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

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()