## 环境管理 (使用 pixi)

### 安装 pixi

```bash
# 安装 pixi
curl -fsSL https://pixi.sh/install.sh | bash

# 重新加载 shell 配置
source ~/.bashrc  # 或 source ~/.zshrc
```

### 初始化项目环境

```bash
# 在项目目录中初始化 pixi 环境
pixi init

# 添加所需的包
pixi add rdkit openbabel meeko

# 激活环境
pixi shell
```

### 使用环境

```bash
# 激活 pixi 环境
pixi shell

# 在环境中运行脚本
pixi run python scripts/your_script.py

# 或者直接使用 pixi 执行命令
pixi run vina --help
```

## AutoDock Vina 安装

### 下载二进制文件

[Download](https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v1.2.7)

for macos:

```bash

wget -O ./bin/vina_1.2.7_mac_aarch64 https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.7/vina_1.2.7_mac_aarch64
wget -O ./bin/vina_split_1.2.7_mac_aarch64 https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.7/vina_split_1.2.7_mac_aarch64

# 或者使用 curl:
curl -L -o ./bin/vina_1.2.7_mac_aarch64 https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.7/vina_1.2.7_mac_aarch64
curl -L -o ./bin/vina_split_1.2.7_mac_aarch64 https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.7/vina_split_1.2.7_mac_aarch64

chmod +x ./bin/vina_*
```

## 项目使用

### 快速开始

```bash
# 1. 克隆项目
git clone <your-repo-url>
cd vinatools

# 2. 初始化 pixi 环境
pixi init
pixi add rdkit openbabel meeko

# 3. 下载 AutoDock Vina 二进制文件
mkdir -p bin
curl -L -o ./bin/vina_1.2.7_mac_aarch64 https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.7/vina_1.2.7_mac_aarch64
curl -L -o ./bin/vina_split_1.2.7_mac_aarch64 https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.7/vina_split_1.2.7_mac_aarch64
chmod +x ./bin/vina_*

# 4. 激活环境并运行
pixi shell
```

### 环境管理命令

```bash
# 查看已安装的包
pixi list

# 添加新包
pixi add package_name

# 移除包
pixi remove package_name

# 更新所有包
pixi update

# 导出环境配置
pixi export --format conda-lock
```

### 项目结构

```
vinatools/
├── bin/                    # AutoDock Vina 二进制文件
│   ├── vina_1.2.7_mac_aarch64
│   └── vina_split_1.2.7_mac_aarch64
├── scripts/                # Python 脚本
│   ├── batch_prepare_ligands.sh
│   ├── batch_docking.sh
│   ├── calculate_qed_values.py
│   └── analyze_results.py
├── pixi.toml               # pixi 环境配置文件
├── docker/                 # Docker 配置文件
│   ├── Dockerfile
│   ├── docker-compose.yml
│   └── README.md
└── README.md
```

## Docker 环境

### 快速使用 Docker

```bash
# 构建并运行 Docker 容器
docker-compose -f docker/docker-compose.yml up -d

# 进入容器
docker-compose -f docker/docker-compose.yml exec vinatools bash

# 运行脚本
docker-compose -f docker/docker-compose.yml exec vinatools pixi run python scripts/calculate_qed_values.py
```

### Docker 服务说明

- **vinatools**: 主服务，包含 pixi 环境和所有依赖包
- **jupyter**: Jupyter Notebook 服务，访问 http://localhost:8888

详细使用说明请参考 [docker/README.md](docker/README.md)