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.