How do I install openbabel for Python 3.6 in Windo

Question

I am using Python for making a script to work with some chemical structures in my PhD. I want to install openbabel libraries for python. I tried my best but I could not install it. It always gives error: Error: SWIG failed. Is Open Babel installed? Here is the Python Path on my PC: C:\Users\malih\AppData\Local\Programs\Python\Python36-32. Openbabel is installed at the following path C:\Program Files (x86)\OpenBabel-2.3.1.

When I run python -m pip install openbabel, it gives the following error:

C:\Users\malih>python -m pip install openbabel
Collecting openbabel
Using cached openbabel-2.4.1.tar.gz
Installing collected packages: openbabel
Running setup.py install for openbabel ... error
Complete output from command C:\Users\malih\AppData\Local\Programs\Python\Python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\malih\\AppData\\Local\\Temp\\pip-build-glr82a7x\\openbabel\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\malih\AppData\Local\Temp\pip-02z3p_a9-record\install-record.txt --single-version-externally-managed --compile:
running install
running build_ext
Warning: pkg-config could not be found.
Guessing Open Babel location:
- include_dirs: ['C:\\Users\\malih\\AppData\\Local\\Programs\\Python\\Python36-32\\include', 'C:\\Users\\malih\\AppData\\Local\\Programs\\Python\\Python36-32\\include', '/usr/local/include/openbabel-2.0']
- library_dirs: ['C:\\Users\\malih\\AppData\\Local\\Programs\\Python\\Python36-32\\libs', 'C:\\Users\\malih\\AppData\\Local\\Programs\\Python\\Python36-32\\PCbuild\\win32', '/usr/local/lib']
building '_openbabel' extension
swigging openbabel-python.i to openbabel-python_wrap.cpp
swig.exe -python -c++ -small -O -templatereduce -naturalvar -IC:\Users\malih\AppData\Local\Programs\Python\Python36-32\include -IC:\Users\malih\AppData\Local\Programs\Python\Python36-32\include -I/usr/local/include/openbabel-2.0 -o openbabel-python_wrap.cpp openbabel-python.i

Error: SWIG failed. Is Open Babel installed?
You may need to manually specify the location of Open Babel include and library directories. For example:
  python setup.py build_ext -I/usr/local/include/openbabel-2.0 -L/usr/local/lib
  python setup.py install

----------------------------------------
Command "C:\Users\malih\AppData\Local\Programs\Python\Python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\malih\\AppData\\Local\\Temp\\pip-build-glr82a7x\\openbabel\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\malih\AppData\Local\Temp\pip-02z3p_a9-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\malih\AppData\Local\Temp\pip-build-glr82a7x\openbabel\

I tried to follow the instructions on this page but they are purely for linux and I could not follow up them for Windows: How do I use python-openbabel in Travis CI?

I also tried to install pkg-config from the following guide but even after that, it gives the same error: How to install pkg config in windows?

Please help me on this as my work is based on this and I am stuck at this point. Thanks in advance for your time.

Answer 1

pip install is notoriously non-windows friendly. Either go to openbabel website and download + install windows binary, then download + install python binding, or use the unoffical official openbabel python windows build, then cd into the downloaded directory, and perform pip install OPENBABEL_FILE_WINDOWS.whl

I recently had do some quite a bit of work on 2D mol file -> 3D mol file translation using openbabel. Let me know how it works out for you.

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edit: I should also add, python3.x is breakingly different to python2.x. So if anything breaks, try it with python2.x