org.biojava.nbio.structure.symmetry.core

Class Helix

java.lang.Object

org.biojava.nbio.structure.symmetry.core.Helix

public class Helix
extends Object

Author:

Peter

Constructor Summary

Constructors

Constructor and Description
Helix()

Method Summary

Methods

Modifier and Type	Method and Description
double	getAngle() Returns the pitch angle of the helix
javax.vecmath.AxisAngle4d	getAxisAngle() Returns the AxisAngle of the helix transformation
int	getContacts()
int	getFold()
List<List<Integer>>	getLayerLines()
int	getnStart()
List<Integer>	getPermutation()
List<List<Integer>>	getRepeatUnits()
double	getRise()
QuatSymmetryScores	getScores()
javax.vecmath.Matrix4d	getTransformation()
void	setContacts(int contacts)
void	setFold(int fold)
void	setnStart(int nStart)
void	setPermutation(List<Integer> permutation)
void	setRepeatUnits(List<List<Integer>> repeatUnits)
void	setRise(double rise)
void	setScores(QuatSymmetryScores scores)
void	setTransformation(javax.vecmath.Matrix4d transformation)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Helix

public Helix()

Method Detail

getScores

public QuatSymmetryScores getScores()

Returns:

the scores

setScores

public void setScores(QuatSymmetryScores scores)

Parameters:

scores - the scores to set

getPermutation

public List<Integer> getPermutation()

Returns:

the permutation

setPermutation

public void setPermutation(List<Integer> permutation)

Parameters:

permutation - the permutation to set

getRepeatUnits

public List<List<Integer>> getRepeatUnits()

setRepeatUnits

public void setRepeatUnits(List<List<Integer>> repeatUnits)

getTransformation

public javax.vecmath.Matrix4d getTransformation()

Returns:

the transformation

setTransformation

public void setTransformation(javax.vecmath.Matrix4d transformation)

Parameters:

transformation - the transformation to set

getRise

public double getRise()

setRise

public void setRise(double rise)

getAngle

public double getAngle()

Returns the pitch angle of the helix

Parameters:

transformation - helix transformation

Returns:

getAxisAngle

public javax.vecmath.AxisAngle4d getAxisAngle()

Returns the AxisAngle of the helix transformation

Parameters:

transformation - helix transformation

Returns:

getnStart

public int getnStart()

setnStart

public void setnStart(int nStart)

getFold

public int getFold()

Returns:

the fold

setFold

public void setFold(int fold)

Parameters:

fold - the fold to set

getContacts

public int getContacts()

setContacts

public void setContacts(int contacts)

toString

public String toString()

Overrides:

toString in class Object

getLayerLines

public List<List<Integer>> getLayerLines()