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A

acceptableInterWordBreaks() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
aceanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
acenaphthene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
acephenanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
aceticacid() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
acrindoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
allowInterpretationOfAcidsWithoutTheWordAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Are acids without the word "acid" interpretable e.g.
AmbiguityDetectionTest - Class in uk.ac.cam.ch.wwmm.opsin
 
AmbiguityDetectionTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.AmbiguityDetectionTest
 
anthratetraphene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
anthrazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
anthyridine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
applyStereochemistryCis() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryLocantedE() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryLocantedRS() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryLocantedZ() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryTrans() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryUnlocantedE() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryUnlocantedZ() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
arsanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
arsanthridine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
arsindole() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
arsindoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
AtomTest - Class in uk.ac.cam.ch.wwmm.opsin
 
AtomTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.AtomTest
 

B

badlyFormedSMILE1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
benzo_cd_azulene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
betacarboline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
BondTest - Class in uk.ac.cam.ch.wwmm.opsin
 
BondTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.BondTest
 
boranthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
bracketedHexachlorohexane() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
bracketedPrimeNotSpecialCase() - Method in class uk.ac.cam.ch.wwmm.opsin.StructureBuildingMethodsTest
 
bracketedPrimeSpecialCase1() - Method in class uk.ac.cam.ch.wwmm.opsin.StructureBuildingMethodsTest
 
bracketedPrimeSpecialCase2() - Method in class uk.ac.cam.ch.wwmm.opsin.StructureBuildingMethodsTest
 

C

cas1() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas10() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas11() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas12() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas13() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas14() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas15() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas16() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas17() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas18() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas19() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas2() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas20() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas21() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas22() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas23() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas24() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas3() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas4() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas5() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas6() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas7() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas8() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas9() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
CASToolsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
CASToolsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
CCCP() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
CCCP_RL() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
chiralityTest1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
cholanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.AmbiguityDetectionTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.VerifyFragmentsTest
 
clone() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
 
ComponentGeneration_AmbiguitiesAndIrregularitiesTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ComponentGeneration_AmbiguitiesAndIrregularitiesTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
ComponentGeneration_MiscTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ComponentGeneration_MiscTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_MiscTest
 
ComponentGeneration_ProcesslocantsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ComponentGeneration_ProcesslocantsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
ComponentGeneration_StereochemistryTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ComponentGeneration_StereochemistryTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
ComponentProcessorTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ComponentProcessorTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
compoundWithInvalidUse1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
compoundWithInvalidUse2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
compoundWithValidUse() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
coronene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
CycleDetectorTest - Class in uk.ac.cam.ch.wwmm.opsin
 
CycleDetectorTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 

D

difficultChain() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
difficultChain2() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
doubleNegativeCharge1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
doubleNegativeCharge2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
doublePositiveCharge1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
doublePositiveCharge2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
DtdTest - Class in uk.ac.cam.ch.wwmm.opsin
 
DtdTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.DtdTest
 

E

equals(Object) - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
 
ethylChloride() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 

F

findStereoCentresBromoChloroFluoroMethane() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
findStereoCentresBut2ene() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
findStereoCentresNacetylleucine() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
FragmentManagerTest - Class in uk.ac.cam.ch.wwmm.opsin
 
FragmentManagerTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
FragmentTest - Class in uk.ac.cam.ch.wwmm.opsin
 
FragmentTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
FusedRingNumbererFunctionsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
FusedRingNumbererFunctionsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererFunctionsTest
 
FusedRingNumbererTest - Class in uk.ac.cam.ch.wwmm.opsin
Tests that fused ring numbering is working as expected.
FusedRingNumbererTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

