Package org.biojava.nbio.aaproperties

Class Constraints

  • public class Constraints
extends Object
    This class is used to support the implementation of properties stated in IPeptideProperties. It initializes several values that would be needed for the computation of properties such as

    Molecular weight
    Instability index
    Hydropathy value
    pKa

    Version:
    2011.05.21
    Author:
    kohchuanhock
    See Also:
    IPeptideProperties

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound A  
      static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2CTerminalPka  
      static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2ExtinctionCoefficient  
      static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2Hydrophathicity  
      static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2MolecularWeight  
      static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2NTerminalPka  
      static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2PKa  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound C  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound D  
      static Map<String,​Double> diAA2Instability  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound E  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound F  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound G  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound H  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound I  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound K  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound L  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound M  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound N  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound P  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound Q  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound R  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound S  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound T  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound V  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound W  
      static org.biojava.nbio.core.sequence.compound.AminoAcidCompound Y  

    • Constructor Summary

      Constructors 
      Constructor Description
      Constraints()  

    • Field Detail

      • A

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound A

      • R

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound R

      • N

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound N

      • D

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound D

      • C

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound C

      • E

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound E

      • Q

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound Q

      • G

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound G

      • H

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound H

      • I

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound I

      • L

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound L

      • K

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound K

      • M

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound M

      • F

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound F

      • P

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound P

      • S

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound S

      • T

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound T

      • W

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound W

      • Y

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound Y

      • V

        public static org.biojava.nbio.core.sequence.compound.AminoAcidCompound V

      • aa2ExtinctionCoefficient

        public static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2ExtinctionCoefficient

      • aa2MolecularWeight

        public static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2MolecularWeight

      • aa2Hydrophathicity

        public static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2Hydrophathicity

      • aa2PKa

        public static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2PKa

      • aa2NTerminalPka

        public static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2NTerminalPka

      • aa2CTerminalPka

        public static Map<org.biojava.nbio.core.sequence.compound.AminoAcidCompound,​Double> aa2CTerminalPka

    • Constructor Detail

      • Constraints

        public Constraints()

    • Method Detail

      • initMolecularWeight

        public static void initMolecularWeight()
        Does the initialization of molecular weights based on http://au.expasy.org/tools/findmod/findmod_masses.html#AA

      • initExtinctionCoefficient

        public static void initExtinctionCoefficient()
        Does the initialization of extinction coefficient based on http://au.expasy.org/tools/protparam-doc.html