3D geometry modeling in CDK 1.1.2

Recently I am experimenting with CDK, the Chemistry Development Kit (CDK), a free, open-source (GNU LGPL) Java toolkit for cheminformatics. An outstanding feature of CDK is its 3D modeller: you provide a 2D (planar) model, and it can generate a true three-dimensional optimized geometry, using a chosen molecular force field. For example, I downloaded a 2-dimensional .mol file of decalin from ChEBI, - this molecule is obviously not planar. Then I used CDK to generate the 3D geometry. Here is a code snippet how I did it:



Here is the 2D image of Decalin, that corresponds to the .mol file from ChEBI:



Here is a pic of the model I generated:



Decalin has two stereoisomers, this is the trans-model which is energetically favourable, compared to the cis-model, so CDK has found the global optimal geometry.