ClusterProteinChains

java.lang.Object

org.biojava.nbio.structure.symmetry.core.ClusterProteinChains

public class ClusterProteinChains extends Object

Clusters the chains of one or two structures by sequence.

Constructor Summary

Constructors

Constructor

Description

ClusterProteinChains(Structure structure1, Structure structure2, QuatSymmetryParameters parameters)

ClusterProteinChains(Structure structure, QuatSymmetryParameters parameters)
Method Summary

Modifier and Type

Method

Description

int

getNucleicAcidChainCount()

int

getProteinChainCount()

List<SequenceAlignmentCluster>

getSequenceAlignmentClusters(double sequenceIdentityThreshold)

Get a non-redundent set of clusters for a given sequence cutoff

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- ClusterProteinChains
  
  public ClusterProteinChains(Structure structure, QuatSymmetryParameters parameters)
- ClusterProteinChains
  
  public ClusterProteinChains(Structure structure1, Structure structure2, QuatSymmetryParameters parameters)
Method Details
- getSequenceAlignmentClusters
  
  public List<SequenceAlignmentCluster> getSequenceAlignmentClusters(double sequenceIdentityThreshold)
  
  Get a non-redundent set of clusters for a given sequence cutoff
  
  Parameters:
  
  sequenceIdentityThreshold -
  
  Returns:
- getProteinChainCount
  
  public int getProteinChainCount()
  
  Returns:
  
  the proteinChainCount
- getNucleicAcidChainCount
  
  public int getNucleicAcidChainCount()
  
  Returns:
  
  the nucleicAcidChainCount