141 lines
3.2 KiB
Markdown
141 lines
3.2 KiB
Markdown
## 环境管理 (使用 pixi)
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### 安装 pixi
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```bash
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# 安装 pixi
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curl -fsSL https://pixi.sh/install.sh | bash
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# 重新加载 shell 配置
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source ~/.bashrc # 或 source ~/.zshrc
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```
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### 初始化项目环境
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```bash
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# 在项目目录中初始化 pixi 环境
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pixi init
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# 添加所需的包
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pixi add rdkit openbabel meeko
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# 激活环境
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pixi shell
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```
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### 使用环境
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```bash
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# 激活 pixi 环境
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pixi shell
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# 在环境中运行脚本
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pixi run python scripts/your_script.py
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# 或者直接使用 pixi 执行命令
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pixi run vina --help
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```
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## AutoDock Vina 安装
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### 下载二进制文件
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[Download](https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v1.2.7)
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for macos:
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```bash
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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
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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
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# 或者使用 curl:
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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
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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
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chmod +x ./bin/vina_*
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```
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## 项目使用
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### 快速开始
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```bash
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# 1. 克隆项目
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git clone <your-repo-url>
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cd vinatools
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# 2. 初始化 pixi 环境
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pixi init
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pixi add rdkit openbabel meeko
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# 3. 下载 AutoDock Vina 二进制文件
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mkdir -p bin
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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
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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
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chmod +x ./bin/vina_*
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# 4. 激活环境并运行
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pixi shell
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```
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### 环境管理命令
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```bash
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# 查看已安装的包
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pixi list
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# 添加新包
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pixi add package_name
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# 移除包
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pixi remove package_name
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# 更新所有包
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pixi update
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# 导出环境配置
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pixi export --format conda-lock
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```
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### 项目结构
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```
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vinatools/
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├── bin/ # AutoDock Vina 二进制文件
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│ ├── vina_1.2.7_mac_aarch64
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│ └── vina_split_1.2.7_mac_aarch64
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├── scripts/ # Python 脚本
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│ ├── batch_prepare_ligands.sh
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│ ├── batch_docking.sh
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│ ├── calculate_qed_values.py
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│ └── analyze_results.py
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├── pixi.toml # pixi 环境配置文件
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├── docker/ # Docker 配置文件
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│ ├── Dockerfile
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│ ├── docker-compose.yml
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│ └── README.md
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└── README.md
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```
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## Docker 环境
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### 快速使用 Docker
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```bash
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# 构建并运行 Docker 容器
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docker-compose -f docker/docker-compose.yml up -d
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# 进入容器
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docker-compose -f docker/docker-compose.yml exec vinatools bash
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# 运行脚本
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docker-compose -f docker/docker-compose.yml exec vinatools pixi run python scripts/calculate_qed_values.py
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```
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### Docker 服务说明
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- **vinatools**: 主服务，包含 pixi 环境和所有依赖包
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- **jupyter**: Jupyter Notebook 服务，访问 http://localhost:8888
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详细使用说明请参考 [docker/README.md](docker/README.md) |