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src/test/org/openscience/cdk/modeling/builder3d/ForceFieldConfiguratorTest.java
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| package org.openscience.cdk.modeling.builder3d; | ||
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| import static junit.framework.Assert.*; | ||
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| import java.util.List; | ||
| import java.util.regex.Matcher; | ||
| import java.util.regex.Pattern; | ||
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| 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; | ||
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| /** | ||
| * @author Daniel Szisz | ||
| * @version 01/04/2012 | ||
| */ | ||
| public class ForceFieldConfiguratorTest { | ||
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| ForceFieldConfigurator forceFieldConfigurator = new ForceFieldConfigurator(); | ||
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| /* | ||
| * 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)); | ||
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| } | ||
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| @Test | ||
| public void testSetForceFieldConfigurator_String() { | ||
| String forceFieldName = "mmff94"; | ||
| try { | ||
| 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()); | ||
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| 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()); | ||
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| } catch(CDKException cdkexp) { | ||
| cdkexp.printStackTrace(); | ||
| } | ||
| } | ||
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| @Test | ||
| public void testSetMM2Parameters() { | ||
| try { | ||
| //FIXME bug : Problem within readParameterSets due | ||
| //to:java.lang.NullPointerException | ||
| 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()); | ||
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| } catch(CDKException cdkexp) { | ||
| cdkexp.printStackTrace(); | ||
| } | ||
| } | ||
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| @Test | ||
| public void testSetMMFF94Parameters() { | ||
| try { | ||
| 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()); | ||
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| } catch(Exception e) { | ||
| e.printStackTrace(); | ||
| } | ||
| } | ||
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| @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); | ||
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| } | ||
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| @Test | ||
| public void testConfigureMM2BasedAtom_IAtom_String_boolean() { | ||
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| } | ||
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| /* | ||
| * bug : mmff94 atom types N and N3OX are given | ||
| */ | ||
| @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()); | ||
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| } | ||
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| @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()); | ||
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| } | ||
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| /* | ||
| * bug : 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()); | ||
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| } | ||
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| /* | ||
| * 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; | ||
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| IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance(); | ||
| SmilesParser smilesParser = new SmilesParser(builder); | ||
| molecule = smilesParser.parseSmiles(smiles); | ||
| ffAtomTypes = new String[molecule.getAtomCount()]; | ||
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| 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); | ||
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| } | ||
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| } |