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 Details

    • QuatSymmetrySubunits

      public QuatSymmetrySubunits(List<SubunitCluster> clusters)
      Converts the List of SubunitCluster to a Subunit object.
      Parameters:
      clusters - List of SubunitCluster
  • Method Details

    • 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()