Class to load abundance information for natural isotopes. More...

#include <abundance.h>

Public Member Functions
size_t	open (const char *file, bool strict=false)
	Attempt to open the abundance data file, return 0 on success, nonzero on failure. More...

size_t	numIsotopes () const
	Return the number of isotopes in the loaded table. More...

size_t	numElements () const
	Return the number of elements in the loaded table. More...

size_t	symbolIndex (const char *symbol, bool caseSensitive=true) const
	Return the element's position in table, starting from 0. More...

void	getSymbolIndices (const std::vector< std::string > &symbols, std::vector< size_t > &indices) const
	Return a vector of symbol indices. More...

void	getSymbolIndices (const std::vector< std::pair< std::string, size_t > > &symbols, std::vector< std::pair< size_t, unsigned int > > &indices) const
	Obtain the symbol indicies for a string,payload type. Resultant pair has first item in index, second is payload. More...

std::string	elementName (size_t elemIdx) const
	Obtain the name of an element from its index. More...

size_t	symbolIdxFromAtomicNumber (size_t atomicNumber) const
	Return the symbol index (offset in vector) for the given atomic number, -1 if it cannot be found. More...

std::string	elementNames (size_t start, size_t end, char separator=',') const
	Obtain a delimited list of element names, using the (optional) supplied separator, over the specified [start,end) range. More...

void	isotopeIndex (size_t elem, float mass, size_t &isotopeIdx) const
	Obtain the atom ID (first) and the isotope value(second). More...

void	isotopeIndex (size_t elem, float mass, float tolerance, size_t &isotopeIdx) const
	Return the first matching element in the table which has a given tolerance to the specified match. More...

unsigned int	getAtomicNumber (size_t elemIdx) const
	Obtain the atomic number for the given element, by element index. More...

const std::vector< ISOTOPE_ENTRY > &	isotopes (size_t offset) const
	Return the isotope at a given position in the table. Offset must exist. More...

void	generateIsotopeDist (const std::vector< size_t > &elementIdx, const std::vector< size_t > &frequency, std::vector< std::pair< float, float > > &massDist) const
	Compute the mass-probability distribution for the grouped set of ions. More...

void	generateGroupedIsotopeDist (const std::vector< size_t > &elementIdx, const std::vector< size_t > &frequency, std::vector< std::pair< float, float > > &massDist, float massTolerance) const
	As per generateIsotopeDist, however, this convenience groups the distribution to limit the effect of minute mass changes. More...

void	generateSingleAtomDist (size_t atomIdx, unsigned int repeatCount, std::vector< std::pair< float, float > > &massDist) const
	Obtain the mass distribution from a single isotope that repeats. Output is not grouped. More...

float	abundanceBetweenLimits (const std::vector< size_t > &elemIdx, const std::vector< size_t > &frequency, float massStart, float massEnd) const
	Obtain the fractional abundance between two limits for the given species [start,end) More...

const ISOTOPE_ENTRY &	isotope (size_t elementIdx, size_t isotopeIdx) const
	Obtain a reference to a particular isotope, using the element's index in the table, and the isotope index. More...

size_t	getMajorIsotopeFromElemIdx (size_t elementIdx) const
	Obtain the most prominent isotope's index from the element index. More...

float	getNominalMass (size_t elementIdx) const
	Obtain the isotope weighted mass for the given element. More...

size_t	getNearestCharge (const std::vector< std::pair< size_t, size_t > > &molecule, float targetMass, size_t maxCharge) const
	Obtain the closest charge state for the given mass and species group. More...

Static Public Member Functions
static const char *	getErrorText (size_t errorCode)
	Obtain a human-readable error message from the open( ) call. More...

Detailed Description

Class to load abundance information for natural isotopes.

Definition at line 54 of file abundance.h.

