OpenMS::NuXLPresets Namespace Reference

Functions
void	getPresets (const String &p, StringList &nucleotides, StringList &mapping, StringList &modifications, StringList &fragment_adducts, String &can_cross_link)

Variables
static constexpr std::array< const char *, 10 >	modifications_RNA_UV
static constexpr std::array< const char *, 29 >	modifications_RNA_UV_EXTENDED
static constexpr std::array< const char *, 6 >	modifications_RNA_UV_4SU
static constexpr std::array< const char *, 14 >	modifications_RNA_UV_4SU_EXTENDED
static constexpr std::array< const char *, 6 >	modifications_RNA_UV_6SG
static constexpr std::array< const char *, 11 >	modifications_RNA_UV_6SG_EXTENDED
static constexpr std::array< const char *, 4 >	modifications_RNA_NM
static constexpr std::array< const char *, 34 >	modifications_RNA_NM_EXTENDED
static constexpr std::array< const char *, 4 >	modifications_RNA_DEB
static constexpr std::array< const char *, 34 >	modifications_RNA_DEB_EXTENDED
static constexpr std::array< const char *, 12 >	modifications_RNA_FA
static constexpr std::array< const char *, 24 >	modifications_RNA_FA_EXTENDED
static constexpr std::array< const char *, 16 >	modifications_DNA_FA
static constexpr std::array< const char *, 28 >	modifications_DNA_FA_EXTENDED
static constexpr std::array< const char *, 12 >	modifications_DNA_UV
static constexpr std::array< const char *, 32 >	modifications_DNA_UV_EXTENDED
static constexpr std::array< const char *, 6 >	modifications_DNA_DEB
static constexpr std::array< const char *, 38 >	modifications_DNA_DEB_EXTENDED
static constexpr std::array< const char *, 6 >	modifications_DNA_NM
static constexpr std::array< const char *, 38 >	modifications_DNA_NM_EXTENDED
static constexpr std::array< const char *, 39 >	fragments_RNA_UV
static constexpr std::array< const char *, 41 >	fragments_RNA_UV_4SU
static constexpr std::array< const char *, 41 >	fragments_RNA_UV_6SG
static constexpr std::array< const char *, 42 >	fragments_DNA_UV
static constexpr std::array< const char *, 47 >	fragments_RNA_DEB
static constexpr std::array< const char *, 50 >	fragments_DNA_DEB
static constexpr std::array< const char *, 43 >	fragments_RNA_NM
static constexpr std::array< const char *, 46 >	fragments_RNA_FA
static constexpr std::array< const char *, 49 >	fragments_DNA_FA
static constexpr std::array< const char *, 46 >	fragments_DNA_NM
static constexpr std::array< const char *, 5 >	DNA_nucleotides {"A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"}
static constexpr std::array< const char *, 4 >	RNA_nucleotides {"A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"}
static constexpr std::array< const char *, 5 >	DNA_mapping {"A->A", "C->C", "G->G", "T->T", "d->d"}
static constexpr std::array< const char *, 4 >	RNA_mapping {"A->A", "C->C", "G->G", "U->U"}
static constexpr std::array< const char *, 23 >	presets_names

Function Documentation

getPresets()

void OpenMS::NuXLPresets::getPresets	(	const String &	p,
		StringList &	nucleotides,
		StringList &	mapping,
		StringList &	modifications,
		StringList &	fragment_adducts,
		String &	can_cross_link
	)

References Residue::addLossFormula(), DNA_mapping, DNA_nucleotides, fragments_DNA_DEB, fragments_DNA_FA, fragments_DNA_NM, fragments_DNA_UV, fragments_RNA_DEB, fragments_RNA_FA, fragments_RNA_NM, fragments_RNA_UV, fragments_RNA_UV_4SU, fragments_RNA_UV_6SG, ResidueDB::getInstance(), ResidueDB::getResidue(), String::hasPrefix(), modifications_DNA_DEB, modifications_DNA_DEB_EXTENDED, modifications_DNA_FA, modifications_DNA_FA_EXTENDED, modifications_DNA_NM, modifications_DNA_NM_EXTENDED, modifications_DNA_UV, modifications_DNA_UV_EXTENDED, modifications_RNA_DEB, modifications_RNA_DEB_EXTENDED, modifications_RNA_FA, modifications_RNA_FA_EXTENDED, modifications_RNA_NM, modifications_RNA_NM_EXTENDED, modifications_RNA_UV, modifications_RNA_UV_4SU, modifications_RNA_UV_4SU_EXTENDED, modifications_RNA_UV_6SG, modifications_RNA_UV_6SG_EXTENDED, modifications_RNA_UV_EXTENDED, presets_names, RNA_mapping, and RNA_nucleotides.

Variable Documentation

DNA_mapping

constexpr std::array<const char*, 5> DNA_mapping {"A->A", "C->C", "G->G", "T->T", "d->d"}

static

Referenced by getPresets().

