biojava · josemduarte · Oct 29, 2021 · Jul 27, 2021 · Jul 31, 2021 · Aug 3, 2021
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,7 +20,7 @@ BioJava 6.0.0 (future release)
 * Removed `org.biojava.nbio.structure.io.mmtf.MmtfUtils.setUpBioJava()`
 * Removed from `org.biojava.nbio.structure.Chain` interface: `getParent()`, `setParent()`, `getAtomLigands()`, `getSwissprotId()`, `setSwissprotId()`, `getInternalChainID()`, `setInternalChainID()`, `getChainID()`, `setChainID()`
 * Removed from `org.biojava.nbio.structure.Structure` interface: `findChain()`, `getId()`, `setId()`, `getChainByPDB()`, `getCompoundById()`, `getResidueRanges()`, `getRanges()`
-* Removed from `org.biojava.nbio.structure.StructureTools` : `isNucleicAcid()`, `isProtein()`, `getPredominantGroupType()`, `isChainWaterOnly()`, `isChainPureNonPolymer()`
+* Removed from `org.biojava.nbio.structure.StructureTools` : `isNucleicAcid()`, `isProtein()`, `getPredominantGroupType()`, `isChainWaterOnly()`, `isChainPureNonPolymer()`, `getReducedStructure()`
 * Removed `org.biojava.nbio.structure.io.SandboxStyleStructureProvider`
 * In `org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser` made all methods private except `parseXMLfile`
 
@@ -32,14 +32,15 @@ BioJava 6.0.0 (future release)
 * Moved all chem-comp model classes from `org.biojava.nbio.structure.io.mmcif.chem` to `org.biojava.nbio.structure.chem`
 * Moved all chem-comp parsing classes from `org.biojava.nbio.structure.io.mmcif.chem` to `org.biojava.nbio.structure.io.cif`
 * Moved classes in `org.biojava.nbio.structure.io.mmcif` to `org.biojava.nbio.structure.chem`
-* Fixed `CRC64Checksum#public void update(byte[] b, int offset, int length)` to use
-the `length` argument correctly as specified in `java.util.zip.Checksum` interface.
-* Removed `DownloadChemCompProvider.useDefaultUrlLayout` with a more flexible system to provide templated URLs `DownloadChemCompProvider.setChemCompPathUrlTemplate()` 
-and `DownloadChemCompProvider.setServerBaseUrl()`
+* Fixed `CRC64Checksum#public void update(byte[] b, int offset, int length)` to use the `length` argument correctly as specified in `java.util.zip.Checksum` interface.
+* In `SubstructureIdentifier`, `StructureName`, `EcodDomain`, `ScopDomain` : `getPdbId()` returns `PdbId` object instead of `String`.
+* Removed `DownloadChemCompProvider.useDefaultUrlLayout` with a more flexible system to provide templated URLs `DownloadChemCompProvider.setChemCompPathUrlTemplate()` and `DownloadChemCompProvider.setServerBaseUrl()`
+* In `Structure` (and `StructureImple`), the accessor methods `String getPdbId()` and `setPdbId(String)` were previously depricated. They were revived in BioJava 6.0.0 but as `PdbId getPdbId()` and `setPdbId(PdbId)` instead.n
 
 ### Added
-* New keywords fields in `PDBHeader` class, populated by PDB and mmCIF parsers #946
+* New `keywords` field in `PDBHeader` class, populated by PDB and mmCIF parsers #946
 * OBO parsing now supports multiple altids, #960
+* New class `PdbId` that wrapps a PDB Identifier and handles conversion between current short PDBID format and upcoming extended PDBID format #930
 
 ### Fixed
 * Correct chain assignment to entities when parsing PDB/mmCIF without entity information (in cases with more than 3 chains per entity) #931

diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java
@@ -67,8 +67,7 @@ public void setUp() throws Exception {
 
 
 	@Test
-	public void test1a4wPDBFile() throws IOException
-	{
+	public void test1a4wPDBFile() throws IOException {
 
 		//		structure = null;
 

diff --git a/...va-integrationtest/src/test/java/org/biojava/nbio/structure/test/cath/CathDomainTest.java b/...va-integrationtest/src/test/java/org/biojava/nbio/structure/test/cath/CathDomainTest.java
@@ -20,6 +20,7 @@
  */
 package org.biojava.nbio.structure.test.cath;
 
