Refactoring of Compound to EntityInfo

abradle · abradle · commit 4a41270d7750 · 2016-03-31T10:21:29.000-07:00
diff --git a/biojava-structure/src/main/java/demo/DemoMMCIFReader.java b/biojava-structure/src/main/java/demo/DemoMMCIFReader.java
@@ -102,7 +102,7 @@ public void loadFromDirectAccess(){
 			System.out.println(h.getAtomSequence());
 			System.out.println(h.getAtomGroups(GroupType.HETATM));
 
-			System.out.println("Compounds: " + s.getEntityInfos());
+			System.out.println("Entities: " + s.getEntityInfos());
 
 		} catch (Exception e) {
 			e.printStackTrace();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
@@ -191,16 +191,16 @@ public interface Chain {
 	public int getSeqResLength();
 
 	/**
-	 * Sets the Compound
-	 * @param compound the Compound
+	 * Sets the Entity information
+	 * @param entityInfo the EntityInfo
 	 * @see #getEntityInfo()
 	*/
-	public void setEntityInfo(EntityInfo compound);
+	public void setEntityInfo(EntityInfo entityInfo);
 
 	/**
-	 * Returns the Compound for this chain.
+	 * Returns the EntityInfo for this chain.
 	 *
-	 * @return the Compound object
+	 * @return the EntityInfo object
 	 * @see #setEntityInfo(EntityInfo)
 	 */
 	public EntityInfo getEntityInfo();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
@@ -157,7 +157,7 @@ public Object clone() {
 		n.setChainID( getChainID());
 		n.setSwissprotId ( getSwissprotId());
 
-		// NOTE the Compound will be reset at the parent level (Structure) if cloning is happening from parent level
+		// NOTE the EntityInfo will be reset at the parent level (Structure) if cloning is happening from parent level
 		// here we don't deep-copy it and just keep the same reference, in case the cloning is happening at the Chain level only
 		n.setEntityInfo(this.mol);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
@@ -523,14 +523,14 @@ public Chain getChainByPDB(String chainId, int modelnr)
 	/**
 	 * Get all the EntityInfo for this Structure.
 	 *
-	 * @return a list of Compounds
+	 * @return a list of EntityInfos
 	 */
 	public List<EntityInfo> getEntityInfos();
 
 	/**
 	 * Add an EntityInfo to this Structure
 	 */
-	public void addEntityInfo(EntityInfo compound);
+	public void addEntityInfo(EntityInfo entityInfo);
 
 	/**
 	 * Set the list of database references for this structure
@@ -550,7 +550,7 @@ public Chain getChainByPDB(String chainId, int modelnr)
 	 * Request a particular entity by its entity id (mol id in legacy PDB format)
 	 *
 	 * @param entityId
-	 * @return a compound
+	 * @return a entityInfo
 	 * @deprecated use {@link #getEntityById(int)} instead
 	 */
 	public EntityInfo getCompoundById(int entityId);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -57,7 +57,7 @@ public class StructureImpl implements Structure, Serializable {
 	private List<List<Chain>> models;
 
 	private List<Map <String,Integer>> connections ;
-	private List<EntityInfo> compounds;
+	private List<EntityInfo> entityInfos;
 	private List<DBRef> dbrefs;
 	private List<Bond> ssbonds;
 	private List<Site> sites;
@@ -79,7 +79,7 @@ public StructureImpl() {
 		models         = new ArrayList<List<Chain>>();
 		name           = "";
 		connections    = new ArrayList<Map<String,Integer>>();
-		compounds      = new ArrayList<EntityInfo>();
+		entityInfos      = new ArrayList<EntityInfo>();
 		dbrefs         = new ArrayList<DBRef>();
 		pdbHeader      = new PDBHeader();
 		ssbonds        = new ArrayList<Bond>();
@@ -167,27 +167,27 @@ public Structure clone() {
 
