@Test
public void testAtomPermutation() throws CDKException {
IAtomContainer pamine = makePropylAmine();
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fp.getBitFingerprint(pamine);
AtomContainerAtomPermutor acp = new AtomContainerAtomPermutor(pamine);
while (acp.hasNext()) {
IAtomContainer container = acp.next();
IBitFingerprint bs2 = fp.getBitFingerprint(container);
Assert.assertTrue(bs1.equals(bs2));
}
}
@Test
public void testFingerprinter_int_int() throws java.lang.Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.assertNotNull(fingerprinter);
IAtomContainer mol = TestMoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
BitSet bs = fingerprinter.getBitFingerprint(mol).asBitSet();
IAtomContainer frag1 = TestMoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag1);
BitSet bs1 = fingerprinter.getBitFingerprint(frag1).asBitSet();
Assert.assertTrue(FingerprinterTool.isSubset(bs, bs1));
}
/**
* @cdk.bug 2819557
* @throws org.openscience.cdk.exception.CDKException
*/
@Test
public void testBug2819557() throws CDKException {
IAtomContainer butane = makeButane();
IAtomContainer propylAmine = makePropylAmine();
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
BitSet b1 = fp.getBitFingerprint(butane).asBitSet();
BitSet b2 = fp.getBitFingerprint(propylAmine).asBitSet();
Assert.assertFalse(FingerprinterTool.isSubset(b2, b1));
Assert.assertFalse(
"butane should not be a substructure of propylamine", FingerprinterTool.isSubset(b2, b1));
}
@Test
public void testAtomPermutation2() throws CDKException {
IAtomContainer pamine = TestMoleculeFactory.makeCyclopentane();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(pamine);
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fp.getBitFingerprint(pamine);
AtomContainerAtomPermutor acp = new AtomContainerAtomPermutor(pamine);
while (acp.hasNext()) {
IAtomContainer container = acp.next();
IBitFingerprint bs2 = fp.getBitFingerprint(container);
Assert.assertTrue(bs1.equals(bs2));
}
}
@Test
public void testRegression() throws Exception {
IAtomContainer mol1 = TestMoleculeFactory.makeIndole();
IAtomContainer mol2 = TestMoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fingerprinter.getBitFingerprint(mol1);
Assert.assertEquals(
"Seems the fingerprint code has changed. This will cause a number of other tests to fail too!",
22,
bs1.cardinality());
IBitFingerprint bs2 = fingerprinter.getBitFingerprint(mol2);
Assert.assertEquals(
"Seems the fingerprint code has changed. This will cause a number of other tests to fail too!",
11,
bs2.cardinality());
}
@Test
public void testFingerprinterBitSetSize() throws Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.assertNotNull(fingerprinter);
IAtomContainer mol = TestMoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
BitSet bs = fingerprinter.getBitFingerprint(mol).asBitSet();
Assert.assertEquals(1024, bs.length()); // highest set bit
Assert.assertEquals(1024, bs.size()); // actual bit set size
}
@Test
public void testgetBitFingerprint_IAtomContainer() throws java.lang.Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IAtomContainer mol = TestMoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
IBitFingerprint bs = fingerprinter.getBitFingerprint(mol);
Assert.assertNotNull(bs);
Assert.assertEquals(fingerprinter.getSize(), bs.size());
}
@Test
public void testGenerateFingerprintNaphthalene() throws InvalidSmilesException, Exception {
String smiles = "C1=CC2=CC=CC=C2C=C1";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
Aromaticity.cdkLegacy().apply(molecule);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitSet fingerprint1;
fingerprint1 = fingerprint.getBitFingerprint(molecule).asBitSet();
org.junit.Assert.assertEquals(8, fingerprint1.cardinality());
}
/**
* Test of ShortestPathFingerprinter method
*
* @throws InvalidSmilesException
* @throws CDKException
*/
@Test
public void testGenerateFingerprintIsSubset() throws InvalidSmilesException, CDKException {
String smilesT = "NC(=O)C1=C2C=CC(Br)=CC2=C(Cl)C=C1";
String smilesQ = "CC1=C2C=CC(Br)=CC2=C(Cl)C=C1";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer moleculeQ = smilesParser.parseSmiles(smilesQ);
IAtomContainer moleculeT = smilesParser.parseSmiles(smilesT);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(moleculeQ);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(moleculeT);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitSet fingerprintQ;
BitSet fingerprintT;
fingerprintQ = fingerprint.getBitFingerprint(moleculeQ).asBitSet();
fingerprintT = fingerprint.getBitFingerprint(moleculeT).asBitSet();
org.junit.Assert.assertTrue(FingerprinterTool.isSubset(fingerprintT, fingerprintQ));
}
/**
* Test of ShortestPathFingerprinter method
*
* @throws InvalidSmilesException
* @throws CDKException
* @throws FileNotFoundException
*/
@Test
public void testGenerateFingerprintIsNotASubset1()
throws InvalidSmilesException, CDKException, FileNotFoundException, FileNotFoundException {
String smilesT = "O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O";
String smilesQ = "OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
smilesParser.kekulise(false);
IAtomContainer moleculeQ = smilesParser.parseSmiles(smilesQ);
IAtomContainer moleculeT = smilesParser.parseSmiles(smilesT);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(moleculeQ);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(moleculeT);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitSet fingerprintQ;
BitSet fingerprintT;
fingerprintQ = fingerprint.getBitFingerprint(moleculeQ).asBitSet();
fingerprintT = fingerprint.getBitFingerprint(moleculeT).asBitSet();
org.junit.Assert.assertFalse(FingerprinterTool.isSubset(fingerprintT, fingerprintQ));
}