Merge remote branch 'upstream/master'

src/test/org/openscience/cdk/modeling/builder3d/ForceFieldConfiguratorTest.java

@@ -0,0 +1,218 @@
+/* Copyright (C) 2000-2007  Christoph Steinbeck 
+ *               2001-2007,2009  Egon Willighagen 
+ *
+ * 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.modeling.builder3d;
+
+
+import static junit.framework.Assert.*;
+
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.junit.Test;
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IRingSet;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.tools.HOSECodeGenerator;
+
+/**
+ * @author Daniel Szisz
+ * @version 01/04/2012
+ * @module test-modelbuilder3d
+ * 
+ */
+public class ForceFieldConfiguratorTest  {
+
+	ForceFieldConfigurator forceFieldConfigurator = new ForceFieldConfigurator();
+
+
+	/**
+	 * @cdk.bug : ArrayIndexOutOfBoundsException because of wrong for loop
+	*/
+	@Test
+	public void testCheckForceFieldType_String() {
+		assertEquals(2, forceFieldConfigurator.getFfTypes().length);
+		String validForceFieldType = "mm2";
+		String invalidForceFieldType = "mmff2001";
+		assertTrue(forceFieldConfigurator.checkForceFieldType(validForceFieldType));
+		assertFalse(forceFieldConfigurator.checkForceFieldType(invalidForceFieldType));
+
+	}
+
+	@Test
+	public void testSetForceFieldConfigurator_String() throws CDKException {
+		String forceFieldName = "mmff94";
+		forceFieldConfigurator.setForceFieldConfigurator(forceFieldName);
+		List<IAtomType> mmff94AtomTypes = forceFieldConfigurator.getAtomTypes();
+		assertNotNull(mmff94AtomTypes);
+		IAtomType atomtype0 = mmff94AtomTypes.get(0);
+		assertEquals("C", atomtype0.getAtomTypeName());
+		IAtomType atomtype1 = mmff94AtomTypes.get(1);
+		assertEquals("Csp2", atomtype1.getAtomTypeName());
+
+		forceFieldName = "mm2";
+		forceFieldConfigurator.setForceFieldConfigurator(forceFieldName);
+		List<IAtomType> mm2AtomTypes = forceFieldConfigurator.getAtomTypes();
+		assertNotNull(mm2AtomTypes);
+		IAtomType atomtype2 = mm2AtomTypes.get(2);
+		assertEquals("C=", atomtype2.getAtomTypeName());
+		IAtomType atomtype3 = mm2AtomTypes.get(3);
+		assertEquals("Csp", atomtype3.getAtomTypeName());
+
+	}
+
+	@Test
+	public void testSetMM2Parameters() throws CDKException {
+		forceFieldConfigurator.setMM2Parameters();
+		assertNotNull(forceFieldConfigurator.getParameterSet());
+		List<IAtomType> atomtypeList = forceFieldConfigurator.getAtomTypes();
+		IAtomType atomtype1 = atomtypeList.get(1);
+		assertEquals("Csp2", atomtype1.getAtomTypeName());
+		assertEquals(6, (int) atomtype1.getAtomicNumber());
+		assertEquals(12, (int) atomtype1.getMassNumber());
+	}
+
+	@Test
+	public void testSetMMFF94Parameters() throws Exception {
+		forceFieldConfigurator.setMMFF94Parameters();
+		assertNotNull(forceFieldConfigurator.getParameterSet());
+		List<IAtomType> atomtypeList = forceFieldConfigurator.getAtomTypes();
+		IAtomType atomtype4 = atomtypeList.get(4);
+		assertEquals("CO2M", atomtype4.getAtomTypeName());
+		assertEquals(6, (int) atomtype4.getAtomicNumber());
+		assertEquals(4, (int) atomtype4.getFormalNeighbourCount());
+		assertEquals(12, (int) atomtype4.getMassNumber());
+
+	}
+
+	@Test
+	public void testRemoveAromaticityFlagsFromHoseCode_String() {
+		String hosecode1 = "***HO*SE*CODE***";
+		String cleanHoseCode = forceFieldConfigurator.removeAromaticityFlagsFromHoseCode(hosecode1);
+		assertEquals("HOSECODE",cleanHoseCode);
+		String hosecode2 = "HOSECODE";
