net.sf.octet.test
Class QueryTest

java.lang.Object
  junit.framework.Assert
      junit.framework.TestCase
          net.sf.octet.test.OctetTestCase
              net.sf.octet.test.QueryTest

All Implemented Interfaces:

junit.framework.Test

public class QueryTest

extends OctetTestCase

A test for MoleculeQuery functionality.

Author:

Richard Apodaca

Constructor Summary

QueryTest()
Default constructor.

Method Summary

void	testAromaticBenzeneMatchesExactKekuleBenzene() Verifies that aromatic benzene is an exact structure match of kekule benzene.
void	testCachedMoleculeQuery() Verifies that CachedMoleculeQuery returns the expected results.
void	testCompare23ButaneDiolIsomers() Constructs all three stereoisomers of 2,3-butanediol and verifies that a query specifying the (R,R) isomer only matches the (R,R) Molecule.
void	testCompareBinaphthylIsomersUsingQuery() Verifies that binpahthyl homomers match and enantiomers do not using MoleculeQuery.
void	testCompareButanoneCyanohydrinEnantiomers()
void	testCompareDimethylalleneIsomersUsingQuery() Verifies that dimethylallene homomers match and enantiomers do not using MoleculeQuery.
void	testCompareIsobutanolEnantiomersUsingQuery() Constructs both enantiomers of isobutanol and verifies that homomers match and enantiomers do not.
void	testComparePlatinIsomers() Constructs a transplatin MoleculeQuery, a transplatin Molecule, and a cisplatin Molecule, and verifies that the query matches only the transplatin Molecule.
void	testCubaneMatchesCubaneExact() Verifies that cubane is an exact structure match of another cubane Molecule.
void	testCyclohexaneMatchesBenzene() Verifies that cyclohexane is not an exact structure match of aromatic benzene.
void	testIsopentaneMatchesTButylCyclohexane() Verifies that isopentane matches t-butlycyclohexane as a substructure, but not as an exact structure.
void	testMatchButanolEnantiomersUsingMoleculeKit() Verifies that matching 2-butanol enantiomers using MoleculeKit gives the expected results.
void	testMatchNapthaleneToBinaphthylUsingMoleculeKit() Verifies that naphthalene matches as a substructure of binaphthyl using MoleculeKit, but that the reverse is not true.
void	testMatchPartialStereoQuery() Verifies that a substructure query matches (R)-2-butanol with (S)-2-cyano-2-butanol.
void	testMatchSerotoninUsingMoleculeKit() Indirectly verifies that two different serotonin Molecules are equivalent as determined by MoleculeKit.exactStructureMatch.
void	testMatchSingletAndTripletDichlorocarbene() Verifies that singlet and triplet dichlorocarbene match themselves, but not each other.
void	testSerotoninMatchesExactSerotonin() Verifies that two different serotonin Molecules exact-match.

Methods inherited from class net.sf.octet.test.OctetTestCase

getMoleculeBuilder

Methods inherited from class junit.framework.TestCase

countTestCases, createResult, getName, run, run, runBare, runTest, setName, setUp, tearDown, toString

Methods inherited from class junit.framework.Assert

assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertFalse, assertFalse, assertNotNull, assertNotNull, assertNotSame, assertNotSame, assertNull, assertNull, assertSame, assertSame, assertTrue, assertTrue, fail, fail

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

QueryTest

public QueryTest()

Default constructor.

Method Detail

testSerotoninMatchesExactSerotonin

public void testSerotoninMatchesExactSerotonin()

Verifies that two different serotonin Molecules exact-match.

testIsopentaneMatchesTButylCyclohexane

public void testIsopentaneMatchesTButylCyclohexane()

Verifies that isopentane matches t-butlycyclohexane as a substructure, but not as an exact structure.

testCubaneMatchesCubaneExact

public void testCubaneMatchesCubaneExact()

Verifies that cubane is an exact structure match of another cubane Molecule.

testAromaticBenzeneMatchesExactKekuleBenzene

public void testAromaticBenzeneMatchesExactKekuleBenzene()

Verifies that aromatic benzene is an exact structure match of kekule benzene.

testCyclohexaneMatchesBenzene

public void testCyclohexaneMatchesBenzene()

Verifies that cyclohexane is not an exact structure match of aromatic benzene.

testCompareIsobutanolEnantiomersUsingQuery

public void testCompareIsobutanolEnantiomersUsingQuery()

Constructs both enantiomers of isobutanol and verifies that homomers match and enantiomers do not.

testCompareButanoneCyanohydrinEnantiomers

public void testCompareButanoneCyanohydrinEnantiomers()

testComparePlatinIsomers

public void testComparePlatinIsomers()

Constructs a transplatin MoleculeQuery, a transplatin Molecule, and a cisplatin Molecule, and verifies that the query matches only the transplatin Molecule.

testCompare23ButaneDiolIsomers

public void testCompare23ButaneDiolIsomers()

Constructs all three stereoisomers of 2,3-butanediol and verifies that a query specifying the (R,R) isomer only matches the (R,R) Molecule.

testCompareBinaphthylIsomersUsingQuery

public void testCompareBinaphthylIsomersUsingQuery()

Verifies that binpahthyl homomers match and enantiomers do not using MoleculeQuery.

testCompareDimethylalleneIsomersUsingQuery

public void testCompareDimethylalleneIsomersUsingQuery()

Verifies that dimethylallene homomers match and enantiomers do not using MoleculeQuery. Note: this method takes orders of magnitude longer to execute than any other test. This is due to the way in which UllmanIsomorphismTraverser is implemented.

testCachedMoleculeQuery

public void testCachedMoleculeQuery()

Verifies that CachedMoleculeQuery returns the expected results.

testMatchSerotoninUsingMoleculeKit

public void testMatchSerotoninUsingMoleculeKit()

Indirectly verifies that two different serotonin Molecules are equivalent as determined by MoleculeKit.exactStructureMatch. Verifies that serotonin is not equivalent to naphthalene.

testMatchPartialStereoQuery

public void testMatchPartialStereoQuery()

Verifies that a substructure query matches (R)-2-butanol with (S)-2-cyano-2-butanol.

testMatchButanolEnantiomersUsingMoleculeKit

public void testMatchButanolEnantiomersUsingMoleculeKit()

Verifies that matching 2-butanol enantiomers using MoleculeKit gives the expected results.

testMatchNapthaleneToBinaphthylUsingMoleculeKit

public void testMatchNapthaleneToBinaphthylUsingMoleculeKit()

Verifies that naphthalene matches as a substructure of binaphthyl using MoleculeKit, but that the reverse is not true.

testMatchSingletAndTripletDichlorocarbene

public void testMatchSingletAndTripletDichlorocarbene()

Verifies that singlet and triplet dichlorocarbene match themselves, but not each other.