Member Function Documentation

◆ abundanceBetweenLimits()

float AtomProbe::AbundanceData::abundanceBetweenLimits	(	const std::vector< size_t > &	elemIdx,
		const std::vector< size_t > &	frequency,
		float	massStart,
		float	massEnd
	)		const

Obtain the fractional abundance between two limits for the given species [start,end)

Definition at line 463 of file abundance.cpp.

References ASSERT, generateIsotopeDist(), and isotope().

Referenced by AtomProbe::leastSquaresOverlapSolve().

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◆ elementName()

std::string AtomProbe::AbundanceData::elementName ( size_t elemIdx ) const

inline

Obtain the name of an element from its index.

Definition at line 107 of file abundance.h.

References AtomProbe::ISOTOPE_ENTRY::atomicNumber, and AtomProbe::ISOTOPE_ENTRY::mass.

Referenced by elementNames().

◆ elementNames()

std::string AtomProbe::AbundanceData::elementNames	(	size_t	start,
		size_t	end,
		char	separator = `','`
	)		const

Obtain a delimited list of element names, using the (optional) supplied separator, over the specified [start,end) range.

Definition at line 593 of file abundance.cpp.

References ASSERT, elementName(), and symbolIdxFromAtomicNumber().

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◆ generateGroupedIsotopeDist()

void AtomProbe::AbundanceData::generateGroupedIsotopeDist	(	const std::vector< size_t > &	elementIdx,
		const std::vector< size_t > &	frequency,
		std::vector< std::pair< float, float > > &	massDist,
		float	massTolerance
	)		const

As per generateIsotopeDist, however, this convenience groups the distribution to limit the effect of minute mass changes.

This groups the masses of nearby isotope combinations together. This is desirable due to species, such as Mo2, which have isotopes within <0.001 amu of one another. The mass centres are computed using a weighted average, and the intensities are summed

Definition at line 395 of file abundance.cpp.

References generateIsotopeDist(), and AtomProbe::weightedMean().

Referenced by AtomProbe::findOverlaps(), getMassDistributions(), getNearestCharge(), and AtomProbe::maxExplainedFraction().

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◆ generateIsotopeDist()

void AtomProbe::AbundanceData::generateIsotopeDist	(	const std::vector< size_t > &	elementIdx,
		const std::vector< size_t > &	frequency,
		std::vector< std::pair< float, float > > &	massDist
	)		const

Compute the mass-probability distribution for the grouped set of ions.

E.g., for C2, this would be elementIdx = elementIdx("C"), and frequency 2. This would return probabilities for each unique mass {C-12 C-12},{C-12 C-13} and {C-13 C-13}.... note an internal "grouping" tolerance is used to group-together very close masses. This may be smaller than what is needed for your application, so if you wish to obtain a more specific distribution use "generateGroupedIsotopeDist"

Definition at line 277 of file abundance.cpp.

References ASSERT, and AtomProbe::vectorMultiErase().

Referenced by abundanceBetweenLimits(), AtomProbe::checkMassRangingCorrectness(), AtomProbe::computeIonDistAdjacency(), AtomProbe::filterPeakNeedBiggerObs(), generateGroupedIsotopeDist(), getNearestCharge(), and AtomProbe::RangeFile::guessChargeState().

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◆ generateSingleAtomDist()

void AtomProbe::AbundanceData::generateSingleAtomDist	(	size_t	atomIdx,
		unsigned int	repeatCount,
		std::vector< std::pair< float, float > > &	massDist
	)		const

Obtain the mass distribution from a single isotope that repeats. Output is not grouped.

Definition at line 517 of file abundance.cpp.

Referenced by AtomProbe::MultiRange::copyDataFromRange().

◆ getAtomicNumber()

unsigned int AtomProbe::AbundanceData::getAtomicNumber ( size_t elemIdx ) const

Obtain the atomic number for the given element, by element index.

Definition at line 503 of file abundance.cpp.

References ASSERT.

