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omsf / plumb Public

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Add `plumbdb` package#1

Draft

ianmkenney wants to merge 24 commits intoomsf:mainomsf/plumb:mainfrom

ianmkenney:plumbdb_pkgianmkenney/plumb:plumbdb_pkgCopy head branch name to clipboard

Conversation Commits24 (24)Checks Files changed

Draft

Add `plumbdb` package#1
ianmkenney wants to merge 24 commits intoomsf:mainfrom
ianmkenney:plumbdb_pkg

Commits

Commits on Oct 27, 2025

Add plumbdb package files
ianmkenney
committed
Add asapdiscovery dependency
ianmkenney
committed
Expose cli entrypoint: plumbline
ianmkenney
committed
Lower Python version constraint
ianmkenney
committed
Add test module
ianmkenney
committed
Add developer docs
ianmkenney
committed
Trim package README
ianmkenney
committed
Add ruff to dev tools
ianmkenney
committed
Replicate commands from old bin/ directory
ianmkenney
committed
Add generate_constrained_ligand_poses command to cli
ianmkenney
committed
Add stubs for unimplemented CLI commands
ianmkenney
committed

Commits on Oct 28, 2025

Fix variable name usage
ianmkenney
committed
Implement prep_cif command
ianmkenney
committed
Implement process_bindingdb command
ianmkenney
committed
Implement visualize-network command
ianmkenney
committed
Updated nextflow to use new plumbline command
ianmkenney
committed
Replace tabs with spaces
ianmkenney
committed

Commits on Nov 14, 2025

added openeye to conda env
arianabrenner
committed
added output option
arianabrenner
committed

Commits on Dec 11, 2025

renamed PDBID field
arianabrenner
committed
add prep-protein-for-docking step to avoid using the asapdiscovery cli which has ML import problems
apayne97
committed
add small command to rename title of ligands so that the openfe cli works
apayne97
committed
renamed field BindingDB monomerid to BindingDB MonomerID
arianabrenner
committed
Merge branch 'plumbdb_pkg' of github.com:ianmkenney/plumb into plumbdb_pkg
arianabrenner
committed

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