biojava · josemduarte · Oct 29, 2021 · Jul 27, 2021 · Jul 31, 2021 · Aug 3, 2021
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
@@ -25,6 +25,7 @@
 package org.biojava.nbio.structure.test;
 
 import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.PDBId.PDBIdException;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.CifFileReader;
 import org.biojava.nbio.structure.io.FileParsingParameters;
@@ -67,7 +68,7 @@ public void setUp() throws Exception {
 
 
 	@Test
-	public void test1a4wPDBFile() throws IOException
+	public void test1a4wPDBFile() throws IOException, PDBIdException
 	{
 
 		//		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/...egrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java b/...egrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
@@ -39,6 +39,7 @@
 import java.util.regex.Pattern;
 
 import org.biojava.nbio.core.util.ConcurrencyTools;
+import org.biojava.nbio.structure.PDBId.PDBIdException;
 import org.biojava.nbio.structure.ResidueNumber;
 import org.biojava.nbio.structure.ResidueRange;
 import org.biojava.nbio.structure.StructureException;
@@ -155,7 +156,7 @@ private void matchNames(String pdbId,String[] expected,List<EcodDomain> actual)
 	}
 
 	@Test
-	public void testParsing() throws IOException {
+	public void testParsing() throws IOException, PDBIdException {
 		EcodDatabase ecod = EcodFactory.getEcodDatabase(VERSION);
 
 		String ecodId;

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 +23,16 @@
 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.PDBId.PDBIdException;
 import org.biojava.nbio.structure.ResidueRange;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -105,31 +108,33 @@ public SelectPDBPanel(boolean show2PDBs) {
 		this.add(vBox);
 	}
 
-	public StructureIdentifier getName1() {
-		String pdbId = f1.getText().trim();
+	public StructureIdentifier getName1() throws PDBIdException {
+		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();
+	public StructureIdentifier getName2() throws PDBIdException {
+		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
@@ -133,9 +133,9 @@ private Structure fromPDB(JTextField f, JTextField c) throws StructureException{
 			if ( debug)
 				System.out.println("using chain " + chain +  " for structure " + structure1.getPDBCode());
 			Chain c1 = structure1.getPolyChainByPDB(chain);
-			tmp1.setPDBCode(structure1.getPDBCode());
+//			tmp1.setPDBId(structure1.getPDBId());  // Isn't it a duplicate?
 			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
@@ -118,9 +118,9 @@ private Structure fromPDB(JTextField f, JTextField c) throws StructureException{
 			if ( debug)
 				System.out.println("using chain " + chain +  " for structure " + structure1.getPDBCode());
 			Chain c1 = structure1.getPolyChainByPDB(chain);
-			tmp1.setPDBCode(structure1.getPDBCode());
+//			tmp1.setPDBId(structure1.getPDBId());  //Isn't it duplicate?
 			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
@@ -66,9 +77,9 @@ public class PDBUploadPanel
 	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);  //FIXME This usage seems wrong and should be changed.
 		reduced.setName(fileURL);
 		return reduced;
 

diff --git a/biojava-structure/src/main/java/demo/DemoMmcifToPdbConverter.java b/biojava-structure/src/main/java/demo/DemoMmcifToPdbConverter.java
@@ -22,6 +22,7 @@
 package demo;
 
 import org.biojava.nbio.structure.Chain;
+import org.biojava.nbio.structure.PDBId.PDBIdException;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.io.cif.CifStructureConverter;
 
@@ -41,7 +42,7 @@ public static void main(String[] args) throws Exception {
 		convert(inFile, outFile);
 	}
 
-	public static void convert(File inFile, File outFile) throws IOException {
+	public static void convert(File inFile, File outFile) throws IOException, PDBIdException {
 		// now get the protein structure.
 		Structure cifStructure = CifStructureConverter.fromPath(inFile.toPath());
 

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
@@ -25,41 +25,51 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.biojava.nbio.structure.PDBId.PDBIdException;
 import org.biojava.nbio.structure.align.util.AtomCache;
 
 public class BioAssemblyIdentifier implements StructureIdentifier {
 
 	private static final long serialVersionUID = -356206725119993449L;
 
