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The protein structure modules of BioJava.
/*
* 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.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import javax.vecmath.Matrix4d;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Calc;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.multiple.Block;
import org.biojava.nbio.structure.align.multiple.BlockImpl;
import org.biojava.nbio.structure.align.multiple.BlockSet;
import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
import org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer;
import org.biojava.nbio.structure.cluster.Subunit;
import org.biojava.nbio.structure.cluster.SubunitCluster;
import org.biojava.nbio.structure.cluster.SubunitClusterer;
import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
import org.biojava.nbio.structure.cluster.SubunitExtractor;
import org.biojava.nbio.structure.contact.Pair;
import org.biojava.nbio.structure.geometry.SuperPositions;
import org.biojava.nbio.structure.geometry.UnitQuaternions;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Quaternary Structure Alignment (QS-Align). The algorithm takes as input two
* protein structures at the quaternary structure level (multiple chains or
* subunits) and calculates the equivalent subunit matching and a residue-based
* alignment, together with usual alignment quality scores.
*
* @author Aleix Lafita
* @since 5.0.0
*
*/
public class QsAlign {
private static final Logger logger = LoggerFactory.getLogger(QsAlign.class);
public static QsAlignResult align(Structure s1, Structure s2,
SubunitClustererParameters cParams, QsAlignParameters aParams)
throws StructureException {
return align(
SubunitExtractor.extractSubunits(s1,
cParams.getAbsoluteMinimumSequenceLength(),
cParams.getMinimumSequenceLengthFraction(),
cParams.getMinimumSequenceLength()),
SubunitExtractor.extractSubunits(s2,
cParams.getAbsoluteMinimumSequenceLength(),
cParams.getMinimumSequenceLengthFraction(),
cParams.getMinimumSequenceLength()), cParams, aParams);
}
public static QsAlignResult align(List s1, List s2,
SubunitClustererParameters cParams, QsAlignParameters aParams)
throws StructureException {
QsAlignResult result = new QsAlignResult(s1, s2);
// SETP 1: cluster each group of subunits O(N^2*L^2) - intra
List c1 = SubunitClusterer.cluster(s1, cParams).getClusters();
List c2 = SubunitClusterer.cluster(s2, cParams).getClusters();
// STEP 2: match each subunit cluster between groups O(N^2*L^2) - inter
Map clusterMap = new HashMap<>();
for (int i = 0; i < c1.size(); i++) {
for (int j = 0; j < c2.size(); j++) {
if (clusterMap.containsKey(i))
break;
if (clusterMap.containsValue(j))
continue;
// Use structural alignment to match the subunit clusters
if (c1.get(i).mergeStructure(c2.get(j),cParams)) {
clusterMap.put(i, j);
}
}
}
logger.info("Cluster Map: " + clusterMap.toString());
result.setClusters(c1);
// STEP 3: Align the assemblies for each cluster match O(N^2*L)
for (int globalKey : clusterMap.keySet()) {
// Obtain the clusters
SubunitCluster clust1 = c1.get(globalKey);
SubunitCluster clust2 = c2.get(clusterMap.get(globalKey));
// Take a cluster match as reference
int index1 = 0;
int index2 = clust1.size() - clust2.size();
Map subunitMap = new HashMap<>();
subunitMap.put(index1, index2);
// Map cluster id to their subunit matching
Map> clustSubunitMap = new HashMap<>();
clustSubunitMap.put(globalKey, subunitMap);
// Change order of key set so that globalKey is first
List keySet = new ArrayList<>(clusterMap.keySet());
keySet.remove((Integer) globalKey);
keySet.add(0, globalKey);
for (int key : clusterMap.keySet()) {
// Recover subunitMap if it is the reference, new one otherwise
if (key == globalKey)
subunitMap = clustSubunitMap.get(key);
else
subunitMap = new HashMap<>();
// Obtain the clusters of each subunit group
clust1 = c1.get(key);
clust2 = c2.get(clusterMap.get(key));
// Get the initial subunit indices of each group
index1 = 0;
index2 = clust1.size() - clust2.size();
for (int i = 0; i < index2; i++) {
for (int j = index2; j < clust1.size(); j++) {
if (subunitMap.containsKey(i))
break;
if (subunitMap.containsValue(j))
continue;
// Obtain cumulative transformation matrix
Matrix4d transform = getTransformForClusterSubunitMap(
c1, clustSubunitMap);
// Obtain Atom arrays of the subunit pair to match
Atom[] atoms1 = clust1.getAlignedAtomsSubunit(i);
Atom[] atoms2 = clust1.getAlignedAtomsSubunit(j);
// Obtain centroids and transform the second
Atom centr1 = Calc.getCentroid(atoms1);
Atom centr2 = Calc.getCentroid(atoms2);
Calc.transform(centr2, transform);
// 1- Check that the distance fulfills maximum
double dCentroid = Calc.getDistance(centr1, centr2);
if (dCentroid > aParams.getdCutoff()) {
logger.debug(String.format("Subunit matching %d "
+ "vs %d of cluster %d could not be "
+ "matched, because centroid distance is "
+ "%.2f", index1, index2, key, dCentroid));
continue;
}
// Transform coordinates of second
Atom[] atoms2c = StructureTools.cloneAtomArray(atoms2);
Calc.transform(atoms2c, transform);
// 2- Check the orientation metric condition
double qOrient = UnitQuaternions.orientationAngle(
