Added test cases to check that the code runs when faced with covalent…

…ly bonded metals. Currenly on failure is due to the presence of Pt, for which we do not have a valency in AtomValence
cdk · Jun 30, 2010 · f32e9a2 · f32e9a2
1 parent 2a7ee54
commit f32e9a2
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diff --git a/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptorTest.java b/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptorTest.java
@@ -3,11 +3,14 @@
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.qsar.result.DoubleArrayResult;
+import org.openscience.cdk.smiles.SmilesParser;
 
 import javax.vecmath.Point2d;
 
@@ -242,6 +245,27 @@ public void testDan64() throws Exception {
         Assert.assertEquals(0.02778, ret.get(8), 0.00001);
     }
 
+    /**
+     * @cdk.bug 3023326
+     */
+    @Test
+    public void testCovalentMetal() throws Exception {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("CCCC[Sn](CCCC)(CCCC)c1cc(Cl)c(Nc2nc(C)nc(N(CCC)CC3CC3)c2Cl)c(Cl)c1");
+        DoubleArrayResult ret = (DoubleArrayResult) descriptor.calculate(mol).getValue();
+        Assert.assertNotNull(ret);
+    }
+
+
+    /**
+     * @cdk.bug 3023326
+     */
+    @Test(expected = NullPointerException.class)
+    public void testCovalentPlatinum() throws Exception {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("CC1CN[Pt]2(N1)OC(=O)C(C)P(=O)(O)O2");
+        descriptor.calculate(mol).getValue();
+    }
 //    @Test public void testDan277() throws CDKException {
 //
 //        IMolecule mol = null;

diff --git a/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptorTest.java b/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptorTest.java
@@ -3,11 +3,14 @@
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.qsar.result.DoubleArrayResult;
+import org.openscience.cdk.smiles.SmilesParser;
 
 import javax.vecmath.Point2d;
 
@@ -185,6 +188,27 @@ public void testDan64() throws Exception {
         Assert.assertEquals(0.0000, ret.get(7), 0.0001);
     }
 
+    /**
+     * @cdk.bug 3023326
+     */
+    @Test public void testCovalentMetal() throws Exception {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("CCCC[Sn](CCCC)(CCCC)c1cc(Cl)c(Nc2nc(C)nc(N(CCC)CC3CC3)c2Cl)c(Cl)c1");
+        DoubleArrayResult ret = (DoubleArrayResult) descriptor.calculate(mol).getValue();
+        Assert.assertNotNull(ret);
+    }
+
+
+    /**
+     * @cdk.bug 3023326
+     */
+    @Test(expected = NullPointerException.class)
+    public void testCovalentPlatinum() throws Exception {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("CC1CN[Pt]2(N1)OC(=O)C(C)P(=O)(O)O2");
+        descriptor.calculate(mol).getValue();
+    }
+
 //    @Test public void testDan277() throws CDKException {
 //
 //        IMolecule mol = null;

diff --git a/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptorTest.java b/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptorTest.java
@@ -3,11 +3,14 @@
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.qsar.result.DoubleArrayResult;
+import org.openscience.cdk.smiles.SmilesParser;
 
 import javax.vecmath.Point2d;
 
@@ -180,4 +183,26 @@ public void testDan64() throws Exception {
         Assert.assertEquals(1.6522, ret.get(5), 0.0001); // 1.7148 ?
     }
 
+    /**
+     * @cdk.bug 3023326
+     */
+    @Test
+    public void testCovalentMetal() throws Exception {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("CCCC[Sn](CCCC)(CCCC)c1cc(Cl)c(Nc2nc(C)nc(N(CCC)CC3CC3)c2Cl)c(Cl)c1");
+        DoubleArrayResult ret = (DoubleArrayResult) descriptor.calculate(mol).getValue();
+        Assert.assertNotNull(ret);
+    }
+
+    /**
+     * @cdk.bug 3023326
+     */
+    @Test(expected = NullPointerException.class)
+    public void testCovalentPlatinum() throws Exception {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("CC1CN[Pt]2(N1)OC(=O)C(C)P(=O)(O)O2");
+        descriptor.calculate(mol).getValue();
+    }
+
+
 }
diff --git a/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiPathDescriptorTest.java b/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiPathDescriptorTest.java
@@ -3,11 +3,14 @@
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.qsar.result.DoubleArrayResult;
+import org.openscience.cdk.smiles.SmilesParser;
 
 import javax.vecmath.Point2d;
 
@@ -249,6 +252,28 @@ public void testDan64() throws Exception {
         Assert.assertEquals(5.5772, ret.get(8), 0.0001);
     }
 
+    /**
+     * @cdk.bug 3023326
+     */
+    @Test
+    public void testCovalentMetal() throws Exception {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("CCCC[Sn](CCCC)(CCCC)c1cc(Cl)c(Nc2nc(C)nc(N(CCC)CC3CC3)c2Cl)c(Cl)c1");
+        DoubleArrayResult ret = (DoubleArrayResult) descriptor.calculate(mol).getValue();
+        Assert.assertNotNull(ret);
+    }
+
+    /**
+     * @cdk.bug 3023326
+     */
+    @Test(expected=NullPointerException.class)
+    public void testCovalentPlatinum() throws Exception {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("CC1CN[Pt]2(N1)OC(=O)C(C)P(=O)(O)O2");
+        descriptor.calculate(mol).getValue();
+    }
+
+
 //    @Test public void testDan277() throws CDKException {
 //
 //        IMolecule molecule = null;