Class: MolecularFormulae

MolecularFormulae()

Code to calculate distribution based on molecular formula

Constructor

new MolecularFormulae()

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Methods

emass(mass, peakDataList, charge)

Function to calculate the emass distrubution fo the given sequence
Parameters:
Name Type Description
mass Double Contains the mass at that position of the sequence
peakDataList Array Contains the peak list provided by the user
charge Float Contains the chrage of the ion
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getMassAndIntensity(totDistributionList, aminoAcidDist)

Logic to calculate distribution
Parameters:
Name Type Description
totDistributionList Array Array with current total distribution
aminoAcidDist Array Array with existing calculated distribution of amino acid
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getMolecularFormula()

Code to get the molecular formular based on the mass. Number of atoms of each atom in the averagine * number of atoms of each atom calculated from mass gives the total number of atoms.
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getMZwithHighInte(totDistributionList, charge, massError, peakDataList)

Code to calculate MZ(mass/charge) and remove low intensity values
Parameters:
Name Type Description
totDistributionList Array Array with total distribution
charge Float Float from mass list
massError Float Calculated massError needed to be added as we taken int values of number of atoms eleminating mass from the float values.
peakDataList Array Array of peak list from user
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getNormalizedIntensity(totDistributionList, peakDataList)

Code to normalize the Intensity. Take the average of intensity from the peaks entered by the user. Take the average of the calculated distribution for each Array element in the Array. Make both of them equal and calculating the rest of the distribution intensity based on the avg value from the peak list.
Parameters:
Name Type Description
totDistributionList Array Total distribution calculated
peakDataList Array Peak Data entered by the user
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