ProteaseDigestion.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow, Xiao Liang $
// $Authors: Marc Sturm, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
 
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ProteaseDigestion: public EnzymaticDigestion
  {
  public:
    using EnzymaticDigestion::setEnzyme;
 
    void setEnzyme(const String& name);
 
    Size digest(const AASequence& protein, std::vector<AASequence>& output, Size min_length = 1, Size max_length = 0) const;
 
    Size digest(const AASequence& protein, std::vector<std::pair<size_t,size_t>>& output, Size min_length = 1, Size max_length = 0) const;
 
    Size peptideCount(const AASequence& protein);
 
    bool isValidProduct(const String& protein, int pep_pos, int pep_length, bool ignore_missed_cleavages = true, bool allow_nterm_protein_cleavage = false, bool allow_random_asp_pro_cleavage = false) const;
 
    bool isValidProduct(const AASequence& protein, int pep_pos, int pep_length, bool ignore_missed_cleavages = true, bool allow_nterm_protein_cleavage = false, bool allow_random_asp_pro_cleavage = false) const;
 
  };
 
} // namespace OpenMS