Upgrading to biojava 5

eppic-cli/pom.xml

@@ -8,7 +8,7 @@
 	<artifactId>eppic-cli</artifactId>
 
 	<properties>
-		<biojava.version>4.2.10</biojava.version>
+		<biojava.version>5.0.0</biojava.version>
 	</properties>
 
 	<repositories>
@@ -261,16 +261,7 @@
 
 			<plugin>
 				<artifactId>maven-surefire-plugin</artifactId>
-				<version>2.19.1</version>
-				<configuration>
-
-					<excludes>
-						<!-- we exclude by default the long tests, they will only be 
-							executed if explicitly called -->
-						<exclude>**/TestLargeStructures.java</exclude>
-
-					</excludes>
-				</configuration>
+				<version>2.21.0</version>
 			</plugin>
 
 			<!-- Buildnumber plugin to get the git SHA hash -->

eppic-cli/src/main/java/eppic/ChainEvolContext.java

@@ -14,9 +14,8 @@
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Compound;
+import org.biojava.nbio.structure.EntityInfo;
 import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.StructureTools;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.xml.sax.SAXException;
@@ -105,7 +104,7 @@ public String toString() {
 
 	private boolean isProtein;
 
-	private Compound compound;
+	private EntityInfo entity;
 
 
 	/**
@@ -122,26 +121,26 @@ public ChainEvolContext(ChainEvolContextList parent, String sequence, String seq
 		this.searchWithFullUniprot = true;
 		this.queryWarnings = new ArrayList<String>();
 		this.isProtein = true;
-		this.compound = null;
+		this.entity = null;
 	}
 
 	/**
 	 * Construct a ChainEvolContext from a Chain
 	 * @param parent
 	 * @param compound
 	 */
-	public ChainEvolContext(ChainEvolContextList parent, Compound compound) {
+	public ChainEvolContext(ChainEvolContextList parent, EntityInfo compound) {
 		this.parent = parent;
 		Chain chain = compound.getRepresentative();
 
-		this.sequenceId = chain.getChainID();
+		this.sequenceId = chain.getName();
 		this.hasQueryMatch = false;
 		this.searchWithFullUniprot = true;
 		this.queryWarnings = new ArrayList<String>();
 
-		this.isProtein = StructureTools.isProtein(chain);
+		this.isProtein = chain.isProtein();
 
-		this.compound = compound;
+		this.entity = compound;
 
 		this.pdbToUniProtMapper = new PdbToUniProtMapper(compound);
 
@@ -156,8 +155,8 @@ public boolean isProtein() {
 		return isProtein;
 	}
 
-	public Compound getCompound() { 
-		return compound;
+	public EntityInfo getCompound() { 
+		return entity;
 	}
 
 	/**
@@ -526,13 +525,13 @@ public void blastForHomologs(EppicParams params)
 		if (searchMode==HomologsSearchMode.GLOBAL) {
 
 			LOGGER.info("Using full UniProt sequence {} {}-{} for blast search (entity {})",
-					query.getUniId(), queryInterv.beg, queryInterv.end, compound.getMolId());
+					query.getUniId(), queryInterv.beg, queryInterv.end, entity.getMolId());
 
 			searchWithFullUniprot = true;
 		} else if (searchMode==HomologsSearchMode.LOCAL) {
 
 			LOGGER.info("Using UniProt {} subsequence {}-{} for blast search (entity {})",
-					query.getUniId(), queryInterv.beg, queryInterv.end, compound.getMolId());
+					query.getUniId(), queryInterv.beg, queryInterv.end, entity.getMolId());
 			searchWithFullUniprot = false;			
 		} 
 

eppic-cli/src/main/java/eppic/ChainEvolContextList.java

@@ -7,9 +7,9 @@
 import java.util.List;
 import java.util.TreeMap;
 
-import org.biojava.nbio.structure.Compound;
+import org.biojava.nbio.structure.EntityInfo;
+import org.biojava.nbio.structure.EntityType;
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -66,14 +66,17 @@ public ChainEvolContextList(Structure pdb, EppicParams params) throws SQLExcepti
 			this.useLocalUniprot = false;
 		}
 
-		for (Compound chainCluster:pdb.getCompounds()) {
-
-			// in mmCIF files some sugars are annotated as compounds with no chains linked to them, e.g. 3s26
-			if (chainCluster.getChains().isEmpty()) continue;
-
-			ChainEvolContext cec = new ChainEvolContext(this, chainCluster);
-
-			cecs.put(cec.getSequenceId(), cec);
+		for (EntityInfo chainCluster:pdb.getEntityInfos()) {
+
+			if (chainCluster.getType() == EntityType.POLYMER) {
+
+				// in mmCIF files some sugars are annotated as compounds with no chains linked to them, e.g. 3s26
+				if (chainCluster.getChains().isEmpty()) continue;
+
+				ChainEvolContext cec = new ChainEvolContext(this, chainCluster);
+
+				cecs.put(cec.getSequenceId(), cec);
+			}
 		}
 
 	}
@@ -115,13 +118,8 @@ public void addChainEvolContext(String representativeChain, ChainEvolContext cec
 	 * @return
 	 */
 	public ChainEvolContext getChainEvolContext(String pdbChainCode) {
-		try {
-			Compound compound = pdb.getChainByPDB(pdbChainCode).getCompound();
-			return cecs.get( compound.getRepresentative().getChainID() );
-		} catch (StructureException e) {
-			LOGGER.error("Unexpected exception",e);
-			return null;
-		}
+		EntityInfo compound = pdb.getPolyChainByPDB(pdbChainCode).getEntityInfo();
+		return cecs.get( compound.getRepresentative().getName() );
 	}
 
 	/**