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.
50 lines
1.7 KiB
Markdown
50 lines
1.7 KiB
Markdown
# Macro Split 文档摘要
|
|
|
|
当前仓库的正式接口全部集中在 `src/macro_lactone_toolkit/`，核心能力包括：
|
|
|
|
- `MacroLactoneAnalyzer`
|
|
- 分子级分类：`standard_macrolactone` / `non_standard_macrocycle` / `not_macrolactone`
|
|
- 12-20 元大环内酯识别
|
|
- 批量统计、DataFrame 分类、动态 SMARTS、基本理化性质
|
|
- `MacrolactoneFragmenter`
|
|
- 标准大环内酯编号
|
|
- 侧链裂解
|
|
- flat JSON/CSV 输出
|
|
- `macro_lactone_toolkit.visualization`
|
|
- 编号分子 SVG/PNG
|
|
- 碎片 SVG/PNG
|
|
- `macro_lactone_toolkit.workflows`
|
|
- CSV 批量裂解
|
|
- `FragmentationResult` 转 DataFrame
|
|
- JSON 导出
|
|
- 编号图片 + 标注 CSV 导出
|
|
- `macro_lactone_toolkit.splicing`
|
|
- 通用大环内酯 scaffold 预处理
|
|
- 片段活化和拼接
|
|
|
|
推荐起步方式：
|
|
|
|
```python
|
|
from macro_lactone_toolkit import MacroLactoneAnalyzer, MacrolactoneFragmenter
|
|
from macro_lactone_toolkit.workflows import fragment_csv, results_to_dataframe
|
|
|
|
analyzer = MacroLactoneAnalyzer()
|
|
classification = analyzer.classify_macrocycle(smiles)
|
|
|
|
fragmenter = MacrolactoneFragmenter()
|
|
result = fragmenter.fragment_molecule(smiles, parent_id="mol_001")
|
|
|
|
results = fragment_csv("molecules.csv")
|
|
fragments_df = results_to_dataframe(results)
|
|
```
|
|
|
|
推荐脚本工作流：
|
|
|
|
```bash
|
|
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
|
|
```
|
|
|
|
活动文档和脚本都基于 `macro_lactone_toolkit.*`。历史 notebook `.ipynb` 快照保留作归档参考，但不再作为当前 API 文档。
|