- 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 frm
- getChildElementsWithTagName(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Finds all child elements whose localname matches one of the strings in elementNames
Equivalent to an xpath of type ./*[local-name() = 'elementName'] from the startingElement
This is equivalent to XOM's getChildElements(String) other than returning an arrayList
- getChildElementsWithTagNameAndAttribute(Element, String, String, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Finds all child elements whose localname matches the given elementName
Additionally the element must have the specified attribute and the value of the attribute must be as specified
Equivalent to an xpath of type ./*[local-name() = 'elementName'][@attribute="attributevalue"] from the startingElement
- getChildElementsWithTagNames(Element, String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Finds all child elements whose localname matches one of the strings in elementNames
Equivalent to an xpath of type ./*[local-name() = 'elementName1']|./*[local-name() = 'elementName2']|./*[local-name() = 'elementName3'] from the startingElement
- getCml() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Lazily evaluates and returns 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
- getDescendantElementsWithTagName(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Finds all descendant elements whose localname matches the given elementName
Equivalent to an xpath of type .//*[local-name() = 'elementName'] from the startingElement
- getDescendantElementsWithTagNameAndAttribute(Element, String, String, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Finds all descendant elements whose localname matches the given elementName
Additionally the element must have the specified attribute and the value of the attribute must be as specified
Equivalent to an xpath of type .//*[local-name() = 'elementName'][@attribute="attributevalue"] from the startingElement
- getDescendantElementsWithTagNames(Element, String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Finds all descendant elements whose localname matches one of the strings in elementNames
Equivalent to an xpath of type .//*[local-name() = 'elementName1']|.//*[local-name() = 'elementName2']|.//*[local-name() = 'elementName3'] from the startingElement
- 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
- getNext(Node) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Gets the next node.
- getNextAdjacentSiblingsOfType(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Returns an arrayList containing sibling elements of the given type after the given element.
- getNextSibling(Node) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Gets the next sibling of a given node.
- getNextSibling(Node, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Gets the first next sibling of a given node whose tagname matches the given string.
- getNextSiblingIgnoringCertainElements(Element, String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Gets the next sibling element of the given element.
- getNextSiblingsOfType(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Returns an arrayList containing sibling elements of the given type after the given element.
- getNextSiblingsOfTypes(Element, String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Returns an arrayList containing sibling elements of the given types after the given element.
- 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
- getPrevious(Node) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Gets the previous node.
- getPreviousSibling(Node) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Gets the previous sibling of a given node.
- getPreviousSibling(Node, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Gets the first previous sibling of a given node whose tagname matches the given string.
- getPreviousSiblingIgnoringCertainElements(Element, String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Gets the previous sibling element of the given element.
- getPreviousSiblingsOfType(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Returns an arrayList containing sibling elements of the given type before the given element.
- getSiblingsUpToElementWithTagName(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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Find all the later siblings of startingElement with the search terminating at the element with string tagName
or if there are not more siblings
- getSmiles() - Method in class uk.ac.cam.ch.wwmm.opsin.OpsinResult
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Lazily evaluates and returns 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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- 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.