Handling some nulls in PdbId creation, #1019

josemduarte · josemduarte · commit c84cf73c23e6 · 2022-01-31T15:23:06.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
@@ -117,8 +117,8 @@ public SubstructureIdentifier(String id) {
 	 * Create a new identifier based on a set of ranges.
 	 *
 	 * If ranges is empty, includes all residues.
-	 * @param pdbId
-	 * @param ranges
+	 * @param pdbId a pdb id, can't be null
+	 * @param ranges the ranges
 	 */
 	public SubstructureIdentifier(String pdbId, List<ResidueRange> ranges) {
 		this(new PdbId(pdbId), ranges);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
@@ -122,7 +122,11 @@ public SubstructureIdentifier toCanonical() throws StructureException{
 			String path = url.getPath();
 			pdbId = guessPDBID(path.substring(path.lastIndexOf("/") + 1));
 		}
-		return new SubstructureIdentifier(new PdbId(pdbId), ranges);
+		PdbId pdbIdObj = null;
+		if (pdbId != null) {
+			pdbIdObj = new PdbId(pdbId);
+		}
+		return new SubstructureIdentifier(pdbIdObj, ranges);
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -167,7 +167,9 @@ public void finalizeStructure() {
 	@Override
 	public void initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGroups,
 			int totalNumChains, int totalNumModels, String modelId) {
-		structure.setPdbId(new PdbId(modelId));
+		if (modelId != null) {
+			structure.setPdbId(new PdbId(modelId));
+		}
 		allAtoms = new Atom[totalNumAtoms];
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
@@ -138,8 +138,10 @@ public PdbId getPdbId() {
 	 */
 	@Deprecated
 	public void setPdbId(String pdbId) {
-		if(pdbId == null) this.pdbId = null;
-		this.pdbId = new PdbId(pdbId);
+		if (pdbId == null)
+			this.pdbId = null;
+		else
+			this.pdbId = new PdbId(pdbId);
 	}
 
 	

Original file line number	Diff line number	Diff line change
`@@ -122,7 +122,11 @@ public SubstructureIdentifier toCanonical() throws StructureException{`
`122`	`122`	`String path = url.getPath();`
`123`	`123`	`pdbId = guessPDBID(path.substring(path.lastIndexOf("/") + 1));`
`124`	`124`	`}`
`125`		`- return new SubstructureIdentifier(new PdbId(pdbId), ranges);`
	`125`	`+ PdbId pdbIdObj = null;`
	`126`	`+ if (pdbId != null) {`
	`127`	`+ pdbIdObj = new PdbId(pdbId);`
	`128`	`+ }`
	`129`	`+ return new SubstructureIdentifier(pdbIdObj, ranges);`
`126`	`130`	`}`
`127`	`131`
`128`	`132`	`@Override`