Package org.biojava.bio.structure

Class AlphaCTools

  • public final class AlphaCTools
extends java.lang.Object
    AlphaCTools is a collection of static convenience methods for dealing with Alpha Carbon Backbone Phi / Psi angles. In BioJava Phi Psi angles are represented as Symbols from the ALPHA CARBON ANGLES alphabet. A Backbone could be represented as a SymbolList. A Ramachandran plot might be represented as a Distribution over Phi Psi Symbols.
    Version:
    1.0
    Author:
    Mark Schreiber

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static double MAX_ANGLE
      MAX_ANGLE .
      static double MIN_ANGLE
      MIN_ANGLE .

    • Constructor Summary

      Constructors 
      Constructor Description
      AlphaCTools()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static Alphabet getAlphaCarbonAngleAlphabet()
      Returns a reference to the Alphabet that contains Symbols that represent PHI, PSI angles.
      static double getPhiAngle​(Symbol phiPsiSym)
      extracts the Phi angle from a Symbol.
      static Symbol getPhiPsiSymbol​(double phiAngle, double psiAngle)
      Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet.
      static double getPsiAngle​(Symbol phiPsiSym)
      extracts the Psi angle from a Symbol.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • AlphaCTools

        public AlphaCTools()

    • Method Detail

      • getAlphaCarbonAngleAlphabet

        public static Alphabet getAlphaCarbonAngleAlphabet()
        Returns a reference to the Alphabet that contains Symbols that represent PHI, PSI angles.
        Returns:
        a reference to the ALPHA CARBON ANGLES alphabet

      • getPhiPsiSymbol

        public static Symbol getPhiPsiSymbol​(double phiAngle,
                                     double psiAngle)
                              throws IllegalSymbolException
        Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet.
        Parameters:
        phiAngle - the phi angle between -180.0 and +180.0
        psiAngle - the psi angle between -180.0 and +180.0
        Returns:
        a reference to the 'fly weight' Symbol.
        Throws:
        IllegalSymbolException - if the bond angles are outside the specified range

      • getPhiAngle

        public static double getPhiAngle​(Symbol phiPsiSym)
                          throws IllegalSymbolException
        extracts the Phi angle from a Symbol.
        Parameters:
        phiPsiSym - a Symbol from the ALPHA CARBON ANGLES Alphabet
        Returns:
        a double between -180.0 and +180.0
        Throws:
        IllegalSymbolException - if the Symbol is not from the ALPHA CARBON ANGLES Alphabet

      • getPsiAngle

        public static double getPsiAngle​(Symbol phiPsiSym)
                          throws IllegalSymbolException
        extracts the Psi angle from a Symbol.
        Parameters:
        phiPsiSym - a Symbol from the ALPHA CARBON ANGLES Alphabet
        Returns:
        a double between -180.0 and +180.0
        Throws:
        IllegalSymbolException - if the Symbol is not from the ALPHA CARBON ANGLES Alphabet