org.biojava.nbio.aaproperties

Class PeptideProperties

java.lang.Object

org.biojava.nbio.aaproperties.PeptideProperties

public class PeptideProperties
extends Object

This is an adaptor class which enable the ease of generating protein properties. At least one adaptor method is written for each available properties provided in IPeptideProperties.

Since:

3.0.2

Version:

2011.08.22

Author:

kohchuanhock

See Also:

IPeptideProperties, PeptidePropertiesImpl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PeptideProperties.SingleLetterAACode Enumeration of 20 standard amino acid code

Field Summary

Fields

Modifier and Type	Field and Description
static Set<Character>	standardAASet Contains the 20 standard AA code in a set

Constructor Summary

Constructors

Constructor and Description
PeptideProperties()

Method Summary

Modifier and Type	Method and Description
static Map<AminoAcidCompound,Double>	getAAComposition(String sequence) An adaptor method to return the composition of the 20 standard amino acid in the sequence.
static Map<Character,Double>	getAACompositionChar(String sequence) An adaptor method to return the composition of the 20 standard amino acid in the sequence.
static Map<String,Double>	getAACompositionString(String sequence) An adaptor method to return the composition of the 20 standard amino acid in the sequence.
static double	getAbsorbance(String sequence, boolean assumeCysReduced) An adaptor method to returns the absorbance (optical density) of sequence.
static double	getApliphaticIndex(String sequence) An adaptor method to return the apliphatic index of sequence.
static double	getAvgHydropathy(String sequence) An adaptor method to return the average hydropathy value of sequence.
static int[]	getChargesOfAminoAcids(String sequence) Returns the array of charges of each amino acid in a protein.
static double	getEnrichment(String sequence, char aminoAcidCode) An adaptor method to return the composition of specified amino acid in the sequence.
static double	getEnrichment(String sequence, PeptideProperties.SingleLetterAACode aminoAcidCode) An adaptor method to return the composition of specified amino acid in the sequence.
static double	getEnrichment(String sequence, String aminoAcidCode) An adaptor method to return the composition of specified amino acid in the sequence.
static double	getExtinctionCoefficient(String sequence, boolean assumeCysReduced) An adaptor method to return the extinction coefficient of sequence.
static double	getInstabilityIndex(String sequence) An adaptor method to return the instability index of sequence.
static double	getIsoelectricPoint(String sequence)
static double	getIsoelectricPoint(String sequence, boolean useExpasyValues) An adaptor method to return the isoelectric point of sequence.
static double	getMolecularWeight(String sequence) An adaptor method to return the molecular weight of sequence.
static double	getMolecularWeight(String sequence, File aminoAcidCompositionFile) An adaptor method to return the molecular weight of sequence.
static double	getMolecularWeight(String sequence, File elementMassFile, File aminoAcidCompositionFile) An adaptor method to return the molecular weight of sequence.
static double	getMolecularWeightBasedOnXML(String sequence, AminoAcidCompositionTable aminoAcidCompositionTable) An adaptor method that returns the molecular weight of sequence.
static double	getNetCharge(String sequence)
static double	getNetCharge(String sequence, boolean useExpasyValues)
static double	getNetCharge(String sequence, boolean useExpasyValues, double pHPoint) An adaptor method to return the net charge of sequence at pH 7.
static int[]	getPolarityOfAminoAcids(String sequence) Returns the array of polarity values of each amino acid in a protein sequence.
static AminoAcidCompositionTable	obtainAminoAcidCompositionTable(File aminoAcidCompositionFile) An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
static AminoAcidCompositionTable	obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile) An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).

Methods inherited from class java.lang.Object

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

Field Detail

standardAASet

public static Set<Character> standardAASet

Contains the 20 standard AA code in a set

Constructor Detail

PeptideProperties

public PeptideProperties()

Method Detail

getMolecularWeight

public static final double getMolecularWeight(String sequence)

An adaptor method to return the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. This method will sum the molecular weight of each amino acid in the sequence. Molecular weights are based on here.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

Returns:

the total molecular weight of sequence + weight of water molecule

getMolecularWeight

public static final double getMolecularWeight(String sequence,
                                              File elementMassFile,
                                              File aminoAcidCompositionFile)
                                       throws FileNotFoundException,
                                              JAXBException

