Package org.biojava.nbio.aaproperties

Class 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

    • 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

      • 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)

      • 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)

      • getAromaticity

        public static final double getAromaticity​(String sequence)
        An adaptor method to return the aromaticity value of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters.

        Calculates the aromaticity value of a protein according to Lobry, 1994. It is simply the relative frequency of Phe+Trp+Tyr. *

        Parameters:
        sequence - a protein sequence consisting of non-ambiguous characters only
        Returns:
        the aromaticity value of sequence