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Added support for min and max seq. identity for pseudosymmetry cases #13

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Jun 4, 2013
Merged

Added support for min and max seq. identity for pseudosymmetry cases #13

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4 changes: 2 additions & 2 deletions src/main/java/demo/DemoOrientBioAssembly.java
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Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@ private static boolean analyzeSymmetry(Structure s,String pdbID, int biolAssembl
System.out.println("=================");
System.out.println("Sequence ID : " + parameters.getSequenceIdentityThreshold() );
System.out.println("Stoichiometry : " + calc.getSubunits().getStoichiometry());
System.out.println("Pseudostoichiometry: " + calc.getSubunits().isPseudoStiochiometric());
System.out.println("Pseudostoichiometry: " + calc.getSubunits().isPseudoStoichiometric());
System.out.println("Point Group : " + calc.getRotationGroup().getPointGroup());

System.out.println("Symmetry RMSD : " + String.format("%.2f",calc.getRotationGroup().getAverageTraceRmsd()));
Expand Down Expand Up @@ -148,7 +148,7 @@ private static boolean analyzeSymmetry(Structure s,String pdbID, int biolAssembl
}

System.out.println("=================");
return calc.getSubunits().isPseudoStiochiometric();
return calc.getSubunits().isPseudoStoichiometric();
} else {
System.out.println("No protein chains found");
return false;
Expand Down
20 changes: 12 additions & 8 deletions src/main/java/org/biojava3/structure/quaternary/analysis/CalcBioAssemblySymmetry.java
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Expand Up @@ -73,10 +73,12 @@ public boolean orient(){
System.out.println("Results for " + Math.round(parameters.getSequenceIdentityThreshold()*100) + "% sequence identity threshold:");
System.out.println();
System.out.println("Global symmetry:");
System.out.println("Stoichiometry : " + globalSymmetry.getSubunits().getStoichiometry());
System.out.println("Pseudostoichiometry : " + globalSymmetry.getSubunits().isPseudoStiochiometric());
System.out.println("Point group : " + globalSymmetry.getRotationGroup().getPointGroup());
System.out.println("Symmetry RMSD : " + (float) globalSymmetry.getRotationGroup().getAverageTraceRmsd());
System.out.println("Stoichiometry : " + globalSymmetry.getSubunits().getStoichiometry());
System.out.println("Pseudostoichiometry : " + globalSymmetry.getSubunits().isPseudoStoichiometric());
System.out.println("Min sequence identity : " + Math.round(globalSymmetry.getSubunits().getMinSequenceIdentity()*100));
System.out.println("Max sequence identity : " + Math.round(globalSymmetry.getSubunits().getMaxSequenceIdentity()*100));
System.out.println("Point group : " + globalSymmetry.getRotationGroup().getPointGroup());
System.out.println("Symmetry RMSD : " + (float) globalSymmetry.getRotationGroup().getAverageTraceRmsd());
}

axisTransformation = new AxisTransformation(globalSymmetry);
Expand All @@ -97,10 +99,12 @@ public boolean orient(){
AxisTransformation at = new AxisTransformation(localSymmetry);
System.out.println();
System.out.println("Results for " + Math.round(parameters.getSequenceIdentityThreshold()*100) + "% sequence identity threshold:");
System.out.println("Stoichiometry : " + localSymmetry.getSubunits().getStoichiometry());
System.out.println("Pseudostoichiometry : " + localSymmetry.getSubunits().isPseudoStiochiometric());
System.out.println("Point group : " + localSymmetry.getRotationGroup().getPointGroup());
System.out.println("Symmetry RMSD : " + (float) localSymmetry.getRotationGroup().getAverageTraceRmsd());
System.out.println("Stoichiometry : " + localSymmetry.getSubunits().getStoichiometry());
System.out.println("Pseudostoichiometry : " + localSymmetry.getSubunits().isPseudoStoichiometric());
System.out.println("Min sequence identity : " + Math.round(localSymmetry.getSubunits().getMinSequenceIdentity()*100));
System.out.println("Max sequence identity : " + Math.round(localSymmetry.getSubunits().getMaxSequenceIdentity()*100));
System.out.println("Point group : " + localSymmetry.getRotationGroup().getPointGroup());
System.out.println("Symmetry RMSD : " + (float) localSymmetry.getRotationGroup().getAverageTraceRmsd());
System.out.println();
JmolSymmetryScriptGenerator gen = JmolSymmetryScriptGenerator.getInstance(at, "l"+count);
if (count == 0) {
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/biojava3/structure/quaternary/analysis/OrientBiologicalAssembly.java
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Expand Up @@ -103,7 +103,7 @@ private void orient(Structure structure) {
// initialize with default parameters
QuatSymmetryParameters params = new QuatSymmetryParameters();
params.setSequenceIdentityThreshold(0.95);
// params.setStructuralAlignmentOnly(true);
params.setStructuralAlignmentOnly(true);
params.setVerbose(verbose);

