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ChiClusterDescriptorTest.java
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ChiClusterDescriptorTest.java
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package org.openscience.cdk.qsar.descriptors.molecular;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.smiles.SmilesParser;
import javax.vecmath.Point2d;
/**
* TestSuite that runs all QSAR tests.
*
* @cdk.module test-qsarmolecular
*/
public class ChiClusterDescriptorTest extends MolecularDescriptorTest {
public ChiClusterDescriptorTest() {
}
@Before
public void setUp() throws Exception {
setDescriptor(ChiClusterDescriptor.class);
}
@Test
public void testDan64() throws Exception {
IMolecule mol = new Molecule();
IAtom a1 = mol.getBuilder().newInstance(IAtom.class,"C");
a1.setPoint2d(new Point2d(0.7500000000000004, 2.799038105676658));
mol.addAtom(a1);
IAtom a2 = mol.getBuilder().newInstance(IAtom.class,"C");
a2.setPoint2d(new Point2d(0.0, 1.5));
mol.addAtom(a2);
IAtom a3 = mol.getBuilder().newInstance(IAtom.class,"C");
a3.setPoint2d(new Point2d(0.0, 0.0));
mol.addAtom(a3);
IAtom a4 = mol.getBuilder().newInstance(IAtom.class,"O");
a4.setPoint2d(new Point2d(-1.2990381056766582, 0.7500000000000001));
mol.addAtom(a4);
IBond b1 = mol.getBuilder().newInstance(IBond.class,a2, a1, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = mol.getBuilder().newInstance(IBond.class,a3, a2, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = mol.getBuilder().newInstance(IBond.class,a4, a3, IBond.Order.SINGLE);
mol.addBond(b3);
IBond b4 = mol.getBuilder().newInstance(IBond.class,a4, a2, IBond.Order.SINGLE);
mol.addBond(b4);
DoubleArrayResult ret = (DoubleArrayResult) descriptor.calculate(mol).getValue();
Assert.assertEquals(0.2887, ret.get(0), 0.0001);
Assert.assertEquals(0.0000, ret.get(1), 0.0001);
Assert.assertEquals(0.0000, ret.get(2), 0.0001);
Assert.assertEquals(0.0000, ret.get(3), 0.0001);
Assert.assertEquals(0.1667, ret.get(4), 0.0001);
Assert.assertEquals(0.0000, ret.get(5), 0.0001);
Assert.assertEquals(0.0000, ret.get(6), 0.0001);
Assert.assertEquals(0.0000, ret.get(7), 0.0001);
}
@Test public void testDan154() throws Exception {
IMolecule mol = new Molecule();
IAtom a1 = mol.getBuilder().newInstance(IAtom.class,"C");
a1.setPoint2d(new Point2d(0.0, 1.5));
mol.addAtom(a1);
IAtom a2 = mol.getBuilder().newInstance(IAtom.class,"C");
a2.setPoint2d(new Point2d(0.0, 0.0));
mol.addAtom(a2);
IAtom a3 = mol.getBuilder().newInstance(IAtom.class,"C");
a3.setPoint2d(new Point2d(-1.2990381056766584, -0.7500000000000001));
mol.addAtom(a3);
IAtom a4 = mol.getBuilder().newInstance(IAtom.class,"C");
a4.setPoint2d(new Point2d(-2.598076211353316, -2.220446049250313E-16));
mol.addAtom(a4);
IAtom a5 = mol.getBuilder().newInstance(IAtom.class,"C");
a5.setPoint2d(new Point2d(-2.5980762113533165, 1.5));
mol.addAtom(a5);
IAtom a6 = mol.getBuilder().newInstance(IAtom.class,"C");
