@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 testBridgedCycloButane() {
String expected = "[C]([C]([C,0])[C]([C,0])[C,0])";
IAtomContainer mol = AbstractSignatureTest.makeBridgedCyclobutane();
String signature = this.canonicalStringFromMolecule(mol);
Assert.assertEquals(expected, signature);
}
@Test
public void testCubane() {
String expected =
"[C]([C]([C,3]([C,2])[C,1]([C,2]))[C]([C,3][C,0]" + "([C,2]))[C]([C,0][C,1]))";
IAtomContainer mol = AbstractSignatureTest.makeCubane();
Assert.assertEquals(expected, this.canonicalStringFromMolecule(mol));
}
@Test
public void cycleWheelTest() {
IAtomContainer mol = AbstractSignatureTest.makeCycleWheel(3, 3);
String expected = "[C]([C]([C]([C,2])[C,2])" + "[C]([C]([C,1])[C,1])" + "[C]([C]([C,0])[C,0]))";
MoleculeSignature molSig = new MoleculeSignature(mol);
String centralSignature = molSig.signatureStringForVertex(0);
Assert.assertEquals(expected, centralSignature);
}
@Test
public void testPropellane() {
String expectedA = "[C]([C]([C,0])[C]([C,0])[C]([C,0])[C,0])";
String expectedB = "[C]([C]([C,2][C,1][C,0])[C,2]([C,1][C,0]))";
IAtomContainer mol = AbstractSignatureTest.makePropellane();
String signature = this.canonicalStringFromMolecule(mol);
Assert.assertEquals(expectedA, signature);
String fullExpected = "2" + expectedA + " + 3" + expectedB;
String fullSignature = fullStringFromMolecule(mol);
Assert.assertEquals(fullExpected, fullSignature);
}
@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);
}
}
@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 testCage() {
String expectedA =
"[C]([C]([C]([C,4][C,3]([C,1]))[C]([C,5][C,3]))"
+ "[C]([C,4]([C]([C,2][C,1]))[C]([C,2]([C,0])[C,6]))"
+ "[C]([C,5]([C]([C,0][C,1]))[C,6]([C,0])))";
String expectedB =
"[C]([C]([C]([C]([C,1]([C,0])[C,4])[C,5])[C,7]"
+ "([C,4]([C,3])))[C]([C]([C,3]([C,0])[C,6])[C,7])"
+ "[C]([C,5]([C]([C,2][C,1]))[C,6]([C,2]([C,0]))))";
IAtomContainer mol = AbstractSignatureTest.makeCage();
String signature = this.canonicalStringFromMolecule(mol);
Assert.assertEquals(expectedA, signature);
String fullSignature = fullStringFromMolecule(mol);
String fullExpected = "8" + expectedA + " + 8" + expectedB;
Assert.assertEquals(fullExpected, fullSignature);
}
@Test
@Category(SlowTest.class)
public void ttprTest() {
String expected =
"[Rh]([P]([C]([C]([C]([C,6]))"
+ "[C]([C]([C,6])))[C]([C]([C]([C,3]))"
+ "[C]([C]([C,3])))[C]([C]([C]([C,2]))"
+ "[C]([C]([C,2]))))[P]([C]([C]([C]([C,7]))"
+ "[C]([C]([C,7])))[C]([C]([C]([C,4]))"
+ "[C]([C]([C,4])))[C]([C]([C]([C,1]))"
+ "[C]([C]([C,1]))))[P]([C]([C]([C]([C,8]))"
+ "[C]([C]([C,8])))[C]([C]([C]([C,5]))"
+ "[C]([C]([C,5])))[C]([C]([C]([C,0]))"
+ "[C]([C]([C,0])))))";
int phosphateCount = 3;
int ringCount = 3;
IAtomContainer ttpr = AbstractSignatureTest.makeRhLikeStructure(phosphateCount, ringCount);
MoleculeSignature molSig = new MoleculeSignature(ttpr);
String centralSignature = molSig.signatureStringForVertex(0);
Assert.assertEquals(expected, centralSignature);
}