uk.ac.cam.ch.wwmm.opsin
Class SMILESFragmentBuilderTest

java.lang.Object
  extended by uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest

public class SMILESFragmentBuilderTest
extends java.lang.Object


Constructor Summary
SMILESFragmentBuilderTest()
           
 
Method Summary
 void badlyFormedSMILE1()
           
 void badlyFormedSMILE2()
           
 void badlyFormedSMILE3()
           
 void badlyFormedSMILE4()
           
 void badlyFormedSMILE5()
           
 void badlyFormedSMILE6()
           
 void badlyFormedSMILE7()
           
 void badlyFormedSMILE8()
           
 void chiralityTest1()
           
 void chiralityTest2()
           
 void chiralityTest3()
           
 void chiralityTest4()
           
 void chiralityTest5()
           
 void chiralityTest6()
           
 void chiralityTest7()
           
 void chiralityTest8()
           
 void doubleNegativeCharge1()
           
 void doubleNegativeCharge2()
           
 void doublePositiveCharge1()
           
 void doublePositiveCharge2()
           
 void hydrogenHandling1()
           
 void hydrogenHandling10()
           
 void hydrogenHandling11()
           
 void hydrogenHandling12()
           
 void hydrogenHandling13()
           
 void hydrogenHandling14()
           
 void hydrogenHandling15()
           
 void hydrogenHandling16()
           
 void hydrogenHandling17()
           
 void hydrogenHandling18()
           
 void hydrogenHandling19()
           
 void hydrogenHandling2()
           
 void hydrogenHandling20()
           
 void hydrogenHandling21()
           
 void hydrogenHandling3()
           
 void hydrogenHandling4()
           
 void hydrogenHandling5()
           
 void hydrogenHandling6()
           
 void hydrogenHandling7()
           
 void hydrogenHandling8()
           
 void hydrogenHandling9()
           
 void indicatedHydrogen1()
           
 void indicatedHydrogen2()
           
 void isotopeSpecified()
           
 void noIsotopeSpecified()
           
 void ringClosureHandling1()
           
 void ringClosureHandling2()
           
 void ringClosureHandling3()
           
 void ringClosureHandling4()
           
 void ringSupportGreaterThan10()
           
 void setUp()
           
 void testBuild()
           
 void testDoubleBondMultiStereo1()
           
 void testDoubleBondMultiStereo2()
           
 void testDoubleBondMultiStereo3()
           
 void testDoubleBondMultiStereo4()
           
 void testDoubleBondNoela()
           
 void testDoubleBondNoelb()
           
 void testDoubleBondNoelc()
           
 void testDoubleBondNoeld()
           
 void testDoubleBondNoele()
           
 void testDoubleBondNoelf()
           
 void testDoubleBondNoelg()
           
 void testDoubleBondNoelLike1()
           
 void testDoubleBondNoelLike2()
           
 void testDoubleBondStereo1()
           
 void testDoubleBondStereo2()
           
 void testDoubleBondStereo3()
           
 void testDoubleBondStereo4()
           
 void testDoubleBondStereo5a()
           
 void testDoubleBondStereo5b()
           
 void testDoubleBondStereo6()
           
 void testSimple1()
           
 void testSimple10()
           
 void testSimple11()
           
 void testSimple2()
           
 void testSimple3()
           
 void testSimple4()
           
 void testSimple5()
           
 void testSimple6()
           
 void testSimple7()
           
 void testSimple8()
           
 void testSimple9()
           
 void unterminatedRingOpening()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SMILESFragmentBuilderTest

public SMILESFragmentBuilderTest()
Method Detail

setUp

public void setUp()

testBuild

public void testBuild()
               throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple1

public void testSimple1()
                 throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple2

public void testSimple2()
                 throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple3

public void testSimple3()
                 throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple4

public void testSimple4()
                 throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple5

public void testSimple5()
                 throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple6

public void testSimple6()
                 throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple7

public void testSimple7()
                 throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple8

public void testSimple8()
                 throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple9

public void testSimple9()
                 throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple10

public void testSimple10()
                  throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testSimple11

public void testSimple11()
                  throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

unterminatedRingOpening

public void unterminatedRingOpening()
                             throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

doublePositiveCharge1

public void doublePositiveCharge1()
                           throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

doublePositiveCharge2

public void doublePositiveCharge2()
                           throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

