centos7安装openbabel踩坑

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openbabel踩坑

源码安装报错，报错信息如下：

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CMakeFiles/xtcformat.dir/xtcformat.cpp.o: In function `OpenBabel::XTCFormat::xdropen(XDR*, char const*, char const*)':
xtcformat.cpp:(.text+0xd2): undefined reference to `xdrstdio_create'
xtcformat.cpp:(.text+0x11b): undefined reference to `xdrstdio_create'
CMakeFiles/xtcformat.dir/xtcformat.cpp.o: In function `OpenBabel::XTCFormat::xdr3dfcoord(XDR*, float*, int*, float*)':
xtcformat.cpp:(.text+0x888): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x8e6): undefined reference to `xdr_float'
xtcformat.cpp:(.text+0x951): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x961): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x971): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x981): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x991): undefined reference to `xdr_int'
CMakeFiles/xtcformat.dir/xtcformat.cpp.o:xtcformat.cpp:(.text+0x9a1): more undefined references to `xdr_int' follow
CMakeFiles/xtcformat.dir/xtcformat.cpp.o: In function `OpenBabel::XTCFormat::xdr3dfcoord(XDR*, float*, int*, float*)':
xtcformat.cpp:(.text+0xab7): undefined reference to `xdr_opaque'
xtcformat.cpp:(.text+0xd33): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0xd5e): undefined reference to `xdr_float'
xtcformat.cpp:(.text+0xd93): undefined reference to `xdr_float'
xtcformat.cpp:(.text+0xd98): undefined reference to `xdr_vector'
xtcformat.cpp:(.text+0xdb2): undefined reference to `xdr_float'
xtcformat.cpp:(.text+0x10ea): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x10fa): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x110a): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x111a): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x112a): undefined reference to `xdr_int'
CMakeFiles/xtcformat.dir/xtcformat.cpp.o:xtcformat.cpp:(.text+0x113a): more undefined references to `xdr_int' follow
CMakeFiles/xtcformat.dir/xtcformat.cpp.o: In function `OpenBabel::XTCFormat::xdr3dfcoord(XDR*, float*, int*, float*)':
xtcformat.cpp:(.text+0x1b0c): undefined reference to `xdr_opaque'
CMakeFiles/xtcformat.dir/xtcformat.cpp.o: In function `OpenBabel::XTCFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)':
xtcformat.cpp:(.text+0x1d67): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x1d80): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x1da4): undefined reference to `xdr_int'
xtcformat.cpp:(.text+0x1db4): undefined reference to `xdr_float'
xtcformat.cpp:(.text+0x1dc4): undefined reference to `xdr_float'
xtcformat.cpp:(.text+0x1dd4): undefined reference to `xdr_float'
xtcformat.cpp:(.text+0x1de4): undefined reference to `xdr_float'
xtcformat.cpp:(.text+0x1df4): undefined reference to `xdr_float'
CMakeFiles/xtcformat.dir/xtcformat.cpp.o:xtcformat.cpp:(.text+0x1e04): more undefined references to `xdr_float' follow
CMakeFiles/xtcformat.dir/xtcformat.cpp.o: In function `OpenBabel::XTCFormat::xdr3dfcoord(XDR*, float*, int*, float*)':
xtcformat.cpp:(.text+0xd74): undefined reference to `xdr_vector'
collect2: error: ld returned 1 exit status
make[2]: *** [src/formats/CMakeFiles/xtcformat.dir/build.make:105: lib/xtcformat.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:4523: src/formats/CMakeFiles/xtcformat.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

没找到解决方法。遂放弃。

conda 安装

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conda install -y -c conda-forge openbabel

安装还挺快。接下来绑定python
从pypi上下载openbabel的源码包（pip install直接安装会报错），下载地址https://pypi.org/project/openbabel/#files
解压后安装命令如下

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cd openbabel-3.1.1.1
# -I 指定conda安装openbabel的include的路径，-L 指定conda安装openbabel的lib的路径
python setup.py build_ext -I$CURR_DIR/envs/Sdocking/include/openbabel3/ -L$CURR_DIR/envs/Sdocking/lib/openbabel/3.1.0
# --prefix指定安装路径，最好指定下，默认会安装到当前目录，后续执行 import openbabel的时候会报错找不到
python setup.py install --prefix=$CURR_DIR/envs/Sdocking/lib/python3.7/site-packages

安装完确认是否安装成功

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python -c 'import openbabel'

参考：https://blog.csdn.net/qq_32115939/article/details/120031684

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