Calc.atomsToPoints(atoms1),
Calc.atomsToPoints(atoms2c), false);
qOrient = Math.min(Math.abs(2*Math.PI - qOrient), qOrient);
if (qOrient > aParams.getMaxOrientationAngle()) {
logger.debug(String.format("Subunit matching %d "
+ "vs %d of cluster %d could not be "
+ "matched, because orientation metric is "
+ "%.2f", i, j, key, qOrient));
continue;
}
// 3- Check the RMSD condition
double rmsd = Calc.rmsd(atoms1, atoms2c);
if (rmsd > aParams.getMaxRmsd()) {
logger.debug(String.format("Subunit matching %d "
+ "vs %d of cluster %d could not be "
+ "matched, because RMSD is %.2f", i,
j, key, rmsd));
continue;
}
logger.info(String.format("Subunit matching %d vs %d"
+ " of cluster %d with centroid distance %.2f"
+ ", orientation metric %.2f and RMSD %.2f",
i, j, key, dCentroid, qOrient, rmsd));
subunitMap.put(i, j);
}
}
clustSubunitMap.put(key, subunitMap);
}
logger.info("Cluster Subunit Map: " + clustSubunitMap.toString());
// Unfold the nested map into subunit map and alignment
subunitMap = new HashMap<>();
List alignRes1 = new ArrayList<>();
List alignRes2 = new ArrayList<>();
List atomArray1 = new ArrayList<>();
List atomArray2 = new ArrayList<>();
for (int key : clustSubunitMap.keySet()) {
// Obtain the cluster and the alignment in it
SubunitCluster cluster = c1.get(key);
List> clusterEqrs = cluster
.getMultipleAlignment().getBlock(0).getAlignRes();
for (Entry pair : clustSubunitMap.get(key)
.entrySet()) {
int i = pair.getKey();
int j = pair.getValue();
// Obtain the indices of the original Subunit Lists
int orig1 = s1.indexOf(cluster.getSubunits().get(i));
int orig2 = s2.indexOf(cluster.getSubunits().get(j));
// Append rescaled aligned residue indices
for (Integer eqr : clusterEqrs.get(i))
alignRes1.add(eqr + atomArray1.size());
for (Integer eqr : clusterEqrs.get(j))
alignRes2.add(eqr + atomArray2.size());
// Apend atoms to the arrays
atomArray1.addAll(Arrays.asList(s1.get(orig1)
.getRepresentativeAtoms()));
atomArray2.addAll(Arrays.asList(s2.get(orig2)
.getRepresentativeAtoms()));
subunitMap.put(orig1, orig2);
}
}
// Evaluate the goodness of the match with an alignment object
MultipleAlignment msa = new MultipleAlignmentImpl();
msa.setEnsemble(new MultipleAlignmentEnsembleImpl());
msa.getEnsemble().setAtomArrays(
Arrays.asList(new Atom[][] {
atomArray1.toArray(new Atom[atomArray1.size()]),
atomArray2.toArray(new Atom[atomArray2.size()]) }));
// Fill in the alignment information
BlockSet bs = new BlockSetImpl(msa);
Block b = new BlockImpl(bs);
List> alignRes = new ArrayList<>(2);
alignRes.add(alignRes1);
alignRes.add(alignRes2);
b.setAlignRes(alignRes);
// Fill in the transformation matrices
new ReferenceSuperimposer().superimpose(msa);
// Calculate some scores
MultipleAlignmentScorer.calculateScores(msa);
// If it is the best match found so far store it
if (subunitMap.size() > result.getSubunitMap().size()) {
result.setSubunitMap(subunitMap);
result.setAlignment(msa);
logger.info("Better result found: " + result.toString());
} else if (subunitMap.size() == result.getSubunitMap().size()) {
if (result.getAlignment() == null) {
result.setSubunitMap(subunitMap);
result.setAlignment(msa);
} else if (msa.getScore(MultipleAlignmentScorer.RMSD) < result.getRmsd()) {
result.setSubunitMap(subunitMap);
result.setAlignment(msa);
logger.info("Better result found: " + result.toString());
}
}
}
return result;
}
/**
* Returns a pair of Atom arrays corresponding to the alignment of subunit
* matchings, in order of appearance. Superposition of the two Atom sets
* gives the transformation of the complex.
*
* Utility method to cumulative calculate the alignment Atoms.
*
* @param clusters
* List of SubunitClusters
* @param clusterSubunitMap
* map from cluster id to subunit matching
* @return pair of atom arrays to be superposed
*/
private static Pair getAlignedAtomsForClusterSubunitMap(
List clusters,
Map> clusterSubunitMap) {
List atomArray1 = new ArrayList<>();
List atomArray2 = new ArrayList<>();
// For each cluster of subunits
for (int key : clusterSubunitMap.keySet()) {
// Obtain the cluster and the alignment in it
SubunitCluster cluster = clusters.get(key);
// For each subunit matching in the cluster
for (Entry pair : clusterSubunitMap.get(key)
.entrySet()) {
int i = pair.getKey();
int j = pair.getValue();
// Apend atoms to the arrays
atomArray1.addAll(Arrays.asList(cluster
.getAlignedAtomsSubunit(i)));
atomArray2.addAll(Arrays.asList(cluster
.getAlignedAtomsSubunit(j)));
}
}
return new Pair<>(
atomArray1.toArray(new Atom[0]),
atomArray2.toArray(new Atom[0]));
}
/**
* Returns the transformation matrix corresponding to the alignment of
* subunit matchings.
*
* Utility method to cumulative calculate the alignment transformation.
*
* @param clusters
* List of SubunitClusters
* @param clusterSubunitMap
* map from cluster id to subunit matching
* @return transformation matrix
*/
private static Matrix4d getTransformForClusterSubunitMap(
List clusters,
Map> clusterSubunitMap) {
Pair pair = getAlignedAtomsForClusterSubunitMap(clusters,
clusterSubunitMap);
return SuperPositions.superpose(Calc.atomsToPoints(pair.getFirst()),
Calc.atomsToPoints(pair.getSecond()));
}
}