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Fixed and cleaned up molecule signature tests
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@gilleain @egonw
gilleain authored and egonw committed Jun 23, 2010
1 parent ff2bdeb commit 3998ed7
Showing 1 changed file with 93 additions and 111 deletions.
204 changes: 93 additions & 111 deletions src/test/org/openscience/cdk/signature/MoleculeSignatureTest.java
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Expand Up @@ -174,31 +174,31 @@ public void testMultipleChildren() throws Exception {
public void testThreeCycle() throws Exception {
String fourCycle = "C1CC1";
String signatureString = this.canonicalStringFromSmiles(fourCycle);
String expected = "[C]([C,2]([C,1])[C,1])";
String expected = "[C]([C]([C,0])[C,0])";
Assert.assertEquals(expected, signatureString);
}

@Test
public void testFourCycle() throws Exception {
String fourCycle = "C1CCC1";
String signatureString = this.canonicalStringFromSmiles(fourCycle);
String expected = "[C]([C]([C,1])[C]([C,1]))";
String expected = "[C]([C]([C,0])[C]([C,0]))";
Assert.assertEquals(expected, signatureString);
}

@Test
public void testMultipleFourCycles() throws Exception {
String bridgedRing = "C1C(C2)CC12";
String signatureString = this.canonicalStringFromSmiles(bridgedRing);
String expected = "[C]([C]([C,1])[C]([C,1])[C]([C,1]))";
String expected = "[C]([C]([C,0])[C]([C,0])[C]([C,0]))";
Assert.assertEquals(expected, signatureString);
}

@Test
public void testFiveCycle() throws Exception {
String fiveCycle = "C1CCCC1";
String signatureString = this.canonicalStringFromSmiles(fiveCycle);
String expected = "[C]([C]([C,2]([C,1]))[C]([C,1]))";
String expected = "[C]([C]([C]([C,0]))[C]([C,0]))";
Assert.assertEquals(expected, signatureString);
}

Expand All @@ -207,57 +207,50 @@ public void testMultipleFiveCycles() throws Exception {
String multipleFiveCycle = "C1C(CC2)CCC12";
String signatureString =
this.canonicalStringFromSmiles(multipleFiveCycle);
String expected = "[C]([C]([C]([C,1]))[C]([C]([C,1]))[C]([C,1]))";
String expected = "[C]([C]([C]([C,0]))[C]([C]([C,0]))[C]([C,0]))";
Assert.assertEquals(expected, signatureString);
}

@Test
public void testSandwich() {
IMolecule sandwich = AbstractSignatureTest.makeSandwich(5, true);
// IMolecule sandwich = AbstractSignatureTest.makeSandwich(5, false);
// toMolfileString(sandwich);
randomPermutationTest(sandwich);
}

@Test
public void testCubane() {
String expected = "[C]([C]([C,4]([C,3])[C,2]([C,3]))[C]([C,4][C,1]" +
"([C,3]))[C]([C,1][C,2]))";
String expected = "[C]([C]([C,3]([C,2])[C,1]([C,2]))[C]([C,3][C,0]" +
"([C,2]))[C]([C,0][C,1]))";
IMolecule mol = AbstractSignatureTest.makeCubane();
Assert.assertEquals(expected, this.canonicalStringFromMolecule(mol));
}

@Test
public void testCage() {
String expectedA = "[C]([C]([C]([C,5][C,4]([C,1]))[C]([C,6][C,4]))" +
"[C]([C,5]([C]([C,1][C,2]))[C]([C,2]([C,3])[C,7]))"+
"[C]([C,6]([C]([C,1][C,3]))[C,7]([C,3])))";
String expectedB = "[C]([C]([C]([C]([C,2]([C,1])[C,5])[C,6])[C,8]" +
"([C,5]([C,4])))[C]([C]([C,4]([C,1])[C,7])[C,8])" +
"[C]([C,6]([C]([C,3][C,2]))[C,7]([C,3]([C,1]))))";
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]))))";
IMolecule mol = AbstractSignatureTest.makeCage();
String signature = this.canonicalStringFromMolecule(mol);
Assert.assertEquals(expectedA, signature);
Assert.assertFalse(expectedB.equals(signature));
String fullSignature = fullStringFromMolecule(mol);
String fullExpected = "8" + expectedA + " + 8" + expectedB;
// System.out.println(fullSignature);
Assert.assertEquals(fullExpected, fullSignature);
}

@Test
public void testPropellane() {
String expectedA = "[C]([C]([C,3])[C,2]([C,1][C,3])[C,2][C,1])";
String expectedB = "[C]([C]([C,1])[C]([C,1])[C]([C,1])[C,1])";
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]))";
IMolecule mol = AbstractSignatureTest.makePropellane();
String signature = this.canonicalStringFromMolecule(mol);
Assert.assertEquals(expectedB, signature);
Assert.assertFalse(expectedA.equals(signature));
Assert.assertEquals(expectedA, signature);
String fullExpected = "2" + expectedA + " + 3" + expectedB;
String fullSignature = fullStringFromMolecule(mol);
Assert.assertEquals(fullExpected, fullSignature);
}

