Package org.biojava.bio.structure
Class AlphaCTools
- java.lang.Object
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- org.biojava.bio.structure.AlphaCTools
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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
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Constructor Summary
Constructors Constructor Description AlphaCTools()
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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 aSymbol
.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 aSymbol
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Field Detail
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MAX_ANGLE
public static final double MAX_ANGLE
MAX_ANGLE .- See Also:
- Constant Field Values
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MIN_ANGLE
public static final double MIN_ANGLE
MIN_ANGLE .- See Also:
- Constant Field Values
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Method Detail
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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
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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 +180.0psiAngle
- 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
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getPhiAngle
public static double getPhiAngle(Symbol phiPsiSym) throws IllegalSymbolException
extracts the Phi angle from aSymbol
.- Parameters:
phiPsiSym
- aSymbol
from the ALPHA CARBON ANGLESAlphabet
- Returns:
- a double between -180.0 and +180.0
- Throws:
IllegalSymbolException
- if theSymbol
is not from the ALPHA CARBON ANGLESAlphabet
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getPsiAngle
public static double getPsiAngle(Symbol phiPsiSym) throws IllegalSymbolException
extracts the Psi angle from aSymbol
.- Parameters:
phiPsiSym
- aSymbol
from the ALPHA CARBON ANGLESAlphabet
- Returns:
- a double between -180.0 and +180.0
- Throws:
IllegalSymbolException
- if theSymbol
is not from the ALPHA CARBON ANGLESAlphabet
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