org.biojava.nbio.structure.cluster

Class SubunitCluster

java.lang.Object

org.biojava.nbio.structure.cluster.SubunitCluster

public class SubunitCluster
extends Object

A SubunitCluster contains a set of equivalent QuatSymmetrySubunits, the set of equivalent residues (EQR) between Subunit and a Subunit representative. It also stores the method used for clustering.

This class allows the comparison and merging of SubunitClusters.

Since:

5.0.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
SubunitCluster(Subunit subunit) A SubunitCluster is always initialized with a single Subunit.

Method Summary

Modifier and Type	Method and Description
boolean	divideInternally(double coverageThreshold, double rmsdThreshold, int minSequenceLength) Analyze the internal symmetry of the SubunitCluster and divide its Subunit into the internal repeats (domains) if they are internally symmetric.
Atom[]	getAlignedAtomsSubunit(int index)
List<Atom[]>	getAlignedAtomsSubunits()
SubunitClustererMethod	getClustererMethod()
MultipleAlignment	getMultipleAlignment() The multiple alignment is calculated from the equivalent residues in the SubunitCluster.
List<Subunit>	getSubunits() Subunits contained in the SubunitCluster.
boolean	isIdenticalTo(SubunitCluster other) Tells whether the other SubunitCluster contains exactly the same Subunit.
int	length()
boolean	mergeIdentical(SubunitCluster other) Merges the other SubunitCluster into this one if it contains exactly the same Subunit.
boolean	mergeSequence(SubunitCluster other, double minSeqid, double minCoverage) Merges the other SubunitCluster into this one if their representatives sequences are similar (higher sequence identity and coverage than the thresholds).
boolean	mergeSequence(SubunitCluster other, double minSeqid, double minCoverage, Alignments.PairwiseSequenceAlignerType alignerType, GapPenalty gapPenalty, SubstitutionMatrix<AminoAcidCompound> subsMatrix) Merges the other SubunitCluster into this one if their representatives sequences are similar (higher sequence identity and coverage than the thresholds).
boolean	mergeStructure(SubunitCluster other, double maxRmsd, double minCoverage) Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (lower RMSD and higher coverage than the thresholds).
boolean	mergeStructure(SubunitCluster other, double maxRmsd, double minCoverage, StructureAlignment aligner) Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (lower RMSD and higher coverage than the thresholds).
int	size()
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SubunitCluster

public SubunitCluster(Subunit subunit)

A SubunitCluster is always initialized with a single Subunit. To obtain a SubunitCluster with multiple Subunits, initialize different SubunitClusters and merge them.

Parameters:

subunit - initial Subunit

Method Detail

getSubunits

public List<Subunit> getSubunits()

Subunits contained in the SubunitCluster.

Returns:

an unmodifiable view of the original List

isIdenticalTo

public boolean isIdenticalTo(SubunitCluster other)

Tells whether the other SubunitCluster contains exactly the same Subunit. This is checked by String equality of their residue one-letter sequences.

Parameters:

other - SubunitCluster

Returns:

true if the SubunitClusters are identical, false otherwise

mergeIdentical

public boolean mergeIdentical(SubunitCluster other)

Merges the other SubunitCluster into this one if it contains exactly the same Subunit. This is checked by isIdenticalTo(SubunitCluster).

Parameters:

other - SubunitCluster

Returns:

true if the SubunitClusters were merged, false otherwise

mergeSequence

public boolean mergeSequence(SubunitCluster other,
                             double minSeqid,
                             double minCoverage)
                      throws CompoundNotFoundException

Merges the other SubunitCluster into this one if their representatives sequences are similar (higher sequence identity and coverage than the thresholds).

The sequence alignment is performed using Smith Waterman, default linear SimpleGapPenalty and BLOSUM62 as scoring matrix.

Parameters:

other - SubunitCluster

minSeqid - sequence identity threshold. Value in [0,1]. Values lower than 0.7 are not recommended. Use mergeStructure(org.biojava.nbio.structure.cluster.SubunitCluster, double, double) for lower values.

minCoverage - coverage (alignment fraction) threshold. Value in [0,1].

