OpenMS  2.4.0
Variables
OpenMS::Constants Namespace Reference
Concept

Mathematical and physical constants namespace. More...

Variables

const unsigned int DEFAULT_NUM_OF_INTERPOLATION_POINTS = 3
 
const double MASS_EPSILON = 1e-4f
 
const double MARR_WAVELET_CUTOFF = 4.f
 
const double PEPTIDE_MASS_RULE_FACTOR = 0.000507f
 
const double PEPTIDE_MASS_RULE_BOUND = 1. / PEPTIDE_MASS_RULE_FACTOR
 
const double PEPTIDE_MASS_RULE_THEO_PPM_BOUND = 200
 
const double IW_NEUTRON_MASS = 1.00866491578f
 
const double IW_HALF_NEUTRON_MASS = 0.5043325f
 
const double IW_QUARTER_NEUTRON_MASS = 0.252166228f
 
const double WAVELET_PERIODICITY = 6.229209734f
 
const double ONEOLOG2E = 0.6931471806f
 
const double IW_PROTON_MASS = 1.00727646688f
 
const double LAMBDA_L_0 = 0.120398590399013419f
 
const double LAMBDA_L_1 = 0.635926795694698589e-3f
 
const double CUT_LAMBDA_Q_0_A = 1.9498e+00f
 
const double CUT_LAMBDA_Q_0_B = 2.4244e-03f
 
const double CUT_LAMBDA_Q_0_C = -2.4183e-07f
 
const double CUT_LAMBDA_Q_1_A = 3.6870e+00f
 
const double CUT_LAMBDA_Q_1_B = 1.1561e-03f
 
const double CUT_LAMBDA_Q_1_C = -1.0329e-08f
 
const double CUT_LAMBDA_L_2_A = 5.7661e+00f
 
const double CUT_LAMBDA_L_2_B = 8.6301e-04f
 
const double CUT_LAMBDA_BREAK_0_1 = 2739.4f
 
const double CUT_LAMBDA_BREAK_1_2 = 1.4187e+04f
 
const int SHIFT23 = (1 << 23)
 
const double SHIFT23_00 = (1.0 / (1 << 23))
 
const double LOG_CONST = 0.346607f
 
const double POW_CONST = 0.33971f
 
Mathematical constants.
const double PI
 PI. More...
 
const double E
 Euler's number - base of the natural logarithm. More...
 
double EPSILON
 
Chemical/physical constants.
const double ELEMENTARY_CHARGE
 
const double e0
 Elementary charge (alias) More...
 
const double ELECTRON_MASS
 
const double ELECTRON_MASS_U
 
const double PROTON_MASS
 
const double PROTON_MASS_U
 
const double C13C12_MASSDIFF_U
 
const double NEUTRON_MASS
 
const double NEUTRON_MASS_U
 
const double AVOGADRO
 
const double NA
 
const double MOL
 
const double BOLTZMANN
 
const double k
 
const double PLANCK
 
const double h
 
const double GAS_CONSTANT
 
const double R
 
const double FARADAY
 
const double F
 
const double BOHR_RADIUS
 
const double a0
 
const double VACUUM_PERMITTIVITY
 
const double VACUUM_PERMEABILITY
 
const double SPEED_OF_LIGHT
 
const double c
 
const double GRAVITATIONAL_CONSTANT
 
const double FINE_STRUCTURE_CONSTANT
 
Conversion factors
const double DEG_PER_RAD
 
const double RAD_PER_DEG
 
const double MM_PER_INCH
 
const double M_PER_FOOT
 
const double JOULE_PER_CAL
 
const double CAL_PER_JOULE
 
const std::string PRECURSOR_ERROR_PPM_USERPARAM
 
const std::string FRAGMENT_ANNOTATION_USERPARAM
 

Detailed Description

Mathematical and physical constants namespace.

This namespace contains definitions for some basic mathematical and physical constants. All constants are double precision.
There are basically two ways of accessing these constants:

Variable Documentation

◆ a0

const double a0

Bohr radius (alias)

◆ AVOGADRO

const double AVOGADRO

Avogadro constant. In units of $mol^{-1}$ ( $6.0221367 \cdot 10^{23} mol^{-1}$).

