Add Kazuya's test case (slightly modified to match the expected behav…

…iour) and add document that pi-systems with a single double bond are not considered conjugated.

descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java

@@ -37,7 +37,8 @@
 /**
  * This class checks if two atoms have pi-contact (this is true when there is
  * one and the same conjugated pi-system which contains both atoms, or directly
- * linked neighbours of the atoms).
+ * linked neighbours of the atoms). Only conjugated systems with more than 2
+ * atoms are considered.
  *
  * <table border="1"><caption>Parameters for this descriptor:</caption>
  *   <tr>

descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptorTest.java

@@ -0,0 +1,75 @@
+/* Copyright (C) 2021 kazuyaujihara
+ *
+ * Contact: cdk-devel@lists.sourceforge.net
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.qsar.descriptors.atompair;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.qsar.DescriptorValue;
+import org.openscience.cdk.qsar.IAtomPairDescriptor;
+import org.openscience.cdk.qsar.result.BooleanResult;
+import org.openscience.cdk.templates.TestMoleculeFactory;
+import org.openscience.cdk.test.qsar.DescriptorTest;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+public class PiContactDetectionDescriptorTest extends DescriptorTest<IAtomPairDescriptor> {
+
+    @Before
+    public void setUp() throws Exception {
+        setDescriptor(PiContactDetectionDescriptor.class);
+    }
+
+    @Test
+    public void testButadiene() {
+        IAtomContainer mol = TestMoleculeFactory.makeAlkane(4);
+        mol.getBond(0).setOrder(IBond.Order.DOUBLE);
+        mol.getBond(2).setOrder(IBond.Order.DOUBLE);
+        for (int i = 0; i < 4; i++)
+            for (int j = 0; j < 4; j++)
+                assertTrue(checkAtomAtom(mol, i, j));
+    }
+
+    @Test
+    public void test137() throws CDKException {
+        IAtomContainer mol = TestMoleculeFactory.makeAlkane(8);
+        mol.getBond(0).setOrder(IBond.Order.DOUBLE);
+        mol.getBond(2).setOrder(IBond.Order.DOUBLE);
+        mol.getBond(6).setOrder(IBond.Order.DOUBLE);
+        for (int i = 0; i < 5; i++)
+            for (int j = 0; j < 5; j++)
+                assertTrue(i + "," + j + " should have pi contact",
+                        checkAtomAtom(mol, i, j));
+        for (int i = 0; i < 5; i++)
+            for (int j = 5; j < 8; j++)
+                assertFalse(i + "," + j + " should NOT have pi contact",
+                        checkAtomAtom(mol, i, j));
+        // a single double bond is not considered see
+        assertFalse(checkAtomAtom(mol, 6, 7));
+    }
+
+    private boolean checkAtomAtom(IAtomContainer mol, int i, int j) {
+        DescriptorValue result = descriptor.calculate(mol.getAtom(i), mol.getAtom(j), mol);
+        BooleanResult val = (BooleanResult)result.getValue();
+        return val.booleanValue();
+    }
+}