+import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.cath.CathDomain;
 import org.biojava.nbio.structure.cath.CathFactory;
 import org.junit.Test;
@@ -33,9 +34,9 @@
  */
 public class CathDomainTest {
 	@Test
-	public void test() {
+	public void test() throws StructureException {
 		String id = "1qvrC03";
 		CathDomain domain = CathFactory.getCathDatabase().getDomainByCathId(id);
-		assertEquals("1qvr.C_332-400,C_514-540", domain.toCanonical().getIdentifier());
+		assertEquals("1QVR.C_332-400,C_514-540", domain.toCanonical().getIdentifier());
 	}
 }
diff --git a/...ava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java b/...ava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
@@ -83,7 +83,7 @@ private static int testVersion(String ecodVersion) throws IOException {
 			Atom[] ca1;
 			Structure struct;
 			try {
-				struct = cache.getStructure(d.getPdbId());
+				struct = cache.getStructure(d.getPdbId().getId());
 				ca1 = StructureTools.getRepresentativeAtomArray(struct);
 			} catch (IOException e) {
 				logger.error("Error getting structure for "+d.getDomainId(),e);

diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
@@ -23,13 +23,15 @@
 import java.awt.BorderLayout;
 import java.awt.Dimension;
 import java.io.IOException;
+import java.util.ArrayList;
 
 import javax.swing.Box;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JTabbedPane;
 import javax.swing.JTextField;
 
+import org.biojava.nbio.structure.PdbId;
 import org.biojava.nbio.structure.ResidueRange;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -106,30 +108,32 @@ public SelectPDBPanel(boolean show2PDBs) {
 	}
 
 	public StructureIdentifier getName1() {
-		String pdbId = f1.getText().trim();
+		String id = f1.getText().trim();
 		String chainId = c1.getText().trim();
 		String range = r1.getText().trim();
-
+
+		PdbId pdbId = new PdbId(id);
 		// Prefer range over chain
 		if( ! range.isEmpty() ) {
 			return new SubstructureIdentifier(pdbId, ResidueRange.parseMultiple(range));
 		} else if ( ! chainId.isEmpty() ){
 			return new SubstructureIdentifier(pdbId, ResidueRange.parseMultiple(chainId));
 		}
-		return new SubstructureIdentifier(pdbId);
+		return new SubstructureIdentifier(pdbId, new ArrayList<ResidueRange>());
 	}
 	public StructureIdentifier getName2() {
-		String pdbId = f2.getText().trim();
+		String id = f2.getText().trim();
 		String chainId = c2.getText().trim();
 		String range = r2.getText().trim();
-
+
+		PdbId pdbId = new PdbId(id);
 		// Prefer range over chain
 		if( ! range.isEmpty() ) {
 			return new SubstructureIdentifier(pdbId, ResidueRange.parseMultiple(range));
 		} else if ( ! chainId.isEmpty() ){
 			return new SubstructureIdentifier(pdbId, ResidueRange.parseMultiple(chainId));
 		}
-		return new SubstructureIdentifier(pdbId);
+		return new SubstructureIdentifier(pdbId, new ArrayList<ResidueRange>());
 	}
 	@Override
 	public Structure getStructure1() throws StructureException, IOException{

diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java
@@ -23,6 +23,7 @@
 package org.biojava.nbio.structure.gui.util;
 
 import org.biojava.nbio.structure.Chain;
+import org.biojava.nbio.structure.PdbId;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureImpl;
@@ -97,17 +98,17 @@ public PDBDirPanel() {
 
 
 	private Structure fromPDB(JTextField f, JTextField c) throws StructureException{
-		String pdb = f.getText();
+		String pdbIdString = f.getText();
 
 
-		if ( pdb.length() < 4) {
+		if ( pdbIdString.length() < 4) {
 			f.setText("!!!");
 			return null;
 		}
 
 		String chain = c.getText();
 		if ( debug )
-			System.out.println("file :" + pdb + " " +  chain);
+			System.out.println("file :" + pdbIdString + " " +  chain);
 		/// prepare structures
 
 		// load them from the file system
@@ -123,19 +124,18 @@ private Structure fromPDB(JTextField f, JTextField c) throws StructureException{
 		Structure tmp1 = new StructureImpl();
 
 		try {
-			Structure structure1 = reader.getStructureById(pdb);
+			Structure structure1 = reader.getStructureById(new PdbId(pdbIdString));
 
 			// no chain has been specified
 			// return whole structure
 			if (( chain == null) || (chain.length()==0)){
 				return structure1;
 			}
 			if ( debug)
-				System.out.println("using chain " + chain +  " for structure " + structure1.getPDBCode());
+				System.out.println("using chain " + chain +  " for structure " + structure1.getPdbId().getId());
 			Chain c1 = structure1.getPolyChainByPDB(chain);
-			tmp1.setPDBCode(structure1.getPDBCode());
 			tmp1.setPDBHeader(structure1.getPDBHeader());
-			tmp1.setPDBCode(structure1.getPDBCode());
+			tmp1.setPdbId(structure1.getPdbId());
 			tmp1.addChain(c1);
 			System.out.println("ok");
 

diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBServerPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBServerPanel.java
@@ -24,6 +24,7 @@
 package org.biojava.nbio.structure.gui.util;
 
 import org.biojava.nbio.structure.Chain;
+import org.biojava.nbio.structure.PdbId;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureImpl;
@@ -86,17 +87,17 @@ public PDBServerPanel() {
 
 
 	private Structure fromPDB(JTextField f, JTextField c) throws StructureException{
-		String pdb = f.getText();
+		String pdbIdString = f.getText();
 
