Chemistry tools tutorials/scripts

Tutorials and scripts for several computational chemistry tools

KBS - Home
Chem. tools tutorials
File conversion

Open Babel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.


Open Babel is available for Windows, Linux and MacOSX. See Open Babel installation for more information.

Command Line Interface

The command line interface for openbabel can be installed from Open Babel website. For usage information:

obabel --help

Single file conversion example from xyz to pdb format for benzene molecule:

obabel -ixyz -opdb -O benzene.pdb

Python bindings

Python bindings for openbabel is available through pip.

pip install openbabel

Here is an example Jupyter Notebook that shows how to use openbabel Python bindings.

Python wrapper (pybel)

There is also a python wrapper for openbabel which is also available through pip. Usage information is available on Pybel website.

pip install pybel

Useful Commands

Converting symmetry to P1 (filling unit cell)

The following command can be used to convert any crystal with symmetry to P1 non-symmetric crystal filling unit cell with all atoms.

obabel -icif non-P1.cif -ocif -O P1.cif --fillUC strict

Exporting rendered molecule image

Using the following command 2D rendering of given atomic coordinates of molecule in any format ( is used to produce an image file (my-molecule.svg).

obabel -O my-molecule.svg -xS -xd -xb none