An adaptor method to return the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. This method will sum the molecular weight of each amino acid in the sequence. Molecular weights are based on the input xml file.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

elementMassFile - xml file that details the mass of each elements and isotopes

aminoAcidCompositionFile - xml file that details the composition of amino acids

Returns:

the total molecular weight of sequence + weight of water molecule

Throws:

FileNotFoundException - thrown if either elementMassFile or aminoAcidCompositionFile are not found

JAXBException - thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile

getMolecularWeight

public static final double getMolecularWeight(String sequence,
                                              File aminoAcidCompositionFile)
                                       throws FileNotFoundException,
                                              JAXBException

An adaptor method to return the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. This method will sum the molecular weight of each amino acid in the sequence. Molecular weights are based on the input files. These input files must be XML using the defined schema. Note that it assumes that ElementMass.xml file can be found in default location.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only xml file that details the mass of each elements and isotopes

aminoAcidCompositionFile - xml file that details the composition of amino acids

Returns:

the total molecular weight of sequence + weight of water molecule

Throws:

JAXBException - thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile

FileNotFoundException - thrown if either elementMassFile or aminoAcidCompositionFile are not found

obtainAminoAcidCompositionTable

public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
                                                                       throws JAXBException,
                                                                              FileNotFoundException

An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable). Note that ElementMass.xml is assumed to be able to be seen in default location.

Parameters:

aminoAcidCompositionFile - xml file that details the composition of amino acids

Returns:

the initialized amino acid composition table

Throws:

JAXBException - thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile

FileNotFoundException - thrown if either elementMassFile or aminoAcidCompositionFile are not found

obtainAminoAcidCompositionTable

public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile,
                                                                              File aminoAcidCompositionFile)
                                                                       throws JAXBException,
                                                                              FileNotFoundException

An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).

Parameters:

elementMassFile - xml file that details the mass of each elements and isotopes

aminoAcidCompositionFile - xml file that details the composition of amino acids

Returns:

the initialized amino acid composition table

Throws:

JAXBException - thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile

FileNotFoundException - thrown if either elementMassFile or aminoAcidCompositionFile are not found

getMolecularWeightBasedOnXML

public static double getMolecularWeightBasedOnXML(String sequence,
                                                  AminoAcidCompositionTable aminoAcidCompositionTable)

An adaptor method that returns the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. This method will sum the molecular weight of each amino acid in the sequence. Molecular weights are based on the AminoAcidCompositionTable. Those input files must be XML using the defined schema.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

aminoAcidCompositionTable - a amino acid composition table obtained by calling IPeptideProperties.obtainAminoAcidCompositionTable

Returns:

the total molecular weight of sequence + weight of water molecule thrown if the method IPeptideProperties.setMolecularWeightXML(File, File) is not successfully called before calling this method.

getAbsorbance

public static final double getAbsorbance(String sequence,
                                         boolean assumeCysReduced)

An adaptor method to returns the absorbance (optical density) of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The computation of absorbance (optical density) follows the documentation in here.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

assumeCysReduced - true if Cys are assumed to be reduced and false if Cys are assumed to form cystines

Returns:

the absorbance (optical density) of sequence

getExtinctionCoefficient

public static final double getExtinctionCoefficient(String sequence,
                                                    boolean assumeCysReduced)

An adaptor method to return the extinction coefficient of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The extinction coefficient indicates how much light a protein absorbs at a certain wavelength. It is useful to have an estimation of this coefficient for following a protein which a spectrophotometer when purifying it. The computation of extinction coefficient follows the documentation in here.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

assumeCysReduced - true if Cys are assumed to be reduced and false if Cys are assumed to form cystines

Returns:

the extinction coefficient of sequence

getInstabilityIndex

public static final double getInstabilityIndex(String sequence)

An adaptor method to return the instability index of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The instability index provides an estimate of the stability of your protein in a test tube. The computation of instability index follows the documentation in here.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

Returns:

the instability index of sequence

getApliphaticIndex

public static final double getApliphaticIndex(String sequence)

An adaptor method to return the apliphatic index of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The aliphatic index of a protein is defined as the relative volume occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins. The computation of aliphatic index follows the documentation in here. A protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

Returns:

the aliphatic index of sequence

getAvgHydropathy

public static final double getAvgHydropathy(String sequence)

An adaptor method to return the average hydropathy value of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The average value for a sequence is calculated as the sum of hydropathy values of all the amino acids, divided by the number of residues in the sequence. Hydropathy values are based on (Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132).

