Using OpenBabel from Java

OpenBabel 2.2.3 has just been released and with that, a new release of the Java bindings. The full details on using OpenBabel from Java are available on our wiki. On Windows openbabel.jar is included with the OpenBabel GUI so no additional installation is necessary. You just start Eclipse, add the jar file and away you go.

The following example shows how to use OpenBabel from Java. It includes an example of file format conversion, iteration over atoms, and using the SMARTS matcher.

import org.openbabel.*;

public class Test {

   public static void main(String[] args) {
       // Initialise
       System.loadLibrary("openbabel_java");

       // Read molecule from SMILES string
       OBConversion conv = new OBConversion();
       OBMol mol = new OBMol();
       conv.SetInFormat("smi");
       conv.ReadString(mol, "C(Cl)(=O)CCC(=O)Cl");
     
       // Print out some general information on the molecule, atoms
       conv.SetOutFormat("can");
       System.out.print("Canonical SMILES: " + conv.WriteString(mol));
       System.out.println("The molecular weight of the molecule is "
                  + mol.GetMolWt());
       for(OBAtom atom : new OBMolAtomIter(mol)) {
           System.out.println("Atom " + atom.GetIdx() +
                              ": atomic number = " + atom.GetAtomicNum() +
                              ", hybridisation = " + atom.GetHyb());
       }

       // What are the indices of the carbon atoms
       // of the acid chloride groups?
       OBSmartsPattern acidpattern = new OBSmartsPattern();
       acidpattern.Init("C(=O)Cl");
       acidpattern.Match(mol);
     
       vvInt matches = acidpattern.GetUMapList();
       System.out.println("There are " + matches.size() +
                          " acid chloride groups");
       System.out.print("The carbon atoms of the matches are: ");
       for(int i=0; i<matches.size(); i++)
           System.out.print(matches.get(i).get(0) + " ");
   }
}

The output is as follows:

Canonical SMILES: ClC(=O)CCC(=O)Cl
The molecular weight of the molecule is 154.97935999999999
Atom 1: atomic number = 6, hybridisation = 2
Atom 2: atomic number = 17, hybridisation = 0
Atom 3: atomic number = 8, hybridisation = 2
Atom 4: atomic number = 6, hybridisation = 3
Atom 5: atomic number = 6, hybridisation = 3
Atom 6: atomic number = 6, hybridisation = 2
Atom 7: atomic number = 8, hybridisation = 2
Atom 8: atomic number = 17, hybridisation = 0
There are 2 acid chloride groups
The carbon atoms of the matches are: 1 6 

Note: although using OpenBabel from Eclipse on Windows works fine, some users have reported problems on Linux with the default OpenBabel build. You probably need to build OpenBabel statically on Linux if you want to use it from Eclipse, but I haven't tested this. In any case, you can just compile it from the command line.