OpenMS  2.8.0
Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
AdductInfo Class Reference

#include <OpenMS/CHEMISTRY/AdductInfo.h>

Collaboration diagram for AdductInfo:
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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...
 
double getMassShift (bool use_avg_mass=false) const
 returns the mass shift caused by this adduct if charges are compensated with protons More...
 
bool isCompatible (EmpiricalFormula db_entry) const
 
int getCharge () const
 get charge of adduct More...
 
const StringgetName () const
 original string used for parsing More...
 
const EmpiricalFormulagetEmpiricalFormula () const
 sum formula of adduct itself. Useful for comparison with feature adduct annotation More...
 
UInt getMolMultiplier () const
 get molecular multiplier More...
 
bool operator== (const AdductInfo &other) const
 equality operator More...
 

Static Public Member Functions

static AdductInfo parseAdductString (const String &adduct)
 

Private Attributes

String name_
 members More...
 
EmpiricalFormula ef_
 Sum formula 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()

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

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

Parameters
nameIdentifier as given in the Positive/Negative-Adducts file, e.g. 'M+2K-H;1+'
adductFormula of the adduct, e.g. '2K-H'
chargeThe charge (must not be 0; can be negative), e.g. 1
mol_multiplierMolecular 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 ( 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.

◆ 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)

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