a6.setPoint2d(new Point2d(-1.2990381056766582, 2.2500000000000004));
mol.addAtom(a6);
IAtom a7 = mol.getBuilder().newInstance(IAtom.class,"Cl");
a7.setPoint2d(new Point2d(-1.2990381056766582, 3.7500000000000004));
mol.addAtom(a7);
IAtom a8 = mol.getBuilder().newInstance(IAtom.class,"Cl");
a8.setPoint2d(new Point2d(1.2990381056766576, -0.7500000000000007));
mol.addAtom(a8);
IBond b1 = mol.getBuilder().newInstance(IBond.class,a2, a1, IBond.Order.DOUBLE);
mol.addBond(b1);
IBond b2 = mol.getBuilder().newInstance(IBond.class,a3, a2, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = mol.getBuilder().newInstance(IBond.class,a4, a3, IBond.Order.DOUBLE);
mol.addBond(b3);
IBond b4 = mol.getBuilder().newInstance(IBond.class,a5, a4, IBond.Order.SINGLE);
mol.addBond(b4);
IBond b5 = mol.getBuilder().newInstance(IBond.class,a6, a5, IBond.Order.DOUBLE);
mol.addBond(b5);
IBond b6 = mol.getBuilder().newInstance(IBond.class,a6, a1, IBond.Order.SINGLE);
mol.addBond(b6);
IBond b7 = mol.getBuilder().newInstance(IBond.class,a7, a6, IBond.Order.SINGLE);
mol.addBond(b7);
IBond b8 = mol.getBuilder().newInstance(IBond.class,a8, a2, IBond.Order.SINGLE);
mol.addBond(b8);
DoubleArrayResult ret = (DoubleArrayResult) descriptor.calculate(mol).getValue();
Assert.assertEquals(0.5774, ret.get(0), 0.0001);
Assert.assertEquals(0.0000, ret.get(1), 0.0001);
Assert.assertEquals(0.0000, ret.get(2), 0.0001);
Assert.assertEquals(0.0000, ret.get(3), 0.0001);
Assert.assertEquals(0.3780, ret.get(4), 0.0001);
Assert.assertEquals(0.0000, ret.get(5), 0.0001);
Assert.assertEquals(0.0000, ret.get(6), 0.0001);
Assert.assertEquals(0.0000, ret.get(7), 0.0001);
}
@Test public void testDan248() throws Exception {
IMolecule mol = new Molecule();
IAtom a1 = mol.getBuilder().newInstance(IAtom.class,"C");
a1.setPoint2d(new Point2d(0.0, 1.5));
mol.addAtom(a1);
IAtom a2 = mol.getBuilder().newInstance(IAtom.class,"C");
a2.setPoint2d(new Point2d(0.0, 0.0));
mol.addAtom(a2);
IAtom a3 = mol.getBuilder().newInstance(IAtom.class,"C");
a3.setPoint2d(new Point2d(-1.2990381056766584, -0.7500000000000001));
mol.addAtom(a3);
IAtom a4 = mol.getBuilder().newInstance(IAtom.class,"C");
a4.setPoint2d(new Point2d(-2.598076211353316, -2.220446049250313E-16));
mol.addAtom(a4);
IAtom a5 = mol.getBuilder().newInstance(IAtom.class,"C");
a5.setPoint2d(new Point2d(-2.5980762113533165, 1.5));
mol.addAtom(a5);
IAtom a6 = mol.getBuilder().newInstance(IAtom.class,"C");
a6.setPoint2d(new Point2d(-1.2990381056766582, 2.2500000000000004));
mol.addAtom(a6);
IAtom a7 = mol.getBuilder().newInstance(IAtom.class,"C");
a7.setPoint2d(new Point2d(-3.897114317029975, 2.249999999999999));
mol.addAtom(a7);
IAtom a8 = mol.getBuilder().newInstance(IAtom.class,"O");
a8.setPoint2d(new Point2d(-1.2990381056766587, -2.25));
mol.addAtom(a8);
IAtom a9 = mol.getBuilder().newInstance(IAtom.class,"C");