◆ BOHR_RADIUS

const double BOHR_RADIUS

Bohr radius. In units m ( $5.29177249 \cdot 10^{-11}$ m).

◆ BOLTZMANN

const double BOLTZMANN

Boltzmann constant. In units of J/K ( $1.380657 \cdot 10^{-23}$ J/K).

◆ c

const double c

Speed of Light (alias)

Referenced by seqan::_consumeChar(), seqan::_createSecondarySpawns(), seqan::_getSpawnRange(), seqan::_masterConsumeChar(), seqan::_spawnConsumeChar(), IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), OpenMS::ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment >(), GridBasedClustering< Metric >::cluster(), IsotopeWaveletTransform< PeakType >::clusterSeeds_(), MSDataTransformingConsumer::consumeChromatogram(), ListUtils::create(), StringUtils::fillLeft(), StringUtils::fillRight(), seqan::find(), OpenMS::Math::gcd(), IsotopeWaveletTransform< PeakType >::getTransform(), IsotopeWaveletTransform< PeakType >::getTransformHighRes(), Precursor::getUnchargedMass(), IsotopeWaveletTransform< PeakType >::identifyCharge(), SignalToNoiseEstimator< ContainerT >::init(), IsotopeWaveletTransform< PeakType >::initializeScan(), seqan::isAmbiguous(), SimpleSearchEngine::main_(), RNPxlSearch::main_(), LayerStatisticsDialog::MetaStatsValue_::MetaStatsValue_(), RNPxlSearch::postScoreHits_(), IsotopeWaveletTransform< PeakType >::push2Box_(), IsotopeWaveletTransform< PeakType >::push2TmpBox_(), StringUtils::removeWhitespaces(), IDConflictResolverAlgorithm::resolveConflict_(), IsotopeWaveletTransform< PeakType >::scoreThis_(), DIntervalBase< D >::setMaxX(), DIntervalBase< D >::setMaxY(), DIntervalBase< D >::setMinX(), DIntervalBase< D >::setMinY(), DPosition< DIMENSION >::setX(), DPosition< DIMENSION >::setY(), IndexedMzMLFileLoader::store(), and OpenMS::StringConversions::toString< const char >().

◆ C13C12_MASSDIFF_U

const double C13C12_MASSDIFF_U

C13C12 mass difference. In units ( $1.0033548$u)

Referenced by MSExperiment::ContainerAdd_< ContainerValueType, true >::addData_(), TOPPOpenPepXLLF::main_(), SimpleSearchEngine::main_(), TOPPOpenPepXL::main_(), and RNPxlSearch::mapPrecursorMassesToScans().

◆ CAL_PER_JOULE

const double CAL_PER_JOULE

Calories per Joule. 1/JOULE_PER_CAL

◆ CUT_LAMBDA_BREAK_0_1

const double CUT_LAMBDA_BREAK_0_1 = 2739.4f

◆ CUT_LAMBDA_BREAK_1_2

const double CUT_LAMBDA_BREAK_1_2 = 1.4187e+04f

◆ CUT_LAMBDA_L_2_A

const double CUT_LAMBDA_L_2_A = 5.7661e+00f

◆ CUT_LAMBDA_L_2_B

const double CUT_LAMBDA_L_2_B = 8.6301e-04f

◆ CUT_LAMBDA_Q_0_A

const double CUT_LAMBDA_Q_0_A = 1.9498e+00f

◆ CUT_LAMBDA_Q_0_B

const double CUT_LAMBDA_Q_0_B = 2.4244e-03f

◆ CUT_LAMBDA_Q_0_C

const double CUT_LAMBDA_Q_0_C = -2.4183e-07f

◆ CUT_LAMBDA_Q_1_A

const double CUT_LAMBDA_Q_1_A = 3.6870e+00f

◆ CUT_LAMBDA_Q_1_B

const double CUT_LAMBDA_Q_1_B = 1.1561e-03f

◆ CUT_LAMBDA_Q_1_C

const double CUT_LAMBDA_Q_1_C = -1.0329e-08f

◆ DEFAULT_NUM_OF_INTERPOLATION_POINTS

const unsigned int DEFAULT_NUM_OF_INTERPOLATION_POINTS = 3

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

◆ DEG_PER_RAD

const double DEG_PER_RAD

Degree per rad. 57.2957795130823209

◆ E

const double E

Euler's number - base of the natural logarithm.

