pwiz::chemistry Namespace Reference

Namespaces
namespace	Element
	scope for declarations related to elements
namespace	detail
namespace	Ion

Classes
struct	MassAbundance
	struct for holding isotope information More...
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	MZTolerance
	struct for expressing m/z tolerance in either amu or ppm More...

Typedefs
typedef std::vector < MassAbundance >	MassDistribution
	struct for holding isotope distribution

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
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)
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)

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

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Typedef Documentation

typedef std::vector<MassAbundance> pwiz::chemistry::MassDistribution

struct for holding isotope distribution

Definition at line 66 of file Chemistry.hpp.

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Function Documentation

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

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

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

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

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

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

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

output a Formula

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

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

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

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

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

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

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

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

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 testIsWithinTolerance().

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)

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Variable Documentation

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().

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().

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().