| 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.
|