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AdductInfo Class Reference

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

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 StringgetName () const
 original string used for parsing 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_
 
double mass_
 
int charge_
 
uint mol_multiplier_
 

Constructor & Destructor Documentation

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
is_intrinsicTrue for a molecule without an explicit adduct, e.g. 'M;-1'
mol_multiplierMolecular multiplier, e.g. for charged dimers '2M+H;+1'
AdductInfo ( )
private

hide default C'tor

Member Function Documentation

int getCharge ( ) const

get charge of adduct

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|)

const String& getName ( ) const

original string used for parsing

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])

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.

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

int charge_
private
EmpiricalFormula ef_
private
double mass_
private
uint mol_multiplier_
private
String name_
private

members


OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:57 using doxygen 1.8.9.1