A B C D E F G H I M N O P Q R S T U V W
All Classes All Packages
All Classes All Packages
All Classes All Packages
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
- APPEARS_AMBIGUOUS - uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
-
OPSIN made a choice that appeared to be ambiguous to give this structure i.e.
- 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
- FAILURE - uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
-
OPSIN failed to interpret the name
- 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 notOpsinResult.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() - 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.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() - 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
- STEREOCHEMISTRY_IGNORED - uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
-
OPSIN ignored stereochemistry from the input name to give this structure.
- 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
- SUCCESS - uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
-
OPSIN successfully interpreted the name
- 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
- WARNING - uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
-
OPSIN interpreted the name but detected a potential problem e.g.
- 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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