◆ e0

const double e0

Elementary charge (alias)

◆ ELECTRON_MASS

const double ELECTRON_MASS

Electron mass. In units of kg ( $9.1093897 \cdot 10^{-31}$ kg).

◆ ELECTRON_MASS_U

const double ELECTRON_MASS_U

Electron mass In units ( $1,822.88850204(77)^{-1}$u).

◆ ELEMENTARY_CHARGE

const double ELEMENTARY_CHARGE

Elementary charge. In units of C ( $1.60217738 \cdot 10^{-19} C$).

◆ EPSILON

double EPSILON

Internal threshold for equality comparisons. Default value is 1e-6.

◆ F

const double F

Faraday constant (alias)

◆ FARADAY

const double FARADAY

Faraday constant (= NA * e0)

◆ FINE_STRUCTURE_CONSTANT

const double FINE_STRUCTURE_CONSTANT

Fine structure constant. Without unit ( $7.29735 \cdot 10^{-3}$).

◆ FRAGMENT_ANNOTATION_USERPARAM

const std::string FRAGMENT_ANNOTATION_USERPARAM

User parameter name for fragment annotations String

◆ GAS_CONSTANT

const double GAS_CONSTANT

Gas constant (= NA * k)

Referenced by AAIndex::calculateGB().

◆ GRAVITATIONAL_CONSTANT

const double GRAVITATIONAL_CONSTANT

Gravitational constant. In units of $Nm^2kg^{-2}$ ( $6.67259 \cdot 10^{-11} Nm^2kg^{-2}$).

◆ h

const double h

Planck constant (alias)

Referenced by EmgGradientDescent_friend::emg_point(), EmgGradientDescent_friend::emg_vector(), and EmgGradientDescent_friend::Loss_function().

◆ IW_HALF_NEUTRON_MASS

const double IW_HALF_NEUTRON_MASS = 0.5043325f

Referenced by IsotopeWaveletTransform< PeakType >::push2Box_(), IsotopeWaveletTransform< PeakType >::push2TmpBox_(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

◆ IW_NEUTRON_MASS

const double IW_NEUTRON_MASS = 1.00866491578f

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

◆ IW_PROTON_MASS

const double IW_PROTON_MASS = 1.00727646688f

Referenced by IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), and IsotopeWavelet::getValueByMass().

◆ IW_QUARTER_NEUTRON_MASS

const double IW_QUARTER_NEUTRON_MASS = 0.252166228f

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::getTransform(), IsotopeWaveletTransform< PeakType >::getTransformHighRes(), IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), and IsotopeWaveletTransform< PeakType >::mapSeeds2Features().

◆ JOULE_PER_CAL

const double JOULE_PER_CAL

Joules per calorie. 4.184

◆ k

const double k

Boltzmann constant (alias)

Referenced by TOPPViewBase::addDataFile(), EmgScoring::calcElutionFitScore(), MRMTransitionGroupPicker::computeQuality_(), MetaProSIPReporting::createCSVReport(), MRMTransitionGroupPicker::createMRMFeature(), MetaProSIPReporting::createPeptideCentricCSVReport(), ChromatogramExtractor::extractChromatograms(), TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), TOPPMetaProSIP::extractIsotopicIntensities(), MetaProSIPXICExtraction::extractXICsOfIsotopeTraces(), TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), TwoDOptimization::optimizeRegions_(), PeakPickerSH::pick(), PeakPickerIterative::pick(), PeakPickerIterative::pickRecenterPeaks_(), MRMTransitionGroupPicker::pickTransitionGroup(), RNPxlSearch::postScoreHits_(), RANSAC< TModelType >::ransac(), MRMTransitionGroupPicker::recalculatePeakBorders_(), MRMTransitionGroupPicker::remove_overlapping_features(), DistanceMatrix< Value >::resize(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), ContinuousWaveletTransformNumIntegration::transform(), MetaProSIPReporting::writeHTML(), and TOPPMetaProSIP::writePeakIntensities_().

