Fixed a bug in reconstructing the bioassembly from pdb format.

josemduarte · josemduarte · commit 38edbb76541f · 2016-05-18T19:51:42.000-07:00
Fixed also compilation error. One test still fails.
diff --git a/biojava-structure-gui/src/main/java/demo/DemoShowBiolAssembly.java b/biojava-structure-gui/src/main/java/demo/DemoShowBiolAssembly.java
@@ -22,7 +22,6 @@
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
-import org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory;
 import org.biojava.nbio.structure.StructureIO;
 
 public class DemoShowBiolAssembly {
@@ -47,7 +46,6 @@ public static void main(String[] args){
 
 			// DNA 173D .. 2
 
-			BioUnitDataProviderFactory.setBioUnitDataProvider(BioUnitDataProviderFactory.pdbProviderClassName);
 			//Structure bioAssembly = StructureIO.getBiologicalAssembly("4A1I",2);
 
 			Structure bioAssembly = StructureIO.getBiologicalAssembly("1pdr",1);
diff --git a/biojava-structure/src/main/java/demo/DemoMMCIFReader.java b/biojava-structure/src/main/java/demo/DemoMMCIFReader.java
@@ -88,7 +88,7 @@ public void loadFromDirectAccess(){
 			List<Chain> hs = s.getNonPolyChainsByPDB("H");
 
 			Chain h = hs.get(0);
-			List<Group> ligands = h.getAtomLigands();
+			List<Group> ligands = h.getAtomGroups();
 
 			System.out.println("These ligands have been found in chain " + h.getName());
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyInfo.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyInfo.java
@@ -80,10 +80,6 @@ public void setTransforms(List<BiologicalAssemblyTransformation> transforms) {
 	 * @return
 	 */
 	public int getMacromolecularSize() {
-		for (BiologicalAssemblyTransformation bat:getTransforms()) {
-			//bat.get
-		}
-		//return getTransforms().size();
 		return macromolecularSize;
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -38,6 +38,7 @@
  *
  * @author Peter Rose
  * @author Andreas Prlic
+ * @author Jose Duarte
  *
  */
 public class BiologicalAssemblyBuilder {
@@ -87,8 +88,13 @@ public Structure rebuildQuaternaryStructure(Structure asymUnit, List<BiologicalA
 			} else {
 				Chain polyC = asymUnit.getPolyChainByPDB(transformation.getChainId());
 				List<Chain> nonPolyCs = asymUnit.getNonPolyChainsByPDB(transformation.getChainId());
-				chainsToTransform.add(polyC);
-				chainsToTransform.addAll(nonPolyCs);
+				Chain waterC = asymUnit.getWaterChainByPDB(transformation.getChainId());
+				if (polyC!=null) 
+					chainsToTransform.add(polyC);
+				if (!nonPolyCs.isEmpty()) 
+					chainsToTransform.addAll(nonPolyCs);
+				if (waterC!=null) 
+					chainsToTransform.add(waterC);
 			}
 			
 			for (Chain c: chainsToTransform) {
