Method searchModifications

src/openms/source/CHEMISTRY/ModificationsDB.cpp:208–253

  }

  void ModificationsDB::searchModifications(set<const ResidueModification*>& mods,
                                            const String& mod_name_,
                                            const String& residue,
                                            ResidueModification::TermSpecificity term_spec) const
  {
    mods.clear();

    String mod_name = mod_name_;

    char res = '?'; // empty
    if (!residue.empty()) res = residue[0];

    #pragma omp critical(OpenMS_ModificationsDB)
    {
      bool found = true;
      auto modifications = modification_names_.find(mod_name);
      if (modifications == modification_names_.end())
      {
        // Try to fix things, Skyline for example uses unimod:10 and not UniMod:10 syntax
        if (mod_name.size() > 6 && mod_name.prefix(6).toLower() == "unimod")
        {
          mod_name = "UniMod" + mod_name.substr(6, mod_name.size() - 6);
        }

        modifications = modification_names_.find(mod_name);
        if (modifications == modification_names_.end())
        {
          OPENMS_LOG_WARN << OPENMS_PRETTY_FUNCTION << "Modification not found: " << mod_name << endl;
          found = false; 
        }
      }

      if (found)
      {
        for (const auto& it : modifications->second)
        {
          if ( residuesMatch_(res, it) &&
               (term_spec == ResidueModification::NUMBER_OF_TERM_SPECIFICITY ||
               (term_spec == it->getTermSpecificity())))
          {
            mods.insert(it);
          }
        }
      }
    } 
  }

  const ResidueModification* ModificationsDB::getModification(const String& mod_name, const String& residue, ResidueModification::TermSpecificity term_spec) const
  {