org.biojava.nbio.aaproperties

Class PeptidePropertiesImpl

java.lang.Object

org.biojava.nbio.aaproperties.PeptidePropertiesImpl

All Implemented Interfaces:

IPeptideProperties

public class PeptidePropertiesImpl
extends Object
implements IPeptideProperties

This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.

Since:

3.0.2

Version:

2011.08.22

Author:

kohchuanhock

See Also:

IPeptideProperties, PeptideProperties

Constructor Summary

Constructors

Constructor and Description
PeptidePropertiesImpl()

Method Summary

Modifier and Type	Method and Description
Map<AminoAcidCompound,Double>	getAAComposition(ProteinSequence sequence) Returns the composition of the 20 standard amino acid in the sequence.
double	getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced) Returns the absorbance (optical density) of sequence.
double	getApliphaticIndex(ProteinSequence sequence) Returns the apliphatic index of sequence.
double	getAvgHydropathy(ProteinSequence sequence) Returns the average hydropathy value of sequence.
double	getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode) Returns the composition of specified amino acid in the sequence.
double	getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced) Returns the extinction coefficient of sequence.
double	getInstabilityIndex(ProteinSequence sequence) Returns the instability index of sequence.
double	getIsoelectricPoint(ProteinSequence sequence)
double	getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues) Returns the isoelectric point of sequence.
double	getMolecularWeight(ProteinSequence sequence) Returns the molecular weight of sequence.
double	getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) Returns the molecular weight of sequence.
double	getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile) Returns the molecular weight of sequence.
double	getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable) Returns the molecular weight of sequence.
double	getNetCharge(ProteinSequence sequence)
double	getNetCharge(ProteinSequence sequence, boolean useExpasyValues)
double	getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint) Returns the net charge of sequence at pH 7.
AminoAcidCompositionTable	obtainAminoAcidCompositionTable(File aminoAcidCompositionFile) This 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).
AminoAcidCompositionTable	obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile) This 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

Constructor Detail

PeptidePropertiesImpl

public PeptidePropertiesImpl()

Method Detail

getMolecularWeight

public double getMolecularWeight(ProteinSequence sequence)

Description copied from interface: IPeptideProperties

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 here.

Specified by:

getMolecularWeight in interface IPeptideProperties

Parameters:

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

Returns:

the total molecular weight of sequence + weight of water molecule

See Also:

ProteinSequence

getMolecularWeight

public double getMolecularWeight(ProteinSequence sequence,
                                 File aminoAcidCompositionFile)
                          throws JAXBException,
                                 FileNotFoundException

Description copied from interface: IPeptideProperties

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 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.

Specified by:

getMolecularWeight in interface IPeptideProperties

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

getMolecularWeight

public double getMolecularWeight(ProteinSequence sequence,
                                 File elementMassFile,
                                 File aminoAcidCompositionFile)
                          throws JAXBException,
                                 FileNotFoundException

Description copied from interface: IPeptideProperties

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 input files. These input files must be XML using the defined schema.

Specified by:

getMolecularWeight in interface IPeptideProperties

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:

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

FileNotFoundException - thrown if either elementMassFile or aminoAcidCompositionFile are not found

getMolecularWeightBasedOnXML

public double getMolecularWeightBasedOnXML(ProteinSequence sequence,
                                           AminoAcidCompositionTable aminoAcidCompositionTable)

Description copied from interface: IPeptideProperties

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.

Specified by:

getMolecularWeightBasedOnXML in interface IPeptideProperties

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

obtainAminoAcidCompositionTable

public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
                                                          throws JAXBException,
                                                                 FileNotFoundException

Description copied from interface: IPeptideProperties

This 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.

Specified by:

obtainAminoAcidCompositionTable in interface IPeptideProperties

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 AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile,
                                                                 File aminoAcidCompositionFile)
                                                          throws JAXBException,
                                                                 FileNotFoundException

Description copied from interface: IPeptideProperties

This 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).

Specified by:

obtainAminoAcidCompositionTable in interface IPeptideProperties

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

getExtinctionCoefficient

public double getExtinctionCoefficient(ProteinSequence sequence,
                                       boolean assumeCysReduced)

Description copied from interface: IPeptideProperties

Returns 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.

Specified by:

getExtinctionCoefficient in interface IPeptideProperties

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

See Also:

ProteinSequence

getAbsorbance

public double getAbsorbance(ProteinSequence sequence,
                            boolean assumeCysReduced)

Description copied from interface: IPeptideProperties

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.

Specified by:

getAbsorbance in interface IPeptideProperties

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

See Also:

ProteinSequence

getInstabilityIndex

public double getInstabilityIndex(ProteinSequence sequence)

Description copied from interface: IPeptideProperties

Returns 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.

Specified by:

getInstabilityIndex in interface IPeptideProperties

Parameters:

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

Returns:

the instability index of sequence

See Also:

ProteinSequence

getApliphaticIndex

public double getApliphaticIndex(ProteinSequence sequence)

Description copied from interface: IPeptideProperties

Returns 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.

Specified by:

getApliphaticIndex in interface IPeptideProperties

Parameters:

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

Returns:

the aliphatic index of sequence

See Also:

ProteinSequence

getAvgHydropathy

public double getAvgHydropathy(ProteinSequence sequence)

Description copied from interface: IPeptideProperties

Returns 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).

Specified by:

getAvgHydropathy in interface IPeptideProperties

Parameters:

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

Returns:

the average hydropathy value of sequence

See Also:

ProteinSequence

getIsoelectricPoint

public double getIsoelectricPoint(ProteinSequence sequence,
                                  boolean useExpasyValues)

Description copied from interface: IPeptideProperties

Returns 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.

Specified by:

getIsoelectricPoint in interface IPeptideProperties

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

See Also:

ProteinSequence

getIsoelectricPoint

public double getIsoelectricPoint(ProteinSequence sequence)

Specified by:

getIsoelectricPoint in interface IPeptideProperties

getNetCharge

public double getNetCharge(ProteinSequence sequence)

Specified by:

getNetCharge in interface IPeptideProperties

getNetCharge

public double getNetCharge(ProteinSequence sequence,
                           boolean useExpasyValues)

Specified by:

getNetCharge in interface IPeptideProperties

getNetCharge

public double getNetCharge(ProteinSequence sequence,
                           boolean useExpasyValues,
                           double pHPoint)

Description copied from interface: IPeptideProperties

Returns 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

Specified by:

getNetCharge in interface IPeptideProperties

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

See Also:

ProteinSequence

getEnrichment

public double getEnrichment(ProteinSequence sequence,
                            AminoAcidCompound aminoAcidCode)

Description copied from interface: IPeptideProperties

Returns 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.

Specified by:

getEnrichment in interface IPeptideProperties

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:

ProteinSequence, AminoAcidCompound

getAAComposition

public Map<AminoAcidCompound,Double> getAAComposition(ProteinSequence sequence)

Description copied from interface: IPeptideProperties

Returns 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.

Specified by:

getAAComposition in interface IPeptideProperties

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:

ProteinSequence, AminoAcidCompound