Referenced by AtomProbe::computeRangeAdjacency(), AtomProbe::findOverlaps(), and AtomProbe::MultiRange::MultiRange().

◆ getErrorText()

const char * AtomProbe::AbundanceData::getErrorText ( size_t errorCode )

static

Obtain a human-readable error message from the open( ) call.

Definition at line 59 of file abundance.cpp.

References ASSERT.

◆ getMajorIsotopeFromElemIdx()

size_t AtomProbe::AbundanceData::getMajorIsotopeFromElemIdx ( size_t elementIdx ) const

Obtain the most prominent isotope's index from the element index.

Definition at line 482 of file abundance.cpp.

References ASSERT.

Referenced by AtomProbe::maxExplainedFraction().

◆ getNearestCharge()

size_t AtomProbe::AbundanceData::getNearestCharge	(	const std::vector< std::pair< size_t, size_t > > &	molecule,
		float	targetMass,
		size_t	maxCharge
	)		const

Obtain the closest charge state for the given mass and species group.

In the "molecule" parameter, the pair is <element index, count>, the target mass is given in Da, and the maximum charge is the maximum the function will search for

Definition at line 642 of file abundance.cpp.

References ASSERT, generateGroupedIsotopeDist(), generateIsotopeDist(), open(), symbolIndex(), and TEST.

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◆ getNominalMass()

float AtomProbe::AbundanceData::getNominalMass ( size_t elementIdx ) const

Obtain the isotope weighted mass for the given element.

Definition at line 626 of file abundance.cpp.

Referenced by AtomProbe::convertMassToMol(), and AtomProbe::convertMolToMass().

◆ getSymbolIndices() [1/2]

void AtomProbe::AbundanceData::getSymbolIndices	(	const std::vector< std::string > &	symbols,
		std::vector< size_t > &	indices
	)		const

Return a vector of symbol indices.

Definition at line 559 of file abundance.cpp.

References symbolIndex().

Referenced by AtomProbe::MultiRange::copyDataFromRange(), AtomProbe::findOverlaps(), getMassDistributions(), and AtomProbe::MultiRange::MultiRange().

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◆ getSymbolIndices() [2/2]

void AtomProbe::AbundanceData::getSymbolIndices	(	const std::vector< std::pair< std::string, size_t > > &	symbols,
		std::vector< std::pair< size_t, unsigned int > > &	indices
	)		const

Obtain the symbol indicies for a string,payload type. Resultant pair has first item in index, second is payload.

◆ isotope()

const ISOTOPE_ENTRY & AtomProbe::AbundanceData::isotope	(	size_t	elementIdx,
		size_t	isotopeIdx
	)		const

Obtain a reference to a particular isotope, using the element's index in the table, and the isotope index.

Definition at line 271 of file abundance.cpp.

References ASSERT.

Referenced by abundanceBetweenLimits(), AtomProbe::MultiRange::copyDataFromRange(), AtomProbe::filterBySolutionPPM(), and AtomProbe::maxExplainedFraction().

◆ isotopeIndex() [1/2]

void AtomProbe::AbundanceData::isotopeIndex	(	size_t	elem,
		float	mass,
		size_t &	isotopeIdx
	)		const

Obtain the atom ID (first) and the isotope value(second).

The mass and element ID must match exactly NOTE: The element and isotope indices are NOT its isotopic number it is the offset to that isotope int the abundance table

Definition at line 238 of file abundance.cpp.

References ASSERT.

◆ isotopeIndex() [2/2]

void AtomProbe::AbundanceData::isotopeIndex	(	size_t	elem,
		float	mass,
		float	tolerance,
		size_t &	isotopeIdx
	)		const

Return the first matching element in the table which has a given tolerance to the specified match.

Definition at line 254 of file abundance.cpp.

References ASSERT.

◆ isotopes()

const std::vector< ISOTOPE_ENTRY > & AtomProbe::AbundanceData::isotopes ( size_t offset ) const

Return the isotope at a given position in the table. Offset must exist.

