org.biojava.nbio.structure.align.quaternary.QsAlignResult Maven / Gradle / Ivy
Show all versions of biojava-structure Show documentation
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.align.quaternary;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import javax.vecmath.Matrix4d;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
import org.biojava.nbio.structure.cluster.Subunit;
import org.biojava.nbio.structure.cluster.SubunitCluster;
/**
* Result of a Quaternary Structure Alignment {@link QsAlign}. The QsAlignResult
* holds the original inputs of the algorithm and the results and scores of the
* alignment.
*
* @author Aleix Lafita
* @since 5.0.0
*
*/
public class QsAlignResult {
private List clusters;
private final List subunits1;
private final List subunits2;
private Map subunitMap;
private MultipleAlignment alignment;
private QsRelation relation;
/**
* The Constructor of the result takes the same inputs as the
* {@link QsAlign} algorithm.
*
* @param subunits1
* @param subunits2
*/
public QsAlignResult(List subunits1, List subunits2) {
this.subunits1 = subunits1;
this.subunits2 = subunits2;
subunitMap = Collections.emptyMap();
relation = QsRelation.DIFFERENT;
}
/**
* Original Subunits of the first group.
*
* @return an unmodifiable view of the original List
*/
public List getSubunits1() {
return Collections.unmodifiableList(subunits1);
}
/**
* Original Subunits of the second group.
*
* @return an unmodifiable view of the original List
*/
public List getSubunits2() {
return Collections.unmodifiableList(subunits2);
}
/**
* Map of Subunit equivalencies from the first to the second group.
*
* @return an unmodifiable view of the original Map
*/
public Map getSubunitMap() {
if (subunitMap == null)
return Collections.emptyMap();
return Collections.unmodifiableMap(subunitMap);
}
/**
* Map of Subunit equivalencies from the first to the second group.
*
* @param subunitMap
*/
public void setSubunitMap(Map subunitMap) {
// Check consistency of the map
if (Collections.max(subunitMap.keySet()) > subunits1.size()
| Collections.max(subunitMap.values()) > subunits2.size())
throw new IndexOutOfBoundsException(
"Subunit Map index higher than Subunit List size.");
// Update the relation enum
if (subunitMap.size() == 0) {
relation = QsRelation.DIFFERENT;
} else if (subunitMap.keySet().size() == subunits1.size()) {
if (subunitMap.values().size() == subunits2.size()) {
relation = QsRelation.EQUIVALENT;
} else {
relation = QsRelation.PARTIAL_COMPLETE;
}
} else {
if (subunitMap.values().size() == subunits2.size()) {
relation = QsRelation.PARTIAL_COMPLETE;
} else {
relation = QsRelation.PARTIAL_INCOMPLETE;
}
}
this.subunitMap = subunitMap;
}
/**
* The length of the alignment is the number of Subunit equivalencies it
* contains. This is equivalent to the size of the Subunit Map.
*
* @return length of the alignment
*/
public int length() {
if (subunitMap == null)
return 0;
return subunitMap.size();
}
/**
* 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).
*
* @return Matrix4d
*/
public Matrix4d getTransform() {
if (alignment == null)
return null;
return alignment.getBlockSet(0).getTransformations().get(1);
}
/**
* The RMSD between the equivalent residues of the equivalent Subunits after
* superposition of the Subunit groups. This is equivalent to
* multipleAlignment.getScore(MultipleAlignmentScorer.RMSD).
*
* @return rmsd
*/
public double getRmsd() {
if (alignment == null)
return -1.0;
if (alignment.getScore(MultipleAlignmentScorer.RMSD) == null)
return MultipleAlignmentScorer.getRMSD(alignment);
return alignment.getScore(MultipleAlignmentScorer.RMSD);
}
/**
* The quaternary structure relation {@link QsRelation} between the two
* groups of Subunits.
*
* @return relation
*/
public QsRelation getRelation() {
return relation;
}
/**
* The quaternary structure relation {@link QsRelation} between the two
* groups of Subunits.
*
* @param relation
*/
public void setRelation(QsRelation relation) {
this.relation = relation;
}
/**
* The alignment that specifies the residue equivalencies of the equivalent
* Subunits.
*
* @return alignment as a MultipleAlignment object
*/
public MultipleAlignment getAlignment() {
return alignment;
}
/**
* The alignment that specifies the residue equivalencies of the equivalent
* Subunits.
*
* @param alignment
* a MultipleAlignment object
*/
public void setAlignment(MultipleAlignment alignment) {
this.alignment = alignment;
}
/**
* Return the aligned subunits of the first Subunit group, in the alignment
* order.
*
* @return a List of Subunits in the alignment order
*/
public List getAlignedSubunits1() {
List aligned = new ArrayList<>(subunitMap.size());
for (Integer key : subunitMap.keySet())
aligned.add(subunits1.get(key));
return aligned;
}
/**
* Return the aligned subunits of the second Subunit group, in the alignment
* order.
*
* @return a List of Subunits in the alignment order
*/
public List getAlignedSubunits2() {
List aligned = new ArrayList<>(subunitMap.size());
for (Integer key : subunitMap.keySet())
aligned.add(subunits2.get(subunitMap.get(key)));
return aligned;
}
public void setClusters(List clusters) {
this.clusters = clusters;
}
public Atom[] getAlignedAtomsForSubunits1(int index) {
// Obtain the indices of the clustered subunits
for (SubunitCluster cluster : clusters) {
if (cluster.getSubunits().contains(subunits1.get(index))) {
return cluster.getAlignedAtomsSubunit(cluster.getSubunits()
.indexOf(subunits1.get(index)));
}
}
return null;
}
public Atom[] getAlignedAtomsForSubunits2(int index) {
// Obtain the indices of the clustered subunits
for (SubunitCluster cluster : clusters) {
if (cluster.getSubunits().contains(subunits2.get(index))) {
return cluster.getAlignedAtomsSubunit(cluster.getSubunits()
.indexOf(subunits2.get(index)));
}
}
return null;
}
@Override
public String toString() {
return "QsAlignResult [relation="
+ relation
+ ", rmsd="
+ getRmsd()
+ ", length="
+ length()
+ ", Aligned 1: "
+ getAlignedSubunits1().stream().map(s -> s.getName())
.collect(Collectors.toList())
+ ", Aligned 2: "
+ getAlignedSubunits2().stream().map(s -> s.getName())
.collect(Collectors.toList()) + "]";
}
}