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

Class ChainClusterer

java.lang.Object
org.biojava.nbio.structure.symmetry.core.ChainClusterer
public class ChainClusterer extends Object
Wraps a sequence clustering with structural information

  • Constructor Details

  • Method Details

    • getCalphaCoordinates

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

    • getCalphaTraces

      public List<Atom[]> getCalphaTraces()

    • getChainIds

      public List<String> getChainIds()

    • getModelNumbers

      public List<Integer> getModelNumbers()

    • getStoichiometry

      public String getStoichiometry()

    • getFolds

      public List<Integer> getFolds()
      Get valid symmetry order for this stoichiometry.
      Returns:

    • getValidFolds

      public static List<Integer> getValidFolds(List<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 List<Integer> getSequenceClusterIds()

    • getSequenceClusterCount

      public int getSequenceClusterCount()

    • getSequenceAlignmentClusters

      public List<SequenceAlignmentCluster> getSequenceAlignmentClusters()

    • getPseudoStoichiometry

      public List<Boolean> getPseudoStoichiometry()

    • getMinSequenceIdentity

      public List<Double> getMinSequenceIdentity()

    • getMaxSequenceIdentity

      public List<Double> getMaxSequenceIdentity()

    • toString

      public String toString()
      Overrides:
      toString in class Object