Package 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:

  • Field Details

    • standardAASet

      public static Set<Character> standardAASet
      Contains the 20 standard AA code in a set

  • Constructor Details

    • PeptideProperties

      public PeptideProperties()

  • Method Details

    • 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, javax.xml.bind.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
      javax.xml.bind.JAXBException - thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile

    • getMolecularWeight

      public static final double getMolecularWeight(String sequence, File aminoAcidCompositionFile) throws FileNotFoundException, javax.xml.bind.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:
      javax.xml.bind.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 javax.xml.bind.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:
      javax.xml.bind.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 javax.xml.bind.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:
      javax.xml.bind.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:

    • 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:

    • 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