Package org.biojava.bio.proteomics

Class MassCalc

java.lang.Object
org.biojava.bio.proteomics.MassCalc
public class MassCalc extends Object
MassCalc calculates the mass of peptides which for our purposes are SymbolLists which contain Symbolsfrom the protein Alphabet. It uses the mono-isotopic and average-isotopic masses identical to those specified at www.micromass.co.uk Note: This class does not handle selenocysteine and pyrrolysine.
Author:
M. Jones sdfsd, Keith James (minor changes), Mark Schreiber, George Waldon - getMolecularWeight

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final double
    Cavg
    Constant value of Carbon average mass
    static final double
    Cmono
    Constant value of Carbon monoisotopic mass
    static final double
    Havg
    Constant value of Hydrogen average mass
    static final double
    Hmono
    Constant value of Hydrogen monoisotopic mass
    static final double
    Navg
    Constant value of Nitrogen average mass
    static final double
    Nmono
    Constant value of Nitrogen monoisotopic mass
    static final double
    Oavg
    Constant value of Oxygen average mass
    static final double
    Omono
    Constant value of Oxygen monoisotopic mass

  • Constructor Summary

    Constructors
    Constructor
    Description
    MassCalc(String isotopicType, boolean MH_PLUS)
    Creates a new MassCalc.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addVariableModification(char residue, double[] masses)
    Add Variable modifications.
    void
    addVariableModification(Symbol residue, double[] masses)
    Add Variable modifications.
    double
    getMass(SymbolList proteinSeq)
    Get the Mass of this peptide.
    static final double
    getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS)
    getMass calculates the mass of this peptide.
    static final double
    getMolecularWeight(SymbolList proteinSeq)
    Calculate the molecular weight of a protein, making estimates whenever it is possible like averaging mass values for ambiguity symbols or counting zero when gaps are encountered.
    double
    getTermMass()
    getTermMass returns the terminal mass being used by the instance methods.
    double[]
    getVariableMasses(SymbolList peptide)
    Get all masses including the variable mass.
    boolean
    removeVariableModifications(char residue)
    Remove all variable modifications assocaited with this residue.
    boolean
    removeVariableModifications(Symbol residue)
    Remove all variable modifications assocaited with this residue.
    void
    setSymbolModification(char symbolToken, double mass)
    Use this to set a post translational modification for the Symbol represented by this character.

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

    • MassCalc

      public MassCalc(String isotopicType, boolean MH_PLUS)
      Creates a new MassCalc.
      Parameters:
      isotopicType - a String. The type of isotopes to calculate. Either mono isotopic or average isotopic. Acceptable values are SymbolPropertyTable.AVG_MASS or SymbolPropertyTable.MONO_MASS.
      MH_PLUS - a boolean.

  • Method Details

    • setSymbolModification

      public void setSymbolModification(char symbolToken, double mass) throws IllegalSymbolException
      Use this to set a post translational modification for the Symbol represented by this character. It will only affect the current MassCalc instance and will not affect the static method.
      Parameters:
      symbolToken - a char representing a Symbol.
      mass - a double to be the new mass of the residue.
      Throws:
      IllegalSymbolException - if the Symbol is not recognised.

    • addVariableModification

      public void addVariableModification(char residue, double[] masses) throws IllegalSymbolException
      Add Variable modifications. If multiple masses are set by this method more then one mass will be returned for a mass calculation. For example if a peptide contains two Mets and the user sets the native and oxidized mass for the Met then the masses returned will be of the peptide with 0, 1 and 2 modified Mets.
      Parameters:
      residue - The one char id for this residue
      masses -
      Throws:
      IllegalSymbolException
      See Also:

    • addVariableModification

      public void addVariableModification(Symbol residue, double[] masses) throws IllegalSymbolException
      Add Variable modifications. If multiple masses are set by this method more then one mass will be returned for a mass calculation. For example if a peptide contains two Mets and the user sets the native and oxidized mass for the Met then the masses returned will be of the peptide with 0, 1 and 2 modified Mets.
      Throws:
      IllegalSymbolException

    • removeVariableModifications

      public boolean removeVariableModifications(char residue) throws IllegalSymbolException
      Remove all variable modifications assocaited with this residue.
      Throws:
      IllegalSymbolException

    • removeVariableModifications

      public boolean removeVariableModifications(Symbol residue)
      Remove all variable modifications assocaited with this residue.

    • getMolecularWeight

      public static final double getMolecularWeight(SymbolList proteinSeq) throws IllegalSymbolException
      Calculate the molecular weight of a protein, making estimates whenever it is possible like averaging mass values for ambiguity symbols or counting zero when gaps are encountered. The method is tolerant for ambiguity symbols as long as they can be resolved to a series of atomic symbols whose mass is available in the ResidueProperties.xml configuration file or they are gaps. The method returns the same value as getMass(SymbolList proteinSeq, SymbolPropertyTable.AVG_MASS, false) when only atomic symbols are found in the polypeptide.
      Throws:
      IllegalSymbolException
      Since:
      1.5

    • getMass

      public static final double getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS) throws IllegalSymbolException
      getMass calculates the mass of this peptide. This only works for the values in the ResidueProperties.xml configuration file. It is probably slightly faster than the instance method, but it does not handle post-translational modifications.
      Parameters:
      proteinSeq - a SymbolList whose mass is to be calculated. This should use the protein alphabet.
      isotopicType - a String The type of isotopes to calculate. Either mono isotopic or average isotopic. Acceptable values are SymbolPropertyTable.AVG_MASS or SymbolPropertyTable.MONO_MASS.
      MH_PLUS - a boolean true if the value needed is the MH+ mass.
      Returns:
      a double mass of the peptide.
      Throws:
      IllegalSymbolException - if the SymbolList contains illegal Symbols.

    • getMass

      public double getMass(SymbolList proteinSeq) throws IllegalSymbolException
      Get the Mass of this peptide. Use this if you want to set fixed modifications and have created an instance of MassCalc. The value is calculated using the value of MH_PLUS defined in the constructor. The static method may be faster.
      Parameters:
      proteinSeq - The sequence for mass calculation
      Returns:
      The mass of the sequence
      Throws:
      IllegalSymbolException

    • getVariableMasses

      public double[] getVariableMasses(SymbolList peptide) throws IllegalSymbolException
      Get all masses including the variable mass. Allgorythm 1 Get the first residue of the sequence create a list of all the standard and non-standard massses for this reidue for each residue mass goto 1 with the sequence of all residues after the current residue add the residue mass to each mass from 1 to the list
      Throws:
      IllegalSymbolException
      See Also:

    • getTermMass

      public double getTermMass()
      getTermMass returns the terminal mass being used by the instance methods.
      Returns:
      a double mass.