@Test
public void methyleneCyclopropeneTest() {
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
AbstractSignatureTest.addCarbons(mol, 4);
AbstractSignatureTest.addHydrogens(mol, 1, 2);
AbstractSignatureTest.addHydrogens(mol, 2, 1);
AbstractSignatureTest.addHydrogens(mol, 3, 1);
mol.addBond(0, 1, IBond.Order.DOUBLE);
mol.addBond(0, 2, IBond.Order.SINGLE);
mol.addBond(0, 3, IBond.Order.SINGLE);
mol.addBond(2, 3, IBond.Order.DOUBLE);
MoleculeSignature molSig = new MoleculeSignature(mol);
String sigFor2Height1 = molSig.signatureStringForVertex(2, 1);
String sigFor3Height1 = molSig.signatureStringForVertex(3, 1);
Assert.assertTrue(
"Height 1 signatures for atoms 2 and 3" + " should be the same",
sigFor2Height1.equals(sigFor3Height1));
String sigFor2Height2 = molSig.signatureStringForVertex(2, 1);
String sigFor3Height2 = molSig.signatureStringForVertex(3, 1);
Assert.assertTrue(
"Height 2 signatures for atoms 2 and 3" + " should be the same",
sigFor2Height2.equals(sigFor3Height2));
}
@Test
public void cyclobuteneTest() {
String expectedA = "[C]([C]([C,0])=[C]([C,0]))";
String expectedB = "[C]([C]([C,0])[C](=[C,0]))";
IAtomContainer cyclobutene = builder.newInstance(IAtomContainer.class);
AbstractSignatureTest.addCarbons(cyclobutene, 4);
cyclobutene.addBond(0, 1, IBond.Order.SINGLE);
cyclobutene.addBond(0, 2, IBond.Order.SINGLE);
cyclobutene.addBond(1, 3, IBond.Order.DOUBLE);
cyclobutene.addBond(2, 3, IBond.Order.SINGLE);
Assert.assertEquals(expectedA, canonicalStringFromMolecule(cyclobutene));
String expectedFullString = "2" + expectedA + " + 2" + expectedB;
String actualFullString = fullStringFromMolecule(cyclobutene);
Assert.assertEquals(expectedFullString, actualFullString);
}
@Test
public void fusedSquareMultipleBondTest() {
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
String expected = "[C]([C]([C,1])[C]([C,0])[C](=[C,1])[C](=[C,0]))";
AbstractSignatureTest.addCarbons(mol, 7);
mol.addBond(0, 1, IBond.Order.SINGLE);
mol.addBond(0, 2, IBond.Order.SINGLE);
mol.addBond(0, 3, IBond.Order.SINGLE);
mol.addBond(0, 4, IBond.Order.SINGLE);
mol.addBond(1, 5, IBond.Order.DOUBLE);
mol.addBond(2, 5, IBond.Order.SINGLE);
mol.addBond(3, 6, IBond.Order.SINGLE);
mol.addBond(4, 6, IBond.Order.DOUBLE);
MoleculeSignature molSig = new MoleculeSignature(mol);
String sigFor0 = molSig.signatureStringForVertex(0);
Assert.assertEquals(expected, sigFor0);
}
@Test
public void testBenzeneWithDoubleBonds() {
IAtomContainer benzene = builder.newInstance(IAtomContainer.class);
AbstractSignatureTest.addCarbons(benzene, 6);
for (int i = 0; i < 6; i++) {
AbstractSignatureTest.addHydrogens(benzene, i, 1);
}
benzene.addBond(0, 1, IBond.Order.SINGLE);
benzene.addBond(1, 2, IBond.Order.DOUBLE);
benzene.addBond(2, 3, IBond.Order.SINGLE);
benzene.addBond(3, 4, IBond.Order.DOUBLE);
benzene.addBond(4, 5, IBond.Order.SINGLE);
benzene.addBond(5, 0, IBond.Order.DOUBLE);
MoleculeSignature signature = new MoleculeSignature(benzene);
String carbonSignature = signature.signatureStringForVertex(0);
for (int i = 1; i < 6; i++) {
String carbonSignatureI = signature.signatureStringForVertex(i);
Assert.assertEquals(carbonSignature, carbonSignatureI);
}
}