-	private String pdbCode;
+	private PDBId pdbId;
 	private int biolNr;
 
 	public static final Pattern BIO_NAME_PATTERN = Pattern.compile("^(?:BIO:)([0-9][a-z0-9]{3})(?::([0-9]+))?$", Pattern.CASE_INSENSITIVE);
 
-	public BioAssemblyIdentifier(String name) {
+	public BioAssemblyIdentifier(String name) throws PDBIdException {
 		Matcher match = BIO_NAME_PATTERN.matcher(name);
 		if(! match.matches() ) {
 			throw new IllegalArgumentException("Invalid BIO identifier");
 		}
-		pdbCode = match.group(1);
+		pdbId = new PDBId(match.group(1));
 		if(match.group(2) != null) {
 			biolNr = Integer.parseInt(match.group(2));
 		} else {
 			biolNr = 1;
 		}
 	}
 
-	public BioAssemblyIdentifier(String pdbCode, int biolNr) {
-		this.pdbCode = pdbCode;
+	/**
+	 * @param pdbCode
+	 * @param biolNr
+	 * @throws PDBIdException
+	 * @Deprecated use {@link #BioAssemblyIdentifier(PDBId, int)} instead
+	 */
+	public BioAssemblyIdentifier(String pdbCode, int biolNr) throws PDBIdException {
+		this(new PDBId(pdbCode), biolNr);
+	}
+	public BioAssemblyIdentifier(PDBId pdbId, int biolNr) {
+		this.pdbId = pdbId;
 		this.biolNr = biolNr;
 	}
 
 	@Override
 	public String getIdentifier() {
 		if( biolNr < 0) {
-			return "BIO:"+pdbCode;
+			return "BIO:"+pdbId.getId();
 		} else {
-			return String.format("BIO:%s:%d",pdbCode,biolNr);
+			return String.format("BIO:%s:%d",pdbId.getId(),biolNr);
 		}
 	}
 	@Override
@@ -70,12 +80,12 @@ public String toString() {
 	@Override
 	public Structure loadStructure(AtomCache cache) throws StructureException,
 			IOException {
-		return cache.getBiologicalAssembly(pdbCode, biolNr, AtomCache.DEFAULT_BIOASSEMBLY_STYLE);
+		return cache.getBiologicalAssembly(pdbId, biolNr, AtomCache.DEFAULT_BIOASSEMBLY_STYLE);
 	}
 
 	@Override
 	public SubstructureIdentifier toCanonical() throws StructureException {
-		return new SubstructureIdentifier(pdbCode, new ArrayList<ResidueRange>());
+		return new SubstructureIdentifier(pdbId, new ArrayList<ResidueRange>());
 	}
 
 	@Override

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
@@ -20,6 +20,7 @@
  */
 package org.biojava.nbio.structure;
 
+import org.biojava.nbio.structure.PDBId.PDBIdException;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -48,7 +49,8 @@ public class PDBHeader implements PDBRecord {
 
 	private String title;
 	private String description;
-	private String idCode;
+//	private String idCode;
+	private PDBId pdbId;
 	private String classification;
 
 	private Date depDate;
@@ -449,20 +451,39 @@ public boolean equals(PDBHeader other){
 	 *
 	 * @return the PDB identifier
 	 * @see #setIdCode(String)
+	 * @deprecated use {@link #getPdbId()}
 	 */
 	public String getIdCode() {
-		return idCode;
+		if(this.pdbId == null)
+			return null;
+		return this.pdbId.getId();
 	}
+
 	/** The PDB code for this protein structure.
 	 *
 	 * @param idCode the PDB identifier
 	 * @see #getIdCode()
-	 *
+	 * @deprecated use {@link #setPDBId(PDBId)}
 	 */
 	public void setIdCode(String idCode) {
-		this.idCode = idCode;
+		if(idCode == null) {
+			this.pdbId = null;
+		}else {
+			try {
+				this.pdbId = new PDBId(idCode);
+			} catch (PDBIdException e) {
+				throw new IllegalArgumentException(e);
+			}
+		}
 	}
 
+	public PDBId getPdbId() {
+		return pdbId;
+	}
+
+	public void setPDBId(PDBId pdbId) {
+		this.pdbId = pdbId;
+	}
 
 	public String getClassification() {
 		return classification;