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lingyuzeng c0ead42384 feat(toolkit): add classification and migration

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.

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__init__.py

first add

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analyze_fragments.py

feat(toolkit): add classification and migration

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batch_process_multi_rings.py

feat(toolkit): add classification and migration

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batch_process_ring16.py

feat(toolkit): add classification and migration

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batch_process.py

feat(toolkit): add classification and migration

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generate_sdf_and_statistics.py

feat(toolkit): add classification and migration

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README.md

feat(toolkit): add classification and migration

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tylosin_splicer.py

feat(toolkit): ship macro_lactone_toolkit package

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README.md

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 flat fragments.csv、errors.csv 和处理摘要 JSON
batch_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 SDF
tylosin_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

README.md Unescape Escape

scripts

README.md