Fixing bug in mmcif writing: ins codes were written as ascii code

josemduarte · josemduarte · commit a191165d0c96 · 2016-04-11T12:04:02.000-07:00
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
@@ -322,7 +322,7 @@ record = "ATOM";
 
 		String insCode = MMCIF_MISSING_VALUE;
 		if (g.getResidueNumber().getInsCode()!=null ) {
-			insCode = Integer.toString(g.getResidueNumber().getInsCode());
+			insCode = Character.toString(g.getResidueNumber().getInsCode());
 		}
 
 		AtomSite atomSite = new AtomSite();
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
@@ -160,5 +160,63 @@ public void test2N3J() throws IOException, StructureException {
 		}
 
 	}
+	
+	@Test
+	public void test1A2C() throws IOException, StructureException {
+		
+		// a structure with insertion codes
+		
+		AtomCache cache = new AtomCache();
+
+		StructureIO.setAtomCache(cache);
+
+		cache.setUseMmCif(true);
+
+		FileParsingParameters params = new FileParsingParameters();
+		params.setAlignSeqRes(true);
+		cache.setFileParsingParams(params);
+
+		Structure originalStruct = StructureIO.getStructure("1A2C");
+
+		File outputFile = File.createTempFile("biojava_testing_", ".cif");
+
+
+		FileWriter fw = new FileWriter(outputFile);
+		fw.write(originalStruct.toMMCIF());
+		fw.close();
+
+
+		MMcifParser parser = new SimpleMMcifParser();
+
+		SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
+
+		FileParsingParameters fileParsingParams = new FileParsingParameters();
+		fileParsingParams.setAlignSeqRes(true);
+
+		consumer.setFileParsingParameters(fileParsingParams);
+
+		parser.addMMcifConsumer(consumer);
+
+		//parser.parse(new BufferedReader(new FileReader(new File("/home/duarte_j/test.cif"))));
+		parser.parse(new BufferedReader(new FileReader(outputFile)));
+
+		Structure readStruct = consumer.getStructure();
+
+		assertNotNull(readStruct);
+
+		assertEquals(originalStruct.getChains().size(), readStruct.getChains().size());
+
+		for (int i=0;i<originalStruct.getChains().size();i++) {
+			assertEquals(originalStruct.getChains().get(i).getAtomGroups().size(),
+							readStruct.getChains().get(i).getAtomGroups().size());
+
+			Chain origChain = originalStruct.getChains().get(i);
+			Chain readChain = readStruct.getChains().get(i);
+
+			assertEquals(origChain.getAtomGroups().size(), readChain.getAtomGroups().size());
+			//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
+		}
+
+	}
 
 }

Original file line number	Diff line number	Diff line change
`@@ -322,7 +322,7 @@ record = "ATOM";`
`322`	`322`
`323`	`323`	`String insCode = MMCIF_MISSING_VALUE;`
`324`	`324`	`if (g.getResidueNumber().getInsCode()!=null ) {`
`325`		`- insCode = Integer.toString(g.getResidueNumber().getInsCode());`
	`325`	`+ insCode = Character.toString(g.getResidueNumber().getInsCode());`
`326`	`326`	`}`
`327`	`327`
`328`	`328`	`AtomSite atomSite = new AtomSite();`