Added handling of '?' and other non integer string for the charge.

abradle · josemduarte · commit f24019f3b522 · 2016-04-29T10:29:30.000-07:00
Added a test to ensure this is handled appropriately.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/ChargeAdder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/ChargeAdder.java
@@ -54,12 +54,21 @@ public static void addCharges(Structure structure) {
 					ChemComp thisChemComp = ChemCompGroupFactory.getChemComp(g.getPDBName());
 					List<ChemCompAtom> chemAtoms = thisChemComp.getAtoms();
 					for(ChemCompAtom chemCompAtom : chemAtoms) {
-						Atom atom = g.getAtom(chemCompAtom.getAtom_id());
-
+						Atom atom = g.getAtom(chemCompAtom.getAtom_id());	
 						String stringCharge = chemCompAtom.getCharge();
 						short shortCharge = 0;
 						if (stringCharge!=null){
-							shortCharge = Short.parseShort(stringCharge);
+							if(!stringCharge.equals("?")){
+								try{
+									shortCharge = Short.parseShort(stringCharge);
+								}
+								catch(NumberFormatException e){
+									logger.warn("Number format exception. Parsing '"+stringCharge+"' to short");
+								}
+							}
+							else{
+								logger.warn("? charge on atom "+chemCompAtom.getAtom_id()+" in group "+thisChemComp.getId());
+							}
 						}
 						else{
 							logger.warn("Null charge on atom "+chemCompAtom.getAtom_id()+" in group "+thisChemComp.getId());
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestChargeAdder.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestChargeAdder.java
@@ -38,6 +38,34 @@ public void testBasic() throws IOException, StructureException {
 			}
 		}
 		// Check that the count is as excpected
-		assertEquals(chargeCount, 425);	
+		assertEquals(425, chargeCount);	
 	}
+	
+	
+	/**
+	 * Test that it can parse '?' values in the CCD.
+	 * @throws StructureException 
+	 * @throws IOException 
+	 */
+	@Test
+	public void testQuestionMark() throws IOException, StructureException {
+		// Get the structure
+		Structure structure = StructureIO.getStructure("3PE6");
+		ChargeAdder.addCharges(structure);
+		// Now count the charges
+		int chargeCount = 0;
+		for(Chain chain : structure.getChains()) {
+			for (Group group : chain.getAtomGroups()) {
+				for (Atom atom : group.getAtoms()) {
+					if (atom.getCharge()!=0) {
+						chargeCount++;
+					}
+				}
+			}
+		}
+		assertEquals(39, chargeCount);
+	}
+	
+	
+	
 }
