NuXLSiteLocalization.h

Go to the documentation of this file.

// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
 
#include <string>
#include <string_view>
#include <vector>
 
namespace OpenMS
{
class NuXLSiteLocalization
{
public:
  static constexpr double DEFAULT_TOLERANCE = 0.1;
 
  struct Site
  {
    int position = -1;                      
    int range_begin = -1;                   
    int range_end = -1;                     
    std::string method = "unlocalized";     
  };
 
  static std::vector<int> supportedResidues(const std::vector<double>& n_shifts,
                                            const std::vector<double>& n_noshifts,
                                            const std::vector<double>& c_shifts,
                                            const std::vector<double>& c_noshifts,
                                            double tolerance = DEFAULT_TOLERANCE);
 
  static Site localizeNHS(const std::string& sequence,
                          bool reactive_protein_n_term,
                          const std::vector<double>& n_shifts,
                          const std::vector<double>& n_noshifts,
                          const std::vector<double>& c_shifts,
                          const std::vector<double>& c_noshifts,
                          double tolerance = DEFAULT_TOLERANCE,
                          const std::vector<bool>& blocked = {});
 
  static void digestProtein(const EnzymaticDigestion& digestion,
                            std::string_view protein,
                            size_t min_length,
                            size_t max_length,
                            bool clip_nterm_methionine,
                            std::vector<std::string_view>& peptides);
 
  struct ProteinTermini
  {
    std::vector<std::string> n_terminal; 
    std::vector<std::string> c_terminal; 
  };
 
  static ProteinTermini proteinTermini(const std::vector<std::string_view>& proteins,
                                       const EnzymaticDigestion& digestion,
                                       size_t min_length,
                                       size_t max_length,
                                       bool clip_nterm_methionine);
 
  static bool isProteinNTerminal(const ProteinTermini& termini, std::string_view peptide);
 
  static bool isProteinCTerminal(const ProteinTermini& termini, std::string_view peptide);
};
} // namespace OpenMS