a9.setPoint2d(new Point2d(1.477211629518312, 1.2395277334996044));
mol.addAtom(a9);
IAtom a10 = mol.getBuilder().newInstance(IAtom.class,"C");
a10.setPoint2d(new Point2d(0.5130302149885025, 2.909538931178863));
mol.addAtom(a10);
IBond b1 = mol.getBuilder().newInstance(IBond.class,a2, a1, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = mol.getBuilder().newInstance(IBond.class,a3, a2, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = mol.getBuilder().newInstance(IBond.class,a4, a3, IBond.Order.SINGLE);
mol.addBond(b3);
IBond b4 = mol.getBuilder().newInstance(IBond.class,a5, a4, IBond.Order.DOUBLE);
mol.addBond(b4);
IBond b5 = mol.getBuilder().newInstance(IBond.class,a6, a5, IBond.Order.SINGLE);
mol.addBond(b5);
IBond b6 = mol.getBuilder().newInstance(IBond.class,a6, a1, IBond.Order.SINGLE);
mol.addBond(b6);
IBond b7 = mol.getBuilder().newInstance(IBond.class,a7, a5, IBond.Order.SINGLE);
mol.addBond(b7);
IBond b8 = mol.getBuilder().newInstance(IBond.class,a8, a3, IBond.Order.DOUBLE);
mol.addBond(b8);
IBond b9 = mol.getBuilder().newInstance(IBond.class,a9, a1, IBond.Order.SINGLE);
mol.addBond(b9);
IBond b10 = mol.getBuilder().newInstance(IBond.class,a10, a1, IBond.Order.SINGLE);
mol.addBond(b10);
DoubleArrayResult ret = (DoubleArrayResult) descriptor.calculate(mol).getValue();
Assert.assertEquals(1.7845, ret.get(0), 0.0001);
Assert.assertEquals(0.2500, ret.get(1), 0.0001);
Assert.assertEquals(0.0000, ret.get(2), 0.0001);
Assert.assertEquals(0.0000, ret.get(3), 0.0001);
Assert.assertEquals(1.4946, ret.get(4), 0.0001);
Assert.assertEquals(0.2500, ret.get(5), 0.0001);
Assert.assertEquals(0.0000, ret.get(6), 0.0001);
Assert.assertEquals(0.0000, ret.get(7), 0.0001);
}
/**
* @cdk.bug 3023326
*/
@Test public void testCovalentMetal() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = sp.parseSmiles("CCCC[Sn](CCCC)(CCCC)c1cc(Cl)c(Nc2nc(C)nc(N(CCC)CC3CC3)c2Cl)c(Cl)c1");
DoubleArrayResult ret = (DoubleArrayResult) descriptor.calculate(mol).getValue();
Assert.assertNotNull(ret);
}
/**
* @cdk.bug 3023326
*/
@Test(expected = NullPointerException.class)
public void testCovalentPlatinum() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = sp.parseSmiles("CC1CN[Pt]2(N1)OC(=O)C(C)P(=O)(O)O2");
descriptor.calculate(mol).getValue();
}
// @Test public void testDan277() throws CDKException {
//
// IMolecule mol = null;
//
// ChiClusterDescriptor desc = new ChiClusterDescriptor();
// DoubleArrayResult ret = (DoubleArrayResult) desc.calculate(mol).getValue();
//
// Assert.assertEquals(0.0000, ret.get(0), 0.0001);
// Assert.assertEquals(0.0000, ret.get(1), 0.0001);
// Assert.assertEquals(0.0000, ret.get(2), 0.0001);
// Assert.assertEquals(0.08333, ret.get(3), 0.00001);
// Assert.assertEquals(0.0000, ret.get(4), 0.0001);
// Assert.assertEquals(0.0000, ret.get(5), 0.0001);
// Assert.assertEquals(0.0000, ret.get(6), 0.0001);
// Assert.assertEquals(0.02778, ret.get(7), 0.00001);
// }
}