DNA_nucleotides

constexpr std::array<const char*, 5> DNA_nucleotides {"A=C10H14N5O6P", "C=C9H14N3O7P", "G=C10H14N5O7P", "T=C10H15N2O8P", "d=C5H9O6P"}

static

Referenced by getPresets().

fragments_DNA_DEB

constexpr std::array<const char*, 50> fragments_DNA_DEB

static

Referenced by getPresets().

fragments_DNA_FA

constexpr std::array<const char*, 49> fragments_DNA_FA

static

Referenced by getPresets().

fragments_DNA_NM

constexpr std::array<const char*, 46> fragments_DNA_NM

static

Referenced by getPresets().

fragments_DNA_UV

constexpr std::array<const char*, 42> fragments_DNA_UV

static

Referenced by getPresets().

fragments_RNA_DEB

constexpr std::array<const char*, 47> fragments_RNA_DEB

static

Referenced by getPresets().

fragments_RNA_FA

constexpr std::array<const char*, 46> fragments_RNA_FA

static

Referenced by getPresets().

fragments_RNA_NM

constexpr std::array<const char*, 43> fragments_RNA_NM

static

Referenced by getPresets().

fragments_RNA_UV

constexpr std::array<const char*, 39> fragments_RNA_UV

static

Referenced by getPresets().

fragments_RNA_UV_4SU

constexpr std::array<const char*, 41> fragments_RNA_UV_4SU

static

Referenced by getPresets().

fragments_RNA_UV_6SG

constexpr std::array<const char*, 41> fragments_RNA_UV_6SG

static

Referenced by getPresets().

modifications_DNA_DEB

constexpr std::array<const char*, 6> modifications_DNA_DEB

static

Initial value:

{
    "T:+C4H6O2",
    "G:+C4H6O2",
    "C:+C4H6O2",
    "A:+C4H6O2",

    "d:", 
    "d:-H2O"
  }

Referenced by getPresets().

modifications_DNA_DEB_EXTENDED

constexpr std::array<const char*, 38> modifications_DNA_DEB_EXTENDED

static

Referenced by getPresets().

modifications_DNA_FA

constexpr std::array<const char*, 16> modifications_DNA_FA

static

Initial value:

{
    "G:+C",
    "G:+C-HPO3",
    "G:+C-H3PO4",
    "G:+C-H2O",
    
    "C:+C",
    "C:+C-H2O",
    "C:+C-HPO3",
    "C:+C-H3PO4",
    
    "A:+C",
    "A:+C-HPO3",
    "A:+C-H2O",
    "A:+C-H3PO4",

    "d:",
    "d:-H2O",
    "d:-H3PO4",
    "d:-HPO3"
  }

Referenced by getPresets().

modifications_DNA_FA_EXTENDED

constexpr std::array<const char*, 28> modifications_DNA_FA_EXTENDED

static

Referenced by getPresets().

modifications_DNA_NM

constexpr std::array<const char*, 6> modifications_DNA_NM

static

Initial value:

{
    "T:+C5H9N1",
    "G:+C5H9N1",
    "C:+C5H9N1",
    "A:+C5H9N1",
    "d:",
    "d:-H2O"
  }

Referenced by getPresets().

modifications_DNA_NM_EXTENDED

constexpr std::array<const char*, 38> modifications_DNA_NM_EXTENDED

static

Referenced by getPresets().

modifications_DNA_UV

constexpr std::array<const char*, 12> modifications_DNA_UV

static

Initial value:

{
    "T:",
    "T:-H2O",

    "G:",
    "G:-H2O",
    "G:-NH3",

    "A:",
    "A:-NH3",

    "C:",
    "C:-H2O",
    "C:-NH3",

    "d:", 
    "d:-H2O"
  }

Referenced by getPresets().

modifications_DNA_UV_EXTENDED

constexpr std::array<const char*, 32> modifications_DNA_UV_EXTENDED

static

Referenced by getPresets().

modifications_RNA_DEB

constexpr std::array<const char*, 4> modifications_RNA_DEB

static

Initial value:

{ 
    "U:+C4H6O2",
    "G:+C4H6O2",
    "C:+C4H6O2",
    "A:+C4H6O2"
  }

Referenced by getPresets().

modifications_RNA_DEB_EXTENDED

constexpr std::array<const char*, 34> modifications_RNA_DEB_EXTENDED

static

Referenced by getPresets().

modifications_RNA_FA

constexpr std::array<const char*, 12> modifications_RNA_FA

static

Initial value:

{
    "G:+C",
    "G:+C-HPO3",
    "G:+C-H3PO4",
    "G:+C-H2O",
    
    "C:+C",
    "C:+C-H2O",
    "C:+C-HPO3",
    "C:+C-H3PO4",
    
    "A:+C",
    "A:+C-HPO3",
    "A:+C-H3PO4",
    "A:+C-H2O",
  }

Referenced by getPresets().

modifications_RNA_FA_EXTENDED

constexpr std::array<const char*, 24> modifications_RNA_FA_EXTENDED

static

Initial value:

