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A

allowInterpretationOfAcidsWithoutTheWordAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Are acids without the word "acid" interpretable e.g.
APPEARS_AMBIGUOUS - uk.ac.cam.ch.wwmm.opsin.OpsinWarning.OpsinWarningType
OPSIN made a choice that appeared to be ambiguous to give this structure i.e.

C

clone() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
 
convertResultToInChI(OpsinResult) - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToInchi
Converts an OPSIN result to InChI.
convertResultToStdInChI(OpsinResult) - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToInchi
Converts an OPSIN result to StdInChI.
convertResultToStdInChIKey(OpsinResult) - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToInchi
Converts an OPSIN result to a StdInChIKey.

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
OPSIN failed to interpret the name

G

getAnnotations() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
 
getChemicalName() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Returns the chemical name that this OpsinResult was generated from
getCml() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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
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
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
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
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
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
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
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
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
Returns an enum indicating whether interpreting the chemical name was successful If an issue was identified but a chemical structure could be still be deduced the status is OpsinResult.OPSIN_RESULT_STATUS.WARNING
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
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
The substring of the name that could not be tokenised at all.
getVersion() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Returns the version of the OPSIN library
getWarnings() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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

InchiPruner - Class in uk.ac.cam.ch.wwmm.opsin
 
InchiPruner() - Constructor for class uk.ac.cam.ch.wwmm.opsin.InchiPruner
 
isAllowRadicals() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Are radicals allowed? e.g.
isDetailedFailureAnalysis() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Should OPSIN attempt reverse parsing to more accurately determine why parsing failed
isOutputRadicalsAsWildCardAtoms() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Are radicals output as wildcard atoms e.g.

M

main(String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Run OPSIN as a command-line application.
mainAndChargeLayers(String) - Static method in class uk.ac.cam.ch.wwmm.opsin.InchiPruner
Return a modified version of the given InChI where the: stereochemistry, fixed hydrogen and reconnected layers have been removed The S indicating standard InChI is also removed
mainChargeAndStereochemistryLayers(String) - Static method in class uk.ac.cam.ch.wwmm.opsin.InchiPruner
Return a modified version of the given InChI where the: fixed hydrogen and reconnected layers have been removed The S indicating standard InChI is also removed

N

nameAppearsToBeAmbiguous() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
Convenience method to check if one of the associated OPSIN warnings was OpsinWarning.OpsinWarningType.APPEARS_AMBIGUOUS
NameToInchi - Class in uk.ac.cam.ch.wwmm.opsin
Allows the conversion of OPSIN's output into (Std)InChIs or StdInChIKeys Also can be used, as a convenience method, to directly convert chemical names to (Std)InChIs or StdInChIKeys
NameToInchi() - Constructor for class uk.ac.cam.ch.wwmm.opsin.NameToInchi
 
NameToStructure - Class in uk.ac.cam.ch.wwmm.opsin
The "master" class, to turn a name into a structure.
NameToStructureConfig - Class in uk.ac.cam.ch.wwmm.opsin
Allows OPSIN to be configured e.g.
NameToStructureConfig() - Constructor for class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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
Thrown if OPSIN failed to initialise

O

OpsinResult - Class in uk.ac.cam.ch.wwmm.opsin
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
Whether parsing the chemical name was successful, encountered problems or was unsuccessful.
If the result is not OpsinResult.OPSIN_RESULT_STATUS.FAILURE then a structure has been generated
OpsinWarning - Class in uk.ac.cam.ch.wwmm.opsin
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
The type of problem OPSIN encountered

P

parseChemicalName(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Parses a chemical name, returning an OpsinResult which represents the molecule.
parseChemicalName(String, NameToStructureConfig) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Parses a chemical name, returning an OpsinResult which represents the molecule.
ParseRules - Class in uk.ac.cam.ch.wwmm.opsin
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
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
Convenience method for converting a name to CML with OPSIN's default options
parseToInchi(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToInchi
Parses a chemical name, returning an InChI representation of the molecule.
ParseTokens - Class in uk.ac.cam.ch.wwmm.opsin
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
Convenience method for converting a name to SMILES with OPSIN's default options
parseToStdInchi(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToInchi
Parses a chemical name, returning a StdInChI representation of the molecule.
parseToStdInchiKey(String) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToInchi
Parses a chemical name, returning a StdInChIKey for the molecule.
ParsingException - Exception in uk.ac.cam.ch.wwmm.opsin
Thrown during finite-state parsing.

S

setAllowRadicals(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Sets whether radicals allowed? e.g.
setDetailedFailureAnalysis(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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
Sets whether acids without the word "acid" interpretable e.g.
setOutputRadicalsAsWildCardAtoms(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
Should radicals be output as wildcard atoms e.g.
setWarnRatherThanFailOnUninterpretableStereochemistry(boolean) - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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
OPSIN ignored stereochemistry from the input name to give this structure.
stereochemistryIgnored() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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
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
 

U

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
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
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
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
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
OPSIN interpreted the name but detected a potential problem e.g.
warnRatherThanFailOnUninterpretableStereochemistry() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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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