Recipe 2.2. Creating modifications

You want to create new modifications.

Modifications can be created mainly from molecular formulae or from masses. Some molecular groups may be ionizable.

Here is a list of examples:

import org.expasy.jpl.core.mol.modif.*;

// create a modification from a formula
ModificationFactory.valueOf("CH3");

// create a modification from a double		
ModificationFactory.valueOf("15.0349");

// with a label and a molecule
ModificationFactory.withLabel("MSO",
	ChemicalFacade.getMolecule("O2"));

// also exists loss modification	
LossModification.valueOf(ModificationFactory.valueOf(-23)
LossModification.valueOf(ModificationFactory
	.valueOf(ChemicalFacade.getMolecule("C-1H-4")));

// or ionizable modification
IonizableModification.newInstance(
	ModificationFactory.withLabel("phosphorylation", ChemicalFacade.getMolecule("H2PO3")),
		new IonizableGroup.Builder(7.21, NeutralMoleculeType.ACID)
			.addPKa(12.67).build());