- skip fused/shared/multi-anchor side systems during extraction
- add fragment library schema and fragment_library.csv export
- make scaffold prep strict for non-spliceable positions
Implement the standard/non-standard/not-macrolactone classification layer
and integrate it into analyzer, fragmenter, and CLI outputs.
Port the remaining legacy package capabilities into new visualization and
workflow modules, restore batch/statistics/SDF scripts on top of the flat
CSV workflow, and update active docs to the new package API.
Unify macrolactone detection, numbering, fragmentation, and
splicing under the installable macro_lactone_toolkit package.
- replace legacy src.* modules with the new package layout
- add analyze/number/fragment CLI entrypoints and pixi tasks
- migrate tests, README, and scripts to the new package API
- Add src/splicing/ module with scaffold_prep, fragment_prep, and engine
- Add tylosin_splicer.py entry script
- Add unit tests for splicing components
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add AGENTS.md with AI assistant guidelines for the project
- Add tests/test_ring_numbering.py to verify ring numbering consistency
- Test confirms atom numbering is fixed and reproducible
Co-Authored-By: Claude <noreply@anthropic.com>