G

getAnnotations() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
 
getChemicalName() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Returns the chemical name that this OpsinResult was generated from
getCml() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Generates the CML corresponding to the molecule described by the name If name generation failed i.e.
getDefaultConfigInstance() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Constructs a NameToStructureConfig with default settings: allowRadicals = false outputRadicalsAsWildCardAtoms = false detailedFailureAnalysis = false interpretAcidsWithoutTheWordAcid = false warnRatherThanFailOnUninterpretableStereochemistry = false
getExplanation() - Method in enum uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
 
getExtendedSmiles() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Experimental function that generates the extended SMILES corresponding to the molecule described by the name If name generation failed i.e.
getInstance() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
 
getMessage() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Returns a message explaining why generation of a molecule from the name failed This string will be blank when no problems were encountered
getMessage() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinWarning
 
getOpsinParser() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Returns an OPSIN parser This can be used to determine whether a word can be interpreted as being part of a chemical name.
getParses(String) - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRules
Determines the possible annotations for a chemical word Returns a list of parses and how much of the word could not be interpreted e.g.
getParseTokensList() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
One ParseTokens object is returned for each possible interpretation of a chemical name If none of the name can be interpreted this list will be empty
getPrettyPrintedCml() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Generates the CML corresponding to the molecule described by the name If name generation failed i.e.
getSmiles() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Generates the SMILES corresponding to the molecule described by the name If name generation failed i.e.
getStatus() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Returns an enum with values SUCCESS, WARNING and FAILURE Currently warning is never used
getTokens() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
 
getType() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinWarning
 
getUninterpretableName() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
The substring of the name that could not be classified into a substituent/full/functionalTerm e.g.
getUnparseableName() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
The substring of the name that could not be tokenised at all.
getVersion() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Returns the version of the OPSIN library
getWarnings() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
A list of warnings encountered when the result was OpsinResult.OPSIN_RESULT_STATUS.WARNING
This list of warnings is immutable

H

hashCode() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
 
HeteroAtomReplacementTest - Class in uk.ac.cam.ch.wwmm.opsin
 
HeteroAtomReplacementTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
hexachlorohexane() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
hexachlorohexaneeeeeee() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
hexane() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
hydrogenHandling1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling11() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling12() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling13() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling14() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling15() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling16() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling17() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling18() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling19() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling20() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling21() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling9() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 

I

indane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
indeno_7_1_cd_azepine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
indicatedHydrogen() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
intialSetup() - Static method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
isAllowRadicals() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Are radicals allowed? e.g.
isDetailedFailureAnalysis() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Should OPSIN attempt reverse parsing to more accurately determine why parsing failed
isoarsindole() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isoarsinoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isophosphindole() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isophosphinoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isotopeSpecified() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
isOutputRadicalsAsWildCardAtoms() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Are radicals output as wildcard atoms e.g.
isoviolanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

M

main(String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Run OPSIN as a command-line application.
mercuranthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
methyl() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 

N

nameAppearsToBeAmbiguous() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Convenience method to check if one of the associated OPSIN warnings was OpsinWarning.OpsinWarningType.APPEARS_AMBIGUOUS
NameToStructure - Class in uk.ac.cam.ch.wwmm.opsin
The "master" class, to turn a name into a structure.
NameToStructureConfig - Class in uk.ac.cam.ch.wwmm.opsin
Allows OPSIN to be configured e.g.
NameToStructureConfig() - Constructor for class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Constructs a NameToStructureConfig with default settings: allowRadicals = false outputRadicalsAsWildCardAtoms = false detailedFailureAnalysis = false interpretAcidsWithoutTheWordAcid = false warnRatherThanFailOnUninterpretableStereochemistry = false
NameToStructureConfigurationsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
NameToStructureConfigurationsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
NameToStructureException - Exception in uk.ac.cam.ch.wwmm.opsin
Thrown if OPSIN failed to initialise
NameToStructureTest - Class in uk.ac.cam.ch.wwmm.opsin
 
NameToStructureTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.NameToStructureTest
 
naphthotetraphene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
noIsotopeSpecified() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
notCas1() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
notCas2() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
notCas3() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
notPhosphoSubstitution() - Method in class uk.ac.cam.ch.wwmm.opsin.StructureBuildingMethodsTest
 

