Class ChainClusterer


  • public class ChainClusterer
    extends java.lang.Object
    Wraps a sequence clustering with structural information
    • Method Detail

      • getCalphaCoordinates

        public java.util.List<javax.vecmath.Point3d[]> getCalphaCoordinates()
      • getCalphaTraces

        public java.util.List<Atom[]> getCalphaTraces()
      • getChainIds

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

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

        public java.lang.String getStoichiometry()
      • getFolds

        public java.util.List<java.lang.Integer> getFolds()
        Get valid symmetry order for this stoichiometry.
        Returns:
      • getValidFolds

        public static java.util.List<java.lang.Integer> getValidFolds​(java.util.List<java.lang.Integer> stoichiometry)
        Find valid symmetry orders for a given stoichiometry. For instance, an A6B4 protein would give [1,2] because (A6B4)1 and (A3B2)2 are valid decompositions.
        Parameters:
        stoichiometry - List giving the number of copies in each chain cluster
        Returns:
        The common factors of the stoichiometry
      • getSequenceClusterIds

        public java.util.List<java.lang.Integer> getSequenceClusterIds()
      • getSequenceClusterCount

        public int getSequenceClusterCount()
      • getPseudoStoichiometry

        public java.util.List<java.lang.Boolean> getPseudoStoichiometry()
      • getMinSequenceIdentity

        public java.util.List<java.lang.Double> getMinSequenceIdentity()
      • getMaxSequenceIdentity

        public java.util.List<java.lang.Double> getMaxSequenceIdentity()
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object