Package org.biojava.nbio.structure.symmetry.internal

Class AngleOrderDetectorPlus

java.lang.Object

org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus

All Implemented Interfaces:

OrderDetector

public class AngleOrderDetectorPlus
extends Object
implements OrderDetector

Guesses an order of rotational symmetry from the angle.

Improves upon the AngleOrderDetector used in the paper by checking all rotations, not just the base one.

Since:

4.2.0

Author:

Spencer Bliven

Constructor Summary

Constructors

Constructor	Description
AngleOrderDetectorPlus(double angleError)
AngleOrderDetectorPlus(int maxOrder)
AngleOrderDetectorPlus(int maxOrder, double angleError)
AngleOrderDetectorPlus(int maxOrder, double angleError, boolean normalize)	Determine order by finding the order (up to the maxOrder) which has the closest rotation angle to the observed rotation.

Method Summary

Modifier and Type	Method	Description
int	calculateOrder(AFPChain afpChain, Atom[] ca)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

AngleOrderDetectorPlus

public AngleOrderDetectorPlus(double angleError)

Parameters:

error - maximum angular error, in radians

AngleOrderDetectorPlus

public AngleOrderDetectorPlus(int maxOrder)

AngleOrderDetectorPlus

public AngleOrderDetectorPlus(int maxOrder,
                              double angleError)

Parameters:

maxOrder - maximum order to consider

error - maximum angular error, in radians

AngleOrderDetectorPlus

public AngleOrderDetectorPlus(int maxOrder,
                              double angleError,
                              boolean normalize)

Determine order by finding the order (up to the maxOrder) which has the closest rotation angle to the observed rotation. If normalized is false, then the error is taken to be the absolute error from the closest ideal angle (in radians). If normalized is true, error is taken to be relative to the fundamental rotation for a given order. For instance, for an error of .25, C2 order would be accepted for angles within .25*pi radians of 0 or pi, while C3 order would be acceptable within .25*2pi/3 radians of 0, 2pi/3, or 4pi/3. In the normalized case, numbers between 0 and .5 are sensible for error.

Parameters:

maxOrder - maximum order to consider

error - maximum angular error

normalize - indicates whether error should be normalized by the order

Method Detail

calculateOrder

public int calculateOrder(AFPChain afpChain,
                          Atom[] ca)
                   throws RefinerFailedException

Specified by:

calculateOrder in interface OrderDetector

Throws:

RefinerFailedException

toString

public String toString()

Overrides:

toString in class Object