O

octalenotetraphene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
OpsinResult - Class in uk.ac.cam.ch.wwmm.opsin
Holds the structure OPSIN has generated from a name Additionally holds a status code for whether name interpretation was successful
OpsinResult.OPSIN_RESULT_STATUS - Enum in uk.ac.cam.ch.wwmm.opsin
Whether parsing the chemical name was successful, encountered problems or was unsuccessful.
If the result is not OpsinResult.OPSIN_RESULT_STATUS.FAILURE then a structure has been generated
OpsinWarning - Class in uk.ac.cam.ch.wwmm.opsin
A warning generated by OPSIN while interpreting a name.
The specifics of the warning may be used to judge whether you want to accept the generated structure.
OpsinWarning.OpsinWarningType - Enum in uk.ac.cam.ch.wwmm.opsin
The type of problem OPSIN encountered
ovalene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
oxanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

P

parseChemicalName(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Parses a chemical name, returning an OpsinResult which represents the molecule.
parseChemicalName(String, NameToStructureConfig) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Parses a chemical name, returning an OpsinResult which represents the molecule.
ParserTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ParserTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
ParseRules - Class in uk.ac.cam.ch.wwmm.opsin
Instantiate via NameToStructure.getOpsinParser() Performs finite-state allocation of roles ("annotations") to tokens: The chemical name is broken down into tokens e.g.
ParseRulesResults - Class in uk.ac.cam.ch.wwmm.opsin
A wrapper for the results from parsing a chemical name or part of a chemical name through ParseRules
ParseRulesResults(List<ParseTokens>, String, String) - Constructor for class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
 
parseToCML(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Convenience method for converting a name to CML with OPSIN's default options
ParseTokens - Class in uk.ac.cam.ch.wwmm.opsin
A "struct" containing data a possible tokenisation of a word in a chemical name.
parseToSmiles(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Convenience method for converting a name to SMILES with OPSIN's default options
ParsingException - Exception in uk.ac.cam.ch.wwmm.opsin
Thrown during finite-state parsing.
partiallyInterpretatableLR() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
partiallyInterpretatableRL1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
partiallyInterpretatableRL2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
perylene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenanthridine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenarsazinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoarsazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenomercazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenomercurazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenomercurine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenophosphazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenophosphazinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoselenazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenotellurazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenothiarsine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenothiarsinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenothiazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxantimonine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxaphosphine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxaphosphinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxarsine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxarsinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxaselenine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxastibinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxatellurine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxathiine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phosphanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phosphindole() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phosphinoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phosphoLocantedSubstitution() - Method in class uk.ac.cam.ch.wwmm.opsin.StructureBuildingMethodsTest
 
phosphoUnlocantedSubstitution() - Method in class uk.ac.cam.ch.wwmm.opsin.StructureBuildingMethodsTest
 
picene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
pleiadene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
PolymerTest - Class in uk.ac.cam.ch.wwmm.opsin
 
PolymerTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.PolymerTest
 
PreProcessorTest - Class in uk.ac.cam.ch.wwmm.opsin
 
PreProcessorTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
pyranthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
pyrrolizine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

Q

quinolizine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

R

RadixTrieTest - Class in uk.ac.cam.ch.wwmm.opsin
 
RadixTrieTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
replaceChargedWithEquallyCharged() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
replaceChargedWithUnEquallyCharged() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
replaceNeutralWithCharged() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
ringClosureHandling1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
ringClosureHandling2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
ringClosureHandling3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
ringClosureHandling4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
ringSupportGreaterThan10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
rubicene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

