Package com.compomics.util.general

Class MassCalc

java.lang.Object
com.compomics.util.general.MassCalc
public class MassCalc extends Object
This class takes care of mass calculation, based on a sequence in IUPAC format.
By default it can handle monoisotopic biochemical element masses and monoisotopic single-letter amino acid masses.
The object can be customized with your own mass lists through the use of a properties file, or by directly passing a HashMap.

Please note: if you decide on your own lists, be sure to follow the following guidelines:
  • An element (key in properties file or HashMap) can be ONE or TWO letters. The first ALWAYS has to be UPPERCASE, the optional second ALWAYS has to be lowercase.
  • A value has to be a parseable number for a properties file, or a Double instance for the HashMap. No other formats are accepted!
Author:
Lennart Martens

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    MONOAA
    Index for the monoisotopic aminoacid masses.
    static final int
    MONOELEMENTS
    Index for the monoisotopic masses of the biochemically relevant elements.
    static final int
    MONONUCLEOTIDES
    Index for the monoisotopic nucleotide masses.
    static final int
    SELFDEFINED
    Value for the self-defined masses.

  • Constructor Summary

    Constructors
    Constructor
    Description
    MassCalc()
    Default constructor.
    MassCalc(int aMassListIdentifier)
    This constructor allows you to specify an identifier to select a element list to use for calculating a mass.
    MassCalc(int aMassListIdentifier, HashMap aSupplElementList)
    This constructor allows the caller to supplement (or to replace elements in) a built-in elementlist with a HashMap of its own design.
    MassCalc(String aFilename)
    This constructor allows the caller to use an elementlist of its own making.
    MassCalc(HashMap aElementList)
    This constructor allows the caller to initialize the elementlist with a HashMap of its own design.

  • Method Summary

    Modifier and Type
    Method
    Description
    double
    calculateMass(String aFormula)
    This method attempts to calculate the mass of a chemical formula.
    static void
    main(String[] args)
    The main method can be used for command-line usage of this class.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • MONOELEMENTS

      public static final int MONOELEMENTS
      Index for the monoisotopic masses of the biochemically relevant elements.
      See Also:

    • MONOAA

      public static final int MONOAA
      Index for the monoisotopic aminoacid masses.
      See Also:

    • MONONUCLEOTIDES

      public static final int MONONUCLEOTIDES
      Index for the monoisotopic nucleotide masses.
      See Also:

    • SELFDEFINED

      public static final int SELFDEFINED
      Value for the self-defined masses.
      See Also:

  • Constructor Details

    • MassCalc

      public MassCalc()
      Default constructor. The mass list to be used defaults to the monoisotopic masses for biochemically relevant elements.

    • MassCalc

      public MassCalc(int aMassListIdentifier)
      This constructor allows you to specify an identifier to select a element list to use for calculating a mass.
      Please use the finalo vriables on this class as identifiers!
      Parameters:
      aMassListIdentifier - int with the identifier for the elementlist to use.

    • MassCalc

      public MassCalc(String aFilename)
      This constructor allows the caller to use an elementlist of its own making. Simply passing the filename of the file suffices.
      Parameters:
      aFilename - String with the name of the file to be loaded. NOTE! this file must be located in the classpath and mst be a simple properties file!

    • MassCalc

      public MassCalc(HashMap aElementList)
      This constructor allows the caller to initialize the elementlist with a HashMap of its own design.
      This HashMap needs be structured in the following way:
      • KEY can be one or two letters, the first has to be uppercase, the second and optional letter has to be lowercase.
      • VALUE must be a Double value
      Parameters:
      aElementList - HashMap with the elementlist to use.

    • MassCalc

      public MassCalc(int aMassListIdentifier, HashMap aSupplElementList)
      This constructor allows the caller to supplement (or to replace elements in) a built-in elementlist with a HashMap of its own design.
      This HashMap needs be structured in the following way:
      • KEY can be one or two letters, the first has to be uppercase, the second and optional letter has to be lowercase.
      • VALUE must be a Double value
      Parameters:
      aMassListIdentifier - int with the identifier for the built-in elementlist to use.
      aSupplElementList - HashMap with the supplementary elementlist to use.

  • Method Details

    • calculateMass

      public double calculateMass(String aFormula) throws UnknownElementMassException
      This method attempts to calculate the mass of a chemical formula. It cannot calculate the mass of an element if it is not known to this class (i.e.: if it does not occur in the Properties instance). In that case it will flag an exception.
      Parameters:
      aFormula - String with the chemical formula (or bruto formula) of the compound in question.
      Returns:
      double with the mass of the compound.
      Throws:
      UnknownElementMassException - when one of the composing elements' mass is unknown to the class.

    • main

      public static void main(String[] args)
      The main method can be used for command-line usage of this class. The parameters should be (a) chemical (or bruto) formula(e) to calculate the mass for.
      Parameters:
      args - String[] at least one chemical formula should be specified, up to as much as you can cramp into a single command-line.