org.biojava.bio.structure
Class AlphaCTools

java.lang.Object
  extended by org.biojava.bio.structure.AlphaCTools

public final class AlphaCTools
extends 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
static double MAX_ANGLE
          MAX_ANGLE .
static double MIN_ANGLE
          MIN_ANGLE .
 
Constructor Summary
AlphaCTools()
           
 
Method Summary
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
 

Field Detail

MAX_ANGLE

public static final double MAX_ANGLE
MAX_ANGLE .

See Also:
Constant Field Values

MIN_ANGLE

public static final double MIN_ANGLE
MIN_ANGLE .

See Also:
Constant Field Values
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