New bioassembly demo

josemduarte · josemduarte · commit d6c1fb353ef6 · 2017-10-04T16:51:39.000-07:00
diff --git a/biojava-structure/src/main/java/demo/DemoBioAssemblies.java b/biojava-structure/src/main/java/demo/DemoBioAssemblies.java
@@ -0,0 +1,48 @@
+package demo;
+
+import java.util.List;
+
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureIO;
+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;
+
+public class DemoBioAssemblies {
+
+	public static void main(String[] args) throws Exception {
+		
+		// 1st method: get 1 bioassembly at a time, parses the file each time
+		System.out.println("Getting one bioassembly at a time");
+		Structure asymUnit = StructureIO.getStructure("2trx");
+		System.out.println("Number of bioassemblies: "+asymUnit.getPDBHeader().getNrBioAssemblies());
+
+		for (int id = 1; id<=asymUnit.getPDBHeader().getNrBioAssemblies(); id++) {
+			Structure bioAssembly = StructureIO.getBiologicalAssembly("2trx", id);
+			findQuatSym(bioAssembly);
+		}
+
+		
+		// 2nd method: get all bioassemblies at once, parses the file only once
+		System.out.println("Getting all bioassemblies");
+		List<Structure> bioAssemblies = StructureIO.getBiologicalAssemblies("2trx");
+		
+		for (Structure bioAssembly : bioAssemblies) {			
+			findQuatSym(bioAssembly);			
+		}
+		
+
+	}
+
+	private static void findQuatSym(Structure bioAssembly) {
+		SubunitClustererParameters clusterParams = new SubunitClustererParameters();
+		QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
+		QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
+				bioAssembly, symmParams, clusterParams);
+
+		// C2 symmetry non pseudosymmetric
+		System.out.println(symmetry.getSymmetry() +" "+ symmetry.getStoichiometry());
+
+	}
+}
