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pwiz::chemistry Namespace Reference

Namespaces

 detail
 
 Element
 scope for declarations related to elements
 
 Ion
 

Classes

class  Formula
 class to represent a chemical formula More...
 
class  IsotopeCalculator
 
class  IsotopeEnvelopeEstimator
 Class used for calculating a theoretical isotope envelope for a given mass, based on an estimate of the elemental composition for that mass. More...
 
class  IsotopeTable
 Class representing a table of isotope distributions for collections of multiple atoms of a single element; the table is computed on instantiation, based on the element's mass distribution, a maximum atom count, and abundance cutoff value. More...
 
struct  MassAbundance
 struct for holding isotope information More...
 
struct  MZTolerance
 struct for expressing m/z tolerance in either amu or ppm More...
 

Typedefs

typedef std::vector< MassAbundanceMassDistribution
 struct for holding isotope distribution More...
 

Functions

PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const MassAbundance &ma)
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const MassDistribution &md)
 
PWIZ_API_DECL Formula operator+ (const Formula &a, const Formula &b)
 
PWIZ_API_DECL Formula operator- (const Formula &a, const Formula &b)
 
PWIZ_API_DECL Formula operator* (const Formula &a, int scalar)
 
PWIZ_API_DECL Formula operator* (int scalar, const Formula &a)
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const Formula &formula)
 output a Formula More...
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const MZTolerance &mzt)
 
PWIZ_API_DECL std::istream & operator>> (std::istream &is, MZTolerance &mzt)
 
PWIZ_API_DECL bool operator== (const MZTolerance &a, const MZTolerance &b)
 
PWIZ_API_DECL bool operator!= (const MZTolerance &a, const MZTolerance &b)
 
PWIZ_API_DECL double & operator+= (double &d, const MZTolerance &tolerance)
 
PWIZ_API_DECL double & operator-= (double &d, const MZTolerance &tolerance)
 
PWIZ_API_DECL double operator+ (double d, const MZTolerance &tolerance)
 
PWIZ_API_DECL double operator- (double d, const MZTolerance &tolerance)
 
PWIZ_API_DECL bool isWithinTolerance (double a, double b, const MZTolerance &tolerance)
 returns true iff a is in (b-tolerance, b+tolerance) More...
 
PWIZ_API_DECL bool lessThanTolerance (double a, double b, const MZTolerance &tolerance)
 returns true iff b - a is greater than the value in tolerance (useful for matching sorted mass lists) More...
 

Variables

const double Proton = 1.00727646688
 the mass of a proton in unified atomic mass units More...
 
const double Neutron = 1.00866491560
 the mass of a neutron in unified atomic mass units More...
 
const double Electron = 0.00054857991
 the mass of an electron in unified atomic mass units More...
 

Typedef Documentation

§ MassDistribution

struct for holding isotope distribution

Definition at line 66 of file Chemistry.hpp.

Function Documentation

§ operator<<() [1/4]

PWIZ_API_DECL std::ostream& pwiz::chemistry::operator<< ( std::ostream &  os,
const MassAbundance ma 
)

§ operator<<() [2/4]

PWIZ_API_DECL std::ostream& pwiz::chemistry::operator<< ( std::ostream &  os,
const MassDistribution md 
)

§ operator+() [1/2]

PWIZ_API_DECL Formula pwiz::chemistry::operator+ ( const Formula a,
const Formula b 
)

§ operator-() [1/2]

PWIZ_API_DECL Formula pwiz::chemistry::operator- ( const Formula a,
const Formula b 
)

§ operator*() [1/2]

PWIZ_API_DECL Formula pwiz::chemistry::operator* ( const Formula a,
int  scalar 
)

§ operator*() [2/2]

PWIZ_API_DECL Formula pwiz::chemistry::operator* ( int  scalar,
const Formula a 
)

§ operator<<() [3/4]

PWIZ_API_DECL std::ostream& pwiz::chemistry::operator<< ( std::ostream &  os,
const Formula formula 
)

output a Formula

§ operator<<() [4/4]

PWIZ_API_DECL std::ostream& pwiz::chemistry::operator<< ( std::ostream &  os,
const MZTolerance mzt 
)

§ operator>>()

PWIZ_API_DECL std::istream& pwiz::chemistry::operator>> ( std::istream &  is,
MZTolerance mzt 
)

§ operator==()

PWIZ_API_DECL bool pwiz::chemistry::operator== ( const MZTolerance a,
const MZTolerance b 
)

§ operator!=()

PWIZ_API_DECL bool pwiz::chemistry::operator!= ( const MZTolerance a,
const MZTolerance b 
)

§ operator+=()

PWIZ_API_DECL double& pwiz::chemistry::operator+= ( double &  d,
const MZTolerance tolerance 
)

§ operator-=()

PWIZ_API_DECL double& pwiz::chemistry::operator-= ( double &  d,
const MZTolerance tolerance 
)

§ operator+() [2/2]

PWIZ_API_DECL double pwiz::chemistry::operator+ ( double  d,
const MZTolerance tolerance 
)

§ operator-() [2/2]

PWIZ_API_DECL double pwiz::chemistry::operator- ( double  d,
const MZTolerance tolerance 
)

§ isWithinTolerance()

PWIZ_API_DECL bool pwiz::chemistry::isWithinTolerance ( double  a,
double  b,
const MZTolerance tolerance 
)

returns true iff a is in (b-tolerance, b+tolerance)

Referenced by pwiz::chemistry::MZTolerance::MZTolerance(), and testIsWithinTolerance().

§ lessThanTolerance()

PWIZ_API_DECL bool pwiz::chemistry::lessThanTolerance ( double  a,
double  b,
const MZTolerance tolerance 
)

returns true iff b - a is greater than the value in tolerance (useful for matching sorted mass lists)

Referenced by pwiz::chemistry::MZTolerance::MZTolerance().

Variable Documentation

§ Proton

const double pwiz::chemistry::Proton = 1.00727646688

the mass of a proton in unified atomic mass units

Definition at line 41 of file Chemistry.hpp.

Referenced by fragmentTest(), pwiz::chemistry::Ion::ionMass(), and pwiz::chemistry::Ion::neutralMass().

§ Neutron

const double pwiz::chemistry::Neutron = 1.00866491560

the mass of a neutron in unified atomic mass units

Definition at line 44 of file Chemistry.hpp.

Referenced by pwiz::chemistry::Ion::ionMass(), and pwiz::chemistry::Ion::neutralMass().

§ Electron

const double pwiz::chemistry::Electron = 0.00054857991

the mass of an electron in unified atomic mass units

Definition at line 47 of file Chemistry.hpp.

Referenced by pwiz::chemistry::Ion::ionMass(), and pwiz::chemistry::Ion::neutralMass().