System.out.println("Default parameters:");
Expand Down
8 changes: 8 additions & 0 deletions src/main/java/org/biojava3/structure/quaternary/core/QuatSymmetryDetector.java
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Expand Up @@ -147,6 +147,8 @@ private Subunits createGlobalSubunits() {
Subunits subunits = new Subunits(chainClusterer.getCalphaCoordinates(),
chainClusterer.getSequenceClusterIds(),
chainClusterer.getPseudoStoichiometry(),
chainClusterer.getMinSequenceIdentity(),
chainClusterer.getMaxSequenceIdentity(),
chainClusterer.getFolds(),
chainClusterer.getChainIds(),
chainClusterer.getModelNumbers());
Expand All @@ -166,13 +168,17 @@ private Subunits createLocalSubunit(List<Integer> subCluster) {
List<Point3d[]> subCalphaCoordinates = new ArrayList<Point3d[]>(subCluster.size());
List<Integer> subSequenceIds = new ArrayList<Integer>(subCluster.size());
List<Boolean> subPseudoStoichiometry = new ArrayList<Boolean>(subCluster.size());
List<Double> subMinSequenceIdentity = new ArrayList<Double>(subCluster.size());
List<Double> subMaxSequenceIdentity = new ArrayList<Double>(subCluster.size());
List<String> subChainIds = new ArrayList<String>(subCluster.size());
List<Integer> subModelNumbers = new ArrayList<Integer>(subCluster.size());

for (int index: subCluster) {
subCalphaCoordinates.add(chainClusterer.getCalphaCoordinates().get(index));
subSequenceIds.add(chainClusterer.getSequenceClusterIds().get(index));
subPseudoStoichiometry.add(chainClusterer.getPseudoStoichiometry().get(index));
subMinSequenceIdentity.add(chainClusterer.getMinSequenceIdentity().get(index));
subMaxSequenceIdentity.add(chainClusterer.getMaxSequenceIdentity().get(index));
subChainIds.add(chainClusterer.getChainIds().get(index));
subModelNumbers.add(chainClusterer.getModelNumbers().get(index));
}
Expand All @@ -184,6 +190,8 @@ private Subunits createLocalSubunit(List<Integer> subCluster) {
Subunits subunits = new Subunits(subCalphaCoordinates,
subSequenceIds,
subPseudoStoichiometry,
subMinSequenceIdentity,
subMaxSequenceIdentity,
subFolds,
subChainIds,
subModelNumbers);
Expand Down
46 changes: 20 additions & 26 deletions src/main/java/org/biojava3/structure/quaternary/core/SequenceAlignmentCluster.java
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Expand Up @@ -22,8 +22,8 @@ public class SequenceAlignmentCluster {

private int alignmentLength = 0;
private boolean pseudoStoichiometric = false;
private double minSequenceIdentity = 100;
private double maxSequenceIdentity = 0;
private double minSequenceIdentity = 1.0;
private double maxSequenceIdentity = 0.0;

private boolean modified = true;

Expand All @@ -36,10 +36,16 @@ public boolean isPseudoStoichiometric() {
}

public double getMinSequenceIdentity() {
if (! isPseudoStoichiometric()) {
return 1.0;
}
return minSequenceIdentity;
}

public double getMaxSequenceIdentity() {
if (! isPseudoStoichiometric()) {
return 1.0;
}
return maxSequenceIdentity;
}

Expand All @@ -49,11 +55,7 @@ public void addUniqueSequenceList(UniqueSequenceList sequenceList) {
}

public int getSequenceCount() {
int count = 0;
for (UniqueSequenceList list: uniqueSequenceList) {
count += list.getChainCount();
}
return count;
return uniqueSequenceList.size();
}

public int getSequenceAlignmentLength() {
Expand All @@ -68,29 +70,23 @@ public List<UniqueSequenceList> getUniqueSequenceList() {
public List<String> getChainIds() {
List<String> ids = new ArrayList<String>();
for (UniqueSequenceList list: uniqueSequenceList) {
for (int i = 0, n = list.getChainCount(); i < n; i++) {
ids.add(list.getChainId(i));
}
ids.add(list.getChainId());
}
return ids;
}

public List<Integer> getModelNumbers() {
List<Integer> numbers = new ArrayList<Integer>();
for (UniqueSequenceList list: uniqueSequenceList) {
for (int i = 0, n = list.getChainCount(); i < n; i++) {
numbers.add(list.getModelNumber(i));
}
numbers.add(list.getModelNumber());
}
return numbers;
}

