[Cdk-commits] SF.net SVN: cdk: [10843] cdk/trunk/src/test/org/openscience/cdk/atomtype/ CDKAtomTypeMatcherTest.java

[<raj...@us...>]

Revision: 10843
          http://cdk.svn.sourceforge.net/cdk/?rev=10843&view=rev
Author:   rajarshi
Date:     2008-05-05 14:09:19 -0700 (Mon, 05 May 2008)

Log Message:
-----------
Added a test case for bug 1957958, in which we make a pyridine as if it came from a SMILES string, i.e., with all single bonds, no explicit hydrogens and all atoms marked as SP2

Modified Paths:
--------------
    cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java

Modified: cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java	2008-05-05 21:08:22 UTC (rev 10842)
+++ cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java	2008-05-05 21:09:19 UTC (rev 10843)
@@ -21,33 +21,22 @@
  */
 package org.openscience.cdk.atomtype;
 
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Map;
-
 import junit.framework.JUnit4TestAdapter;
-
 import org.junit.Assert;
 import org.junit.Test;
-import org.openscience.cdk.Atom;
-import org.openscience.cdk.Bond;
-import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.Molecule;
-import org.openscience.cdk.PseudoAtom;
-import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.*;
 import org.openscience.cdk.config.AtomTypeFactory;
 import org.openscience.cdk.config.Symbols;
 import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomType;
-import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.interfaces.IAtomType.Hybridization;
 import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
 import org.openscience.cdk.templates.MoleculeFactory;
 
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+
 /**
  * This class tests the matching of atom types defined in the
  * CDK atom type list.
@@ -1410,8 +1399,53 @@
 		mol.addBond(0,5,IBond.Order.DOUBLE);
     	assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
-    
-	/**
+
+
+    /**
+     * @cdk.bug 1957958
+     */
+    @Test
+    public void testPyridineWithSP2() throws Exception {
+        String[] expectedTypes = {
+                "N.sp2",
+                "C.sp2",
+                "C.sp2",
+                "C.sp2",
+                "C.sp2",
+                "C.sp2"
+        };
+        IMolecule mol = new Molecule();
+        IAtom a1 = mol.getBuilder().newAtom("N");
+        IAtom a2 = mol.getBuilder().newAtom("C");
+        IAtom a3 = mol.getBuilder().newAtom("C");
+        IAtom a4 = mol.getBuilder().newAtom("C");
+        IAtom a5 = mol.getBuilder().newAtom("C");
+        IAtom a6 = mol.getBuilder().newAtom("C");
+
+        a1.setHybridization(Hybridization.SP2);
+        a2.setHybridization(Hybridization.SP2);
+        a3.setHybridization(Hybridization.SP2);
+        a4.setHybridization(Hybridization.SP2);
+        a5.setHybridization(Hybridization.SP2);
+        a6.setHybridization(Hybridization.SP2);
+
+        mol.addAtom(a1);
+        mol.addAtom(a2);
+        mol.addAtom(a3);
+        mol.addAtom(a4);
+        mol.addAtom(a5);
+        mol.addAtom(a6);
+
+        mol.addBond(0, 1, IBond.Order.SINGLE);
+        mol.addBond(1, 2, IBond.Order.SINGLE);
+        mol.addBond(2, 3, IBond.Order.SINGLE);
+        mol.addBond(3, 4, IBond.Order.SINGLE);
+        mol.addBond(4, 5, IBond.Order.SINGLE);
+        mol.addBond(0, 5, IBond.Order.SINGLE);
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
+    /**
 	 * @cdk.bug 1879589
 	 */
     @Test public void testChargedSulphurSpecies() throws Exception {


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