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.
The command line interface for openbabel can be installed from Open Babel website. For usage information:
Single file conversion example from xyz to pdb format for benzene molecule:
obabel -ixyz benzene.xyz -opdb -O benzene.pdb
Python bindings for openbabel is available through pip.
pip install openbabel
There is also a python wrapper for openbabel which is also available through pip. Usage information is available on Pybel website.
pip install pybel
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
Using the following command 2D rendering of given atomic coordinates of molecule in any format (
my-molecule.xyz) is used to produce an image file (
obabel my-molecule.xyz -O my-molecule.svg -xS -xd -xb none