Added test case for CircularFingerprint smarts

descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprintSmartsTest.java

@@ -0,0 +1,139 @@
+package org.openscience.cdk.fingerprint;
+
+import junit.framework.TestCase;
+
+import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.fingerprint.CircularFingerprinter.FP;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.tools.ILoggingTool;
+import org.openscience.cdk.tools.LoggingToolFactory;
+
+public class CircularFingerprintSmartsTest extends TestCase {
+
+    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(CircularFingerprintSmartsTest.class);
+
+    public void testMol1() throws Exception
+    {
+    	String molSmiles = "CC";
+    	String expectedFPSmarts [][]  = {
+    			{"C*"},
+    			{"CC"}
+    	};
+    	checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+    }
+
+    public void testMol2() throws Exception
+    {
+    	String molSmiles = "CCC";
+    	String expectedFPSmarts [][]  = {
+    			{"C*"},
+    			{"C(*)*"},
+    			{"CC*", "C(*)C"},
+    			{"CCC"},
+    	};
+    	checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+    }
+
+    public void testMol3() throws Exception
+    {
+    	String molSmiles = "CCN";
+    	String expectedFPSmarts [][]  = {
+    			{"C*"},
+    			{"C(*)*"},
+    			{"N*"},
+    			{"CC*", "C(*)C"},
+    			{"C(*)N", "NC*"},
+    			{"CCN", "NCC", "C(C)N", "C(N)C"},
+    	};
+    	checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+    }
+
+    public void testMol4() throws Exception
+    {
+    	String molSmiles = "C1CC1";
+    	String expectedFPSmarts [][]  = {
+
+    			{"C(*)*"},
+    			{"C1CC1", "C(C1)C1"}
+    	};
+    	checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+    }
+
+    public void testMol5() throws Exception
+    {
+    	String molSmiles = "C1CCC1";
+    	String expectedFPSmarts [][]  = {
+
+    			{"C(*)*"},
+    			{"C(C*)C*", "C(CC*)*", "C(*)CC*" },
+    			{"C1CCC1", "C(CC1)C1", "C(C1)CC1"}
+    	};
+    	checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+    }
+
+    public void testMol6() throws Exception
+    {
+    	String molSmiles = "CC[C-]";
+    	String expectedFPSmarts [][]  = {
+
+    			{"C*"},
+    			{"C(*)*"},
+    			{"[C-]*"},
+    			{"CC*", "C(*)C"},
+    			{"[C-]C*", "C(*)[C-]"},
+    			{"CC[C-]", "C(C)[C-]", "[C-]CC", "C([C-])C" }
+    	};
+    	checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+    }
+
+    public void testMol7() throws Exception
+    {
+    	String molSmiles = "c1ccccc1";
+    	String expectedFPSmarts [][]  = {
+
+    			{"c(:a):a"},
+    			{"c(:a)cc:a", "c(c:a)c:a", "c(cc:a):a"},
+    			{"c(:a)cccc:a", "c(c:a)ccc:a", "c(cc:a)cc:a", "c(ccc:a)c:a", "c(cccc:a):a"},
+    			{"c1ccccc1", "c(c1)cccc1", "c(cc1)ccc1", "c(ccc1)cc1", "c(cccc1)c1" }
+    	};
+    	checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+    }
+
+
+    private void checkFPSmartsForMolecule(String moleculeSmiles, String expectedFPSmarts[][]) throws Exception
+    {
+    	//expectedFPSmarts[][] is a double array because for each smarts several equivalent variants
+    	//of the smarts are given e.g. CCC C(C)C
+    	SmilesParser parser = new SmilesParser(SilentChemObjectBuilder.getInstance());
+    	IAtomContainer mol = parser.parseSmiles(moleculeSmiles);
+
+    	CircularFingerprinter circ = new CircularFingerprinter();
+    	circ.calculate(mol);
+    	int numFP =  circ.getFPCount();
+    	for (int i = 0; i < numFP; i++)
+    	{
+    		FP fp = circ.getFP(i);
+    		String smarts = circ.getFPSmarts(fp, mol);
+    		int res = findSmarts(smarts, expectedFPSmarts);
+    		assertEquals("serching fp smarts: " + smarts, true, res >=0);
+    	}
+    }
+
+    private int findSmarts(String smarts, String smartsSet[][])
+    {
+    	for (int i = 0; i < smartsSet.length; i++)
+    	{
+    		String s[] = smartsSet[i];
+    		for (int k = 0; k < s.length; k++)
+    			if (s[k].equals(smarts))
+    				return i;
+    	}
+    	return -1;
+    }
+
+
+
+
+}