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

Class Subunits

java.lang.Object
org.biojava.nbio.structure.symmetry.core.Subunits
public class Subunits extends Object
A bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment.
Author:
Peter Rose

  • Constructor Details

    • Subunits

      public Subunits(List<javax.vecmath.Point3d[]> caCoords, List<Integer> sequenceClusterIds, List<Boolean> pseudoStoichiometry, List<Double> minSequenceIdentity, List<Double> maxSequenceIdentity, List<Integer> folds, List<String> chainIds, List<Integer> modelNumbers)
      All inputs should contain one element per subunit.
      Parameters:
      caCoords - CA coordinates of all subunits
      sequenceClusterIds - ID of the cluster that each subunit belongs to
      pseudoStoichiometry - Whether pseudosymmetry was used when clustering the subunit
      minSequenceIdentity - Minimum sequence identity to other cluster members
      maxSequenceIdentity - Maximum sequence identity to other cluster members
      folds - Valid symmetry orders for this stoichiometry
      chainIds - Chain ID for the subunit
      modelNumbers - Model number for the subunit

  • Method Details

    • getTraces

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

    • getSubunitCount

      public int getSubunitCount()

    • getSequenceClusterIds

      public List<Integer> getSequenceClusterIds()

    • isPseudoStoichiometric

      public boolean isPseudoStoichiometric()

    • isPseudoSymmetric

      public boolean isPseudoSymmetric()

    • setPseudoSymmetric

      public void setPseudoSymmetric(boolean pseudoSymmetric)

    • getMinSequenceIdentity

      public double getMinSequenceIdentity()

    • getMaxSequenceIdentity

      public double getMaxSequenceIdentity()

    • getChainIds

      public List<String> getChainIds()

    • getModelNumbers

      public List<Integer> getModelNumbers()

    • getFolds

      public List<Integer> getFolds()

    • getStoichiometry

      public String getStoichiometry()

    • 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()

    • getNucleicAcidChainCount

      public int getNucleicAcidChainCount()
      Returns:
      the nucleicAcidChainCount

    • setNucleicAcidChainCount

      public void setNucleicAcidChainCount(int nucleicAcidChainCount)
      Parameters:
      nucleicAcidChainCount - the nucleicAcidChainCount to set

    • overlaps

      public boolean overlaps(Subunits subunits)

    • contains

      public boolean contains(Subunits subunits)

    • getLowerBound

      public javax.vecmath.Point3d getLowerBound()

    • getUpperBound

      public javax.vecmath.Point3d getUpperBound()