S

selenanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
selenochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
selenochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
selenoisochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
selenoisochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
setAllowRadicals(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Sets whether radicals allowed? e.g.
setDetailedFailureAnalysis(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Sets whether OPSIN should attempt reverse parsing to more accurately determine why parsing failed
setInterpretAcidsWithoutTheWordAcid(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Sets whether acids without the word "acid" interpretable e.g.
setOutputRadicalsAsWildCardAtoms(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Should radicals be output as wildcard atoms e.g.
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.AmbiguityDetectionTest
 
setUp() - Method in class uk.ac.cam.ch.wwmm.opsin.AtomTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
setUp() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
setUp() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
setUp() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
setup() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
setup() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.VerifyFragmentsTest
 
setUpSubstituent() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
setWarnRatherThanFailOnUninterpretableStereochemistry(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Sets whether if OPSIN cannot understand the stereochemistry in a name whether OPSIN's result should be a warning and structure with incomplete stereochemistry, or should failure be returned (Default)
silanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
SMILESFragmentBuilderTest - Class in uk.ac.cam.ch.wwmm.opsin
 
SMILESFragmentBuilderTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
SMILESWriterTest - Class in uk.ac.cam.ch.wwmm.opsin
 
SMILESWriterTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
SSSRTest - Class in uk.ac.cam.ch.wwmm.opsin
 
SSSRTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.SSSRTest
 
stereochemistryIgnored() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Convenience method to check if one of the associated OPSIN warnings was OpsinWarning.OpsinWarningType.STEREOCHEMISTRY_IGNORED
StereochemistryTest - Class in uk.ac.cam.ch.wwmm.opsin
 
StereochemistryTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
StructureBuildingMethodsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
StructureBuildingMethodsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.StructureBuildingMethodsTest
 
sulfanida() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
sulfanuida() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
sulfanylia() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 

T

telluranthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
tellurochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
tellurochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
telluroisochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
telluroisochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
testAchiralDueToResonance() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testAchiralDueToTautomerism() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testAddAtom() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testAddBond() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testAddedHydrogen() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testAddedHydrogen2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testAddLocantHasLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.AtomTest
 
testAddWithBranchFindPrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testAllowRadicals() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
testAlphaBeta() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAlphaBetaNotDirectlyPrecedingANaturalProduct1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAlphaBetaNotDirectlyPrecedingANaturalProduct2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAlphaBetaNotDirectlyPrecedingANaturalProduct3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAlphaBetaStereoMixedWithNormalLocants() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAminoAcidStyleLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testAnti() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAssignCyclic1() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic2() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic3() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic4() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic5() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic6() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAtom() - Method in class uk.ac.cam.ch.wwmm.opsin.AtomTest
 
testAtomParityEquivalence1() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testAtomParityEquivalence2() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testAxial1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAxial2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testBond() - Method in class uk.ac.cam.ch.wwmm.opsin.BondTest
 
testBondMutation() - Method in class uk.ac.cam.ch.wwmm.opsin.BondTest
 
testBracketedEndo() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testBracketedExo() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testBracketedLocantedCisTrans() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testBracketedUnlocantedCisTrans() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testBrackettedAlphaBeta() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testBuild() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testCarbohydrateStyleLocants() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCarbohydrateStyleLocantsCounterExample() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCarbohydrateStyleLocantsNoNumericComponent() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCardinalNumber() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCardinalNumberWithHyphen() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCharged1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testCharged2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testCharged3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testCharged4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testChiralAtomWhichBecomesAchiral() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testChiralBondWhichBecomesAchiral() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority1() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority10() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority11() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority12() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority13() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority14() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority15() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority2() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority3() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority4() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority5() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority6() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority7() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority8() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority9() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCipUnassignable() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCis() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testCisTransAmbiguous() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCisTransUnambiguous() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCloneFragment() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
testCompoundLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testConvertSpareValenciesToDoubleBonds() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testConvertStringToComponentRatios1() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testConvertStringToComponentRatios2() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testConvertStringToComponentRatios3() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testCorrectlyTokenisedAlkane() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testCorrectlyTokenisedAlkane2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testCorrectlyTokenisedAlkane3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testDashInsteadOfComma() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testDLStereochemistryDLOnAminoAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryDOnAchiralAminoAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryDOnAminoAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryDOnCarbohydrate() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryDOnCarbohydratePrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryInvertedNaturalOnCarbohydrate1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryInvertedNaturalOnCarbohydrate2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryLOnAminoAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryLOnCarbohydrate() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDoubleBondCornerCase1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondCornerCase2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondCornerCase3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondCornerCase4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondCornerCase5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondCornerCase6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondMultiStereo1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondMultiStereo2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondMultiStereo3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondMultiStereo4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoela() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelb() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelc() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoeld() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoele() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelf() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelg() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo5a() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo5b() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondSupport1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDStereochemistryDOnCarbohydratePrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testEandZUnbrackettedBeforeEne() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testEandZUnbrackettedBeforeYlidene() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testEandZUnbrackettedLocanted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testElementSymbol() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testFindBond() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testFindPathBetweenAtoms1() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testFindPathBetweenAtoms2() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testFindPathBetweenAtoms3() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testFindPseudoAsymmetricCarbon1() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testFindPseudoAsymmetricCarbon2() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testFindSSSR() - Method in class uk.ac.cam.ch.wwmm.opsin.SSSRTest
 
