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java.lang.Objectorg.biojava.bio.structure.AlphaCTools
public final class AlphaCTools
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.
Field Summary | |
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static double |
MAX_ANGLE
MAX_ANGLE . |
static double |
MIN_ANGLE
MIN_ANGLE . |
Constructor Summary | |
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AlphaCTools()
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Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final double MAX_ANGLE
public static final double MIN_ANGLE
Constructor Detail |
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public AlphaCTools()
Method Detail |
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public static Alphabet getAlphaCarbonAngleAlphabet()
public static Symbol getPhiPsiSymbol(double phiAngle, double psiAngle) throws IllegalSymbolException
phiAngle
- the phi angle between -180.0 and +180.0psiAngle
- the psi angle between -180.0 and +180.0
IllegalSymbolException
- if the bond angles are outside the specified rangepublic static double getPhiAngle(Symbol phiPsiSym) throws IllegalSymbolException
Symbol
.
phiPsiSym
- a Symbol
from the ALPHA CARBON ANGLES
Alphabet
IllegalSymbolException
- if the Symbol
is not from
the ALPHA CARBON ANGLES Alphabet
public static double getPsiAngle(Symbol phiPsiSym) throws IllegalSymbolException
Symbol
.
phiPsiSym
- a Symbol
from the ALPHA CARBON ANGLES
Alphabet
IllegalSymbolException
- if the Symbol
is not from
the ALPHA CARBON ANGLES Alphabet
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