Added missing files

Signed-off-by: John May <john.wilkinsonmay@gmail.com>

descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/FractionalPSADescriptorTest.java

@@ -0,0 +1,97 @@
+
+/* $Revision$ $Author$ $Date$
+ *
+ * Copyright (c) 2014 Collaborative Drug Discovery, Inc. <alex@collaborativedrug.com>
+ *
+ * Implemented by Alex M. Clark, produced by Collaborative Drug Discovery, Inc.
+ * Made available to the CDK community under the terms of the GNU LGPL.
+ *
+ *    http://collaborativedrug.com
+ *
+ * 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.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * 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.molecular;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.openscience.cdk.*;
+import org.openscience.cdk.qsar.*;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.io.*;
+import org.openscience.cdk.qsar.result.*;
+import org.openscience.cdk.tools.*;
+import org.openscience.cdk.annotations.*;
+
+import java.util.*;
+import java.util.zip.*;
+import java.io.*;
+
+/**
+ * Test for fractional PSA descriptor.
+ *
+ * @cdk.module test-qsarmolecular
+ */
+
+public class FractionalPSADescriptorTest extends MolecularDescriptorTest 
+{
+	private static ILoggingTool logger=LoggingToolFactory.createLoggingTool(FractionalPSADescriptorTest.class);
+
+    public FractionalPSADescriptorTest()
+    {
+    }
+
+    @Before
+    public void setUp() throws Exception 
+    {
+    	setDescriptor(FractionalPSADescriptor.class);
+    }
+
+    @Test
+    public void testDescriptors() throws Exception
+    {
+    	String fnmol="data/cdd/pyridineacid.mol";
+    	MDLReader mdl=new MDLReader(this.getClass().getClassLoader().getResourceAsStream(fnmol));
+		AtomContainer mol=new AtomContainer();
+		mdl.read(mol);
+		mdl.close();
+
+		FractionalPSADescriptor fpsa=new FractionalPSADescriptor();
+		DescriptorValue results=fpsa.calculate(mol);
+
+		// note: test currently assumes that just one descriptor is calculated
+		String[] names=results.getNames();
+		if (names.length!=1 || !names[0].equals("tpsaEfficiency")) throw new CDKException("Only expecting 'tpsaEfficiency'");
+		DoubleResult value=(DoubleResult)results.getValue();
+		double tpsaEfficiency=value.doubleValue();
+		final double ANSWER=0.4036,ANSWER_LO=ANSWER*0.999,ANSWER_HI=ANSWER*1.001; // (we can tolerate rounding errors)
+		if (tpsaEfficiency<ANSWER_LO || tpsaEfficiency>ANSWER_HI)
+		{
+			throw new CDKException("Got "+tpsaEfficiency+", expected "+ANSWER);
+		}
+    }
+
+    // included to shutdown the warning messages for not having tests for trivial methods
+    @Test
+    public void nop() throws Exception {}
+}
+

descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/SmallRingDescriptorTest.java

