Merge pull request #683 from josemduarte/bugfixes-4.2

josemduarte · web-flow · commit 9291fab5c9d9 · 2017-07-06T13:53:26.000-07:00
Updating to latest RCSB URLs for 4.2.x
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
@@ -67,7 +67,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 
 	public static final String CHEM_COMP_CACHE_DIRECTORY = "chemcomp";
 
-	public static final String SERVER_LOCATION = "http://www.rcsb.org/pdb/files/ligand/";
+	public static final String SERVER_LOCATION = "http://files.rcsb.org/ligands/download/";
 
 
 	private static File path;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
@@ -31,6 +31,7 @@
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.zip.GZIPInputStream;
 
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.ResidueNumber;
@@ -95,8 +96,11 @@ public static List<SecStrucState> fetch(String pdb,
 			Structure structure, boolean assign)
 					throws IOException, StructureException {
 
-		InputStream in = new URL("http://www.rcsb.org/pdb/files/"+
-				pdb+".dssp").openStream();
+		URL url = new URL("http://files.rcsb.org/dssp/" + 
+				pdb.toLowerCase().substring(1, 3) + "/" + 
+				pdb.toLowerCase() + "/" +
+				pdb + ".dssp.gz");
+		InputStream in = new GZIPInputStream(url.openStream());
 		Reader read = new InputStreamReader(in);
 		BufferedReader reader = new BufferedReader(read);
 		return generalParse(reader, structure, assign);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java
@@ -20,9 +20,9 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertEquals;
 
 import java.io.IOException;
 
@@ -55,7 +55,7 @@ public void test2JA5() throws IOException, StructureException {
 		// assertTrue(StructureTools.getNrAtoms(s1) == 0);
 
 		// SeqRes contains 15 chains, but since we cannot align Chain N to AtomGroups => 14.
-		assertTrue(s1.getChains().size() == 14);
+		assertEquals(14, s1.getChains().size());
 
 		Chain nChain = null;
 		try {
@@ -84,15 +84,15 @@ public void test2JA5noHeader() throws IOException, StructureException {
 		// This is not applicable anymore, we need to parse atoms to have chains to match.
 		assertTrue(StructureTools.getNrAtoms(s1) == 0);
 
-		// All 15 seqres chains will be store.
-		assertTrue(s1.getChains().size() == 15);
+		// 2ja5 has been remediated on March 2017, now it has 14 chains in seqres matching the 14 chains in atoms (chain N has been removed)
+		assertEquals(14, s1.getChains().size());
 
 		Chain nChain = null;
 		try {
 			nChain = s1.getChainByPDB("N");
 		} catch (StructureException e){
 			// this is expected here, since there is no chain N
 		}
-		assertNotNull(nChain);
+		assertNull(nChain);
 	}
 }
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
@@ -101,7 +101,7 @@ public void testURLParameters() throws StructureException, IOException {
 		assertEquals("wrong length for chainId=A", 94, StructureTools.getRepresentativeAtomArray(reduced).length);
 
 		try {
-			url = new URL("http://www.rcsb.org/pdb/files/1B8G.pdb.gz");
+			url = new URL("http://files.rcsb.org/download/1B8G.pdb.gz");
 			id = new URLIdentifier(url);
 
 			full = id.loadStructure(cache);
