lingyuzeng
3e07402f4e
Add a public numbering module and route fragmenting, validation, and scaffold preparation through the canonical numbering entry. Rewrite the repository entry docs around the fixed numbering contract, add MkDocs landing pages, and document the mirror mapping used for medicinal-chemistry comparisons. Also refresh the validation analysis reports to explain the canonical-versus-mirrored numbering relationship.
scripts
这些脚本都基于 macro_lactone_toolkit.* 的正式包接口，不再依赖旧的 src.* 模块。
batch_process.py: 读取分子 CSV，输出 flatfragments.csv、errors.csv和处理摘要 JSONbatch_process_ring16.py: 固定--ring-size 16的批处理入口batch_process_multi_rings.py: 自动识别 12-20 元环的批处理入口analyze_fragments.py: 读取 flat fragment CSV，生成位置统计、性质汇总和频率图generate_sdf_and_statistics.py: 读取 flat fragment CSV，生成 cleavage 统计 JSON 和 3D SDFtylosin_splicer.py: 使用macro_lactone_toolkit.splicing.*做简单拼接
推荐工作流：
python scripts/batch_process.py --input molecules.csv --output fragments.csv --errors-output errors.csv
python scripts/analyze_fragments.py --input fragments.csv --output-dir analysis
python scripts/generate_sdf_and_statistics.py --input fragments.csv --output-dir sdf_output