Class Subunits


  • public class Subunits
    extends java.lang.Object
    A bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment.
    Author:
    Peter Rose
    • Constructor Detail

      • Subunits

        public Subunits​(java.util.List<javax.vecmath.Point3d[]> caCoords,
                        java.util.List<java.lang.Integer> sequenceClusterIds,
                        java.util.List<java.lang.Boolean> pseudoStoichiometry,
                        java.util.List<java.lang.Double> minSequenceIdentity,
                        java.util.List<java.lang.Double> maxSequenceIdentity,
                        java.util.List<java.lang.Integer> folds,
                        java.util.List<java.lang.String> chainIds,
                        java.util.List<java.lang.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 Detail

      • getTraces

        public java.util.List<javax.vecmath.Point3d[]> getTraces()
      • getSubunitCount

        public int getSubunitCount()
      • getSequenceClusterIds

        public java.util.List<java.lang.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 java.util.List<java.lang.String> getChainIds()
      • getModelNumbers

        public java.util.List<java.lang.Integer> getModelNumbers()
      • getFolds

        public java.util.List<java.lang.Integer> getFolds()
      • getStoichiometry

        public java.lang.String getStoichiometry()
      • getCalphaCount

        public int getCalphaCount()
      • getLargestSubunit

        public int getLargestSubunit()
      • getCenters

        public java.util.List<javax.vecmath.Point3d> getCenters()
      • getUnitVectors

        public java.util.List<javax.vecmath.Vector3d> getUnitVectors()
      • getOriginalCenters

        public java.util.List<javax.vecmath.Point3d> getOriginalCenters()
      • getCentroid

        public javax.vecmath.Point3d getCentroid()
      • 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()