SimonyanG
diff --git a/‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java‎
Lines changed: 41 additions & 15 deletions b/‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java‎
Lines changed: 41 additions & 15 deletions
@@ -54,7 +54,7 @@
 import org.biojava.nbio.structure.Author;
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.Compound;
+import org.biojava.nbio.structure.EntityInfo;
 import org.biojava.nbio.structure.DBRef;
 import org.biojava.nbio.structure.Element;
 import org.biojava.nbio.structure.Group;
@@ -179,8 +179,8 @@ public class PDBFileParser  {
 
 	private boolean isLastCompndLine = false;
 	private boolean isLastSourceLine = false;
-	private Compound current_compound;
-	private List<Compound> compounds = new ArrayList<Compound>();
+	private EntityInfo current_compound;
+	private List<EntityInfo> compounds = new ArrayList<EntityInfo>();
 	private HashMap<Integer,List<String>> compoundMolIds2chainIds = new HashMap<Integer, List<String>>();
 	private List<String> compndLines = new ArrayList<String>();
 	private List<String> sourceLines = new ArrayList<String>();
@@ -1012,7 +1012,7 @@ private void compndValueSetter(String field, String value) {
 
 				logger.debug("Initialising new Compound with mol_id {}", i);
 
-				current_compound = new Compound();
+				current_compound = new EntityInfo();
 
 				current_compound.setMolId(i);
 
@@ -1027,7 +1027,7 @@ private void compndValueSetter(String field, String value) {
 		}
 
 		if (field.equals("MOLECULE:")) {
-			current_compound.setMolName(value);
+			current_compound.setDescription(value);
 
 		}
 		if (field.equals("CHAIN:")) {
@@ -2758,11 +2758,37 @@ else if ( params.isParseSecStruc()) {
 		if ( params.isParseSecStruc() && !params.isHeaderOnly())
 			setSecStruc();
 
+		// Now correct the alternate location group
+		correctAltLocGroups();
 
 		return structure;
 
 			}
+	
+	
+	/**
+	 * Ensure that all the alt loc groups have all the atoms in the main group
+	 */
+	private void correctAltLocGroups() {
+		for (int i =0; i< structure.nrModels() ; i++){
+			for (Chain chain : structure.getModel(i)) {
+				for (Group group : chain.getAtomGroups()) {
+					for (Group altLocGroup : group.getAltLocs()) { 
+						for ( Atom groupAtom : group.getAtoms()) {
+							// If this alt loc doesn't have this atom
+							if (! altLocGroup.hasAtom(groupAtom.getName())) {
+								altLocGroup.addAtom(groupAtom);
+							}
+						}
+					}
+				}
+			}
+		}
+	}
 
+	/**
+	 * Add the charges to the Structure
+	 */
 	private void addCharges() {
 		ChargeAdder adder = new ChargeAdder(structure);
 		adder.addCharges();
@@ -2789,7 +2815,7 @@ private void makeCompounds(List<String> compoundList,
 		//		System.out.println("[makeCompounds] adding sources to compounds from sourceLines");
 		// since we're starting again from the first compound, reset it here
 		if ( compounds.size() == 0){
-			current_compound = new Compound();
+			current_compound = new EntityInfo();
 		} else {
 			current_compound = compounds.get(0);
 		}
@@ -2919,7 +2945,7 @@ private void triggerEndFileChecks(){
 
 		// to make sure we have Compounds linked to chains, we call getCompounds() which will lazily initialise the
 		// compounds using heuristics (see CompoundFinder) in the case that they were not explicitly present in the file
-		structure.getCompounds();
+		structure.getEntityInformation();
 	}
 
 	private void setSecStruc(){
@@ -3002,15 +3028,15 @@ private void setSecElement(List<Map<String,String>> secList, String assignment,
 	}
 
 
-	/** After the parsing of a PDB file the {@link Chain} and  {@link Compound}
+	/** After the parsing of a PDB file the {@link Chain} and  {@link EntityInfo}
 	 * objects need to be linked to each other.
 	 *
 	 * @param s the structure
 	 */
 	public void linkChains2Compound(Structure s){
 
 
-		for(Compound comp : compounds){
+		for(EntityInfo comp : compounds){
 			List<Chain> chains = new ArrayList<Chain>();
 			List<String> chainIds = compoundMolIds2chainIds.get(comp.getMolId());
 			if ( chainIds == null)
@@ -3036,7 +3062,7 @@ public void linkChains2Compound(Structure s){
 		}
 
 		if ( compounds.size() == 1) {
-			Compound comp = compounds.get(0);
+			EntityInfo comp = compounds.get(0);
 			if ( compoundMolIds2chainIds.get(comp.getMolId()) == null){
 				List<Chain> chains = s.getChains(0);
 				if ( chains.size() == 1) {
@@ -3047,7 +3073,7 @@ public void linkChains2Compound(Structure s){
 			}
 		}
 
-		for (Compound comp: compounds){
+		for (EntityInfo comp: compounds){
 			if ( compoundMolIds2chainIds.get(comp.getMolId()) == null) {
 				// could not link to chain
 				// TODO: should this be allowed to happen?
@@ -3073,7 +3099,7 @@ public void linkChains2Compound(Structure s){
 			for (Chain c: s.getChains()) {
 				if (c.getCompound() == null) {
 
-					Compound compound = new Compound();
+					EntityInfo compound = new EntityInfo();
 					compound.addChain(c);
 					compound.setMolId(findMaxCompoundId(compounds)+1);
 					c.setCompound(compound);
@@ -3085,13 +3111,13 @@ public void linkChains2Compound(Structure s){
 		}
 	}
 
-	private static int findMaxCompoundId(List<Compound> compounds) {
+	private static int findMaxCompoundId(List<EntityInfo> compounds) {
 
 		return
 
-		Collections.max(compounds, new Comparator<Compound>() {
+		Collections.max(compounds, new Comparator<EntityInfo>() {
 			@Override
-			public int compare(Compound o1, Compound o2) {
+			public int compare(EntityInfo o1, EntityInfo o2) {
 				return new Integer(o1.getMolId()).compareTo(o2.getMolId());
 			}
 		}).getMolId();