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OpenMS::Constants Namespace Reference

Mathematical and physical constants namespace. More...

Namespaces

 UserParam
 

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 = 3.14159265358979323846
 PI. More...
 
const double E = 2.718281828459045235
 Euler's number - base of the natural logarithm. More...
 
double EPSILON = 1e-6
 
Chemical/physical constants.
const double ELEMENTARY_CHARGE = 1.60217738E-19
 
const double e0 = ELEMENTARY_CHARGE
 Elementary charge (alias) More...
 
const double ELECTRON_MASS = 9.1093897E-31
 
const double ELECTRON_MASS_U = 1.0 / 1822.8885020477
 
const double PROTON_MASS = 1.6726230E-27
 
const double PROTON_MASS_U = 1.0072764667710
 
const double C13C12_MASSDIFF_U = 1.0033548378
 
const double ISOTOPE_MASSDIFF_55K_U = 1.002371
 
const double NEUTRON_MASS = 1.6749286E-27
 
const double NEUTRON_MASS_U = 1.00866491566
 
const double AVOGADRO = 6.0221367E+23
 
const double NA = AVOGADRO
 
const double MOL = AVOGADRO
 
const double BOLTZMANN = 1.380657E-23
 
const double k = BOLTZMANN
 
const double PLANCK = 6.6260754E-34
 
const double h = PLANCK
 
const double GAS_CONSTANT = NA * k
 
const double R = GAS_CONSTANT
 
const double FARADAY = NA * e0
 
const double F = FARADAY
 
const double BOHR_RADIUS = 5.29177249E-11
 
const double a0 = BOHR_RADIUS
 
const double VACUUM_PERMITTIVITY = 8.85419E-12
 
const double VACUUM_PERMEABILITY = (4 * PI * 1E-7)
 
const double SPEED_OF_LIGHT = 2.99792458E+8
 
const double c = SPEED_OF_LIGHT
 
const double GRAVITATIONAL_CONSTANT = 6.67259E-11
 
const double FINE_STRUCTURE_CONSTANT = 7.29735E-3
 
Conversion factors
const double DEG_PER_RAD = 57.2957795130823209
 
const double RAD_PER_DEG = 0.0174532925199432957
 
const double MM_PER_INCH = 25.4
 
const double M_PER_FOOT = 3.048
 
const double JOULE_PER_CAL = 4.184
 
const double CAL_PER_JOULE = (1 / 4.184)
 

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
inline

Bohr radius (alias)

◆ AVOGADRO

const double AVOGADRO = 6.0221367E+23
inline

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

◆ BOHR_RADIUS

const double BOHR_RADIUS = 5.29177249E-11
inline

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

◆ BOLTZMANN

const double BOLTZMANN = 1.380657E-23
inline

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

◆ c

const double c = SPEED_OF_LIGHT
inline

Speed of Light (alias)

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), OpenMS::ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment >(), GridBasedClustering< Metric >::cluster(), IsotopeWaveletTransform< PeakType >::clusterSeeds_(), SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), SignalToNoiseEstimatorMedian< Container >::computeSTN_(), ListUtils::create(), OpenMS::StringUtils::fillLeft(), OpenMS::StringUtils::fillRight(), OpenMS::Math::gcd(), IsotopeWaveletTransform< PeakType >::getTransform(), IsotopeWaveletTransform< PeakType >::getTransformHighRes(), Precursor::getUnchargedMass(), IsotopeWaveletTransform< PeakType >::identifyCharge(), SignalToNoiseEstimator< Container >::init(), IsotopeWaveletTransform< PeakType >::initializeScan(), IsotopeWaveletTransform< PeakType >::push2Box_(), IsotopeWaveletTransform< PeakType >::push2TmpBox_(), OpenMS::StringUtils::removeWhitespaces(), IDConflictResolverAlgorithm::resolveConflict_(), IsotopeWaveletTransform< PeakType >::scoreThis_(), DIntervalBase< D >::setMaxX(), DIntervalBase< D >::setMaxY(), DIntervalBase< D >::setMinX(), DIntervalBase< D >::setMinY(), DPosition< D, TCoordinateType >::setX(), DPosition< D, TCoordinateType >::setY(), and OpenMS::StringConversions::toString().

◆ C13C12_MASSDIFF_U

const double C13C12_MASSDIFF_U = 1.0033548378
inline

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

Referenced by MSExperiment::ContainerAdd_< ContainerValueType, true >::addData_(), NucleicAcidSearchEngine::calculatePrecursorMass_(), and NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_().

◆ CAL_PER_JOULE

const double CAL_PER_JOULE = (1 / 4.184)
inline

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 = 57.2957795130823209
inline

Degree per rad. 57.2957795130823209

◆ E

const double E = 2.718281828459045235
inline

Euler's number - base of the natural logarithm.

