lingyuzeng
c0ead42384
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.
19 lines
965 B
Markdown
19 lines
965 B
Markdown
# scripts
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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。
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- `batch_process.py`: 读取分子 CSV，输出 flat `fragments.csv`、`errors.csv` 和处理摘要 JSON
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- `batch_process_ring16.py`: 固定 `--ring-size 16` 的批处理入口
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- `batch_process_multi_rings.py`: 自动识别 12-20 元环的批处理入口
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- `analyze_fragments.py`: 读取 flat fragment CSV，生成位置统计、性质汇总和频率图
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- `generate_sdf_and_statistics.py`: 读取 flat fragment CSV，生成 cleavage 统计 JSON 和 3D SDF
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- `tylosin_splicer.py`: 使用 `macro_lactone_toolkit.splicing.*` 做简单拼接
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推荐工作流：
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```bash
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python scripts/batch_process.py --input molecules.csv --output fragments.csv --errors-output errors.csv
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python scripts/analyze_fragments.py --input fragments.csv --output-dir analysis
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python scripts/generate_sdf_and_statistics.py --input fragments.csv --output-dir sdf_output
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```
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