testFragment() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetAtomByID() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetAtomByLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetAtomNeighbours() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetChainLength() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetIDFromLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetIncomingValency() - Method in class uk.ac.cam.ch.wwmm.opsin.AtomTest
 
testGetOppositeDirection() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererFunctionsTest
 
testGetUnifiedFrags() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
testGreek() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testHtmlGreeks() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testHydrogenNotBondedToAnyNonHydrogen1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testHydrogenNotBondedToAnyNonHydrogen2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testHydrogenNotBondedToAnyNonHydrogen3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testHydrogenNotBondedToAnyNonHydrogen4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testImportFrag() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testImportFragWithIntraFragBonds1() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testImportFragWithIntraFragBonds2() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testIndicatedHydrogen() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testInterpretAcidsWithoutTheWordAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
testIsCharacteristicAtomAldehyde() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testIsCharacteristicAtomFunctionalAtom() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testIsCharacteristicAtomHydroxy() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testIsCharacteristicAtomSuffix() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testIsotope() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testIsTetrahedral() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testIUPAC2004() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testLabelAcetoanilide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelCarbamimidamido() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelCarbonicDihydrazide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelCarbonimidoyl() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelCarboximidohydrazide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelDiimidooxalicDiamide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHexanDiamide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHydrazinecarbohydrazide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHydrazonate() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHydrazonicAmide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHydrazonoHydrazide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelling1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testLabelling2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testLabelPiperazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelPyridine() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelSulfonoThioate() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLocantedCisTrans() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testLocantedExo() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testLocantedExoOn() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testLocantedR() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testLocantedZ() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testLocantsIndicatingTokenizationIsCorrect() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testLocantsIndicatingTokenizationIsIncorrect() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testLStereochemistryDOnCarbohydratePrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testMisTokenisedAlkane() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testMultipleCardinals() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testMultipleHits() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testMultipleHits2() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testMultipleParsesAmbiguousWordTokenisationTerminalFunctionalTerm() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testMultipleParsesTerminalFunctionalTerm() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testMultipleRorSLocanted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testMultipleRorSorEorZ() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testMultipleTypesTogether() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testMultipleUnLocanted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testNamesThatShouldBeDetectedAsAmbiguous() - Method in class uk.ac.cam.ch.wwmm.opsin.AmbiguityDetectionTest
 
testNameToStructure() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureTest
 
testNoParseForOneComponentSalt() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testNormalCase() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testNormalCase2() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testNormalCase3() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testNormalCase4() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testNotlowercase1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testNotlowercase2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testNumericallyMultipliedSaltComponent() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_MiscTest
 
testOrganic1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic9() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOutputRadicalsAsWildCards() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
testParseReturnsOneWordRuleForEachMixtureComponent() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testParseThrowsWhenNameIsSubstituentOnly() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testParseThrowsWhenNameIsUninterpretable() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testParseToCML() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureTest
 
