Updating dssp urls to latest RCSB convention

josemduarte · josemduarte · commit 4bdd304dbb8e · 2017-07-05T16:40:58.000-07:00
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);