doubleNegativeCharge1

public void doubleNegativeCharge1()
                           throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

doubleNegativeCharge2

public void doubleNegativeCharge2()
                           throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

noIsotopeSpecified

public void noIsotopeSpecified()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

isotopeSpecified

public void isotopeSpecified()
                      throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

badlyFormedSMILE1

public void badlyFormedSMILE1()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

badlyFormedSMILE2

public void badlyFormedSMILE2()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

badlyFormedSMILE3

public void badlyFormedSMILE3()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

badlyFormedSMILE4

public void badlyFormedSMILE4()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

badlyFormedSMILE5

public void badlyFormedSMILE5()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

badlyFormedSMILE6

public void badlyFormedSMILE6()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

badlyFormedSMILE7

public void badlyFormedSMILE7()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

badlyFormedSMILE8

public void badlyFormedSMILE8()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

ringClosureHandling1

public void ringClosureHandling1()
                          throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

ringClosureHandling2

public void ringClosureHandling2()
                          throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

ringClosureHandling3

public void ringClosureHandling3()
                          throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

ringClosureHandling4

public void ringClosureHandling4()
                          throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

ringSupportGreaterThan10

public void ringSupportGreaterThan10()
                              throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling1

public void hydrogenHandling1()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling2

public void hydrogenHandling2()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling3

public void hydrogenHandling3()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling4

public void hydrogenHandling4()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling5

public void hydrogenHandling5()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling6

public void hydrogenHandling6()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling7

public void hydrogenHandling7()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling8

public void hydrogenHandling8()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling9

public void hydrogenHandling9()
                       throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling10

public void hydrogenHandling10()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling11

public void hydrogenHandling11()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling12

public void hydrogenHandling12()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling13

public void hydrogenHandling13()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling14

public void hydrogenHandling14()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling15

public void hydrogenHandling15()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling16

public void hydrogenHandling16()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling17

public void hydrogenHandling17()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling18

public void hydrogenHandling18()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling19

public void hydrogenHandling19()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling20

public void hydrogenHandling20()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

hydrogenHandling21

public void hydrogenHandling21()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

indicatedHydrogen1

public void indicatedHydrogen1()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

indicatedHydrogen2

public void indicatedHydrogen2()
                        throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

chiralityTest1

public void chiralityTest1()
                    throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

chiralityTest2

public void chiralityTest2()
                    throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

chiralityTest3

public void chiralityTest3()
                    throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

chiralityTest4

public void chiralityTest4()
                    throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

chiralityTest5

public void chiralityTest5()
                    throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

chiralityTest6

public void chiralityTest6()
                    throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

chiralityTest7

public void chiralityTest7()
                    throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

chiralityTest8

public void chiralityTest8()
                    throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondStereo1

public void testDoubleBondStereo1()
                           throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondStereo2

public void testDoubleBondStereo2()
                           throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondStereo3

public void testDoubleBondStereo3()
                           throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondStereo4

public void testDoubleBondStereo4()
                           throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondStereo5a

public void testDoubleBondStereo5a()
                            throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondStereo5b

public void testDoubleBondStereo5b()
                            throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondStereo6

public void testDoubleBondStereo6()
                           throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondMultiStereo1

public void testDoubleBondMultiStereo1()
                                throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondMultiStereo2

public void testDoubleBondMultiStereo2()
                                throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondMultiStereo3

public void testDoubleBondMultiStereo3()
                                throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondMultiStereo4

public void testDoubleBondMultiStereo4()
                                throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondNoela

public void testDoubleBondNoela()
                         throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondNoelb

public void testDoubleBondNoelb()
                         throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondNoelc

public void testDoubleBondNoelc()
                         throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondNoeld

public void testDoubleBondNoeld()
                         throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondNoele

public void testDoubleBondNoele()
                         throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondNoelf

public void testDoubleBondNoelf()
                         throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondNoelg

public void testDoubleBondNoelg()
                         throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondNoelLike1

public void testDoubleBondNoelLike1()
                             throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException

testDoubleBondNoelLike2

public void testDoubleBondNoelLike2()
                             throws uk.ac.cam.ch.wwmm.opsin.StructureBuildingException
Throws:
uk.ac.cam.ch.wwmm.opsin.StructureBuildingException