@Test
public void testBridgedCycloButane() {
String expected = "[C]([C]([C,1])[C]([C,1])[C,1])";
String expected = "[C]([C]([C,0])[C]([C,0])[C,0])";
IMolecule mol = AbstractSignatureTest.makeBridgedCyclobutane();
String signature = this.canonicalStringFromMolecule(mol);
for (String atomicSignature : this.getAtomicSignatures(mol)) {
Expand All @@ -266,46 +259,19 @@ public void testBridgedCycloButane() {
Assert.assertEquals(expected, signature);
}

@Test
public void testCageAtVariousHeights() {
IMolecule cage = AbstractSignatureTest.makeCage();
MoleculeSignature molSig;
molSig = new MoleculeSignature(cage, 2);
System.out.println(molSig.signatureStringForVertex(0, 2));
molSig = new MoleculeSignature(cage, 3);
System.out.println(molSig.signatureStringForVertex(0, 3));
}

@Test
public void testCyclohexaneWithHydrogens() {
IMolecule cyclohexane = MoleculeFactory.makeCyclohexane();
for (int i = 0; i < 6; i++) {
addHydrogens(cyclohexane, cyclohexane.getAtom(i), 2);
}
String expected = "[C]([C]([C]([C,1]([H][H])[H][H])[H][H])" +
"[C]([C]([C,1][H][H])[H][H])[H][H])";
String expected = "[C]([C]([C]([C,0]([H][H])[H][H])[H][H])" +
"[C]([C]([C,0][H][H])[H][H])[H][H])";

String actual = this.canonicalStringFromMolecule(cyclohexane);
Assert.assertEquals(expected, actual);
}

public void testSmiles(String smiles) {
try {
IMolecule molecule = this.parser.parseSmiles(smiles);
MoleculeSignature sig = new MoleculeSignature(molecule);
// System.out.println(sig.toFullString());
System.out.println(sig.toCanonicalString());
} catch (Exception e) {

}
}

@Test
public void testCuneane() {
String cuneaneSmiles = "C1C2C3CC4C1C4C23";
testSmiles(cuneaneSmiles);
}

@Test
public void testBenzeneWithDoubleBonds() {
IMolecule benzene = builder.newInstance(IMolecule.class);
Expand All @@ -330,15 +296,19 @@ public void testBenzeneWithDoubleBonds() {

@Test
public void cyclobuteneTest() {
String expectedA = "[C]([C]([C,0])=[C]([C,0]))";
String expectedB = "[C]([C]([C,0])[C](=[C,0]))";
IMolecule cyclobutene = builder.newInstance(IMolecule.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);
// toMolfileString(cyclobutene);
randomPermutationTest(cyclobutene);
// System.out.println(fullStringFromMolecule(cyclobutene));
Assert.assertEquals(expectedA, canonicalStringFromMolecule(cyclobutene));

String expectedFullString = "2" + expectedA + " + 2" + expectedB;
String actualFullString = fullStringFromMolecule(cyclobutene);
Assert.assertEquals(expectedFullString, actualFullString);
}

@Test
Expand All @@ -353,17 +323,22 @@ public void methyleneCyclopropeneTest() {
mol.addBond(0, 3, IBond.Order.SINGLE);
mol.addBond(2, 3, IBond.Order.DOUBLE);
MoleculeSignature molSig = new MoleculeSignature(mol);
for (int i = 0; i < 4; i++) {
String sigForIHeight2 = molSig.signatureStringForVertex(i, 2);
System.out.println(i + " " + sigForIHeight2);
}
// AbstractSignatureTest.print(mol);
// toMolfileString(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 fusedSquareMultipleBondTest() {
IMolecule mol = builder.newInstance(IMolecule.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);
Expand All @@ -373,42 +348,49 @@ public void fusedSquareMultipleBondTest() {
mol.addBond(2, 5, IBond.Order.SINGLE);
mol.addBond(3, 6, IBond.Order.SINGLE);
mol.addBond(4, 6, IBond.Order.DOUBLE);
// toMolfileString(mol);
// MoleculeSignature molSig = new MoleculeSignature(mol);
// String sigFor0 = molSig.signatureStringForVertex(0);
// System.out.println(sigFor0);
randomPermutationTest(mol);
MoleculeSignature molSig = new MoleculeSignature(mol);
String sigFor0 = molSig.signatureStringForVertex(0);
Assert.assertEquals(expected, sigFor0);
}