+		cleanHoseCode = forceFieldConfigurator.removeAromaticityFlagsFromHoseCode(hosecode2);
+		assertEquals("HOSECODE", cleanHoseCode);
+
+	}
+
+	/**
+	 * @cdk.bug  #3515122:  N atom type instead of NC=O
+	 */
+	@Test
+	public void testConfigureMMFF94BasedAtom_IAtom_String_boolean_hydroxyurea() throws CDKException {
+		String husmi = "NC(=O)NO";
+		IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+		SmilesParser parser = new SmilesParser(builder);
+		IAtomContainer hu = parser.parseSmiles(husmi);
+		ForceFieldConfigurator ffc = new ForceFieldConfigurator();
+		ffc.setForceFieldConfigurator("mmff94");
+		IAtom N1= hu.getAtom(0);
+		IAtom N2 = hu.getAtom(3);
+		ffc.configureAtom(N1, 
+				new HOSECodeGenerator().getHOSECode(hu, N1, 3),
+				false);
+		ffc.configureAtom(N2, 
+				new HOSECodeGenerator().getHOSECode(hu, N2, 3),
+				false);
+		assertEquals("NC=O", N1.getAtomTypeName());
+		assertEquals("N2OX", N2.getAtomTypeName());
+
+	}
+
+	@Test
+	public void testConfigureMMFF94BasedAtom_IAtom_String_boolean_propanamide() throws CDKException {
+		String pasmi = "NC(=O)CC";
+		IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+		SmilesParser parser = new SmilesParser(builder);
+		IAtomContainer pa = parser.parseSmiles(pasmi);
+		ForceFieldConfigurator ffc = new ForceFieldConfigurator();
+		ffc.setForceFieldConfigurator("mmff94");
+		IAtom amideN = pa.getAtom(0);
+		ffc.configureMMFF94BasedAtom(amideN, 
+				new HOSECodeGenerator().getHOSECode(pa, amideN, 3), 
+				false);
+	    assertEquals("NC=O", amideN.getAtomTypeName());	
+
+	}
+
+	/**
+	 * @cdk.bug  #3515122 : mmff94 atomtype N instead of NC=O
+	 */
+	@Test
+	public void testConfigureMMFF94BasedAtom_IAtom_String_boolean_urea() throws CDKException {
+		String usmi = "NC(N)=O";
+		IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+		SmilesParser parser = new SmilesParser(builder);
+		IAtomContainer urea = parser.parseSmiles(usmi);
+		ForceFieldConfigurator ffc = new ForceFieldConfigurator();
+		ffc.setForceFieldConfigurator("mmff94");
+		IAtom amideN = urea.getAtom(0);
+		ffc.configureMMFF94BasedAtom(amideN, 
+				new HOSECodeGenerator().getHOSECode(urea, amideN, 3), 
+				false);
+//		System.err.println(amideN.getAtomTypeName());
+		assertEquals("NC=O", amideN.getAtomTypeName());
+
+	}
+
+	/**
+	 * @cdk.bug : bad atom types
+	 */
+	@Test 
+	public void testAssignAtomTyps_test4_hydroxyurea() throws CDKException {
+		String smiles = "C(=O)(NO)N";
+	    String[] originalAtomTypes = {"C.sp2","O.sp2","N.amide","O.sp3","N.amide"}; 
+        String[] expectedAtomTypes = {"C=","O=","NC=O","O","N2OX"};
+    	IAtomContainer molecule = null;
+    	String[] ffAtomTypes=null;
+
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+		SmilesParser smilesParser = new SmilesParser(builder);
+		molecule = smilesParser.parseSmiles(smiles);
+		ffAtomTypes = new String[molecule.getAtomCount()];
+
+		for(int i=0; i<molecule.getAtomCount(); i++) {
+			assertEquals(originalAtomTypes[i],molecule.getAtom(i).getAtomTypeName());	
+		     }
+		forceFieldConfigurator.setForceFieldConfigurator("mmff94");	
+		IRingSet moleculeRingSet = forceFieldConfigurator.assignAtomTyps(molecule);
+		//no rings
+		assertEquals(0, moleculeRingSet.getAtomContainerCount());
+		for(int i=0; i< molecule.getAtomCount(); i++) {
+			IAtom mmff94atom = molecule.getAtom(i);
+			assertTrue(mmff94atom.getFlag(CDKConstants.ISALIPHATIC));
+			ffAtomTypes[i] = mmff94atom.getAtomTypeName();
+		 }
+		 assertEquals(expectedAtomTypes, ffAtomTypes);
+
+	}
+
+}