◆ e0

const double e0 = ELEMENTARY_CHARGE
inline

Elementary charge (alias)

◆ ELECTRON_MASS

const double ELECTRON_MASS = 9.1093897E-31
inline

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

◆ ELECTRON_MASS_U

const double ELECTRON_MASS_U = 1.0 / 1822.8885020477
inline

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

◆ ELEMENTARY_CHARGE

const double ELEMENTARY_CHARGE = 1.60217738E-19
inline

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

◆ EPSILON

double EPSILON = 1e-6
inline

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

◆ F

const double F = FARADAY
inline

Faraday constant (alias)

◆ FARADAY

const double FARADAY = NA * e0
inline

Faraday constant (= NA * e0)

◆ FINE_STRUCTURE_CONSTANT

const double FINE_STRUCTURE_CONSTANT = 7.29735E-3
inline

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

◆ GAS_CONSTANT

const double GAS_CONSTANT = NA * k
inline

Gas constant (= NA * k)

Referenced by AAIndex::calculateGB().

◆ GRAVITATIONAL_CONSTANT

const double GRAVITATIONAL_CONSTANT = 6.67259E-11
inline

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

◆ h

const double h = PLANCK
inline

Planck constant (alias)

Referenced by EmgGradientDescent_friend::applyEstimatedParameters(), Annotation1DPeakItem< DataPoint >::draw(), EmgGradientDescent_friend::emg_point(), EmgGradientDescent_friend::Loss_function(), OpenMS::Math::quantile(), and PeakIntegrator::simpson_().

◆ ISOTOPE_MASSDIFF_55K_U

const double ISOTOPE_MASSDIFF_55K_U = 1.002371
inline

Average mass difference between consecutive isotopes for proteins of mass 55kDa. Referred to the values used in TopPIC. In units ( \(1.002371\)u)

Referenced by SpectraMerger::areMassesMatched().

◆ 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 = 4.184
inline

Joules per calorie. 4.184

◆ k

const double k = BOLTZMANN
inline

Boltzmann constant (alias)

Referenced by TOPPViewBase::addDataFile(), EmgScoring::calcElutionFitScore(), MRMTransitionGroupPicker::computeQuality_(), OpenSwathHelper::computeTransitionGroupId(), ChromatogramExtractor::extractChromatograms(), TOPPFLASHDeconv::main_(), TOPPOpenSwathBase::performCalibration(), PeakPickerIterative::pick(), PeakPickerSH::pick(), MRMTransitionGroupPicker::pickApex(), MRMTransitionGroupPicker::pickFragmentChromatograms(), MRMTransitionGroupPicker::pickPrecursorChromatograms(), PeakPickerIterative::pickRecenterPeaks_(), MRMTransitionGroupPicker::pickTransitionGroup(), RANSAC< TModelType >::ransac(), MRMTransitionGroupPicker::recalculatePeakBorders_(), MRMTransitionGroupPicker::remove_overlapping_features(), DistanceMatrix< Value >::resize(), TOPPViewBase::showCurrentPeaksAsDIA(), PeakIntegrator::simpson_(), and ContinuousWaveletTransformNumIntegration::transform().

◆ 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 = 3.048
inline

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 = 25.4
inline

mm per inch. 25.4

◆ MOL

const double MOL = AVOGADRO
inline

Avogadro constant (alias)

◆ NA

const double NA = AVOGADRO
inline

Avogadro constant (alias)

◆ NEUTRON_MASS

const double NEUTRON_MASS = 1.6749286E-27
inline

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

◆ NEUTRON_MASS_U

const double NEUTRON_MASS_U = 1.00866491566
inline

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 = 3.14159265358979323846
inline

PI.

◆ PLANCK

const double PLANCK = 6.6260754E-34
inline

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

◆ POW_CONST

const double POW_CONST = 0.33971f

◆ PROTON_MASS

const double PROTON_MASS = 1.6726230E-27
inline

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

◆ PROTON_MASS_U

const double PROTON_MASS_U = 1.0072764667710
inline

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

Referenced by SpectraMerger::areMassesMatched(), NucleicAcidSearchEngine::calculatePrecursorMass_(), NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_(), Precursor::getUnchargedMass(), and DTAFile::load().

◆ R

const double R = GAS_CONSTANT
inline

Gas constant (alias)

Referenced by AAIndex::calculateGB(), and KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >::visit_within_range().

◆ RAD_PER_DEG

const double RAD_PER_DEG = 0.0174532925199432957
inline

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 = 2.99792458E+8
inline

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

◆ VACUUM_PERMEABILITY

const double VACUUM_PERMEABILITY = (4 * PI * 1E-7)
inline

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 = 8.85419E-12
inline

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