{
    "G:+C",
    "G:+C-HPO3",
    "G:+C-H3PO4",
    "G:+C-H2O",
    "G:+C2",
    "G:+C2-HPO3",
    "G:+C2-H2O",
    "G:+C2-H3PO4",
    
    "C:+C",
    "C:+C-H2O",
    "C:+C-HPO3",
    "C:+C-H3PO4",
    "C:+C2",
    "C:+C2-HPO3",
    "C:+C2-H2O",
    "C:+C2-H3PO4",
    
    "A:+C",
    "A:+C-HPO3",
    "A:+C-H3PO4",
    "A:+C-H2O",
    "A:+C2",
    "A:+C2-HPO3",
    "A:+C2-H2O",
    "A:+C2-H3PO4"
  }

Referenced by getPresets().

modifications_RNA_NM

constexpr std::array<const char*, 4> modifications_RNA_NM

static

Initial value:

{
    "U:+C5H9N1",
    "G:+C5H9N1",
    "C:+C5H9N1",
    "A:+C5H9N1"
  }

Referenced by getPresets().

modifications_RNA_NM_EXTENDED

constexpr std::array<const char*, 34> modifications_RNA_NM_EXTENDED

static

Referenced by getPresets().

modifications_RNA_UV

constexpr std::array<const char*, 10> modifications_RNA_UV

static

Initial value:

{
    "U:", 
    "U:-H2O", 

    "C:", 
    "C:-H2O",
    "C:-NH3",

    "G:", 
    "G:-H2O", 
    "G:-NH3", 

    "A:", 
    "A:-NH3"
  }

Referenced by getPresets().

modifications_RNA_UV_4SU

constexpr std::array<const char*, 6> modifications_RNA_UV_4SU

static

Initial value:

{   
    "S:",
    "S:-H2O",
    "S:-H2S",
    "S:-C5H8O4",
    "S:-C5H8O4-H2O",
    "S:-C5H8O4-H2S"
  }

Referenced by getPresets().

modifications_RNA_UV_4SU_EXTENDED

constexpr std::array<const char*, 14> modifications_RNA_UV_4SU_EXTENDED

static

Initial value:

{   
    "S:",
    "S:-H2O",
    "S:-H3PO4",
    "S:-HPO3",
    "S:-H2S",
    "S:+HPO3-H2S", 
    "S:-HPO3-H2S", 
    "S:+HPO3", 

    "S:-C5H8O4",
    "S:-C5H8O4-H2O",
    "S:-C5H8O4-H3PO4",
    "S:-C5H8O4-HPO3",
    "S:-C5H8O4-HPO3-H2S", 
    "S:-C5H8O4-H2S"
  }

Referenced by getPresets().

modifications_RNA_UV_6SG

constexpr std::array<const char*, 6> modifications_RNA_UV_6SG

static

Initial value:

{   
    "X:",
    "X:-H2O",
    "X:-H2S",
    "X:-C5H8O4",
    "X:-C5H8O4-H2O",
    "X:-C5H8O4-H2S"
  }

Referenced by getPresets().

modifications_RNA_UV_6SG_EXTENDED

constexpr std::array<const char*, 11> modifications_RNA_UV_6SG_EXTENDED

static

Initial value:

{   
    "X:",
    "X:-H2O",
    "X:-H3PO4",
    "X:-HPO3",
    "X:-H2S",
    "X:-HPO3-H2S", 
    

    "X:-C5H8O4",
    "X:-C5H8O4-H2O",
    "X:-C5H8O4-HPO3",
    "X:-C5H8O4-HPO3-H2S", 
    "X:-C5H8O4-H2S"    
  }

Referenced by getPresets().

modifications_RNA_UV_EXTENDED

constexpr std::array<const char*, 29> modifications_RNA_UV_EXTENDED

static

Referenced by getPresets().

presets_names

constexpr std::array<const char*, 23> presets_names

static

Initial value:

{
      "none", 
      "RNA-UV (U)", 
      "RNA-UV (UCGA)",
      "RNA-UV Extended (U)", 
      "RNA-UV Extended (UCGA)", 
      "RNA-UV (4SU)", 
      "RNA-UV Extended (4SU)",
      "RNA-UV (6SG)", 
      "RNA-UV Extended (6SG)",
      "RNA-DEB",
      "RNA-DEB Extended", 
      "RNA-NM",
      "RNA-NM Extended", 
      "DNA-UV", 
      "DNA-UV Extended", 
      "DNA-DEB", 
      "DNA-DEB Extended",
      "DNA-NM",
      "DNA-NM Extended",
      "RNA-FA",
      "RNA-FA Extended",
      "DNA-FA",
      "DNA-FA Extended"
   }

Referenced by getPresets().

RNA_mapping

constexpr std::array<const char*, 4> RNA_mapping {"A->A", "C->C", "G->G", "U->U"}

static

Referenced by getPresets().

RNA_nucleotides

constexpr std::array<const char*, 4> RNA_nucleotides {"A=C10H14N5O7P", "C=C9H14N3O8P", "G=C10H14N5O8P", "U=C9H13N2O9P"}

static

Referenced by getPresets().