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

Returns:

the average hydropathy value of sequence

getIsoelectricPoint

public static final double getIsoelectricPoint(String sequence,
                                               boolean useExpasyValues)

An adaptor method to return the isoelectric point of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The isoelectric point is the pH at which the protein carries no net electrical charge. The isoelectric point will be computed based on approach stated in here pKa values used will be either those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539" OR A.Lehninger, Principles of Biochemistry, 4th Edition (2005), Chapter 3, page78, Table 3-1.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

useExpasyValues - whether to use Expasy values (Default) or Innovagen values

Returns:

the isoelectric point of sequence

getIsoelectricPoint

public static final double getIsoelectricPoint(String sequence)

getNetCharge

public static final double getNetCharge(String sequence,
                                        boolean useExpasyValues,
                                        double pHPoint)

An adaptor method to return the net charge of sequence at pH 7. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The net charge will be computed using the approach stated in here pKa values used will be either those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539" OR A.Lehninger, Principles of Biochemistry, 4th Edition (2005), Chapter 3, page78, Table 3-1.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

useExpasyValues - whether to use Expasy values (Default) or Innovagen values

pHPoint - the pH value to use for computation of the net charge. Default at 7.

Returns:

the net charge of sequence at given pHPoint

getNetCharge

public static final double getNetCharge(String sequence,
                                        boolean useExpasyValues)

getNetCharge

public static final double getNetCharge(String sequence)

getEnrichment

public static final double getEnrichment(String sequence,
                                         PeptideProperties.SingleLetterAACode aminoAcidCode)

An adaptor method to return the composition of specified amino acid in the sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The aminoAcidCode must be a non-ambiguous character. The composition of an amino acid is the total number of its occurrence, divided by the total length of the sequence.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

aminoAcidCode - the code of the amino acid to compute

Returns:

the composition of specified amino acid in the sequence

See Also:

PeptideProperties.SingleLetterAACode

getEnrichment

public static final double getEnrichment(String sequence,
                                         char aminoAcidCode)

An adaptor method to return the composition of specified amino acid in the sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The aminoAcidCode must be a non-ambiguous character. The composition of an amino acid is the total number of its occurrence, divided by the total length of the sequence.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

aminoAcidCode - the code of the amino acid to compute

Returns:

the composition of specified amino acid in the sequence

getEnrichment

public static final double getEnrichment(String sequence,
                                         String aminoAcidCode)

An adaptor method to return the composition of specified amino acid in the sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The aminoAcidCode must be a non-ambiguous character. The composition of an amino acid is the total number of its occurrence, divided by the total length of the sequence.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

aminoAcidCode - the code of the amino acid to compute

Returns:

the composition of specified amino acid in the sequence

getAAComposition

public static final Map<AminoAcidCompound,Double> getAAComposition(String sequence)

An adaptor method to return the composition of the 20 standard amino acid in the sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The composition of an amino acid is the total number of its occurrence, divided by the total length of the sequence.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

Returns:

the composition of the 20 standard amino acid in the sequence

See Also:

AminoAcidCompound

getAACompositionString

public static final Map<String,Double> getAACompositionString(String sequence)

An adaptor method to return the composition of the 20 standard amino acid in the sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The composition of an amino acid is the total number of its occurrence, divided by the total length of the sequence.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

Returns:

the composition of the 20 standard amino acid in the sequence

getAACompositionChar

public static final Map<Character,Double> getAACompositionChar(String sequence)

An adaptor method to return the composition of the 20 standard amino acid in the sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters. The composition of an amino acid is the total number of its occurrence, divided by the total length of the sequence.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

Returns:

the composition of the 20 standard amino acid in the sequence

getChargesOfAminoAcids

public static final int[] getChargesOfAminoAcids(String sequence)

Returns the array of charges of each amino acid in a protein. At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains), and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

Returns:

the array of charges of amino acids in the protein (1 if amino acid is positively charged, -1 if negatively charged, 0 if not charged)

getPolarityOfAminoAcids

public static final int[] getPolarityOfAminoAcids(String sequence)

Returns the array of polarity values of each amino acid in a protein sequence.

Parameters:

sequence - a protein sequence consisting of non-ambiguous characters only

Returns:

the array of polarity of amino acids in the protein (1 if amino acid is polar, 0 if not)