Constructor Detail

• ChainClusterer

  public ChainClusterer​(java.util.List<SequenceAlignmentCluster> seqClusters)

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()

• getSequenceAlignmentClusters

  public java.util.List<SequenceAlignmentCluster> getSequenceAlignmentClusters()

• 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