1) Updated the mmtf test data to v0.2.0

abradle · abradle · commit 699c8866545a · 2016-06-03T08:17:23.000-07:00
2) Updated the mmtf structure reader to use the given single letter code
3) mmCIF tests use mmCIF atom cache.
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
@@ -186,7 +186,7 @@ public void setGroupInfo(String groupName, int groupNumber,
 		case 1:
 			AminoAcid aa = new AminoAcidImpl();
 			// Now set the one letter code
-			aa.setAminoType(StructureTools.get1LetterCodeAmino(groupName));
+			aa.setAminoType(singleLetterCode);
 			group = aa;
 			break;
 		case 2:
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFFeatures.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFFeatures.java
@@ -142,6 +142,12 @@ private void assertDisulfideBond(String expectedChainId1, String expectedChainId
 
 	@Test
 	public void testSites()throws IOException, StructureException {
+
+		AtomCache cache = new AtomCache();
+
+		StructureIO.setAtomCache(cache);
+
+		cache.setUseMmCif(true);
 		Structure sCif = StructureIO.getStructure("4HHB");
 
 		assertNotNull(sCif);
@@ -171,6 +177,11 @@ public void testSites()throws IOException, StructureException {
 
 	@Test
 	public void testSites1a4w()throws IOException, StructureException {
+		AtomCache cache = new AtomCache();
+
+		StructureIO.setAtomCache(cache);
+
+		cache.setUseMmCif(true);
 		Structure sCif = StructureIO.getStructure("1A4W");
 
 		assertNotNull(sCif);
diff --git a/biojava-structure/src/test/resources/org/biojava/nbio/structure/io/mmtf/4CUP.mmtf b/biojava-structure/src/test/resources/org/biojava/nbio/structure/io/mmtf/4CUP.mmtf
