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

• group2

  public static final char group2

  See Also:

  Constant Field Values

• group3

  public static final char group3

  See Also:

  Constant Field Values

• unknownGroup

  public static final char unknownGroup

  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 java.lang.String[] getGrouping​()

  Returns the groupings of the attribute

  Returns:

  the groupings of the attribute

• getAttribute

  public abstract java.lang.String getAttribute​()

  Return the attribute of the grouping

  Returns:

  the attribute of the grouping

• convert

  public java.lang.String convert​(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