public List<Integer> getStructureIds() {
List<Integer> numbers = new ArrayList<Integer>();
for (UniqueSequenceList list: uniqueSequenceList) {
for (int i = 0, n = list.getChainCount(); i < n; i++) {
numbers.add(list.getStructureId(i));
}
numbers.add(list.getStructureId());
}
return numbers;
}
Expand Down Expand Up @@ -129,7 +125,7 @@ public boolean identityMatch(Atom[] cAlphaAtoms, String chainId, int modelNumber
if (seqMatch) {
List<Integer> alig1 = new ArrayList<Integer>();
List<Integer> alig2 = new ArrayList<Integer>();
Atom[] referenceAtoms = u.getReferenceChain();
Atom[] referenceAtoms = u.getCalphaAtoms();
int inCommon = alignIdenticalSequence(referenceAtoms, cAlphaAtoms, alig1, alig2);
// System.out.println("in common: " + inCommon);

Expand All @@ -154,8 +150,8 @@ public int[][][] alignClustersByStructure(SequenceAlignmentCluster cluster) {
pseudoStoichiometric = false;

int[][][] alignment = null;
Atom[] referenceAtoms1 = this.getUniqueSequenceList().get(0).getReferenceChain();
Atom[] referenceAtoms2 = cluster.getUniqueSequenceList().get(0).getReferenceChain();
Atom[] referenceAtoms1 = this.getUniqueSequenceList().get(0).getCalphaAtoms();
Atom[] referenceAtoms2 = cluster.getUniqueSequenceList().get(0).getCalphaAtoms();

double alignmentLengthFraction = (double)Math.min(referenceAtoms1.length, referenceAtoms2.length) /
Math.max(referenceAtoms1.length, referenceAtoms2.length);
Expand Down Expand Up @@ -318,14 +314,12 @@ private void createAlignedCAlphaAtoms() {
alignmentIndices.add(alignment2.get(i));
}
}
for (int i = 0; i < u.getChainCount(); i++) {
Atom[] unalignedAtoms = u.getChain(i);
Atom[] alignedAtoms = new Atom[alignmentIndices.size()];
for (int j = 0; j < alignedAtoms.length; j++) {
alignedAtoms[j] = unalignedAtoms[alignmentIndices.get(j)];
}
alignedCAlphaAtoms.add(alignedAtoms);
Atom[] unalignedAtoms = u.getCalphaAtoms();
Atom[] alignedAtoms = new Atom[alignmentIndices.size()];
for (int j = 0; j < alignedAtoms.length; j++) {
alignedAtoms[j] = unalignedAtoms[alignmentIndices.get(j)];
}
alignedCAlphaAtoms.add(alignedAtoms);
}
}

Expand Down
36 changes: 26 additions & 10 deletions src/main/java/org/biojava3/structure/quaternary/core/Subunits.java
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Expand Up @@ -25,6 +25,8 @@ public class Subunits {
private List<Point3d[]> caCoords = Collections.emptyList();
private List<Integer> sequenceClusterIds = Collections.emptyList();
private List<Boolean> pseudoStoichiometry = Collections.emptyList();
private List<Double> minSequenceIdentity = Collections.emptyList();
private List<Double> maxSequenceIdentity = Collections.emptyList();
private List<String> chainIds = Collections.emptyList();
private List<Integer> modelNumbers = Collections.emptyList();
private List<Integer> folds = Collections.emptyList();
Expand All @@ -35,13 +37,15 @@ public class Subunits {
private Point3d centroid;
private MomentsOfInertia momentsOfInertia = new MomentsOfInertia();

public Subunits(List<Point3d[]> caCoords, List<Integer> sequenceClusterIds, List<Boolean> pseudoStoichiometry, List<Integer> folds, List<String> chainIds, List<Integer> modelNumbers) {
this.caCoords = caCoords;
this.sequenceClusterIds = sequenceClusterIds;
this.pseudoStoichiometry = pseudoStoichiometry;
this.folds = folds;
this.chainIds = chainIds;
this.modelNumbers = modelNumbers;
public Subunits(List<Point3d[]> caCoords, List<Integer> sequenceClusterIds, List<Boolean> pseudoStoichiometry, List<Double> minSequenceIdentity, List<Double> maxSequenceIdentity, List<Integer> folds, List<String> chainIds, List<Integer> modelNumbers) {
this.caCoords = caCoords;
this.sequenceClusterIds = sequenceClusterIds;
this.pseudoStoichiometry = pseudoStoichiometry;
this.minSequenceIdentity = minSequenceIdentity;
this.maxSequenceIdentity = maxSequenceIdentity;
this.folds = folds;
this.chainIds = chainIds;
this.modelNumbers = modelNumbers;
}

