Install Python bindings

Windows

Install the bindings

1. First you need to download and install the main Open Babel executable and library as described in Install a binary package.

2. Next, use pip to install the Python bindings:

   pip install -U openbabel
   

Note: Python is available as either a 32-bit or 64-bit version. You need to install the corresponding version of Open Babel in step 1.

Install Pillow (optional)

If you want to display 2D depictions using Pybel (rather than just write to a file), you need to install the Pillow library:

pip install -U pillow

Test the installation

Open a Windows command prompt, and type the following commands to make sure that everything is installed okay. If you get an error message, there’s something wrong and you should email the mailing list with the output from these commands.

C:\Documents and Settings\Noel> obabel -V
Open Babel 3.0.0 -- Oct  7 2019 -- 20:18:16

C:\Documents and Settings\Noel> obabel -Hsdf
sdf  MDL MOL format
Reads and writes V2000 and V3000 versions

Read Options, e.g. -as
 s  determine chirality from atom parity flags
...
...

C:\Documents and Settings\Noel> dir "%BABEL_DATADIR%"\mr.txt
 Volume in drive C has no label.
 Volume Serial Number is 68A3-3CC9

 Directory of C:\Users\Noel\AppData\Roaming\OpenBabel-3.0.0\data

06/10/2019  16:37             4,295 mr.txt
               1 File(s)          4,295 bytes
               0 Dir(s)  58,607,575,040 bytes free

C:\Documents and Settings\Noel> py
Python 2.7.16 (v2.7.16:413a49145e, Mar  4 2019, 01:37:19) [MSC v.1500 64
bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from openbabel import pybel
>>> mol = pybel.readstring("smi", "CC(=O)Br")
>>> mol.make3D()
>>> print(mol.write("sdf"))

 OpenBabel01010918183D

  7  6  0  0  0  0  0  0  0  0999 V2000
    1.0166   -0.0354   -0.0062 C   0  0  0  0  0
    2.5200   -0.1269    0.0003 C   0  0  0  0  0
    3.0871   -1.2168    0.0026 O   0  0  0  0  0
    3.2979    1.4258    0.0015 Br  0  0  0  0  0
    0.6684    1.0007    0.0052 H   0  0  0  0  0
    0.6255   -0.5416    0.8803 H   0  0  0  0  0
    0.6345   -0.5199   -0.9086 H   0  0  0  0  0
  1  2  1  0  0  0
  1  5  1  0  0  0
  1  6  1  0  0  0
  1  7  1  0  0  0
  2  4  1  0  0  0
  2  3  2  0  0  0
M  END
$$$$
>>> mol.draw() # If you installed PIL, this will display its structure
>>> (Hit CTRL+Z followed by Enter to exit)

Linux and MacOSX

See Compile language bindings for information on how to configure CMake to compile the Python bindings. This can be done either globally or locally.

You may need to add the location of libopenbabel.so (on my system, the location is /usr/local/lib) to the environment variable LD_LIBRARY_PATH if you get the following error when you try to import the OpenBabel library at the Python prompt:

$ python
>>> from openbabel import openbabel
Traceback (most recent call last):
  File "<stdin>", line 1, in
  File "/usr/lib/python2.4/site-packages/openbabel.py", line 9, in
   import _openbabel
ImportError: libopenbabel.so.3: cannot open shared object file: No such file or directory

Install Pillow (optional)

If you want to display 2D depictions using Pybel (rather than just write to a file), you need the Pillow library, and the Python Tkinter library (part of the standard library). These should be available through your package manager, e.g. on Ubuntu, Pillow is provided by ‘python-pil’ and ‘python-pil.imagetk’, while Tkinter is provided by ‘python-tk’.