A new dome for quat symmetry detection

josemduarte · josemduarte · commit 885600670be7 · 2017-10-05T15:30:44.000-07:00
diff --git a/biojava-structure/src/main/java/demo/DemoSymmetry.java b/biojava-structure/src/main/java/demo/DemoSymmetry.java
@@ -0,0 +1,96 @@
+package demo;
+
+import java.util.List;
+
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.cluster.SubunitCluster;
+import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+
+/**
+ * A demo on how to use the quaternary symmetry detection algorithms.
+ * 
+ * @author Jose Duarte
+ *
+ */
+public class DemoSymmetry {
+
+	public static void main(String[] args) throws Exception {
+		
+		System.out.println("Getting all bioassemblies");
+		List<Structure> bioAssemblies = StructureIO.getBiologicalAssemblies("4hhb");
+		
+		for (Structure bioAssembly : bioAssemblies) {			
+			findQuatSym(bioAssembly);			
+		}
+		
+
+	}
+
+	private static void findQuatSym(Structure bioAssembly) throws StructureException {
+
+		QuatSymmetryParameters symmParams = new QuatSymmetryParameters();		
+		
+		System.out.println("GLOBAL SYMMETRY, NO CLUSTERING");
+		SubunitClustererParameters clusterParams = new SubunitClustererParameters();
+		clusterParams.setSequenceIdentityThreshold(0.95);
+		clusterParams.setRmsdThreshold(0.0);
+
+		QuatSymmetryResults globalResults = QuatSymmetryDetector.calcGlobalSymmetry(bioAssembly, symmParams, clusterParams);	
+		
+		
+		
+		System.out.println(globalResults.getSymmetry() + (globalResults.isPseudosymmetric()?"(pseudo)":""));
+		
+		System.out.println("There are "+globalResults.getSubunitClusters().size()+" subunit clusters");
+		int i = 1;
+		for (SubunitCluster suc : globalResults.getSubunitClusters()) {
+			//System.out.println(suc.getClustererMethod());
+			MultipleAlignment ma = suc.getMultipleAlignment();
+						
+			System.out.printf("Cluster %d (clustered by %s), RMSD = %4.2f\n", i, suc.getClustererMethod(), ma.getScore("RMSD"));
+			
+			i++;
+		}
+
+		System.out.println("\nGLOBAL SYMMETRY, WITH CLUSTERING (PSEUDO-SYMMETRY)");
+		clusterParams = new SubunitClustererParameters();
+		// we can either set sequence identity to 40% or rmsd to 2, both would have the same effect of clustering the alpha/beta subunits together
+		clusterParams.setSequenceIdentityThreshold(0.40);
+		clusterParams.setRmsdThreshold(0.0); 
+
+		globalResults = QuatSymmetryDetector.calcGlobalSymmetry(bioAssembly, symmParams, clusterParams);	
+		
+		
+		
+		System.out.println(globalResults.getSymmetry() + (globalResults.isPseudosymmetric()?"(pseudo)":""));
+		
+		System.out.println("There are "+globalResults.getSubunitClusters().size()+" subunit clusters");
+		i = 1;
+		for (SubunitCluster suc : globalResults.getSubunitClusters()) {
+			//System.out.println(suc.getClustererMethod());
+			MultipleAlignment ma = suc.getMultipleAlignment();
+						
+			System.out.printf("Cluster %d (clustered by %s), RMSD = %4.2f\n", i, suc.getClustererMethod(), ma.getScore("RMSD"));
+			
+			i++;
+		}
+
+		
+		System.out.println("\n\nLOCAL SYMMETRIES");
+		List<QuatSymmetryResults> localResults = QuatSymmetryDetector.calcLocalSymmetries(bioAssembly, symmParams, clusterParams);
+
+		System.out.println("Number of local symmetries: "+localResults.size());
+		
+		for (QuatSymmetryResults results : localResults) {
+			System.out.println(results.getSymmetry()+" "+results.getStoichiometry());
+		}
+
+
+	}
+}