@Test
public void testPolyPhenylMolecule() throws Exception {
String smiles = "C1=CC=C(C=C1)P(C2=CC=CC=C2)(C3=CC=CC=C3)[RhH]" +
"(P(C4=CC=CC=C4)(C5=CC=CC=C5)C6=CC=CC=C6)(P(C7=CC=CC=C7)" +
"(C8=CC=CC=C8)C9=CC=CC=C9)P(C%10=CC=CC=C%10)" +
"(C%11=CC=CC=C%11)C%12=CC=CC=C%12";
// testSmiles(smiles);
IMolecule mol = parser.parseSmiles(smiles);
int rhIndex = 0;
for (int i = 0; i < mol.getAtomCount(); i++) {
if (mol.getAtom(i).getSymbol().equals("Rh")) {
rhIndex = i;
break;
public int findFirstAtomIndexForSymbol(
IAtomContainer container, String symbol) {
for (int i = 0; i < container.getAtomCount(); i++) {
if (container.getAtom(i).getSymbol().equals(symbol)) {
return i;
}
}
// System.out.println("rh index = " + rhIndex);
MoleculeSignature molSig = new MoleculeSignature(mol);
String signatureForRh = molSig.signatureStringForVertex(rhIndex);
System.out.println(signatureForRh);
// toMolfileString(mol);
}
return -1;
}

// XXX commented out this test for now, as it takes a long time - this
// is a known weakness of the current implementation
// @Test
// public void testPolyPhenylMolecule() throws Exception {
// String smiles = "C1=CC=C(C=C1)P(C2=CC=CC=C2)(C3=CC=CC=C3)[RhH]" +
// "(P(C4=CC=CC=C4)(C5=CC=CC=C5)C6=CC=CC=C6)(P(C7=CC=CC=C7)" +
// "(C8=CC=CC=C8)C9=CC=CC=C9)P(C%10=CC=CC=C%10)" +
// "(C%11=CC=CC=C%11)C%12=CC=CC=C%12";
//// testSmiles(smiles);
// IMolecule mol = parser.parseSmiles(smiles);
// int rhIndex = findFirstAtomIndexForSymbol(mol, "Rh");

// MoleculeSignature molSig = new MoleculeSignature(mol);
// String signatureForRh = molSig.signatureStringForVertex(rhIndex);
// System.out.println(signatureForRh);
// }

@Test
public void methylFerroceneTest() throws Exception {
String smiles = "CC12C3C4C5C1[Fe]23456789C%10C6C7C8C9%10";
// testSmiles(smiles);
IMolecule mol = parser.parseSmiles(smiles);
// toMolfileString(mol);
randomPermutationTest(mol);
MoleculeSignature molSig = new MoleculeSignature(mol);
int feIndex = findFirstAtomIndexForSymbol(mol, "Fe");
String sigForIron = molSig.signatureStringForVertex(feIndex);
String expected = "[Fe]([C]([C,3][C,4])[C,3]([C,1])[C,4]([C,0])" +
"[C]([C,5][C,6])[C,5]([C,2])[C,6]([C,7])" +
"[C,7]([C][C,2])[C,0]([C,1])[C,1][C,2])";
Assert.assertEquals(expected, sigForIron);
}

@Test
Expand All @@ -420,26 +402,33 @@ public void threeMethylSulphanylPropanal() throws Exception {
@Test
public void cycleWheelTest() {
IMolecule mol = AbstractSignatureTest.makeCycleWheel(3, 3);
// AbstractSignatureTest.print(mol);
// toMolfileString(mol);
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);
System.out.println(centralSignature);
// for (String signature : getAtomicSignatures(threeThreeWheel)) {
// System.out.println(signature);
// }
Assert.assertEquals(expected, centralSignature);
}

@Test
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;
IMolecule ttpr =
AbstractSignatureTest.makeRhLikeStructure(phosphateCount, ringCount);
// toMolfileString(ttpr);
MoleculeSignature molSig = new MoleculeSignature(ttpr);
String centralSignature = molSig.signatureStringForVertex(0);
System.out.println(centralSignature);
Assert.assertEquals(expected, centralSignature);
}

@Test
Expand Down Expand Up @@ -474,9 +463,6 @@ public void napthaleneSkeletonHeightTest() {
}
orbit.addAtom(i);
}
// for (String key : orbits.keySet()) {
// System.out.println(orbits.get(key));
// }
Assert.assertEquals(3, orbits.size());
}

Expand Down Expand Up @@ -516,14 +502,10 @@ public void napthaleneWithDoubleBondsAndHydrogenHeightTest() {
napthalene.addBond(9, 17, IBond.Order.SINGLE);

int height = 2;
// MoleculeSignature molSig = new MoleculeSignature(napthalene);
// for (int i = 0; i < napthalene.getAtomCount(); i++) {
// String sigString = molSig.signatureStringForVertex(i, height);
// System.out.println(i + " " + sigString);
// }
SignatureQuotientGraph mqg =
new SignatureQuotientGraph(napthalene, height);
System.out.println(mqg);

Assert.assertEquals(4, mqg.getVertexCount());
Assert.assertEquals(6, mqg.getEdgeCount());
Assert.assertEquals(2, mqg.numberOfLoopEdges());
}
}

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