public List<Point3d[]> getTraces() {
Expand All @@ -60,7 +64,7 @@ public List<Integer> getSequenceClusterIds() {
return sequenceClusterIds;
}

public boolean isPseudoStiochiometric() {
public boolean isPseudoStoichiometric() {
for (Boolean b: pseudoStoichiometry) {
if (b) {
return true;
Expand All @@ -69,10 +73,22 @@ public boolean isPseudoStiochiometric() {
return false;
}

public List<Boolean> getPseudoStoichiometry() {
return pseudoStoichiometry;
public double getMinSequenceIdentity() {
double minId = 1.0;
for (double seqId: minSequenceIdentity) {
minId = Math.min(seqId, minId);
}
return minId;
}

public double getMaxSequenceIdentity() {
double maxId = 1.0;
for (double seqId: maxSequenceIdentity) {
maxId = Math.min(seqId, maxId);
}
return maxId;
}

public List<String> getChainIds() {
return chainIds;
}
Expand Down
60 changes: 20 additions & 40 deletions src/main/java/org/biojava3/structure/quaternary/core/UniqueSequenceList.java
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Expand Up @@ -11,23 +11,24 @@ public class UniqueSequenceList {
private String seqResSequence = "";
private List<Integer> alignment1 = null;
private List<Integer> alignment2 = null;
private List<Atom[]> caAtoms = new ArrayList<Atom[]>();
private List<String> chainIds = new ArrayList<String>();
private List<Integer> modelNumbers = new ArrayList<Integer>();
private List<Integer> structureIds = new ArrayList<Integer>();
private Atom[] caAtoms = null;
private String chainId = null;
private Integer modelNumber = null;
private Integer structureId = null;

public UniqueSequenceList(Atom[] cAlphaAtoms, String chainId, int modelNumber, int structureId, String seqResSequence) {
this.caAtoms.add(cAlphaAtoms);
this.chainIds.add(chainId);
this.modelNumbers.add(modelNumber);
this.structureIds.add(structureId);
this.caAtoms = cAlphaAtoms;
this.chainId = chainId;
this.modelNumber = modelNumber;
this.structureId = structureId;
this.seqResSequence = seqResSequence;
this.sequenceString = getSequenceString(cAlphaAtoms);
this.alignment1 = new ArrayList<Integer>(cAlphaAtoms.length);
this.alignment2 = new ArrayList<Integer>(cAlphaAtoms.length);
for (int i = 0; i < cAlphaAtoms.length; i++) {
this.alignment1.add(i);
this.alignment2.add(i);
}
this.alignment2 = alignment1;
}

/**
Expand All @@ -41,43 +42,21 @@ public boolean isMatch(Atom[] caAlphaAtoms) {
return sequenceString.equals(getSequenceString(caAlphaAtoms));
}

public void addChain(Atom[] cAlphaAtoms, String chainId, int modelNumber, int structureId) {
this.caAtoms.add(cAlphaAtoms);
this.chainIds.add(chainId);
this.modelNumbers.add(modelNumber);
this.structureIds.add(structureId);
public String getChainId() {
return chainId;
}

public int getChainCount() {
return caAtoms.size();
}

public Atom[] getChain(int index) {
return caAtoms.get(index);
}

public String getChainId(int index) {
return chainIds.get(index);
}

public int getModelNumber(int index) {
return modelNumbers.get(index);
public int getModelNumber() {
return modelNumber;
}

public int getStructureId(int index) {
return structureIds.get(index);
public int getStructureId() {
return structureId;
}

public Atom[] getReferenceChain() {
return caAtoms.get(0);
public Atom[] getCalphaAtoms() {
return caAtoms;
}

/**
* @return the sequenceString
*/
public String getSequenceString() {
return sequenceString;
}

public String getSeqResSequence() {
return seqResSequence;
Expand Down Expand Up @@ -119,6 +98,7 @@ public static String getSequenceString(Atom[] caAlphaAtoms) {

for (Atom a: caAlphaAtoms) {
Group g = a.getGroup();
// TODO is the check for UNK required? UNK should have been filtered already in ChainClusterer?
if (! g.getPDBName().equals("UNK")) {
builder.append(g.getResidueNumber());
builder.append(g.getPDBName());
Expand All @@ -132,7 +112,7 @@ public static String getSequenceString(Atom[] caAlphaAtoms) {
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("#: ");
builder.append(caAtoms.size());
builder.append(caAtoms.length);
builder.append(" seq: ");
builder.append(sequenceString);
builder.append("\n");
Expand Down
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