Fix StructureToolsTest to pass according to changes

lafita · lafita · commit 2927b321308c · 2015-08-04T12:21:19.000+02:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java
@@ -44,13 +44,7 @@ protected void setUp() throws IOException
 		InputStream inStream = this.getClass().getResourceAsStream("/5pti.pdb");
 		assertNotNull(inStream);
 
-
 		PDBFileParser pdbpars = new PDBFileParser();
-		FileParsingParameters params = new FileParsingParameters();
-		params.setAlignSeqRes(false);
-		params.setLoadChemCompInfo(false);
-
-		pdbpars.setFileParsingParameters(params);
 
 		structure = pdbpars.parsePDBFile(inStream) ;
 
@@ -96,6 +90,10 @@ public void testGetCAAtoms(){
 
 	public void testGetAtomsConsistency() throws IOException, StructureException{
 		AtomCache cache = new AtomCache();
+		FileParsingParameters params = new FileParsingParameters();
+		params.setLoadChemCompInfo(true);
+		cache.setFileParsingParams(params);
+		
 		Structure hivA = cache.getStructure("1hiv.A");
 		Atom[] caSa = StructureTools.getRepresentativeAtomArray(hivA);
 		Atom[] caCa = StructureTools.getRepresentativeAtomArray(hivA.getChain(0));
@@ -110,6 +108,7 @@ public void testGetAtomsConsistency() throws IOException, StructureException{
 		assertEquals(caSa.length,99);
 		assertEquals("did not find the same number of Atoms in both chains...",
 				caSa.length,caCb.length);
+		assertEquals(caSa.length, 99);
 	}
 
 	public void testGetNrAtoms(){
@@ -430,8 +429,16 @@ public void testCAmmCIF() throws StructureException {
 		//mmCIF files left justify their atom names (eg "CA  "), so can have different behavior
 		AtomCache pdbCache = new AtomCache();
 		pdbCache.setUseMmCif(false);
+		FileParsingParameters params = new FileParsingParameters();
+		params.setLoadChemCompInfo(true);
+		pdbCache.setFileParsingParams(params);
+		
 		AtomCache mmcifCache = new AtomCache();
 		mmcifCache.setUseMmCif(true);
+		FileParsingParameters params2 = new FileParsingParameters();
+		params2.setLoadChemCompInfo(true);
+		mmcifCache.setFileParsingParams(params2);
+		
 
 		Structure pdb=null, mmcif=null;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -613,8 +613,7 @@ public static final Atom[] getRepresentativeAtomArray(Chain c) {
 				}
 			}
 			else {
-				if (ResidueType.lPeptideLinking.equals(cc.getResidueType()) ||
-						PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType())){
+				if (PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType())){
 					
 					if (g.hasAtom(CA_ATOM_NAME) && g.getAtom(CA_ATOM_NAME).getElement()==Element.C) {
 						atoms.add(g.getAtom(CA_ATOM_NAME));

Original file line number	Diff line number	Diff line change
`@@ -613,8 +613,7 @@ public static final Atom[] getRepresentativeAtomArray(Chain c) {`
`613`	`613`	`}`
`614`	`614`	`}`
`615`	`615`	`else {`
`616`		`- if (ResidueType.lPeptideLinking.equals(cc.getResidueType()) \|\|`
`617`		`- PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType())){`
	`616`	`+ if (PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType())){`
`618`	`617`
`619`	`618`	`if (g.hasAtom(CA_ATOM_NAME) && g.getAtom(CA_ATOM_NAME).getElement()==Element.C) {`
`620`	`619`	`atoms.add(g.getAtom(CA_ATOM_NAME));`