A C E F G H I M N O P S T U V W
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All Classes All Packages
All Classes All Packages
A
- allowInterpretationOfAcidsWithoutTheWordAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Are acids without the word "acid" interpretable e.g.
- APPEARS_AMBIGUOUS - uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
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OPSIN made a choice that appeared to be ambiguous to give this structure i.e.
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- clone() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
E
- equals(Object) - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
F
- FAILURE - uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
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OPSIN failed to interpret the name
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- getAnnotations() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
- getChemicalName() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Returns the chemical name that this OpsinResult was generated from
- getCml() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Generates the CML corresponding to the molecule described by the name If name generation failed i.e.
- getDefaultConfigInstance() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Constructs a NameToStructureConfig with default settings: allowRadicals = false outputRadicalsAsWildCardAtoms = false detailedFailureAnalysis = false interpretAcidsWithoutTheWordAcid = false warnRatherThanFailOnUninterpretableStereochemistry = false
- getExplanation() - Method in enum uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
- getExtendedSmiles() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Experimental function that generates the extended SMILES corresponding to the molecule described by the name If name generation failed i.e.
- getInstance() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
- getMessage() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Returns a message explaining why generation of a molecule from the name failed This string will be blank when no problems were encountered
- getMessage() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinWarning
- getOpsinParser() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
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Returns an OPSIN parser This can be used to determine whether a word can be interpreted as being part of a chemical name.
- getParses(String) - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRules
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Determines the possible annotations for a chemical word Returns a list of parses and how much of the word could not be interpreted e.g.
- getParseTokensList() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
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One ParseTokens object is returned for each possible interpretation of a chemical name If none of the name can be interpreted this list will be empty
- getPrettyPrintedCml() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Generates the CML corresponding to the molecule described by the name If name generation failed i.e.
- getSmiles() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Generates the SMILES corresponding to the molecule described by the name If name generation failed i.e.
- getStatus() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Returns an enum with values SUCCESS, WARNING and FAILURE Currently warning is never used
- getTokens() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
- getType() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinWarning
- getUninterpretableName() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
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The substring of the name that could not be classified into a substituent/full/functionalTerm e.g.
- getUnparseableName() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
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The substring of the name that could not be tokenised at all.
- getVersion() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
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Returns the version of the OPSIN library
- getWarnings() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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A list of warnings encountered when the result was
OpsinResult.OPSIN_RESULT_STATUS.WARNING
This list of warnings is immutable
H
- hashCode() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
I
- isAllowRadicals() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Are radicals allowed? e.g.
- isDetailedFailureAnalysis() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Should OPSIN attempt reverse parsing to more accurately determine why parsing failed
- isOutputRadicalsAsWildCardAtoms() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Are radicals output as wildcard atoms e.g.
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- main(String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
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Run OPSIN as a command-line application.
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- nameAppearsToBeAmbiguous() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Convenience method to check if one of the associated OPSIN warnings was
OpsinWarning.OpsinWarningType.APPEARS_AMBIGUOUS
- NameToStructure - Class in uk.ac.cam.ch.wwmm.opsin
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The "master" class, to turn a name into a structure.
- NameToStructureConfig - Class in uk.ac.cam.ch.wwmm.opsin
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Allows OPSIN to be configured e.g.
- NameToStructureConfig() - Constructor for class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Constructs a NameToStructureConfig with default settings: allowRadicals = false outputRadicalsAsWildCardAtoms = false detailedFailureAnalysis = false interpretAcidsWithoutTheWordAcid = false warnRatherThanFailOnUninterpretableStereochemistry = false
- NameToStructureException - Exception in uk.ac.cam.ch.wwmm.opsin
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Thrown if OPSIN failed to initialise
O
- OpsinResult - Class in uk.ac.cam.ch.wwmm.opsin
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Holds the structure OPSIN has generated from a name Additionally holds a status code for whether name interpretation was successful
- OpsinResult.OPSIN_RESULT_STATUS - Enum in uk.ac.cam.ch.wwmm.opsin
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Whether parsing the chemical name was successful, encountered problems or was unsuccessful.
If the result is notOpsinResult.OPSIN_RESULT_STATUS.FAILURE
then a structure has been generated - OpsinWarning - Class in uk.ac.cam.ch.wwmm.opsin
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A warning generated by OPSIN while interpreting a name.
The specifics of the warning may be used to judge whether you want to accept the generated structure. - OpsinWarning.OpsinWarningType - Enum in uk.ac.cam.ch.wwmm.opsin
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The type of problem OPSIN encountered
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- parseChemicalName(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
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Parses a chemical name, returning an OpsinResult which represents the molecule.
- parseChemicalName(String, NameToStructureConfig) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
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Parses a chemical name, returning an OpsinResult which represents the molecule.
- ParseRules - Class in uk.ac.cam.ch.wwmm.opsin
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Instantiate via NameToStructure.getOpsinParser() Performs finite-state allocation of roles ("annotations") to tokens: The chemical name is broken down into tokens e.g.
- ParseRulesResults - Class in uk.ac.cam.ch.wwmm.opsin
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A wrapper for the results from parsing a chemical name or part of a chemical name through ParseRules
- ParseRulesResults(List<ParseTokens>, String, String) - Constructor for class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
- parseToCML(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
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Convenience method for converting a name to CML with OPSIN's default options
- ParseTokens - Class in uk.ac.cam.ch.wwmm.opsin
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A "struct" containing data a possible tokenisation of a word in a chemical name.
- parseToSmiles(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
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Convenience method for converting a name to SMILES with OPSIN's default options
- ParsingException - Exception in uk.ac.cam.ch.wwmm.opsin
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Thrown during finite-state parsing.
S
- setAllowRadicals(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Sets whether radicals allowed? e.g.
- setDetailedFailureAnalysis(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Sets whether OPSIN should attempt reverse parsing to more accurately determine why parsing failed
- setInterpretAcidsWithoutTheWordAcid(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Sets whether acids without the word "acid" interpretable e.g.
- setOutputRadicalsAsWildCardAtoms(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Should radicals be output as wildcard atoms e.g.
- setWarnRatherThanFailOnUninterpretableStereochemistry(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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Sets whether if OPSIN cannot understand the stereochemistry in a name whether OPSIN's result should be a warning and structure with incomplete stereochemistry, or should failure be returned (Default)
- STEREOCHEMISTRY_IGNORED - uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
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OPSIN ignored stereochemistry from the input name to give this structure.
- stereochemistryIgnored() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Convenience method to check if one of the associated OPSIN warnings was
OpsinWarning.OpsinWarningType.STEREOCHEMISTRY_IGNORED
- SUCCESS - uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
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OPSIN successfully interpreted the name
T
- toString() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
- toString() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
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- uk.ac.cam.ch.wwmm.opsin - package uk.ac.cam.ch.wwmm.opsin
V
- valueOf(String) - Static method in enum uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
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Returns the enum constant of this type with the specified name.
- values() - Static method in enum uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
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Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
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Returns an array containing the constants of this enum type, in the order they are declared.
W
- WARNING - uk.ac.cam.ch.wwmm.opsin.OpsinResult.OPSIN_RESULT_STATUS
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OPSIN interpreted the name but detected a potential problem e.g.
- warnRatherThanFailOnUninterpretableStereochemistry() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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If OPSIN cannot understand the stereochemistry in a name should OPSIN's result be a warning and structure with incomplete stereochemistry, or should failure be returned (Default)
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