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 double	Cavg	Constant value of Carbon average mass
static double	Cmono	Constant value of Carbon monoisotopic mass
static double	Havg	Constant value of Hydrogen average mass
static double	Hmono	Constant value of Hydrogen monoisotopic mass
static double	Navg	Constant value of Nitrogen average mass
static double	Nmono	Constant value of Nitrogen monoisotopic mass
static double	Oavg	Constant value of Oxygen average mass
static 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 double	getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS)	getMass calculates the mass of this peptide.
static 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 Detail

Cmono

public static final double Cmono

Constant value of Carbon monoisotopic mass

See Also:

Constant Field Values

Hmono

public static final double Hmono

Constant value of Hydrogen monoisotopic mass

See Also:

Constant Field Values

Nmono

public static final double Nmono

Constant value of Nitrogen monoisotopic mass

See Also:

Constant Field Values

Omono

public static final double Omono

Constant value of Oxygen monoisotopic mass

See Also:

Constant Field Values

Cavg

public static final double Cavg

Constant value of Carbon average mass

See Also:

Constant Field Values

Havg

public static final double Havg

Constant value of Hydrogen average mass

See Also:

Constant Field Values

Navg

public static final double Navg

Constant value of Nitrogen average mass

See Also:

Constant Field Values

Oavg

public static final double Oavg

Constant value of Oxygen average mass

See Also:

Constant Field Values

Constructor Detail

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 Detail

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:

getVariableMasses(SymbolList peptide), addVariableModification(Symbol residue,double[] masses)

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:

addVariableModification(char, double[])

getTermMass

public double getTermMass()

getTermMass returns the terminal mass being used by the instance methods.

Returns:

a double mass.