primary_ligands_in_df
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feat: Add Dockerfile for setting up PoseBench environment with dependencies
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fix: Remove unnecessary package 'libconeangle' from Conda dependencies in Dockerfile
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fix: Update scipy version to 1.13.0 in posebench_environment.yaml
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fix: Update lightning and related packages to latest versions in posebench_environment.yaml
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Commits on Mar 13, 2026
fix: Update pdbeccdutils version to 1.0.0 in posebench_environment.yaml
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fix: Update pdbeccdutils to version 1.0.3 and scipy to version 1.14.1 in posebench_environment.yaml
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update: refactor code structure for improved readability and maintainability
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feat: add interaction analysis script and configuration for method-dataset preprocessing with SLURM
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update: add SLURM-based method interaction analysis scripts
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update: remove 'casp15' from datasets to sweep in interaction analysis script
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update: correct output script directory in interaction analysis script configuration
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update: add interaction scripts to .gitignore
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Commits on Mar 14, 2026
update: remove relative path references in data directory configurations across multiple analysis scripts
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update: fix file path for PoseBusters benchmark deposition dates CSV in SLURM plotting script
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update: add openff-toolkit and openbabel to Conda dependencies in Dockerfile
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update: speed up Dockerfile build by removing openff
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update: remove biotraj dependency from posebench environment
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update: add biotraj dependency to posebench environment
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Commits on Mar 15, 2026
update: add bioconda reduce package installation in Dockerfile
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update: add loguru for cleaner logging and tables for data file parsing
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update: update file paths to include 'notebooks' directory for interaction dataframes
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Commits on Mar 20, 2026
update: regenerate results and plots with ligand scoring bug fix
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chore: update to version 1.1.0 with bug fix documentation
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update: adjust line references in documentation includes for consistency, and update PoseBench image
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Commits on Mar 21, 2026
chore: clean up before opening PR
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