增加多阶段构建，并在镜像中构建指定版本的vina 便于使用。

docker/Dockerfile

@@ -1,69 +1,167 @@
-# 使用 Ubuntu 22.04 作为基础镜像（使用腾讯云镜像源）
-FROM ccr.ccs.tencentyun.com/library/ubuntu:22.04
+# ============ 构建阶段 ============
+FROM ubuntu:24.04 AS builder
 
-# 设置环境变量
 ENV DEBIAN_FRONTEND=noninteractive
-ENV PATH="/root/.pixi/bin:$PATH"
 
-# 配置 APT 镜像源（使用阿里云镜像）
-RUN sed -i 's@//.*archive.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list && \
-    sed -i 's@//.*security.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+# 配置镜像源（使用阿里云镜像）
+RUN <<EOF
+sed -i 's@//.*archive.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+sed -i 's@//.*security.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+EOF
 
-# 安装系统依赖
-RUN apt-get update && apt-get install -y \
-    curl \
-    wget \
+# 安装构建依赖
+RUN <<EOF
+apt-get update
+apt-get install -y \
     git \
     build-essential \
-    ca-certificates \
-    gnupg \
-    lsb-release \
-    && rm -rf /var/lib/apt/lists/*
+    libboost-all-dev \
+    swig \
+    python3-dev \
+    python3-pip \
+    python3-venv
+rm -rf /var/lib/apt/lists/*
+EOF
+
+# 创建构建虚拟环境并安装必要的 Python 包
+RUN <<EOF
+echo "创建构建虚拟环境..."
+python3 -m venv /opt/build-venv
+echo "配置 pip 镜像源..."
+/opt/build-venv/bin/pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
+echo "安装构建依赖包..."
+/opt/build-venv/bin/pip install numpy packaging setuptools wheel
+echo "构建环境准备完成"
+EOF
+
+# 克隆 AutoDock Vina 源码
+ARG VINA_VERSION=1.2.7
+RUN <<EOF
+git clone https://github.com/ccsb-scripps/AutoDock-Vina.git /tmp/AutoDock-Vina
+cd /tmp/AutoDock-Vina
+git checkout v${VINA_VERSION}
+EOF
+
+# 编译 Python wheel 包
+RUN <<EOF
+cd /tmp/AutoDock-Vina
+echo "AutoDock Vina 源码结构:"
+find . -name "setup.py" -type f
+echo "检查 build/python 目录:"
+ls -la build/python/ 2>/dev/null || echo "build/python 目录不存在"
+echo "检查根目录的 setup.py:"
+ls -la setup.py 2>/dev/null || echo "根目录没有 setup.py"
+
+# 尝试在根目录构建
+if [ -f "setup.py" ]; then
+    echo "在根目录构建 wheel 包..."
+    /opt/build-venv/bin/python setup.py bdist_wheel
+else
+    echo "在 build/python 目录构建 wheel 包..."
+    cd build/python
+    /opt/build-venv/bin/python setup.py bdist_wheel
+fi
+
+echo "构建完成，查找所有 wheel 文件:"
+find /tmp/AutoDock-Vina -name "*.whl" -type f
+mkdir -p /wheels
+find /tmp/AutoDock-Vina -name "*.whl" -type f -exec cp {} /wheels/ \;
+echo "复制的 wheel 文件:"
+ls -la /wheels/
+EOF
+
+# 编译二进制可执行文件
+RUN <<EOF
+cd /tmp/AutoDock-Vina/build/linux/release
+make
+mkdir -p /binaries
+cp vina /binaries/
+cp vina_split /binaries/
+EOF
+
+# ============ 运行阶段 ============
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# 配置镜像源（使用阿里云镜像）
+RUN <<EOF
+sed -i 's@//.*archive.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+sed -i 's@//.*security.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+EOF
+
+# 安装运行时依赖
+RUN <<EOF
+apt-get update
+apt-get install -y \
+    python3 \
+    python3-pip \
+    python3-venv \
+    libboost-system1.83.0 \
+    libboost-thread1.83.0 \
+    libboost-serialization1.83.0 \
+    libboost-filesystem1.83.0 \
+    libboost-program-options1.83.0
+rm -rf /var/lib/apt/lists/*
+EOF
 
