Package org.biojava.nbio.aaproperties.profeat.convertor

Class Convertor

    • Field Detail

      • group1

        public static final char group1
        Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
        An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
        The seven different attributes are

        Hydrophobicity (Polar, Neutral, Hydrophobicity)
        Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)
        Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)
        Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)
        Charge (Positive, Neutral, Negative)
        Secondary structure (Helix, Strand, Coil)
        Solvent accessibility (Buried, Exposed, Intermediate)

        See Also:
        Constant Field Values

    • Constructor Detail

      • Convertor

        public Convertor()

    • Method Detail

      • convert

        public abstract char convert​(char aminoAcid)
        Returns the grouping of the amino acid character. The aminoAcid argument is preferably of non-ambiguous characters. Standard amino acids will be converted to '1', '2' or '3' depending on its grouping Non-standard amino acids are simply converted to '0'.
        Parameters:
        aminoAcid - an amino acid character preferably of non-ambiguous characters
        Returns:
        its grouping

      • getGrouping

        public abstract String[] getGrouping()
        Returns the groupings of the attribute
        Returns:
        the groupings of the attribute

      • getAttribute

        public abstract String getAttribute()
        Return the attribute of the grouping
        Returns:
        the attribute of the grouping

      • convert

        public String convert​(org.biojava.nbio.core.sequence.ProteinSequence sequence)
        Returns the converted sequence. The sequence argument must be a protein sequence consisting of preferably non-ambiguous characters only. Standard amino acids will be converted to '1', '2' or '3' depending on its grouping Non-standard amino acids are simply converted to '0'.
        Parameters:
        sequence - a protein sequence consisting of preferably non-ambiguous characters only
        Returns:
        the converted sequence