Returns:

true if the SubunitClusters were merged, false otherwise

Throws:

CompoundNotFoundException

mergeSequence

public boolean mergeSequence(SubunitCluster other,
                             double minSeqid,
                             double minCoverage,
                             Alignments.PairwiseSequenceAlignerType alignerType,
                             GapPenalty gapPenalty,
                             SubstitutionMatrix<AminoAcidCompound> subsMatrix)
                      throws CompoundNotFoundException

Merges the other SubunitCluster into this one if their representatives sequences are similar (higher sequence identity and coverage than the thresholds).

The sequence alignment is performed using Smith Waterman, default linear SimpleGapPenalty and BLOSUM62 as scoring matrix.

Parameters:

other - SubunitCluster

minSeqid - sequence identity threshold. Value in [0,1]. Values lower than 0.7 are not recommended. Use mergeStructure(org.biojava.nbio.structure.cluster.SubunitCluster, double, double) for lower values.

minCoverage - coverage (alignment fraction) threshold. Value in [0,1].

alignerType - parameter for the sequence alignment algorithm

gapPenalty - parameter for the sequence alignment algorithm

subsMatrix - parameter for the sequence alignment algorithm

Returns:

true if the SubunitClusters were merged, false otherwise

Throws:

CompoundNotFoundException

mergeStructure

public boolean mergeStructure(SubunitCluster other,
                              double maxRmsd,
                              double minCoverage)
                       throws StructureException

Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (lower RMSD and higher coverage than the thresholds).

The structure alignment is performed using FatCatRigid, with default parameters.

Parameters:

other - SubunitCluster

maxRmsd - RMSD threshold.

minCoverage - coverage (alignment fraction) threshold. Value in [0,1].

Returns:

true if the SubunitClusters were merged, false otherwise

Throws:

StructureException

mergeStructure

public boolean mergeStructure(SubunitCluster other,
                              double maxRmsd,
                              double minCoverage,
                              StructureAlignment aligner)
                       throws StructureException

Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (lower RMSD and higher coverage than the thresholds).

The structure alignment is performed using FatCatRigid, with default parameters.

Parameters:

other - SubunitCluster

maxRmsd - RMSD threshold.

minCoverage - coverage (alignment fraction) threshold. Value in [0,1].

aligner - StructureAlignment algorithm

Returns:

true if the SubunitClusters were merged, false otherwise

Throws:

StructureException

divideInternally

public boolean divideInternally(double coverageThreshold,
                                double rmsdThreshold,
                                int minSequenceLength)
                         throws StructureException

Analyze the internal symmetry of the SubunitCluster and divide its Subunit into the internal repeats (domains) if they are internally symmetric.

Parameters:

coverageThreshold - the minimum coverage of all repeats in the Subunit

rmsdThreshold - the maximum allowed RMSD between the repeats

minSequenceLength - the minimum length of the repeating units

Returns:

true if the cluster was internally symmetric, false otherwise

Throws:

StructureException

size

public int size()

Returns:

the number of Subunits in the cluster

length

public int length()

Returns:

the number of aligned residues between Subunits of the cluster

getClustererMethod

public SubunitClustererMethod getClustererMethod()

Returns:

the SubunitClustererMethod used for clustering the Subunits

getAlignedAtomsSubunits

public List<Atom[]> getAlignedAtomsSubunits()

Returns:

A List of size size() of Atom arrays of length length() with the aligned Atoms for each Subunit in the cluster

getAlignedAtomsSubunit

public Atom[] getAlignedAtomsSubunit(int index)

Parameters:

index - Subunit index in the Cluster

Returns:

An Atom array of length length() with the aligned Atoms from the selected Subunit in the Cluster

getMultipleAlignment

public MultipleAlignment getMultipleAlignment()
                                       throws StructureException

The multiple alignment is calculated from the equivalent residues in the SubunitCluster. The alignment is recalculated every time the method is called (no caching).

Returns:

MultipleAlignment representation of the aligned residues in this Subunit Cluster

Throws:

StructureException

toString

public String toString()

Overrides:

toString in class Object