sbliven · Jun 18, 2018 · Jun 4, 2018 · Jun 4, 2018 · Jun 8, 2018 · Jun 8, 2018
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -636,6 +636,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
 
 	protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{
 //        System.out.println("downloading " + remoteURL + " to: " + localFile);
+		LOGGER.info("Downloaded file {} to local file {}", remoteURL, localFile);
 
 		long timeS = System.currentTimeMillis();
 		File tempFile  = File.createTempFile(FileDownloadUtils.getFilePrefix(localFile), "."+ FileDownloadUtils.getFileExtension(localFile));
@@ -665,7 +666,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx
 			disp = disp / 1024.0;
 		}
 		long timeE = System.currentTimeMillis();
-		LOGGER.info("Downloaded file {} ({}) to local file {} in {} sec.", remoteURL, String.format("%.1f",disp) + unit, localFile, (timeE - timeS)/1000);
+		LOGGER.info("Downloaded {} in {} sec. to {}", String.format("%.1f",disp) + unit, (timeE - timeS)/1000, localFile);
 	}
 
 	private boolean domainDescriptionFileAvailable(){

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -127,6 +127,9 @@ public static enum FetchBehavior {
 
 	protected static final String lineSplit = System.getProperty("file.separator");
 
+	/** Minimum size for a valid structure file (CIF or PDB), in bytes */
+	public static final long MIN_PDB_FILE_SIZE = 40;  // Empty gzip files are 20bytes. Add a few more for buffer.
+
 	private File path;
 	private List<String> extensions;
 
@@ -687,6 +690,14 @@ public File getLocalFile(String pdbId) {
 				for(String ex : getExtensions() ){
 					File f = new File(searchdir,prefix + pdbId.toLowerCase() + ex) ;
 					if ( f.exists()) {
+						// delete files that are too short to have contents
+						if( f.length() < MIN_PDB_FILE_SIZE ) {
+							boolean success = f.delete();
+							if( ! success) {
+								return null;
+							}
+							assert(!f.exists());
+						}
 						return f;
 					}
 				}

diff --git a/...ava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java b/...ava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
@@ -68,9 +68,8 @@ public static ChemComp getChemComp(String recordName){
 	 * again. Note that this change can have unexpected behavior of
 	 * code executed afterwards.
 	 * <p>
-	 * Changing the provider does not reset the cache, so Chemical
-	 * Component definitions already downloaded from previous providers
-	 * will be used. To reset the cache see {@link #getCache()).
+	 * Changing the provider also resets the cache, so any groups
+	 * previously accessed will be re-downloaded and reread.
 	 *
 	 * @param provider
 	 */
@@ -84,6 +83,13 @@ public static void setChemCompProvider(ChemCompProvider provider) {
 	public static ChemCompProvider getChemCompProvider(){
 		return chemCompProvider;
 	}
+
+	/**
+	 * Force the cache to be reset.
+	 */
+	public static void clearCache() {
+		cache.clear();
+	}
 
 	public static Group getGroupFromChemCompDictionary(String recordName) {
 

diff --git a/...structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/...structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
@@ -42,6 +42,7 @@
 import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.align.util.HTTPConnectionTools;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
+import org.biojava.nbio.structure.io.LocalPDBDirectory;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -85,6 +86,8 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 		protectedIDs.add("AUX");
 		protectedIDs.add("NUL");
 	}
+
+	private static ChemCompProvider fallback = null; // Fallback provider if the download fails
 
 	/** by default we will download only some of the files. User has to request that all files should be downloaded...
 	 *
@@ -272,7 +275,10 @@ public  ChemComp getChemComp(String recordName) {
 
 				ChemComp chemComp = dict.getChemComp(recordName);
 
-				return chemComp;
+				// May be null if the file was corrupt. Fall back on ReducedChemCompProvider in that case
+				if(chemComp != null) {
+					return chemComp;
+				}
 
 			} catch (IOException e) {
 
@@ -296,9 +302,11 @@ public  ChemComp getChemComp(String recordName) {
 
 		// see https://github.com/biojava/biojava/issues/315
 		// probably a network error happened. Try to use the ReducedChemCOmpProvider
-		ReducedChemCompProvider reduced = new ReducedChemCompProvider();
+		if( fallback == null) {
+			fallback = new ReducedChemCompProvider();
+		}
 
-		return reduced.getChemComp(recordName);
+		return fallback.getChemComp(recordName);
 
 	}
 
@@ -337,6 +345,12 @@ private static  boolean fileExists(String recordName){
 
 		File f = new File(fileName);
 
+		// delete files that are too short to have contents
+		if( f.length() < LocalPDBDirectory.MIN_PDB_FILE_SIZE ) {
+			f.delete();
+			return false;
+		}
+
 		return f.exists();
 
 	}

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -328,7 +328,13 @@ public void newAtomSite(AtomSite atom) {
 
 		String recordName    = atom.getGroup_PDB();
 		String residueNumberS = atom.getAuth_seq_id();
-		Integer residueNrInt = Integer.parseInt(residueNumberS);
+		Integer residueNrInt;
+		if(residueNumberS != null) {
+			residueNrInt = Integer.parseInt(residueNumberS);
+		} else {
+			String label_seq_id = atom.getLabel_seq_id();
+			residueNrInt = Integer.parseInt(label_seq_id);
+		}
 
 		// the 3-letter name of the group:
 		String groupCode3    = atom.getLabel_comp_id();

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -212,6 +212,9 @@ public void parse(BufferedReader buf)
 
 		// the first line is a data_PDBCODE line, test if this looks like a mmcif file
 		line = buf.readLine();
+		while( line != null && (line.isEmpty() || line.startsWith(COMMENT_CHAR))) {
+			line = buf.readLine();
+		}
 		if (line == null || !line.startsWith(MMCIF_TOP_HEADER)){
 			logger.error("This does not look like a valid mmCIF file! The first line should start with 'data_', but is: '" + line+"'");
 			triggerDocumentEnd();

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/FileDownloadUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/FileDownloadUtils.java
@@ -21,9 +21,6 @@
  */
 package org.biojava.nbio.structure.io.util;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -36,6 +33,15 @@
 import java.nio.channels.Channels;
 import java.nio.channels.FileChannel;
 import java.nio.channels.ReadableByteChannel;
+import java.nio.file.FileVisitResult;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.SimpleFileVisitor;
+import java.nio.file.attribute.BasicFileAttributes;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class FileDownloadUtils {
 
@@ -240,6 +246,41 @@ public static URLConnection prepareURLConnection(String url, int timeout) throws
 		connection.setConnectTimeout(timeout);
 		return connection;
 	}
+
+	/**
+	 * Recursively delete a folder & contents
+	 *
+	 * @param dir directory to delete
+	 */
+	public static void deleteDirectory(Path dir) throws IOException {
+		if(dir == null || !Files.exists(dir))
+			return;
+		Files.walkFileTree(dir, new SimpleFileVisitor<Path>() {
+	        @Override
+	        public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
+	            Files.delete(file);
+	            return FileVisitResult.CONTINUE;
+	        }
+
+	        @Override
+	        public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOException {
+	            if (e != null) {
+	                throw e;
+	            }
+	            Files.delete(dir);
+	            return FileVisitResult.CONTINUE;
+	        }
+	    });
+	}
+	/**
+	 * Recursively delete a folder & contents
+	 *
+	 * @param dir directory to delete
+	 */
+	public static void deleteDirectory(String dir) throws IOException {
+		deleteDirectory(Paths.get(dir));
+	}
+
 
 	public static void main(String[] args) {
 		String url;