AdductInfo Class Reference

#include <OpenMS/ANALYSIS/ID/AccurateMassSearchEngine.h>

Collaboration diagram for AdductInfo:

Public Member Functions
	AdductInfo (const String &name, const EmpiricalFormula &adduct, int charge, UInt mol_multiplier=1)
double	getNeutralMass (double observed_mz) const
	returns the neutral mass of the small molecule without adduct (creates monomer from nmer, decharges and removes the adduct (given m/z of [nM+Adduct]/|charge| returns mass of [M]) More...
double	getMZ (double neutral_mass) const
	returns the m/z of the small molecule with neutral mass neutral_mass if the adduct is added (given mass of [M] returns m/z of [nM+Adduct]/|charge|) More...
bool	isCompatible (EmpiricalFormula db_entry) const
int	getCharge () const
	get charge of adduct More...
const String &	getName () const
	original string used for parsing More...
const EmpiricalFormula &	getEmpiricalFormula () const
	EF of adduct itself. Useful for comparison with feature adduct annotation. More...

Static Public Member Functions
static AdductInfo	parseAdductString (const String &adduct)

Private Member Functions
	AdductInfo ()
	hide default C'tor More...

Private Attributes
String	name_
	members More...
EmpiricalFormula	ef_
	EF for the actual adduct e.g. 'H' in 2M+H;+1. More...
double	mass_
	computed from ef_.getMonoWeight(), but stored explicitly for efficiency More...
int	charge_
	negative or positive charge; must not be 0 More...
UInt	mol_multiplier_
	Mol multiplier, e.g. 2 in 2M+H;+1. More...

Constructor & Destructor Documentation

AdductInfo() [1/2]

AdductInfo	(	const String &	name,
		const EmpiricalFormula &	adduct,
		int	charge,
		UInt	mol_multiplier = 1
	)

C'tor, to build a representation of an adduct.

Parameters

name	Identifier as given in the Positive/Negative-Adducts file, e.g. 'M+2K-H;1+'
adduct	Formula of the adduct, e.g. '2K-H'
charge	The charge (must not be 0; can be negative), e.g. 1
is_intrinsic	True for a molecule without an explicit adduct, e.g. 'M;-1'
mol_multiplier	Molecular multiplier, e.g. for charged dimers '2M+H;+1'

AdductInfo() [2/2]

AdductInfo ( )

private

hide default C'tor

Member Function Documentation

getCharge()

int getCharge

(

)

const

get charge of adduct

getEmpiricalFormula()

const EmpiricalFormula& getEmpiricalFormula

(

)

const

EF of adduct itself. Useful for comparison with feature adduct annotation.

getMZ()

double getMZ

(

double

neutral_mass

)

const

returns the m/z of the small molecule with neutral mass neutral_mass if the adduct is added (given mass of [M] returns m/z of [nM+Adduct]/|charge|)

getName()

const String& getName

(

)

const

original string used for parsing

getNeutralMass()

double getNeutralMass

(

double

observed_mz

)

const

returns the neutral mass of the small molecule without adduct (creates monomer from nmer, decharges and removes the adduct (given m/z of [nM+Adduct]/|charge| returns mass of [M])

isCompatible()

bool isCompatible

(

EmpiricalFormula

db_entry

)

const

checks if an adduct (e.g.a 'M+2K-H;1+') is valid, i.e if the losses (==negative amounts) can actually be lost by the compound given in db_entry. If the negative parts are present in db_entry, true is returned.

parseAdductString()

static AdductInfo parseAdductString ( const String &  adduct )

static

parse an adduct string containing a formula (must contain 'M') and charge, separated by ';'. e.g. M+H;1+ 'M' can have multipliers, e.g. '2M + H;1+' (for a singly charged dimer)

Member Data Documentation

charge_

int charge_

private

negative or positive charge; must not be 0

ef_

EmpiricalFormula ef_

private

EF for the actual adduct e.g. 'H' in 2M+H;+1.

mass_

double mass_

private

computed from ef_.getMonoWeight(), but stored explicitly for efficiency

mol_multiplier_

UInt mol_multiplier_

private

Mol multiplier, e.g. 2 in 2M+H;+1.

name_

String name_

private

members

arbitrary name, only used for error reporting