Recipe 2.9. Shuffling a peptide

You want to shuffle a peptide.

PeptideResidueManager propose methods to shuffle Peptides:

import org.expasy.jpl.core.mol.polymer.pept.PeptideResidueManager;

// the peptide to shuffle
Peptide peptide =
	new Peptide.Builder("H_A({128.10})CHUHEUHU({11.90})RHE_OH")
		.build();

// generate 5 peptides
for (int i = 0; i < 5; i++) {
	Peptide shuffled = manager.shuffle(peptide);
	System.out.println(shuffled);
}

// output
H_EHRA({128.10})CHHHUUU({11.90})E_HO
H_HU({11.90})HHREUA({128.10})CHUE_HO
H_HUU({11.90})HREEUCHA({128.10})H_HO
H_CEHU({11.90})A({128.10})HHRHUUE_HO
H_RA({128.10})HHEUEU({11.90})HUHC_HO

It is also possible to fixed some positions and while scrambling the others:

// the peptide to shuffle
Peptide peptide =
	new Peptide.Builder("H_A({128.10})CHUHEUHU({11.90})RHE_OH")
		.build();
		
// generate 5 peptides with positions 0 and 8 fixed
for (int i = 0; i < 5; i++) {
	Peptide shuffled =
		manager.shuffle(peptide, new HashSet<Integer>(Arrays.asList(0,8)));
			
	System.out.println(shuffled);
}

// output
H_A({128.10})CHHHUUEU({11.90})RHE_HO
H_A({128.10})HCEEHURU({11.90})HUH_HO
H_A({128.10})ERHHUUHU({11.90})HEC_HO
H_A({128.10})UUCHEEHU({11.90})HRH_HO
H_A({128.10})EHHCURHU({11.90})EUH_HO