@@ -0,0 +1,170 @@
+
+/* $Revision$ $Author$ $Date$
+ *
+ * Copyright (c) 2014 Collaborative Drug Discovery, Inc. <alex@collaborativedrug.com>
+ *
+ * Implemented by Alex M. Clark, produced by Collaborative Drug Discovery, Inc.
+ * Made available to the CDK community under the terms of the GNU LGPL.
+ *
+ *    http://collaborativedrug.com
+ *
+ * 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.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * 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.molecular;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.openscience.cdk.*;
+import org.openscience.cdk.qsar.*;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.io.MDLReader;
+import org.openscience.cdk.io.MDLV2000Writer;
+import org.openscience.cdk.qsar.result.*;
+import org.openscience.cdk.tools.*;
+import org.openscience.cdk.annotations.*;
+
+import java.util.*;
+import java.util.zip.*;
+import java.io.*;
+
+/**
+ * Test for small rings descriptor.
+ *
+ * @cdk.module test-qsarmolecular
+ */
+
+public class SmallRingDescriptorTest extends MolecularDescriptorTest 
+{
+	private static ILoggingTool logger=LoggingToolFactory.createLoggingTool(SmallRingDescriptorTest.class);
+
+    public SmallRingDescriptorTest()
+    {
+    }
+
+    @Before
+    public void setUp() throws Exception 
+    {
+    	setDescriptor(SmallRingDescriptor.class);
+    }
+
+    @Test
+    public void testDescriptors() throws Exception
+    {
+    	logger.info("CircularFingerprinter test: loading source materials");
+
+        String fnzip="data/cdd/aromring_validation.zip";
+        logger.info("Loading source content: "+fnzip);
+        InputStream in=this.getClass().getClassLoader().getResourceAsStream(fnzip);
+    	validate(in);
+    	in.close();
+
+		logger.info("CircularFingerprinter test: completed without any problems");
+    }
+
+    // included to shutdown the warning messages for not having tests for trivial methods
+    @Test
+    public void nop() throws Exception {}
+
+    // run through the cases
+	private void validate(InputStream in) throws Exception
+	{
+		ZipInputStream zip=new ZipInputStream(in);
+
+		// stream the contents form the zipfile: these are all short
+		HashMap<String,byte[]> content=new HashMap<String,byte[]>();
+		while (true)
+		{
+			ZipEntry ze=zip.getNextEntry();
+			if (ze==null) break;
+			String fn=ze.getName();
+			ByteArrayOutputStream buff=new ByteArrayOutputStream();
+			while (true)
+			{
+				int b=zip.read();
+				if (b<0) break;
+				buff.write(b);
+			}
+			content.put(fn,buff.toByteArray());
+		}
+
+		zip.close();
+
+		for (int idx=1;;idx++)
+		{
+			String basefn=String.valueOf(idx);
+			while (basefn.length()<6) basefn="0"+basefn;
+			byte[] molBytes=content.get(basefn+".mol");
+			if (molBytes==null) break;
+
+    		AtomContainer mol=new AtomContainer();
+    		MDLReader mdl=new MDLReader(new ByteArrayInputStream(molBytes));
+    		mdl.read(mol);
+    		mdl.close();
+
+			ByteArrayInputStream rin=new ByteArrayInputStream(content.get(basefn+".rings"));
+    		BufferedReader rdr=new BufferedReader(new InputStreamReader(rin));
+    		String[] bits=rdr.readLine().split(" ");
+    		rdr.close();
+    		int wantSmallRings=Integer.parseInt(bits[0]);
+    		int wantRingBlocks=Integer.parseInt(bits[1]);
+    		int wantAromRings=Integer.parseInt(bits[2]);
+    		int wantAromBlocks=Integer.parseInt(bits[3]);
+
+    		logger.info("FN="+basefn+" MOL="+mol.getAtomCount()+","+mol.getBondCount()+
+    		   " nSmallRings="+wantSmallRings+" nRingBlocks="+wantRingBlocks+
+    		   " nAromRings="+wantAromRings+" nAromBlocks="+wantAromBlocks);
+
+			SmallRingDescriptor descr=new SmallRingDescriptor();
+			DescriptorValue results=descr.calculate(mol);
+			String[] names=results.getNames();
+			IntegerArrayResult values=(IntegerArrayResult)results.getValue();
+
+			int gotSmallRings=0,gotRingBlocks=0,gotAromRings=0,gotAromBlocks=0;
+			for (int n=0;n<names.length;n++)
+			{
+				if (names[n].equals("nSmallRings")) gotSmallRings=values.get(n);
+				else if (names[n].equals("nRingBlocks")) gotRingBlocks=values.get(n);
+				else if (names[n].equals("nAromRings")) gotAromRings=values.get(n);
+				else if (names[n].equals("nAromBlocks")) gotAromBlocks=values.get(n);
+			}
+
+			String error=null;
+			if (gotSmallRings!=wantSmallRings) error="Got "+gotSmallRings+" small rings, expected "+wantSmallRings;
+			else if (gotRingBlocks!=wantRingBlocks) error="Got "+gotRingBlocks+" ring blocks, expected "+wantRingBlocks;
+			else if (gotAromRings!=wantAromRings) error="Got "+gotAromRings+" aromatic rings, expected "+wantAromRings;
+			else if (gotAromBlocks!=wantAromBlocks) error="Got "+gotAromBlocks+" aromatic blocks, expected "+wantAromBlocks;
+
+			if (error!=null)
+			{
+				StringWriter str=new StringWriter();
+				MDLV2000Writer wtr=new MDLV2000Writer(str);
+				wtr.write(mol);
+				wtr.close();
+				error+="\nMolecule:\n"+str.toString();
+				throw new CDKException(error);
+			}
+		}
+	}
+
+}
+