{

ProteaseDigestion protease;

// in this example, we don't produce peptides with missed cleavages

protease.setMissedCleavages(0);

// output the number of tryptic peptides (no cut before proline)

protease.setEnzyme("Trypsin");

cout << protease.peptideCount(AASequence::fromString("ACKPDE")) << " "

<< protease.peptideCount(AASequence::fromString("ACRPDEKA"))

<< endl;

// digest C-terminally amidated peptide

vector<AASequence> products;

auto aa_seq = AASequence::fromString("ARCDRE.(Amidated)");

protease.digest(aa_seq, products);

// output digestion products

std::cout << "digesting " << aa_seq.toString() << " into:\n";

for (const AASequence& p : products)

{

cout << "--> " << p.toString() << "\n";

}

cout << endl;

// allow many miss-cleavages

protease.setMissedCleavages(10);

protease.digest(aa_seq, products);

// output digestion products

std::cout << "digesting " << aa_seq.toString() << " with 10 MCs into:\n";

for (const AASequence& p : products)

{

cout << "--> " << p.toString() << "\n";

}

cout << endl;

// verify an infix of a protein is a digestion product:

String peptide = "FFFRAAA";

cout << "Is '" << peptide.prefix(4) << "' a valid digestion product of '" << peptide << "'? "

<< std::boolalpha << protease.isValidProduct(peptide, 0, 4); // yes it is!