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scripts/README.md
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scripts/README.md
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# 批量处理脚本使用说明
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## 概述
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本文件夹包含两个批量处理脚本，用于对大环内酯分子进行编号、裂解和保存。
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## 脚本列表
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### 1. `batch_process_ring16.py` - 处理16元环分子
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**功能：**
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- 处理已过滤的1241个16元环分子
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- 对每个分子进行环原子编号
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- 进行侧链断裂
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- 保存JSON文件
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**输入文件：**
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- `ring16/temp_filtered_complete.csv`
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**输出文件夹：**
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- `output/ring16_fragments/`
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- `ring16_mol_{idx}/` - 每个分子的文件夹
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- `ring16_mol_{idx}_all_fragments.json` - 所有碎片信息
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- `{fragment_id}.json` - 单个碎片文件
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- `metadata.json` - 分子元数据
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- `processing_log_*.txt` - 处理日志
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- `error_log_*.txt` - 错误日志
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- `processing_statistics.json` - 统计信息
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**使用方法：**
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```bash
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cd /home/zly/project/macro_split
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# 方法1: 直接运行Python脚本
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python scripts/batch_process_ring16.py
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# 方法2: 作为可执行文件运行
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chmod +x scripts/batch_process_ring16.py
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./scripts/batch_process_ring16.py
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```
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**预期运行时间：** 10-30分钟（取决于计算机性能）
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---
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### 2. `batch_process_multi_rings.py` - 处理12-20元环分子
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**功能：**
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- 处理12-20元环的所有大环内酯分子
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- 按环大小自动分类（12元、13元、14元...20元）
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- 检测并剔除含有多个内酯键的分子
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- 对每种环大小分别编号和裂解
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- 保存到对应的文件夹
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**输入文件：**
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- `data/ring12_20/temp.csv`
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**输出文件夹：**
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- `output/ring12_fragments/` - 12元环碎片
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- `output/ring13_fragments/` - 13元环碎片
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- `output/ring14_fragments/` - 14元环碎片
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- ...
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- `output/ring20_fragments/` - 20元环碎片
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每个文件夹包含：
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- `ring{N}_mol_{idx}/` - 每个分子的文件夹
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- `ring{N}_mol_{idx}_all_fragments.json`
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- `{fragment_id}.json`
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- `metadata.json`
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- `processing_log_*.txt` - 处理日志
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- `error_log_*.txt` - 错误日志
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- `multiple_lactone_log_*.txt` - 多内酯键分子记录
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- `processing_statistics.json` - 统计信息
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**使用方法：**
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```bash
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cd /home/zly/project/macro_split
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# 确保输入文件存在
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ls data/ring12_20/temp.csv
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# 运行脚本
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python scripts/batch_process_multi_rings.py
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```
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**预期运行时间：** 根据数据集大小，可能需要30分钟-2小时
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---
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## 输出文件说明
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### JSON文件格式
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#### 1. `{parent_id}_all_fragments.json`
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包含所有碎片的完整信息：
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```json
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{
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"parent_id": "ring16_mol_0",
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"parent_smiles": "...",
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"fragments": [
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{
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"fragment_smiles": "CC(C)C",
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"parent_smiles": "...",
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"cleavage_position": 5,
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"fragment_id": "ring16_mol_0_frag_0",
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"parent_id": "ring16_mol_0",
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"atom_count": 4,
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"molecular_weight": 58.12
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},
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...
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]
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}
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```
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#### 2. `{fragment_id}.json`
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单个碎片的信息：
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```json
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{
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"fragment_smiles": "CC(C)C",
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"parent_smiles": "...",
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"cleavage_position": 5,
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"fragment_id": "ring16_mol_0_frag_0",
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"parent_id": "ring16_mol_0",
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"atom_count": 4,
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"molecular_weight": 58.12
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}
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```
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#### 3. `metadata.json`
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分子的元数据：
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```json
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{
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"parent_id": "ring16_mol_0",
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"molecule_id": "CHEMBL94657",
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"molecule_name": "PATUPILONE",
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"smiles": "C/C(=C\\c1csc(C)n1)...",
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"ring_size": 16,
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"num_fragments": 11,
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"processing_date": "2025-11-06T10:30:00"
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}
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```
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#### 4. `processing_statistics.json`
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处理统计信息：
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```json
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{
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"ring_size": 16,
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"total": 1241,
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"success": 1200,
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"failed_parse": 5,
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"failed_numbering": 10,
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"failed_validation": 8,
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"failed_cleavage": 18,
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"total_fragments": 12500
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}
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```
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---
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## 日志文件
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### 1. `processing_log_*.txt`
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记录所有处理过程：
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```
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[2025-11-06 10:30:00] 开始批量处理 1241 个16元环分子
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[2025-11-06 10:30:05] 分子 0 处理成功
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...
