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

Class Summary

AtomTest
BondTest
CASToolsTest
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.
StructureBuildingMethodsTest
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

CipOrderingException	Thrown if the ordering of ligands can now be determined by OPSIN's implementation of the CIP rules.
NameToStructureException	Thrown if OPSIN failed to initialise
ParsingException	Thrown during finite-state parsing.