 
-		if ( pdb.length() < 4) {
+		if ( pdbIdString.length() < 4) {
 			f.setText("!!!");
 			return null;
 		}
 
 		String chain = c.getText();
 		if ( debug )
-			System.out.println("file :" + pdb + " " +  chain);
+			System.out.println("file :" + pdbIdString + " " +  chain);
 		/// prepare structures
 
 		// load them from the file system
@@ -108,19 +109,18 @@ private Structure fromPDB(JTextField f, JTextField c) throws StructureException{
 		Structure tmp1 = new StructureImpl();
 
 		try {
-			Structure structure1 = reader.getStructureById(pdb);
+			Structure structure1 = reader.getStructureById(new PdbId(pdbIdString));
 
 			// no chain has been specified
 			// return whole structure
 			if (( chain == null) || (chain.length()==0)){
 				return structure1;
 			}
 			if ( debug)
-				System.out.println("using chain " + chain +  " for structure " + structure1.getPDBCode());
+				System.out.println("using chain " + chain +  " for structure " + structure1.getPdbId().getId());
 			Chain c1 = structure1.getPolyChainByPDB(chain);
-			tmp1.setPDBCode(structure1.getPDBCode());
 			tmp1.setPDBHeader(structure1.getPDBHeader());
-			tmp1.setPDBCode(structure1.getPDBCode());
+			tmp1.setPdbId(structure1.getPdbId());
 			tmp1.addChain(c1);
 			System.out.println("ok");
 

diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
@@ -22,23 +22,34 @@
 package org.biojava.nbio.structure.gui.util;
 
 
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.util.Arrays;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+import org.biojava.nbio.structure.ResidueRange;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.SubstructureIdentifier;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.structure.io.CifFileReader;
 import org.biojava.nbio.structure.io.PDBFileReader;
 import org.biojava.nbio.structure.io.StructureIOFile;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.swing.*;
-import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.io.File;
-import java.io.IOException;
-import java.net.URL;
-
 /** A JPanel to upload 2 custom PDB files.
  *
  * @author Andreas Prlic
@@ -59,16 +70,16 @@ public class PDBUploadPanel
 
 
 
-	private JComboBox fileType ;
+	private JComboBox<String> fileType ;
 
 	JTextField filePath1;
 	JTextField filePath2;
 	JTextField chain1;
 	JTextField chain2;
 
-	public static JComboBox getFileFormatSelect(){
-		JComboBox fileType = new JComboBox();
-			fileType = new JComboBox(new String[] {UserConfiguration.PDB_FORMAT,UserConfiguration.MMCIF_FORMAT});
+	public static JComboBox<String> getFileFormatSelect(){
+		JComboBox<String> fileType = new JComboBox<>();
+			fileType = new JComboBox<String>(new String[] {UserConfiguration.PDB_FORMAT,UserConfiguration.MMCIF_FORMAT});
 			fileType.setSelectedIndex(0);
 			fileType.setMaximumSize(new Dimension(10,50));
 
@@ -150,7 +161,10 @@ private Structure getStructure(JTextField filePath,JTextField chainId) throws St
 			throw new StructureException(e);
 		}
 
-		Structure reduced = StructureTools.getReducedStructure(s, chainId.getText());
+//		Structure reduced = StructureTools.getReducedStructure(s, chainId.getText());
+//		Structure reduced = new SubstructureIdentifier(s.getPdbId().getId()+"."+ chainId.getText()).reduce(s);  //TODO double check this
+		Structure reduced = new SubstructureIdentifier(s.getPdbId(),
+				Arrays.asList(new ResidueRange(chainId.getText(), (String) null, null))).reduce(s);
 
 		String fileURL = "";
 		try {
@@ -169,7 +183,7 @@ private Structure getStructure(JTextField filePath,JTextField chainId) throws St
 			e.printStackTrace();
 		}
 
-		reduced.setPDBCode(fileURL);
+		reduced.setPDBCode(fileURL);  //TODO FIXME This usage seems wrong and should be changed.
 		reduced.setName(fileURL);
 		return reduced;
 

diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
@@ -105,7 +105,6 @@
     		<artifactId>log4j-core</artifactId>
   		</dependency>
 		<!--  Testing related dependencies -->
-
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
@@ -117,6 +116,19 @@
 			<version>1.6</version>
 			<scope>test</scope>
 		</dependency>
+		<!-- Junit5 dependencies, defined in parent pom. -->
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-engine</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-params</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.junit.vintage</groupId>
+			<artifactId>junit-vintage-engine</artifactId>
+		</dependency>
 
 	</dependencies>
-Original file line number
+Diff line change
@@ Expand Up / @@ -67,8 +67,7 @@ public void setUp() throws Exception { @@
     	@Test
-    	public void test1a4wPDBFile() throws IOException
-    	{
+    	public void test1a4wPDBFile() throws IOException {
     		//		structure = null;
@@ Expand Down @@