Recipe 2.10. Generate modified peptides from a peptide and a set of rules

You want to generate all possible modified peptides given an initial peptide and a set of rules defining the site(s) of modification and the nature of applied modifs.

The PeptideEditorFactory creates new instances of modified Peptides given the set of EditionRules and the initial Peptide.

A EditionRule is composed of 2 parts:

1. a AAMotifMatcher specify site of editions
2. a EditionAction specify the modification to add in the specific mode (fixed or variable)

import org.expasy.jpl.core.mol.polymer.pept.rule.*;
import import org.apache.commons.collections15.Transformer;

// the initial peptide
Peptide peptide = new Peptide.Builder("MQRSTATGCFKL").build();

// the rules to apply
EditionRule ruleFixed =
	new EditionRule("1", AAMotifMatcher.newInstance("[KNQR]"),
		EditionAction.newFixedModifAction(LossModification.AMMONIUM_LOSS));
		
EditionRule ruleVariable =
	new EditionRule("2", AAMotifMatcher.newInstance("[ST]"),
		EditionAction.newVariableModifAction(LossModification.WATER_LOSS));

List<EditionRule> rules = new ArrayList<EditionRule>();
rules.add(ruleFixed);
rules.add(ruleVariable);

// the factory makes the process
PeptideEditorFactory factory =
	PeptideEditorFactory.newInstance(rules);

List<Peptide> peptides = factory.transform(peptide);

// display:
// H_MQ(H-3N-1)R(H-3N-1)STAT(H-2O-1)GCFK(H-3N-1)L_HO
// H_MQ(H-3N-1)R(H-3N-1)ST(H-2O-1)ATGCFK(H-3N-1)L_HO
// H_MQ(H-3N-1)R(H-3N-1)ST(H-2O-1)AT(H-2O-1)GCFK(H-3N-1)L_HO
// H_MQ(H-3N-1)R(H-3N-1)S(H-2O-1)TATGCFK(H-3N-1)L_HO
// H_MQ(H-3N-1)R(H-3N-1)S(H-2O-1)TAT(H-2O-1)GCFK(H-3N-1)L_HO
// H_MQ(H-3N-1)R(H-3N-1)S(H-2O-1)T(H-2O-1)ATGCFK(H-3N-1)L_HO
// H_MQ(H-3N-1)R(H-3N-1)S(H-2O-1)T(H-2O-1)AT(H-2O-1)GCFK(H-3N-1)L_HO		
for (Peptide peptide : peptides) {
	System.out.println(peptide);
}
Assert.assertEquals(7, peptides.size());

By now EditionAction is only able to handle modifications adds. In the future, I would like to integrate protein/peptide digestion here as a cut is an edition.

See also how to generate tuples and how to create modifs or to add them in peptides.