 # 配置 pip 镜像源
-RUN mkdir -p /root/.pip && \
-    echo "[global]" > /root/.pip/pip.conf && \
-    echo "index-url = https://pypi.tuna.tsinghua.edu.cn/simple" >> /root/.pip/pip.conf && \
-    echo "trusted-host = pypi.tuna.tsinghua.edu.cn" >> /root/.pip/pip.conf
+RUN pip3 config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
 
-# 安装 pixi
-RUN curl -fsSL https://pixi.sh/install.sh | bash
+# 创建虚拟环境（解决 Python 3.12 PEP 668 保护问题）
+RUN <<EOF
+echo "创建虚拟环境..."
+python3 -m venv /opt/venv
+echo "虚拟环境创建完成，检查路径:"
+ls -la /opt/venv/bin/
+echo "升级 pip..."
+/opt/venv/bin/pip install --upgrade pip
+echo "虚拟环境准备完成"
+EOF
+
+# 从构建阶段复制 wheel 包并安装到虚拟环境
+COPY --from=builder /wheels/*.whl /tmp/
+RUN <<EOF
+/opt/venv/bin/pip install /tmp/*.whl
+rm -rf /tmp/*.whl
+EOF
+
+# 设置虚拟环境路径
+ENV PATH="/opt/venv/bin:$PATH"
+
+# 从构建阶段复制二进制文件
+COPY --from=builder /binaries/* /usr/local/bin/
+RUN chmod +x /usr/local/bin/vina*
 
 # 设置工作目录
 WORKDIR /app
 
-# 复制项目文件
-COPY . .
-
-# 创建 bin 目录
-RUN mkdir -p bin
-
-# 下载 AutoDock Vina 二进制文件
-ARG VINA_VERSION=1.2.7
-ARG VINA_PLATFORM=mac_aarch64
-ARG DOWNLOAD_VINA=true
-
-RUN if [ "$DOWNLOAD_VINA" = "true" ]; then \
-        curl -L -o ./bin/vina_${VINA_VERSION}_${VINA_PLATFORM} https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v${VINA_VERSION}/vina_${VINA_VERSION}_${VINA_PLATFORM} && \
-        curl -L -o ./bin/vina_split_${VINA_VERSION}_${VINA_PLATFORM} https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v${VINA_VERSION}/vina_split_${VINA_VERSION}_${VINA_PLATFORM} && \
-        chmod +x ./bin/vina_*; \
-    fi
-
-# 添加平台支持并安装 pixi 包
-RUN /root/.pixi/bin/pixi workspace platform add linux-aarch64 && \
-    /root/.pixi/bin/pixi add rdkit openbabel meeko
-
-# 设置环境变量
-ENV PATH="/root/.pixi/bin:/app/bin:$PATH"
-
 # 创建启动脚本
-RUN echo '#!/bin/bash\n\
-source /root/.bashrc\n\
-exec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
+RUN <<EOF
+cat > /entrypoint.sh << 'SCRIPT_EOF'
+#!/bin/bash
+echo "AutoDock Vina 环境已准备就绪 (Ubuntu 24.04 + Python 3.12 + Boost 1.83.0)"
+echo "虚拟环境: \$(which python)"
+echo "Python 版本: \$(python --version 2>&1)"
+echo "Python 绑定测试:"
+python -c "from vina import Vina; print('Vina Python 绑定可用')" 2>/dev/null || echo "Python 绑定不可用"
+echo "命令行工具: vina --version"
+vina --version 2>/dev/null || echo "vina 命令不可用"
+echo "Boost 库信息:"
+ldd /usr/local/bin/vina | grep boost || echo "无法获取 Boost 信息"
+if [ "\$#" -eq 0 ]; then
+    echo "进入交互模式..."
+    exec /bin/bash
+else
+    echo "执行命令: \$@"
+    exec "\$@"
+fi
+SCRIPT_EOF
+chmod +x /entrypoint.sh
+EOF
 
 # 设置入口点
 ENTRYPOINT ["/entrypoint.sh"]
 
 # 默认命令
-CMD ["/root/.pixi/bin/pixi", "shell"]
+CMD ["bash"]