Package uk.ac.cam.ch.wwmm.opsin

Class Summary
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
OpsinResult.OPSIN_RESULT_STATUS Whether parsing the chemical name was successful, encountered problems or was unsuccessful.
 

Exception Summary
NameToStructureException Thrown if OPSIN failed to initialise
ParsingException Thrown during finite-state parsing.