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+## 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)