Definition at line 621 of file abundance.cpp.

References ASSERT.

Referenced by AtomProbe::leastSquaresOverlapSolve().

◆ numElements()

size_t AtomProbe::AbundanceData::numElements ( ) const

Return the number of elements in the loaded table.

Definition at line 74 of file abundance.cpp.

◆ numIsotopes()

size_t AtomProbe::AbundanceData::numIsotopes ( ) const

Return the number of isotopes in the loaded table.

Definition at line 65 of file abundance.cpp.

◆ open()

size_t AtomProbe::AbundanceData::open	(	const char *	file,
		bool	strict = `false`
	)

Attempt to open the abundance data file, return 0 on success, nonzero on failure.

If nonzero, a human readable message can be obtained from getErrorText(...)

Definition at line 79 of file abundance.cpp.

References AtomProbe::ISOTOPE_ENTRY::abundance, AtomProbe::ISOTOPE_ENTRY::abundanceError, AtomProbe::ISOTOPE_ENTRY::atomicNumber, AtomProbe::ISOTOPE_ENTRY::mass, AtomProbe::ISOTOPE_ENTRY::massError, AtomProbe::ISOTOPE_ENTRY::massNumber, AtomProbe::ISOTOPE_ENTRY::symbol, AtomProbe::XMLHelpFwdToElem(), and AtomProbe::XMLHelpGetProp().

Referenced by AtomProbe::checkMassRangingCorrectness(), AtomProbe::computeRangeAdjacency(), AtomProbe::findOverlaps(), getNearestCharge(), AtomProbe::RangeFile::guessChargeState(), AtomProbe::leastSquaresOverlapSolve(), main(), AtomProbe::maxExplainedFraction(), AtomProbe::parseCompositionData(), and runTests().

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◆ symbolIdxFromAtomicNumber()

size_t AtomProbe::AbundanceData::symbolIdxFromAtomicNumber ( size_t atomicNumber ) const

Return the symbol index (offset in vector) for the given atomic number, -1 if it cannot be found.

Definition at line 609 of file abundance.cpp.

Referenced by AtomProbe::computeIonDistAdjacency(), elementNames(), and AtomProbe::leastSquaresOverlapSolve().

◆ symbolIndex()

size_t AtomProbe::AbundanceData::symbolIndex	(	const char *	symbol,
		bool	caseSensitive = `true`
	)		const

Return the element's position in table, starting from 0.

Notes

Input is case insensitive.
returns (unsigned) -1 if the symbol cannot be found

Definition at line 214 of file abundance.cpp.

References ASSERT, and AtomProbe::lowercase().

Referenced by AtomProbe::computeRangeAdjacency(), AtomProbe::MultiRange::copyDataFromRange(), getNearestCharge(), AtomProbe::getRangeMolecule(), getSymbolIndices(), AtomProbe::RangeFile::guessChargeState(), AtomProbe::leastSquaresOverlapSolve(), AtomProbe::maxExplainedFraction(), and AtomProbe::parseCompositionData().

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The documentation for this class was generated from the following files:

include/atomprobe/isotopes/abundance.h
src/isotopes/abundance.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ abundanceBetweenLimits()

◆ elementName()

◆ elementNames()

◆ generateGroupedIsotopeDist()

◆ generateIsotopeDist()

◆ generateSingleAtomDist()

◆ getAtomicNumber()

◆ getErrorText()

◆ getMajorIsotopeFromElemIdx()

◆ getNearestCharge()

◆ getNominalMass()

◆ getSymbolIndices() [1/2]

◆ getSymbolIndices() [2/2]

◆ isotope()

◆ isotopeIndex() [1/2]

◆ isotopeIndex() [2/2]

◆ isotopes()

◆ numElements()

◆ numIsotopes()

◆ open()

◆ symbolIdxFromAtomicNumber()

◆ symbolIndex()