mdtraj库安装

Installation

• 官网推荐conda安装：

  1	conda install -c conda-forge mdtraj

• PIP安装：

  1	pip install mdtraj

Windows环境python安装失败

• 不想装conda，直接pip install mdtraj报错：

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  Looking in indexes: http://pypi.douban.com/simple/ Collecting mdtraj Downloading http://pypi.doubanio.com/packages/2f/03/c174bfb6471f796472ce1d8695f6c0d1a20ad6516cb789b70052df45b7a6/mdtraj-1.9.7.tar.gz (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 3.7 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... error error: subprocess-exited-with-error × Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [34 lines of output] ... ... ...

• 直接源码安装：

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  git clone https://github.com/mdtraj/mdtraj cd mdtraj pip install -e .

  • 跟上面直接pip报同样的错误

• 在mdtraj文件夹下直接python .\setup.py install出现了不同的错误：

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  ... ... ... cc.initialize() File "D:\softwares\Python\Python311\Lib\site-packages\setuptools\_distutils\_msvccompiler.py", line 253, in initialize vc_env = _get_vc_env(plat_spec) ^^^^^^^^^^^^^^^^^^^^^^ File "D:\softwares\Python\Python311\Lib\site-packages\setuptools\msvc.py", line 214, in msvc14_get_vc_env return _msvc14_get_vc_env(plat_spec) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "D:\softwares\Python\Python311\Lib\site-packages\setuptools\msvc.py", line 168, in _msvc14_get_vc_env raise distutils.errors.DistutilsPlatformError( distutils.errors.DistutilsPlatformError: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/

  • 看样子需要安装：Microsoft C++ Build Tools

• 下载安装 Microsoft C++ Build Tools 后（默认安装），再次安装

  1	python .\setup.py install

• 成功一部分，显示Cython包未安装：

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  C compiler: 用于 x64 的 Microsoft (R) C/C++ 优化编译器 19.35.32217.1 版 版权所有(C) Microsoft Corporation。保留所有权利。 用法: cl [ 选项... ] 文件名... [ /link 链接选项... ] Attempting to autodetect OpenMP support... Compiler supports OpenMP mdtrajs setup depends on Cython (>=0.29). Install it prior invoking setup.py No module named 'Cython'

• 安装Cython包后再次安装

  1 2	pip install cython python .\setup.py install

• 以为安装成功了，又报错：

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  ... ... ... mdtraj/formats/tng/src/lib/tng_io.c(32): fatal error C1083: 无法打开包括文件: “zlib.h”: No such file or directory error: command 'D:\\Program Files (x86)\\Microsoft Visual Studio\\2022\\BuildTools\\VC\\Tools\\MSVC\\14.35.32215\\bin\\HostX86\\x64\\cl.exe' failed with exit code 2

• Windows下ZLib的编译（使用VS2019）

• Windows中zlib的安装与配置

• 安装zlib：

  1	git clone https://github.com/madler/zlib.git

  • 安装cmake

  • Windows下ZLib的编译（使用VS2019）

  • Windows中zlib的安装与配置

• 不想装vs，太臃肿了，所以这里我不尝试了（有机会再试），还是用Linux版的吧

Ubuntu环境python安装

• PIP安装成功：

  1	pip install mdtraj

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  Collecting mdtraj Using cached mdtraj-1.9.7.tar.gz (2.1 MB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... done Requirement already satisfied: scipy in /home/cup/.local/lib/python3.8/site-packages (from mdtraj) (1.7.3) ...... Building wheels for collected packages: mdtraj Building wheel for mdtraj (PEP 517) ... done Created wheel for mdtraj: filename=mdtraj-1.9.7-cp38-cp38-linux_x86_64.whl size=8473679 sha256=31b82b30935b14413c5d62fe126d29f8837dcc745bb46ba030902d8ba54facfc Stored in directory: /home/cup/.cache/pip/wheels/68/ff/96/5d9a2efac5e5918e5c8fd799e8703e2f8b804a029bcbbd2431 Successfully built mdtraj Installing collected packages: astunparse, mdtraj Successfully installed astunparse-1.6.3 mdtraj-1.9.7

mdtraj测试

• 安装测试包

  1	pip install pytest

• 测试

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  git clone https://github.com/mdtraj/mdtraj.git cd mdtraj # If using conda, make sure to have your conda environment active py.test