TheoreticalGlycanSpectrumGenerator.h File Reference

#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CHEMISTRY/GlycanStructure.h>
#include <map>

Go to the source code of this file.

Classes
class	TheoreticalGlycanSpectrumGenerator
	Generate positive-mode glycan and singly glycosylated peptide fragments. More...
struct	TheoreticalGlycanSpectrumGenerator::PeptideRetention
	Independent choices of glycan material retained by a backbone ion. More...
struct	TheoreticalGlycanSpectrumGenerator::Options
	Generation settings; all size and charge ranges are inclusive. More...
struct	TheoreticalGlycanSpectrumGenerator::Fragment
	One interpretation of a fragment, including its charge and attachment. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::TheoreticalGlycanSpectrumGenerator::PeptideRetention

struct OpenMS::TheoreticalGlycanSpectrumGenerator::PeptideRetention

Independent choices of glycan material retained by a backbone ion.

Class Members
bool	intact = false	Include the complete glycan.
bool	stripped = true	Include the peptide with no glycan.
vector< Composition >	stubs	Explicit retained compositions, each a subset of the input.

OpenMS::TheoreticalGlycanSpectrumGenerator::Options

struct OpenMS::TheoreticalGlycanSpectrumGenerator::Options

Generation settings; all size and charge ranges are inclusive.

Class Members
bool	add_b_ions = true
bool	add_c_ions = false
bool	add_diagnostic_ions = true
bool	add_internal_fragments = true
bool	add_y_ions = true
bool	add_z_ions = false
bool	allow_structural = true	False selects the composition fallback even for a tree.
Int	max_charge = 2
Size	max_cleavages = 2	Includes the root cleavage of B/internal fragments.
Size	max_composition_size = 3	Y0 is included separately when Y is enabled.
Size	max_fragments = 10000	Includes charge states, losses and peptide fragments.
Int	max_oxonium_charge = 1
Size	max_states = 100000	Also bounds enumeration work, including rejected candidates.
Int	min_charge = 1
Size	min_composition_size = 1	Retained residues for both composition B and Y.
Int	min_oxonium_charge = 1
vector< EmpiricalFormula >	neutral_losses	Single losses, not a combinatorial loss ladder.
map< char, PeptideRetention >	peptide_retention	Optional overrides for b/y/c/z.
map< string, vector< EmpiricalFormula > >	specific_neutral_losses	Applied only if that residue is retained.