Package 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	Description
SubunitCluster(List<Subunit> subunits, List<List<Integer>> subunitEQR)	Create the cluster manually by specifying subunits and the equivalent residues
SubunitCluster(Subunit subunit)	A constructor from a single Subunit.
SubunitCluster(SubunitCluster other, List<Integer> subunitsToRetain)	A copy constructor with the possibility of removing subunits.

Method Summary

Modifier and Type	Method	Description
boolean	divideInternally(SubunitClustererParameters clusterParams)	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()
String	getAlpha()	A letter that is assigned to this cluster in stoichiometry.
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	isIdenticalByEntityIdTo(SubunitCluster other)	Tells whether the other SubunitCluster contains exactly the same Subunit.
boolean	isIdenticalTo(SubunitCluster other)	Tells whether the other SubunitCluster contains exactly the same Subunit.
boolean	isPseudoStoichiometric()
int	length()
boolean	mergeIdentical(SubunitCluster other)	Merges the other SubunitCluster into this one if it contains exactly the same Subunit.
boolean	mergeIdenticalByEntityId(SubunitCluster other)	Merges the other SubunitCluster into this one if it contains exactly the same Subunit.
boolean	mergeSequence(SubunitCluster other, SubunitClustererParameters params)	Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).
boolean	mergeSequence(SubunitCluster other, SubunitClustererParameters params, Alignments.PairwiseSequenceAlignerType alignerType, GapPenalty gapPenalty, SubstitutionMatrix<AminoAcidCompound> subsMatrix)	Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).
boolean	mergeStructure(SubunitCluster other, SubunitClustererParameters params)	Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (according to the criteria in params).
void	setAlpha(String alpha)	A letter that is assigned to this cluster in stoichiometry.
int	size()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

SubunitCluster

public SubunitCluster(Subunit subunit)

A constructor from a single Subunit. To obtain a SubunitCluster with multiple Subunits, initialize different SubunitClusters and merge them.

Parameters:

subunit - initial Subunit

SubunitCluster

public SubunitCluster(SubunitCluster other,
 List<Integer> subunitsToRetain)

A copy constructor with the possibility of removing subunits. No re-clustering is done.

Parameters:

other - reference SubunitCluster

subunitsToRetain - which subunits to copy to this cluster

SubunitCluster

public SubunitCluster(List<Subunit> subunits,
 List<List<Integer>> subunitEQR)

Create the cluster manually by specifying subunits and the equivalent residues

Parameters:

subunits - List of aligned subunits

subunitEQR - Double list giving the aligned residue indices in each subunit

Method Details

getAlpha

public String getAlpha()

A letter that is assigned to this cluster in stoichiometry.

Returns:

alpha String

setAlpha

public void setAlpha(String alpha)

A letter that is assigned to this cluster in stoichiometry.

Parameters:

alpha - String

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

isIdenticalByEntityIdTo

public boolean isIdenticalByEntityIdTo(SubunitCluster other)

Tells whether the other SubunitCluster contains exactly the same Subunit. This is checked by equality of their entity identifiers if they are present.

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

mergeIdenticalByEntityId

public boolean mergeIdenticalByEntityId(SubunitCluster other)

Merges the other SubunitCluster into this one if it contains exactly the same Subunit. This is checked by comparing the entity identifiers of the subunits if one can be found. Thus this only makes sense when the subunits are complete chains of a deposited PDB entry.

Parameters:

other - SubunitCluster

Returns:

true if the SubunitClusters were merged, false otherwise

mergeSequence

public boolean mergeSequence(SubunitCluster other,
 SubunitClustererParameters params)
                      throws CompoundNotFoundException

Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).

The sequence alignment is performed using linear SimpleGapPenalty and BLOSUM62 as scoring matrix.

Parameters:

other - SubunitCluster

params - SubunitClustererParameters, with information whether to use local or global alignment, sequence identity and coverage thresholds. Threshold values lower than 0.7 are not recommended. Use mergeStructure(org.biojava.nbio.structure.cluster.SubunitCluster, org.biojava.nbio.structure.cluster.SubunitClustererParameters) for lower values.

Returns:

true if the SubunitClusters were merged, false otherwise

Throws:

CompoundNotFoundException

mergeSequence

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

Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).

The sequence alignment is performed using linear SimpleGapPenalty and BLOSUM62 as scoring matrix.

Parameters:

other - SubunitCluster

params - SubunitClustererParameters, with information whether to use local or global alignment, sequence identity and coverage thresholds. Threshold values lower than 0.7 are not recommended. Use mergeStructure(org.biojava.nbio.structure.cluster.SubunitCluster, org.biojava.nbio.structure.cluster.SubunitClustererParameters) for lower values.

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,
 SubunitClustererParameters params)
                       throws StructureException

Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (according to the criteria in params).

Parameters:

other - SubunitCluster

params - SubunitClustererParameters, with information on what alignment algorithm to use, RMSD/TMScore and structure coverage thresholds.

Returns:

true if the SubunitClusters were merged, false otherwise

Throws:

StructureException

divideInternally

public boolean divideInternally(SubunitClustererParameters clusterParams)
                         throws StructureException

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

Parameters:

clusterParams - SubunitClustererParameters with fields used as follows: structureCoverageThreshold the minimum coverage of all repeats in the Subunit rmsdThreshold the maximum allowed RMSD between the repeats minimumSequenceLength 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

isPseudoStoichiometric

public boolean isPseudoStoichiometric()

Returns:

true if this cluster is considered pseudo-stoichiometric (i.e., was either clustered by structure, or by sequence with low scores), false otherwise.