testParseToSmiles() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureTest
 
testParseUninvertsCASNomenclature() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testPreProcessBlankThrows() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarA() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarB() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarD() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarE() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarG() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarL() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsGreekLetterToWord() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsSulphToSulf() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testRacemate1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate10() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate2_ci() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate4() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate5() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate6() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate7() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate8() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate9() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemateEz1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemateEz2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemateEz3_unbracketted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemateEz4_unbracketted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRegexes() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testRegexTokens() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testRejectSingleComponentSaltComponent() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_MiscTest
 
testRelabelFusedRingSystem() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
testRelabelSuffixLocants() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testRelativeCisTrans() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRelativeStereoChemistry1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRelativeStereoChemistry2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRelativeStereoChemistry3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRemovalOfDotsFromGreekWords1() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testRemovalOfDotsFromGreekWords2() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testReverseMatching() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testRGroup1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRGroup2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRingOpeningsGreaterThan10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip11() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip12() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip9() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testSimple1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple11() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple9() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimpleAddFindPrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testSimpleAddSimpleGet() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testSimplePolymer() - Method in class uk.ac.cam.ch.wwmm.opsin.PolymerTest
 
testSpareValenciesOnAromaticAtoms() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testStartingFunctionalTerm1() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testStartingFunctionalTerm2() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testStereochemistryInLocant1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testStereochemistryInLocant2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testStereochemistryInLocant3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testStereochemistryInLocant4() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testStereochemistryInLocant5() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testStereochemistryInLocant6() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSubtractiveBiochemicalPreferredToRightMost() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSubtractiveRightMostPreferred() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSubtractiveWithBiochemicalToAttachTo() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSubtractiveWithMultiplierAndLocants() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSubtractiveWithNoGroupToAttachTo() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSuffixApplicability() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testSuffixRules() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testSuperscript1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript4() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript5() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript6() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript7() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testTerminalFunctionalTerm() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testTetrahedralChirality1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetraphenShouldBeTetra_Phen1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testTetraphenShouldBeTetra_Phen2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testTetraphenShouldBeTetraphen1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testTetraphenShouldBeTetraphen2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testTetraphenShouldBeTetraphen3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testTokenFiles() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testTokenFilesValueValidity() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testUnAmbiguousCounterExamples() - Method in class uk.ac.cam.ch.wwmm.opsin.AmbiguityDetectionTest
 
testUnLocantedE() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testUnlocantedS() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testWarnRatherThanFailOnUninterpretableStereochemistry() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
testWordRules() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testZeroLengthToken() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testZUnbracketted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
thia() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
thianthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thiochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thiochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thioisochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thioisochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thionia() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
tokenizeDoesNotTokenizeUnTokenizableName() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUninterpretableNameLR1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUninterpretableNameLR2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUninterpretableNameRL1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUninterpretableNameRL2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsableNameLR1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsableNameLR2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsableNameRL1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsableNameRL2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsedNameLR1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsedNameLR2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsedNameRL1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsedNameRL2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
TokenizerTest - Class in uk.ac.cam.ch.wwmm.opsin
 
TokenizerTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
toString() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
 
toString() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
 
trindene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
tripleSubstituedSevenMembered() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

U

uk.ac.cam.ch.wwmm.opsin - package uk.ac.cam.ch.wwmm.opsin
 
unterminatedRingOpening() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 

V

validate(URI) - Static method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
valueOf(String) - Static method in enum uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
Returns the enum constant of this type with the specified name.
values() - Static method in enum uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
Returns an array containing the constants of this enum type, in the order they are declared.
VerifyFragmentsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
VerifyFragmentsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.VerifyFragmentsTest
 
verifySMILES() - Method in class uk.ac.cam.ch.wwmm.opsin.VerifyFragmentsTest
 
violanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

W

warnRatherThanFailOnUninterpretableStereochemistry() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
If OPSIN cannot understand the stereochemistry in a name should OPSIN's result be a warning and structure with incomplete stereochemistry, or should failure be returned (Default)
WordToolsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
WordToolsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
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