non-null atomic numbers when reading from InChi [bug:1293]

Change-Id: Ib6c5e9291913705ccb6f8ef6bd2813f3dd77745c Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Mar 15, 2013 · 3117f4c · 3117f4c
1 parent 471a20c
commit 3117f4c
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Showing 2 changed files with 28 additions and 8 deletions.
diff --git a/src/main/org/openscience/cdk/inchi/InChIToStructure.java b/src/main/org/openscience/cdk/inchi/InChIToStructure.java
@@ -46,6 +46,7 @@
 import org.openscience.cdk.interfaces.IAtomParity;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.tools.periodictable.PeriodicTable;
 
 /**
  * <p>This class generates a CDK IAtomContainer from an InChI string.  It places 
@@ -163,9 +164,10 @@ protected void generateAtomContainerFromInchi(IChemObjectBuilder builder) throws
 
             cAt.setID("a" + i);
             cAt.setSymbol(iAt.getElementType());
+            cAt.setAtomicNumber(PeriodicTable.getAtomicNumber(cAt.getSymbol()));
 
             // Ignore coordinates - all zero
-            
+
             int charge = iAt.getCharge();
             if (charge != 0) {
                 cAt.setFormalCharge(charge);

diff --git a/src/test/org/openscience/cdk/inchi/InChIToStructureTest.java b/src/test/org/openscience/cdk/inchi/InChIToStructureTest.java
@@ -25,11 +25,14 @@
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.silent.AtomContainer;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
 
+import static org.junit.Assert.assertNotNull;
+
 /**
  * TestCase for the {@link InChIToStructure} class.
  *
@@ -44,7 +47,7 @@ public void testConstructor_String_IChemObjectBuilder()
 			"InChI=1S/CH4/h1H4",
 			DefaultChemObjectBuilder.getInstance()
 		);
-		Assert.assertNotNull(parser);
+		assertNotNull(parser);
 	}
 
 	@Test
@@ -54,18 +57,33 @@ public void testGetAtomContainer() throws CDKException {
 			DefaultChemObjectBuilder.getInstance()
 		);
 		IAtomContainer container = parser.getAtomContainer();
-		Assert.assertNotNull(container);
+		assertNotNull(container);
 		Assert.assertEquals(1, container.getAtomCount());
 	}
 
+    /** @cdk.bug 1293 */
+    @Test
+    public void nonNullAtomicNumbers() throws CDKException {
+        InChIToStructure parser = new InChIToStructure(
+                "InChI=1S/CH4/h1H4",
+                DefaultChemObjectBuilder.getInstance()
+        );
+        IAtomContainer container = parser.getAtomContainer();
+        for(IAtom atom : container.atoms()){
+            assertNotNull(atom.getAtomicNumber());
+        }
+        assertNotNull(container);
+        Assert.assertEquals(1, container.getAtomCount());
+    }
+
 	@Test
 	public void testFixedHydrogens() throws CDKException {
 		InChIToStructure parser = new InChIToStructure(
 			"InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)/f/h2H",
 			DefaultChemObjectBuilder.getInstance()
 		);
 		IAtomContainer container = parser.getAtomContainer();
-		Assert.assertNotNull(container);
+		assertNotNull(container);
 		Assert.assertEquals(3, container.getAtomCount());
 		Assert.assertEquals(2, container.getBondCount());
 		Assert.assertTrue(
@@ -82,7 +100,7 @@ public void testGetReturnStatus_EOF() throws CDKException {
 		);
 		parser.getAtomContainer();
 		INCHI_RET returnStatus = parser.getReturnStatus();
-		Assert.assertNotNull(returnStatus);
+		assertNotNull(returnStatus);
 		Assert.assertEquals(INCHI_RET.EOF, returnStatus);
 	}
 
@@ -93,7 +111,7 @@ public void testGetMessage() throws CDKException {
 		);
 		parser.getAtomContainer();
 		String message = parser.getMessage();
-		Assert.assertNotNull(message);
+		assertNotNull(message);
 	}
 
 	@Test
@@ -113,7 +131,7 @@ public void testGetLog() throws CDKException {
 		);
 		parser.getAtomContainer();
 		String message = parser.getMessage();
-		Assert.assertNotNull(message);
+		assertNotNull(message);
 	}
 
 	@Test
@@ -123,7 +141,7 @@ public void testGetWarningFlags() throws CDKException {
 		);
 		parser.getAtomContainer();
 		long[][] flags = parser.getWarningFlags();
-		Assert.assertNotNull(flags);
+		assertNotNull(flags);
 		Assert.assertEquals(2, flags.length);
 		Assert.assertEquals(2, flags[0].length);
 		Assert.assertEquals(2, flags[1].length);