Resolving a warning that should not appear

josemduarte · josemduarte · commit d568743ad66f · 2019-01-26T18:47:57.000-08:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestMMCIFWriting.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestMMCIFWriting.java
@@ -26,4 +26,11 @@ public void testBiounitWriting1STP() throws IOException, StructureException {
         assertTrue(mmcif.contains("A_2"));
     }
 
+    @Test
+    public void testStructWriting1STP() throws IOException, StructureException {
+        Structure s = StructureIO.getStructure("1STP");
+        String mmcif = s.toMMCIF();
+        assertNotNull(mmcif);
+        assertTrue(mmcif.contains("A"));
+    }
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
@@ -294,9 +294,11 @@ public List<String> getChainIds() {
 	}
 
 	/**
-	 * Given a Group g of Chain c (member of this EnityInfo) return the corresponding position in the
+	 * Given a Group g of Chain c (member of this EntityInfo) return the corresponding position in the
 	 * alignment of all member sequences (1-based numbering), i.e. the index (1-based) in the SEQRES sequence.
-	 * This allows for comparisons of residues belonging to different chains of the same EnityInfo (entity).
+	 * This allows for comparisons of residues belonging to different chains of the same EntityInfo (entity).
+	 * <p>
+	 * Note this method should only be used for entities of type {@link EntityType#POLYMER}
 	 * <p>
 	 * If {@link FileParsingParameters#setAlignSeqRes(boolean)} is not used or SEQRES not present, a mapping
 	 * will not be available and this method will return {@link ResidueNumber#getSeqNum()} for all residues, which
@@ -310,7 +312,7 @@ public List<String> getChainIds() {
 	 * is returned as a fall-back, if the group is not found in the SEQRES groups then -1 is returned
 	 * for the given group and chain
 	 * @throws IllegalArgumentException if the given Chain is not a member of this EnityInfo
-	 * @see {@link Chain#getSeqResGroup(int)}
+	 * @see Chain#getSeqResGroup(int)
 	 */
 	public int getAlignedResIndex(Group g, Chain c) {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
@@ -27,6 +27,7 @@
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.Element;
+import org.biojava.nbio.structure.EntityType;
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.GroupType;
 import org.biojava.nbio.structure.Structure;
@@ -375,10 +376,13 @@ record = "ATOM";
 		String labelSeqId = Integer.toString(g.getResidueNumber().getSeqNum());
 		if (g.getChain()!=null && g.getChain().getEntityInfo()!=null) {
 			entityId = Integer.toString(g.getChain().getEntityInfo().getMolId());
-			labelSeqId = Integer.toString(g.getChain().getEntityInfo().getAlignedResIndex(g, g.getChain()));
+			if (g.getChain().getEntityInfo().getType() == EntityType.POLYMER) {
+				// this only makes sense for polymeric chains, non-polymer chains will never have seqres groups and there's no point in calling getAlignedResIndex
+				labelSeqId = Integer.toString(g.getChain().getEntityInfo().getAlignedResIndex(g, g.getChain()));
+			}
 		}
 
-		Character  altLoc = a.getAltLoc()           ;
+		Character  altLoc = a.getAltLoc();
 		String altLocStr;
 		if (altLoc==null || altLoc == ' ') {
 			altLocStr = MMCIF_DEFAULT_VALUE;
@@ -473,7 +477,7 @@ public static List<AtomSite> convertChainToAtomSites(Chain c, int model, String
 		List<AtomSite> list = new ArrayList<>();
 
 		if (c.getEntityInfo()==null) {
-			logger.warn("No Compound (entity) found for chain {}: entity_id will be set to 0, label_seq_id will be the same as auth_seq_id", c.getName());
+			logger.warn("No entity found for chain {}: entity_id will be set to 0, label_seq_id will be the same as auth_seq_id", c.getName());
 		}
 
 		for ( int h=0; h<c.getAtomLength();h++){

Original file line number	Diff line number	Diff line change
`@@ -26,4 +26,11 @@ public void testBiounitWriting1STP() throws IOException, StructureException {`
`26`	`26`	`assertTrue(mmcif.contains("A_2"));`
`27`	`27`	`}`
`28`	`28`
	`29`	`+ @Test`
	`30`	`+ public void testStructWriting1STP() throws IOException, StructureException {`
	`31`	`+ Structure s = StructureIO.getStructure("1STP");`
	`32`	`+ String mmcif = s.toMMCIF();`
	`33`	`+ assertNotNull(mmcif);`
	`34`	`+ assertTrue(mmcif.contains("A"));`
	`35`	`+ }`
`29`	`36`	`}`