In this post, I will introduce how to install openbabel package and use it through python.

Installation

Before you install the openbabel, you need to make sure that you have: (1) Eigen package and (2) SWIG.

Prerequists

Eigen

You can download the Eigen package through this command: git clone https://gitlab.com/libeigen/eigen.git. Then you can use cd eigen to go into the folder, you will find something like this:

Then the procedure is in below:

Step 1. mkdir build
Step 2. cd build
Step 3. cmake ..
Step 4. make -j4 (or jusr make)
Step 5. make install

Then you will install the Eigen package, which will be used in openbabel.

SWIG

The SWIG package can be installed by using the brew: brew install swig

Install openbabel with python binding

The Github Repository of openbabel is:

Open Babel
Interconverting chemical data since 2001. Open Babel has 10 repositories available. Follow their code on GitHub.
GitHub
Github repository for Open Babel

Then we can download it by using:

git clone https://github.com/openbabel/openbabel.git

Once we have downloaded all the code, then we should go into the openbabel folder. You should see something like this:

Then you should build a new folder named build: mkdir build. Then go into it: cd build.

Then you can type this command:

cmake -DRUN_SWIG=ON -DPYTHON_BINDINGS=ON ..

The -DPYTHON_BINDINGS=ON means you want to use python bindings, so that you can import openbabel in python.

After the cmake, you can do the following steps:

  • Step 1: make -j4
  • Step 2: make test (optional)
  • Step 3: sudo make install

Once you have finished the above steps, then you need to export the location where the openbabel package is installed to PYTHONPATH, add this line into your ~/.bashrc:

export PYTHONPATH=$PYTHONPATH:your/location/in/here/openbabel

Then use source ~/.bashrc to make the change happen.

After everything is finished, then you can use openbabel in Python.

Usage of openbabel in python

In below is a short tutorial that can show you how to use openbabel in Python: (convert SMILES to cif file)

from openbabel import openbabel
from ase.io import read, write
import numpy as np

ft = 'xyz'
f = open('babel.'+ft, 'w')

gen3d = openbabel.OBOp.FindType('gen3D')
mol = openbabel.OBMol()

obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats('smi', ft)
obConversion.ReadString(mol, '[N+](=O)([O-])[O-]')

gen3d.Do(mol, '--best')

print(mol.NumAtoms())

outMDL = obConversion.WriteString(mol)
f.write(outMDL)
f.close()

atoms = read('babel.'+ft)

a = 20
r_origin = np.array([a/2,a/2,a/2]) - atoms[0].position
print("r_origin is: {}".format(r_origin))
atoms.cell = [a, a, a]
atoms.pbc = [True, True, True]
for atom in atoms:
    atom.position += r_origin 
print(atom.position)
print(atoms)
write('babel.cif', atoms)

If you want to create the molecules, MolView is a great tool. You can draw the structure yourself, and it will output the SMILES for you.