Package org.biojava.nbio.structure.symmetry.core

Class QuatSymmetrySubunits

java.lang.Object

org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

public class QuatSymmetrySubunits
extends Object

A bean to represent information about the set of Subunits being considered for symmetry detection. This class is a helper for the QuatSymmetryDetector algorithm, since it calculates and caches the MomentsOfInertia and the centroids of each Subunit.

Author:

Peter Rose, Aleix Lafita

Constructor Summary

Constructors

Constructor	Description
QuatSymmetrySubunits(List<SubunitCluster> clusters)	Converts the List of SubunitCluster to a Subunit object.

Method Summary

Modifier and Type	Method	Description
int	getCalphaCount()
List<javax.vecmath.Point3d>	getCenters()
javax.vecmath.Point3d	getCentroid()
List<String>	getChainIds()	This method is provisional and should only be used for coloring Subunits.
List<Integer>	getClusterIds()
List<Integer>	getFolds()
int	getLargestSubunit()
javax.vecmath.Point3d	getLowerBound()
List<Integer>	getModelNumbers()	This method is provisional and should only be used for coloring Subunits.
MomentsOfInertia	getMomentsOfInertia()
List<javax.vecmath.Point3d>	getOriginalCenters()
int	getSubunitCount()
List<javax.vecmath.Point3d[]>	getTraces()
List<javax.vecmath.Vector3d>	getUnitVectors()
javax.vecmath.Point3d	getUpperBound()

Methods inherited from class java.lang.Object

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

Constructor Detail

QuatSymmetrySubunits

public QuatSymmetrySubunits(List<SubunitCluster> clusters)

Converts the List of SubunitCluster to a Subunit object.

Parameters:

clusters - List of SubunitCluster

Method Detail

getTraces

public List<javax.vecmath.Point3d[]> getTraces()

getClusterIds

public List<Integer> getClusterIds()

getChainIds

public List<String> getChainIds()

This method is provisional and should only be used for coloring Subunits. A new coloring schema has to be implemented to allow the coloring of Subunits, without implying one Subunit = one Chain.

Returns:

A List of the Chain Ids of each Subunit

getModelNumbers

public List<Integer> getModelNumbers()

This method is provisional and should only be used for coloring Subunits. A new coloring schema has to be implemented to allow the coloring of Subunits, without implying one Subunit = one Chain.

Returns:

A List of the Model number of each Subunit

getSubunitCount

public int getSubunitCount()

getFolds

public List<Integer> getFolds()

getCalphaCount

public int getCalphaCount()

getLargestSubunit

public int getLargestSubunit()

getCenters

public List<javax.vecmath.Point3d> getCenters()

getUnitVectors

public List<javax.vecmath.Vector3d> getUnitVectors()

getOriginalCenters

public List<javax.vecmath.Point3d> getOriginalCenters()

getCentroid

public javax.vecmath.Point3d getCentroid()

getMomentsOfInertia

public MomentsOfInertia getMomentsOfInertia()

getLowerBound

public javax.vecmath.Point3d getLowerBound()

getUpperBound

public javax.vecmath.Point3d getUpperBound()