- getAnnotations() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
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- 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
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- 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
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- 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
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- 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
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- getType() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinWarning
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- 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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