lingyuzeng
5e7b236f31
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
68 lines
2.0 KiB
Markdown
68 lines
2.0 KiB
Markdown
# macro_lactone_toolkit
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`macro_lactone_toolkit` 是一个正式可安装的 Python 包，用于 12-20 元有效大环内酯的识别、环编号、侧链裂解和简单拼接回组装。
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## 核心能力
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- 默认自动识别 12-20 元有效大环内酯，也允许显式指定 `ring_size`
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- 环编号规则固定为：
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- 位置 1 = 内酯羰基碳
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- 位置 2 = 环上的酯键氧
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- 位置 3-N = 沿统一方向连续编号
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- 侧链裂解同时输出两套 SMILES：
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- `fragment_smiles_labeled`，例如 `[5*]`
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- `fragment_smiles_plain`，例如 `*`
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- dummy 原子与连接原子的原始键型保持一致
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- 提供正式 CLI：
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- `macro-lactone-toolkit analyze`
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- `macro-lactone-toolkit number`
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- `macro-lactone-toolkit fragment`
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## 环境
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推荐使用 `pixi`，项目已固定到 Python 3.12，并支持 `osx-arm64` 与 `linux-64`。
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```bash
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pixi install
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pixi run pytest
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pixi run python -c "import macro_lactone_toolkit"
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```
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## Python API
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```python
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from macro_lactone_toolkit import MacroLactoneAnalyzer, MacrolactoneFragmenter
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analyzer = MacroLactoneAnalyzer()
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valid_ring_sizes = analyzer.get_valid_ring_sizes("O=C1CCCCCCCCCCCCCCO1")
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fragmenter = MacrolactoneFragmenter()
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numbering = fragmenter.number_molecule("O=C1CCCCCCCCCCCCCCO1")
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result = fragmenter.fragment_molecule("O=C1CCCC(C)CCCCCCCCCCO1", parent_id="mol_001")
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```
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## CLI
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单分子分析：
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```bash
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pixi run macro-lactone-toolkit analyze --smiles "O=C1CCCCCCCCCCCCCCO1"
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pixi run macro-lactone-toolkit number --smiles "O=C1CCCCCCCCCCCCCCO1"
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pixi run macro-lactone-toolkit fragment --smiles "O=C1CCCC(C)CCCCCCCCCCO1" --parent-id mol_001
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```
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CSV 批处理：
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```bash
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pixi run macro-lactone-toolkit fragment \
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--input molecules.csv \
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--output fragments.csv \
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--errors-output fragment_errors.csv
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```
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默认读取 `smiles` 列；若存在 `id` 列则将其作为 `parent_id`，否则自动生成 `row_<index>`。
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## Legacy Scripts
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`scripts/` 目录保留为薄封装或迁移提示，不再承载核心实现。正式接口以 `macro_lactone_toolkit.*` 与 `macro-lactone-toolkit` CLI 为准。
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