◆ LAMBDA_L_0

const double LAMBDA_L_0 = 0.120398590399013419f

◆ LAMBDA_L_1

const double LAMBDA_L_1 = 0.635926795694698589e-3f

◆ LOG_CONST

const double LOG_CONST = 0.346607f

◆ M_PER_FOOT

const double M_PER_FOOT

m per foot. 3.048

◆ MARR_WAVELET_CUTOFF

const double MARR_WAVELET_CUTOFF = 4.f

◆ MASS_EPSILON

const double MASS_EPSILON = 1e-4f

◆ MM_PER_INCH

const double MM_PER_INCH

mm per inch. 25.4

◆ MOL

const double MOL

Avogadro constant (alias)

◆ NA

const double NA

Avogadro constant (alias)

◆ NEUTRON_MASS

const double NEUTRON_MASS

Neutron mass. In units of kg ( $1.6749286 \cdot 10^{-27}$ kg).

◆ NEUTRON_MASS_U

const double NEUTRON_MASS_U

Neutron mass. In units ( $1.0086649156(6)$u)

◆ ONEOLOG2E

const double ONEOLOG2E = 0.6931471806f

◆ PEPTIDE_MASS_RULE_BOUND

const double PEPTIDE_MASS_RULE_BOUND = 1. / PEPTIDE_MASS_RULE_FACTOR

Referenced by IsotopeWaveletTransform< PeakType >::peptideMassRule_().

◆ PEPTIDE_MASS_RULE_FACTOR

const double PEPTIDE_MASS_RULE_FACTOR = 0.000507f

Referenced by IsotopeWaveletTransform< PeakType >::peptideMassRule_().

◆ PEPTIDE_MASS_RULE_THEO_PPM_BOUND

const double PEPTIDE_MASS_RULE_THEO_PPM_BOUND = 200

Referenced by IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_().

◆ PI

const double PI

PI.

◆ PLANCK

const double PLANCK

Planck constant. In units of Js ( $6.6260754 \cdot 10^{-34}$ Js).

◆ POW_CONST

const double POW_CONST = 0.33971f

◆ PRECURSOR_ERROR_PPM_USERPARAM

const std::string PRECURSOR_ERROR_PPM_USERPARAM

User parameter name for precursor mz error in ppm String

◆ PROTON_MASS

const double PROTON_MASS

Proton mass. In units of kg ( $1.6726230 \cdot 10^{-27}$ kg).

◆ PROTON_MASS_U

const double PROTON_MASS_U

Proton mass. In units ( $1.00727646677(10)$u)

Referenced by RNPxlSearch::RNPxlFragmentIonGenerator::addMS2MarkerIons(), RNPxlSearch::RNPxlFragmentIonGenerator::addPrecursorWithCompleteRNA_(), Precursor::getUnchargedMass(), DTAFile::load(), TOPPOpenPepXLLF::main_(), SimpleSearchEngine::main_(), TOPPOpenPepXL::main_(), TOPPMetaProSIP::main_(), and RNPxlSearch::mapPrecursorMassesToScans().

◆ R

const double R

Gas constant (alias)

Referenced by AAIndex::calculateGB(), and KDTree< 2, KDTreeFeatureNode >::visit_within_range().

◆ RAD_PER_DEG

const double RAD_PER_DEG

Rad per degree. 0.0174532925199432957

◆ SHIFT23

const int SHIFT23 = (1 << 23)

◆ SHIFT23_00

const double SHIFT23_00 = (1.0 / (1 << 23))

◆ SPEED_OF_LIGHT

const double SPEED_OF_LIGHT

Speed of light. In units of m/s ( $2.99792458 \cdot 10^8 ms^{-1}$).

◆ VACUUM_PERMEABILITY

const double VACUUM_PERMEABILITY

Vacuum permeability. In units of $Js^2C^{-2}m^{-1}$ ( $4\pi \cdot 10^{-7} Js^2C^{-2}m^{-1}$).

◆ VACUUM_PERMITTIVITY

const double VACUUM_PERMITTIVITY

Vacuum permittivity. In units of $C^2J^{-1}m^{-1}$ ( $8.85419 \cdot 10^{-12} C^2J^{-1}m^{-1}$).

◆ WAVELET_PERIODICITY

const double WAVELET_PERIODICITY = 6.229209734f
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