org.biojava.nbio.structure.symmetry.core

Class 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 and Description
ClusterProteinChains(Structure structure, QuatSymmetryParameters parameters)
ClusterProteinChains(Structure structure1, Structure structure2, QuatSymmetryParameters parameters)

Method Summary

Modifier and Type	Method and 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 Detail

ClusterProteinChains

public ClusterProteinChains(Structure structure,
                            QuatSymmetryParameters parameters)

ClusterProteinChains

public ClusterProteinChains(Structure structure1,
                            Structure structure2,
                            QuatSymmetryParameters parameters)

Method Detail

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