 		}
 
-		// deep-copying of Compounds is tricky: there's cross references also in the Chains
-		// beware: if we copy the compounds we would also need to reset the references to compounds in the individual chains
-		List<EntityInfo> newCompoundList = new ArrayList<EntityInfo>();
-		for (EntityInfo compound:this.compounds) {
-			EntityInfo newCompound = new EntityInfo(compound); // this sets everything but the chains
-			for (String chainId:compound.getChainIds()) {
+		// deep-copying of entityInfofos is tricky: there's cross references also in the Chains
+		// beware: if we copy the entityInfos we would also need to reset the references to entityInfos in the individual chains
+		List<EntityInfo> newEntityInfoList = new ArrayList<EntityInfo>();
+		for (EntityInfo entityInfo : this.entityInfos) {
+			EntityInfo newEntityInfo = new EntityInfo(entityInfo); // this sets everything but the chains
+			for (String chainId:entityInfo.getChainIds()) {
 
 					for (int modelNr=0;modelNr<n.nrModels();modelNr++) {
 						try {
 							Chain newChain = n.getChainByPDB(chainId,modelNr);
-							newChain.setEntityInfo(newCompound);
-							newCompound.addChain(newChain);
+							newChain.setEntityInfo(newEntityInfo);
+							newEntityInfo.addChain(newChain);
 						} catch (StructureException e) {
 							// this actually happens for structure 1msh, which has no chain B for model 29 (clearly a deposition error)
-							logger.warn("Could not find chain id "+chainId+" of model "+modelNr+" while cloning compound "+compound.getMolId()+". Something is wrong!");
+							logger.warn("Could not find chain id "+chainId+" of model "+modelNr+" while cloning entityInfo "+entityInfo.getMolId()+". Something is wrong!");
 						}
 					}
 			}
-			newCompoundList.add(newCompound);
+			newEntityInfoList.add(newEntityInfo);
 		}
-		n.setEntityInfos(newCompoundList);
+		n.setEntityInfos(newEntityInfoList);
 		// TODO ssbonds are complicated to clone: there are deep references inside Atom objects, how would we do it? - JD 2016-03-03
 
 		return n ;
@@ -464,7 +464,7 @@ public String toString(){
 			str.append(dbref.toPDB()).append(newline);
 		}
 		str.append("Molecules: ").append(newline);
-		for (EntityInfo mol : compounds) {
+		for (EntityInfo mol : entityInfos) {
 			str.append(mol).append(newline);
 		}
 
@@ -665,33 +665,33 @@ public boolean hasChain(String chainId) {
 	/** {@inheritDoc} */
 	@Override
 	public void setEntityInfos(List<EntityInfo> molList){
-		this.compounds = molList;
+		this.entityInfos = molList;
 	}
 
 	/** {@inheritDoc} */
 	@Override
-	public void addEntityInfo(EntityInfo compound) {
-		this.compounds.add(compound);
+	public void addEntityInfo(EntityInfo entityInfo) {
+		this.entityInfos.add(entityInfo);
 	}
 
 	/** {@inheritDoc} */
 	@Override
 	public List<EntityInfo> getEntityInfos() {
-		// compounds are parsed from the PDB/mmCIF file normally
-		// but if the file is incomplete, it won't have the Compounds information and we try
+		// entity information is parsed from the PDB/mmCIF file normally
+		// but if the file is incomplete, it won't have the entityInfo information and we try
 		// to guess it from the existing seqres/atom sequences
-		if (compounds==null || compounds.isEmpty()) {
+		if (entityInfos==null || entityInfos.isEmpty()) {
 			EntityFinder cf = new EntityFinder(this);
-			this.compounds = cf.findEntities();
+			this.entityInfos = cf.findEntities();
 
 			// now we need to set references in chains:
-			for (EntityInfo compound:compounds) {
+			for (EntityInfo compound:entityInfos) {
 				for (Chain c:compound.getChains()) {
 					c.setEntityInfo(compound);
 				}
 			}
 		}
-		return compounds;
+		return entityInfos;
 	}
 
 	/** {@inheritDoc} */
@@ -703,7 +703,7 @@ public EntityInfo getCompoundById(int molId) {
 	/** {@inheritDoc} */
 	@Override
 	public EntityInfo getEntityById(int entityId) {
-		for (EntityInfo mol : this.compounds){
+		for (EntityInfo mol : this.entityInfos){
 			if (mol.getMolId()==entityId){
 				return mol;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -1078,7 +1078,7 @@ public static final Structure getReducedStructure(Structure s,
 			for (EntityInfo comp : s.getEntityInfos()) {
 				if (comp.getChainIds() != null
 						&& comp.getChainIds().contains(c.getChainID())) {
-					// found matching compound. set description...
+					// found matching entity info. set description...
 					newS.getPDBHeader().setDescription(
 							"Chain " + c.getChainID() + " of " + s.getPDBCode()
 									+ " " + comp.getDescription());
