org.biojava.bio.structure

Class AlphaCTools

java.lang.Object

org.biojava.bio.structure.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 and Description
static double	MAX_ANGLE MAX_ANGLE .
static double	MIN_ANGLE MIN_ANGLE .

Constructor Summary

Constructors

Constructor and Description
AlphaCTools()

Method Summary

Methods

Modifier and Type	Method and 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

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