Class | Description |
---|---|
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 | Description |
---|---|
OpsinResult.OPSIN_RESULT_STATUS |
Whether parsing the chemical name was successful,
encountered problems or was unsuccessful.
|
Exception | Description |
---|---|
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.
|