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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
//! [Enzyme]
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/ProteaseDigestion.h>
#include <vector>
#include <iostream>
using namespace OpenMS;
using namespace std;
int main()
{
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;
protease.digest(AASequence::fromString("ARCDRE.(Amidated)"), products);
// output digestion products
for (const AASequence p : products)
{
cout << p.toString() << " ";
}
cout << endl;
// allow many miss-cleavages
protease.setMissedCleavages(10);
protease.digest(AASequence::fromString("ARCDRE.(Amidated)"), products);
// output digestion products
for (const AASequence p : products)
{
cout << p.toString() << " ";
}
cout << endl;
// ... many more
return 0;
}
//! [Enzyme]
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