AdductInfo Class Reference

#include <OpenMS/CHEMISTRY/AdductInfo.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])
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|)
double	getMassShift (bool use_avg_mass=false) const
	returns the mass shift caused by this adduct if charges are compensated with protons
bool	isCompatible (const EmpiricalFormula &db_entry) const
int	getCharge () const
	get charge of adduct
const String &	getName () const
	original string used for parsing
const EmpiricalFormula &	getEmpiricalFormula () const
	sum formula of adduct itself. Useful for comparison with feature adduct annotation
UInt	getMolMultiplier () const
	get molecular multiplier
bool	operator== (const AdductInfo &other) const
	equality operator

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

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

Constructor & Destructor Documentation

AdductInfo()

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

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

Parameters

[in]	name	Identifier as given in the Positive/Negative-Adducts file, e.g. 'M+2K-H;1+'
[in]	adduct	Formula of the adduct, e.g. '2K-H'
[in]	charge	The charge (must not be 0; can be negative), e.g. 1
[in]	mol_multiplier	Molecular multiplier, e.g. for charged dimers '2M+H;+1'

Member Function Documentation

getCharge()

int getCharge

(

)

const

get charge of adduct

Referenced by AdductCompare::operator()().

getEmpiricalFormula()

const EmpiricalFormula & getEmpiricalFormula

(

)

const

sum formula of adduct itself. Useful for comparison with feature adduct annotation

Referenced by AdductCompare::operator()().

getMassShift()

double getMassShift

(

bool

use_avg_mass = false

)

const

returns the mass shift caused by this adduct if charges are compensated with protons

Referenced by NucleicAcidSearchEngine::main_().

getMolMultiplier()

UInt getMolMultiplier

(

)

const

get molecular multiplier

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

(

const 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.

Parameters

[in]

db_entry

The empirical formula to check compatibility with

operator==()

bool operator==

(

const AdductInfo &

other

)

const

equality operator

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)

Parameters

[in]

adduct

The adduct string to parse

Member Data Documentation

charge_

int charge_

private

negative or positive charge; must not be 0

ef_

EmpiricalFormula ef_

private

Sum formula 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