C# Class ImsInformed.Util.MoleculeUtil

The molecule utilities.

Datei anzeigen Open project: PNNL-Comp-Mass-Spec/IMS-Informed-Library

Public Methods

Method	Description
AreCompositionsEqual ( InformedProteomics.Backend.Data.Composition.Composition A, InformedProteomics.Backend.Data.Composition.Composition B ) : bool	The are compositions equal.
ComputeCrossSectionalArea ( double averageTemperatureInKelvin, double mobility, int chargeState, double reducedMass ) : double	The math to compute collision cross sectional area.
ComputeReducedMass ( double targetMz, InformedProteomics.Backend.Data.Composition.Composition bufferGas ) : double	The reduced mass.
MaxGlobalIntensities2 ( VoltageGroup group, DataReader reader ) : double	The max global intensities 2.
ReadEmpiricalFormula ( string empiricalFormula ) : Composition	Convert the empirical formula string to CompositionWithoutAdduct object defined Informed Proteomics

Private Methods

Method	Description
CloseParenthesis ( string stringToBeClosed, string &leftOver ) : InformedProteomics.Backend.Data.Composition.Composition	The close parenthesis.
IsBalanced ( string input ) : bool	The is balanced.
IsBalanced ( string input, string stack ) : bool	Check the balance of parenthesis given a empirical formula
IsClose ( char ch ) : bool	The character is a closing parenthesis.
IsMatching ( char open, char close ) : bool
IsOpen ( char ch ) : bool	The character is an open parenthesis.
ParseEmpiricalFormula ( string empiricalFormula ) : Composition	This method can parse empirical formulas with parentheses
ParseEmpiricalFormulaString ( string chemicalFormula ) : int>.IDictionary	The parse empirical formula string.
ReadEmpiricalFormulaNoParenthesis ( string empiricalFormula ) : Composition	This method only parse empirical formulas without parenthethese Examples, CHOCOOH, H2O, CO2, FeS

Method Details

AreCompositionsEqual() public static method

The are compositions equal.

public static AreCompositionsEqual ( InformedProteomics.Backend.Data.Composition.Composition A, InformedProteomics.Backend.Data.Composition.Composition B ) : bool
A	InformedProteomics.Backend.Data.Composition.Composition	/// The a. ///
B	InformedProteomics.Backend.Data.Composition.Composition	/// The b. ///
return	bool

ComputeCrossSectionalArea() public static method

The math to compute collision cross sectional area.

public static ComputeCrossSectionalArea ( double averageTemperatureInKelvin, double mobility, int chargeState, double reducedMass ) : double
averageTemperatureInKelvin	double	/// The average temperature in kelvin. ///
mobility	double	/// The mobility. ///
chargeState	int	/// The charge state. ///
reducedMass	double	/// The reduced mass. ///
return	double

ComputeReducedMass() public static method

The reduced mass.

public static ComputeReducedMass ( double targetMz, InformedProteomics.Backend.Data.Composition.Composition bufferGas ) : double
targetMz	double	/// The Target MZ. ///
bufferGas	InformedProteomics.Backend.Data.Composition.Composition	/// The buffer gas composition. /// Example: N2 ///
return	double

MaxGlobalIntensities2() public static method

The max global intensities 2.

public static MaxGlobalIntensities2 ( VoltageGroup group, DataReader reader ) : double
group	VoltageGroup	/// The group. ///
reader	DataReader	/// The reader. ///
return	double

ReadEmpiricalFormula() public static method

Convert the empirical formula string to CompositionWithoutAdduct object defined Informed Proteomics

///

public static ReadEmpiricalFormula ( string empiricalFormula ) : Composition
empiricalFormula	string	/// The empirical formula. ///
return	Composition