org.biojava.nbio.structure.align.quaternary

Class QsAlignResult

java.lang.Object

org.biojava.nbio.structure.align.quaternary.QsAlignResult

public class QsAlignResult
extends Object

Result of a Quaternary Structure Alignment QsAlign. The QsAlignResult holds the original inputs of the algorithm and the results and scores of the alignment.

Since:

5.0.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
QsAlignResult(List<Subunit> subunits1, List<Subunit> subunits2) The Constructor of the result takes the same inputs as the QsAlign algorithm.

Method Summary

Modifier and Type	Method and Description
Atom[]	getAlignedAtomsForSubunits1(int index)
Atom[]	getAlignedAtomsForSubunits2(int index)
List<Subunit>	getAlignedSubunits1() Return the aligned subunits of the first Subunit group, in the alignment order.
List<Subunit>	getAlignedSubunits2() Return the aligned subunits of the second Subunit group, in the alignment order.
MultipleAlignment	getAlignment() The alignment that specifies the residue equivalencies of the equivalent Subunits.
QsRelation	getRelation() The quaternary structure relation QsRelation between the two groups of Subunits.
double	getRmsd() The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups.
Map<Integer,Integer>	getSubunitMap() Map of Subunit equivalencies from the first to the second group.
List<Subunit>	getSubunits1() Original Subunits of the first group.
List<Subunit>	getSubunits2() Original Subunits of the second group.
javax.vecmath.Matrix4d	getTransform() The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.
int	length() The length of the alignment is the number of Subunit equivalencies it contains.
void	setAlignment(MultipleAlignment alignment) The alignment that specifies the residue equivalencies of the equivalent Subunits.
void	setClusters(List<SubunitCluster> clusters)
void	setRelation(QsRelation relation) The quaternary structure relation QsRelation between the two groups of Subunits.
void	setSubunitMap(Map<Integer,Integer> subunitMap) Map of Subunit equivalencies from the first to the second group.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

QsAlignResult

public QsAlignResult(List<Subunit> subunits1,
                     List<Subunit> subunits2)

The Constructor of the result takes the same inputs as the QsAlign algorithm.

Parameters:

subunits1 -

subunits2 -

Method Detail

getSubunits1

public List<Subunit> getSubunits1()

Original Subunits of the first group.

Returns:

an unmodifiable view of the original List

getSubunits2

public List<Subunit> getSubunits2()

Original Subunits of the second group.

Returns:

an unmodifiable view of the original List

getSubunitMap

public Map<Integer,Integer> getSubunitMap()

Map of Subunit equivalencies from the first to the second group.

Returns:

an unmodifiable view of the original Map

setSubunitMap

public void setSubunitMap(Map<Integer,Integer> subunitMap)

Map of Subunit equivalencies from the first to the second group.

Parameters:

subunitMap -

length

public int length()

The length of the alignment is the number of Subunit equivalencies it contains. This is equivalent to the size of the Subunit Map.

Returns:

length of the alignment

getTransform

public javax.vecmath.Matrix4d getTransform()

The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.

This is equivalent to multipleAlignment.getBlockSet(0).getTransformations().get(1).

Returns:

Matrix4d

getRmsd

public double getRmsd()

The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups. This is equivalent to multipleAlignment.getScore(MultipleAlignmentScorer.RMSD).

Returns:

rmsd

getRelation

public QsRelation getRelation()

The quaternary structure relation QsRelation between the two groups of Subunits.

Returns:

relation

setRelation

public void setRelation(QsRelation relation)

The quaternary structure relation QsRelation between the two groups of Subunits.

Parameters:

relation -

getAlignment

public MultipleAlignment getAlignment()

The alignment that specifies the residue equivalencies of the equivalent Subunits.

Returns:

alignment as a MultipleAlignment object

setAlignment

public void setAlignment(MultipleAlignment alignment)

The alignment that specifies the residue equivalencies of the equivalent Subunits.

Parameters:

alignment - a MultipleAlignment object

getAlignedSubunits1

public List<Subunit> getAlignedSubunits1()

Return the aligned subunits of the first Subunit group, in the alignment order.

Returns:

a List of Subunits in the alignment order

getAlignedSubunits2

public List<Subunit> getAlignedSubunits2()

Return the aligned subunits of the second Subunit group, in the alignment order.

Returns:

a List of Subunits in the alignment order

setClusters

public void setClusters(List<SubunitCluster> clusters)

getAlignedAtomsForSubunits1

public Atom[] getAlignedAtomsForSubunits1(int index)

getAlignedAtomsForSubunits2

public Atom[] getAlignedAtomsForSubunits2(int index)

toString

public String toString()

Overrides:

toString in class Object