refactored to junit4

cdk · Oct 6, 2016 · 1f4b09e · 1f4b09e
1 parent 72c4a65
commit 1f4b09e
Showing 1 changed file with 103 additions and 126 deletions.
diff --git a/...gerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprintSmartsTest.java b/...gerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprintSmartsTest.java
@@ -1,7 +1,7 @@
 package org.openscience.cdk.fingerprint;
 
-import junit.framework.TestCase;
-
+import org.junit.Assert;
+import org.junit.Test;
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.fingerprint.CircularFingerprinter.FP;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -10,130 +10,107 @@
 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;
-    }
-
-
+public class CircularFingerprintSmartsTest extends CDKTestCase {
+
+	private static ILoggingTool logger = LoggingToolFactory
+			.createLoggingTool(CircularFingerprintSmartsTest.class);
+
+	@Test
+	public void testMol1() throws Exception {
+		String molSmiles = "CC";
+		String expectedFPSmarts[][] = { { "C*" }, { "CC" } };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	@Test
+	public void testMol2() throws Exception {
+		String molSmiles = "CCC";
+		String expectedFPSmarts[][] = { { "C*" }, { "C(*)*" },
+				{ "CC*", "C(*)C" }, { "CCC" }, };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	@Test
+	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);
+	}
+
+	@Test
+	public void testMol4() throws Exception {
+		String molSmiles = "C1CC1";
+		String expectedFPSmarts[][] = {
+
+		{ "C(*)*" }, { "C1CC1", "C(C1)C1" } };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	@Test
+	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);
+	}
+
+	@Test
+	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);
+	}
+
+	@Test
+	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);
+			Assert.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;
+	}
 
 }