Recipe 2.1.2. Creating a molecule with a modification

You want to create a modified molecule.

You just need a Molecule and a Modification and the class JPLModifiedMolecule:

import org.expasy.jpl.core.mol.chem.impl.ModifiedMolecule;

// get a molecule
Molecule molec = ChemicalFacade.getMolecule("CH3");

// a new simple modification
Modification modif = ModificationFactory.valueOf(12.0);

// a new modified molecule (sorry for this non realistic example :))
Molecule modMol = 
	new ModifiedMolecule.Builder(molec, modif).build();

Assert.assertEquals("CH3({12.0000})", modMol.getId());

See also how to create a peptide from a list of ModifiedMolecule.