Tests pass now, except for TestLongPdbVsMmcif

josemduarte · josemduarte · commit a73d6f53b7a1 · 2016-03-07T22:26:53.000-08:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
@@ -108,11 +108,16 @@ public void testReadPDBFile() throws Exception {
 		Chain c = structure.getChain(0);
 		assertEquals("did not find the expected 58 amino acids!",58,c.getAtomGroups(GroupType.AMINOACID).size());
 
-		assertTrue(c.getAtomGroups(GroupType.HETATM).size()     == 0);
+		assertEquals(0 , c.getAtomGroups(GroupType.HETATM).size());
 
 		Chain c2 = structure.getChain(1);
-		assertTrue(c2.getAtomGroups(GroupType.HETATM).size()     == 65);
-		assertTrue(c2.getAtomGroups(GroupType.NUCLEOTIDE).size() == 0 );
+		
+		// The second (unnamed) chain in te file contains 63 molecules of deutarated 
+		// water + 1 PO4 molecule + 1 UNK hetatom molecule
+		// Since the UNK chemcomp is considered a peptide linked molecule (unknown aminoacid), 
+		// then we have only 64 HETATMs
+		assertEquals(64, c2.getAtomGroups(GroupType.HETATM).size());
+		assertEquals(0, c2.getAtomGroups(GroupType.NUCLEOTIDE).size());
 
 		List<Compound> compounds= structure.getCompounds();
 		
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
@@ -124,7 +124,7 @@ public void testVeryLongPdbVsMmCif() throws IOException, StructureException {
 	
 	@Test
 	public void testSingle() throws IOException, StructureException {
-		testAll(Arrays.asList("4imj"));
+		testAll(Arrays.asList("1jnv"));
 	}
 	
 	@After
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -418,12 +418,14 @@ else if (atomCode.equals("CA") || atomCode.equals("CB") ||
 
 			// not any of the expected atoms
 		} else {
-			// we log at info level for the MSE case (Selenomethionine), because it is too usual			
-			if (aa == 'M' && atomCode.equals("SE")) {  
-				logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");
+			// non standard aas, (e.g. MSE, LLP) will always have this problem, 
+			// thus we log at info level for them, at warn for others		
+			if (amino.getChemComp()!=null && amino.getChemComp().isStandard()) {
+				logger.warn("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
 			} else {
-				logger.warn("Unexpected atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");				
+				logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
 			}
+			
 			return atom.getElement().getVDWRadius();
 		}
 	}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
@@ -58,14 +58,15 @@ public void testAsa3PIU() throws StructureException, IOException {
 		}
 		
 		for (GroupAsa groupAsa: groupAsas) {
+			//System.out.println(groupAsa.getGroup().getPDBName() + " " + groupAsa.getGroup().getResidueNumber() + " " + groupAsa.getAsaU());
 			totResidues+=groupAsa.getAsaU();
 			
 			assertTrue(groupAsa.getRelativeAsaU()<=1.0);
 		}
 		
 		assertEquals(totAtoms, totResidues,0.000001);
 		
-		assertEquals(17638.0, totAtoms, 1.0);
+		assertEquals(17462.0, totAtoms, 1.0);
 		
 	}
 }

Original file line number	Diff line number	Diff line change
`@@ -124,7 +124,7 @@ public void testVeryLongPdbVsMmCif() throws IOException, StructureException {`
`124`	`124`
`125`	`125`	`@Test`
`126`	`126`	`public void testSingle() throws IOException, StructureException {`
`127`		`- testAll(Arrays.asList("4imj"));`
	`127`	`+ testAll(Arrays.asList("1jnv"));`
`128`	`128`	`}`
`129`	`129`
`130`	`130`	`@After`
Original file line number	Diff line number	Diff line change
`@@ -418,12 +418,14 @@ else if (atomCode.equals("CA") \|\| atomCode.equals("CB") \|\|`
`418`	`418`
`419`	`419`	`// not any of the expected atoms`
`420`	`420`	`} else {`
`421`		`- // we log at info level for the MSE case (Selenomethionine), because it is too usual`
`422`		`- if (aa == 'M' && atomCode.equals("SE")) {`
`423`		`- logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");`
	`421`	`+ // non standard aas, (e.g. MSE, LLP) will always have this problem,`
	`422`	`+ // thus we log at info level for them, at warn for others`
	`423`	`+ if (amino.getChemComp()!=null && amino.getChemComp().isStandard()) {`
	`424`	`+ logger.warn("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");`
`424`	`425`	`} else {`
`425`		`- logger.warn("Unexpected atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");`
	`426`	`+ logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");`
`426`	`427`	`}`
	`428`	`+`
`427`	`429`	`return atom.getElement().getVDWRadius();`
`428`	`430`	`}`
`429`	`431`	`}`
Original file line number	Diff line number	Diff line change
`@@ -58,14 +58,15 @@ public void testAsa3PIU() throws StructureException, IOException {`
`58`	`58`	`}`
`59`	`59`
`60`	`60`	`for (GroupAsa groupAsa: groupAsas) {`
	`61`	`+ //System.out.println(groupAsa.getGroup().getPDBName() + " " + groupAsa.getGroup().getResidueNumber() + " " + groupAsa.getAsaU());`
`61`	`62`	`totResidues+=groupAsa.getAsaU();`
`62`	`63`
`63`	`64`	`assertTrue(groupAsa.getRelativeAsaU()<=1.0);`
`64`	`65`	`}`
`65`	`66`
`66`	`67`	`assertEquals(totAtoms, totResidues,0.000001);`
`67`	`68`
`68`		`- assertEquals(17638.0, totAtoms, 1.0);`
	`69`	`+ assertEquals(17462.0, totAtoms, 1.0);`
`69`	`70`
`70`	`71`	`}`
`71`	`72`	`}`