Check for molecular descriptors modifying mol/atom/bond flags.

cdk · Jan 3, 2018 · 7ea64b4 · 7ea64b4
1 parent dd8823a
commit 7ea64b4
Showing 1 changed file with 39 additions and 0 deletions.
diff --git a/...src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java b/...src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java
@@ -20,6 +20,7 @@
 
 import javax.vecmath.Point3d;
 
+import org.hamcrest.CoreMatchers;
 import org.junit.Assert;
 import org.junit.Ignore;
 import org.junit.Test;
@@ -29,6 +30,8 @@
 import org.openscience.cdk.dict.Dictionary;
 import org.openscience.cdk.dict.DictionaryDatabase;
 import org.openscience.cdk.dict.Entry;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;
@@ -45,9 +48,13 @@
 import org.openscience.cdk.qsar.result.IDescriptorResult;
 import org.openscience.cdk.qsar.result.IntegerArrayResult;
 import org.openscience.cdk.qsar.result.IntegerResult;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.templates.TestMoleculeFactory;
 import org.openscience.cdk.tools.diff.AtomContainerDiff;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
+import java.util.Iterator;
+
 /**
  * Tests for molecular descriptors.
  *
@@ -60,6 +67,38 @@ public abstract class MolecularDescriptorTest extends DescriptorTest<IMolecularD
 
     public MolecularDescriptorTest() {}
 
+    private Number[] getAtomFlags(IAtomContainer mol) {
+        Number[] flags = new Number[mol.getAtomCount()];
+        for (int i = 0; i < mol.getAtomCount(); i++) {
+            flags[i] = mol.getAtom(i).getFlagValue();
+        }
+        return flags;
+    }
+
+    private Number[] getBondFlags(IAtomContainer mol) {
+        Number[] flags = new Number[mol.getBondCount()];
+        for (int i = 0; i < mol.getBondCount(); i++) {
+            flags[i] = mol.getBond(i).getFlagValue();
+        }
+        return flags;
+    }
+
+    @Test
+    public void descriptorDoesNotChangeFlags() throws CDKException {
+        IAtomContainer mol = TestMoleculeFactory.makeBenzene();
+        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
+        Number   mflags = mol.getFlagValue();
+        Number[] aflags = getAtomFlags(mol);
+        Number[] bflags = getBondFlags(mol);
+        descriptor.calculate(mol);
+        Assert.assertThat("Molecule flags were modified by descriptor!",
+                          mol.getFlagValue(), CoreMatchers.is(mflags));
+        Assert.assertThat("Molecule's Atom flags were modified by descriptor!",
+                          getAtomFlags(mol), CoreMatchers.is(aflags));
+        Assert.assertThat("Molecule's Bond flags were modified by descriptor!",
+                          getBondFlags(mol), CoreMatchers.is(bflags));
+    }
+
     @Test
     public void testDescriptorIdentifierExistsInOntology() {
         Entry ontologyEntry = dict.getEntry(descriptor.getSpecification().getSpecificationReference()