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[2025-11-06 11:00:00] 处理完成: 成功 1200/1241
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```
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### 2. `error_log_*.txt`
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记录所有错误：
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```
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[2025-11-06 10:35:12] ❌ 分子 125 (CHEMBL12345) SMILES解析失败
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[2025-11-06 10:36:45] ❌ 分子 256 (CHEMBL67890) 编号验证失败
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```
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### 3. `multiple_lactone_log_*.txt`
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记录含有多个内酯键的分子（仅在multi_rings脚本中）：
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```
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[2025-11-06 10:40:00] 分子 350 (CHEMBL11111, Molecule Name) 有多个内酯键，已剔除。内酯碳索引: [15, 28, 42]
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```
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---
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## 常见问题
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### Q1: 如何检查处理进度？
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**A:** 脚本会显示实时进度条。你也可以查看日志文件：
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```bash
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tail -f output/ring16_fragments/processing_log_*.txt
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```
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### Q2: 如何查看处理结果？
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**A:** 查看统计文件：
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```bash
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cat output/ring16_fragments/processing_statistics.json
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```
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### Q3: 处理失败了怎么办？
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**A:**
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1. 查看 `error_log_*.txt` 了解失败原因
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2. 脚本会跳过失败的分子，继续处理其他分子
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3. 可以手动处理失败的分子
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### Q4: 如何重新处理？
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**A:**
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1. 删除输出文件夹：`rm -rf output/ring16_fragments`
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2. 重新运行脚本
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### Q5: 内存不足怎么办？
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**A:**
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- 脚本已优化为逐个处理分子，内存占用很小
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- 如果仍有问题，可以修改脚本分批处理
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---
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## 后续分析
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处理完成后，可以进行以下分析：
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### 1. 统计碎片多样性
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```python
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import json
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from pathlib import Path
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from collections import Counter
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# 读取所有碎片
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all_fragments = []
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for mol_dir in Path('output/ring16_fragments').iterdir():
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if mol_dir.is_dir() and mol_dir.name.startswith('ring16_mol_'):
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fragments_file = mol_dir / f"{mol_dir.name}_all_fragments.json"
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if fragments_file.exists():
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with open(fragments_file) as f:
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data = json.load(f)
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all_fragments.extend([frag['fragment_smiles'] for frag in data['fragments']])
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# 统计
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fragment_counts = Counter(all_fragments)
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print(f"总碎片数: {len(all_fragments)}")
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print(f"独特碎片数: {len(fragment_counts)}")
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print(f"\n最常见的10个碎片:")
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for smiles, count in fragment_counts.most_common(10):
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print(f" {smiles}: {count}次")
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```
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### 2. 分析位置分布
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```python
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from collections import defaultdict
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position_fragments = defaultdict(list)
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for mol_dir in Path('output/ring16_fragments').iterdir():
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if mol_dir.is_dir() and mol_dir.name.startswith('ring16_mol_'):
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fragments_file = mol_dir / f"{mol_dir.name}_all_fragments.json"
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if fragments_file.exists():
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with open(fragments_file) as f:
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data = json.load(f)
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for frag in data['fragments']:
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position = frag['cleavage_position']
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position_fragments[position].append(frag['fragment_smiles'])
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# 统计每个位置的碎片多样性
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for pos in sorted(position_fragments.keys()):
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unique_frags = set(position_fragments[pos])
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print(f"位置 {pos:2d}: {len(position_fragments[pos])} 个碎片, {len(unique_frags)} 种不同结构")
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```
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---
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## 性能优化
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如果需要处理大量数据，可以考虑：
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1. **并行处理：** 使用 `multiprocessing` 模块
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2. **分批处理：** 将数据集分成多个批次
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3. **增量处理：** 只处理新增的分子
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---
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## 联系与支持
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如有问题，请查看：
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- 错误日志文件
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- `BRIDGE_RING_ANALYSIS.md` - 详细技术文档
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- `QUICK_GUIDE.md` - 快速参考指南
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---
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**最后更新：** 2025-11-06
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**版本：** 1.0
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