org.biojava.nbio.structure.symmetry.internal

Class SymmetryAxes.Axis

java.lang.Object

org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

Enclosing class:

SymmetryAxes

public static class SymmetryAxes.Axis
extends Object

Represents an axis of symmetry

Author:

Spencer Bliven

Constructor Summary

Constructors

Constructor and Description
SymmetryAxes.Axis(javax.vecmath.Matrix4d operator, int order, CESymmParameters.SymmetryType type, int level, int firstRepeat)

Method Summary

Methods

Modifier and Type	Method and Description
int	getFirstRepeat() Get the index of the first repeat used by this axis
int	getLevel()
javax.vecmath.Matrix4d	getOperator() Get the transformation operator for this axis as an homogeneous matrix
int	getOrder() Get the order of this axis (closed symm) or the number of repeats (open symm)
RotationAxis	getRotationAxis() Get the transformation operator as a rotation axis.
CESymmParameters.SymmetryType	getSymmType()
void	setFirstRepeat(int firstRepeat)
void	setLevel(int level)
void	setOperator(javax.vecmath.Matrix4d op)

Methods inherited from class java.lang.Object

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

Constructor Detail

SymmetryAxes.Axis

public SymmetryAxes.Axis(javax.vecmath.Matrix4d operator,
                 int order,
                 CESymmParameters.SymmetryType type,
                 int level,
                 int firstRepeat)

Method Detail

getOperator

public javax.vecmath.Matrix4d getOperator()

Get the transformation operator for this axis as an homogeneous matrix

Returns:

the transformation operator

setOperator

public void setOperator(javax.vecmath.Matrix4d op)

getOrder

public int getOrder()

Get the order of this axis (closed symm) or the number of repeats (open symm)

Returns:

the order

getSymmType

public CESymmParameters.SymmetryType getSymmType()

Returns:

the symmType (OPEN or CLOSED only)

getRotationAxis

public RotationAxis getRotationAxis()

Get the transformation operator as a rotation axis. For open symmetry this will have a non-zero screw component.

Returns:

a RotationAxis for this Axis

getLevel

public int getLevel()

Returns:

The level of this axis within it's parent hierarchy, or -1 if unset

setLevel

public void setLevel(int level)

Parameters:

level - The level of this axis within it's parent hierarchy. Must be positive

getFirstRepeat

public int getFirstRepeat()

Get the index of the first repeat used by this axis

Returns:

the firstRepeat

setFirstRepeat

public void setFirstRepeat(int firstRepeat)

Parameters:

firstRepeat - the index of the first repeat used by this axis