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Class Summary | |
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AtomTest | |
BondTest | |
CASToolsTest | |
CMLFragmentBuilderTest | |
ComponentGeneration_AmbiguitiesAndIrregularitiesTest | |
ComponentGeneration_ProcesslocantsTest | |
ComponentGeneration_StereochemistryTest | |
ComponentProcessorTest | |
CycleDetectorTest | |
DtdTest | |
FragmentManagerTest | |
FragmentTest | |
FusedRingNumbererFunctionsTest | |
FusedRingNumbererTest | Tests that fused ring numbering is working as expected. |
HeteroAtomReplacementTest | |
NameToStructure | The "master" class, to turn a name into a structure. |
NameToStructureConfig | Allows OPSIN to be configured e.g. |
NameToStructureConfigurationsTest | |
NameToStructureTest | |
OpsinResult | Holds the structure OPSIN has generated from a name Additionally holds a status code for whether name interpretation was successful |
ParserTest | |
ParseRules | Instantiate via NameToStructure.getOpsinParser() Performs finite-state allocation of roles ("annotations") to tokens: The chemical name is broken down into tokens e.g. |
ParseRulesResults | A wrapper for the results from parsing a chemical name or part of a chemical name through ParseRules |
ParseTokens | A "struct" containing data a possible tokenisation of a word in a chemical name. |
PreProcessorTest | |
RadixTrieTest | |
SMILESFragmentBuilderTest | |
SMILESWriterTest | |
SSSRTest | |
StereochemistryTest | |
StreamSerializer | |
StringTools | Static routines for string manipulation. |
StructureBuilderTest | |
TokenizerTest | |
VerifyFragmentsTest | |
WordToolsTest | |
XOMFormatter | Turns a XOM Element into a pretty indented string. |
XOMTools | Accessory functions for the manipulation of XOM Nodes/Elements Only those that are necessary for OPSIN's execution |
Enum Summary | |
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OpsinResult.OPSIN_RESULT_STATUS | Whether parsing the chemical name was successful, encountered problems or was unsuccessful. |
Exception Summary | |
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NameToStructureException | Thrown if OPSIN failed to initialise |
ParsingException | Thrown during finite-state parsing. |
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