A B C D E F G H I M N O P Q R S T U V W X 

A

acceptableInterWordBreaks() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
aceanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
acenaphthene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
acephenanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
aceticacid() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
acrindoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
anthratetraphene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
anthrazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
anthyridine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
applyStereochemistryCis() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryLocantedE() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryLocantedRS() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryLocantedZ() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryTrans() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryUnlocantedE() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
applyStereochemistryUnlocantedZ() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
arrayToList(String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
Converts a string array to an ArrayList.
arrayToString(String[], String) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
Joins an array of strings into a single string.
arsanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
arsanthridine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
arsindole() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
arsindoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
AtomTest - Class in uk.ac.cam.ch.wwmm.opsin
 
AtomTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.AtomTest
 

B

badlyFormedSMILE1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
badlyFormedSMILE8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
betacarboline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
BondTest - Class in uk.ac.cam.ch.wwmm.opsin
 
BondTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.BondTest
 
boranthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
bracketedHexachlorohexane() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 

C

cas1() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas10() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas11() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas12() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas13() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas14() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas15() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas16() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas17() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas18() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas2() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas3() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas4() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas5() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas6() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas7() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas8() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cas9() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
CASToolsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
CASToolsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
CCCP() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
CCCP_RL() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
charListToString(List<Character>) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
Converts a list of characters into a string.
chiralityTest1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
chiralityTest8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
cholanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.CMLFragmentBuilderTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
cleanUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
clone() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
 
CMLFragmentBuilderTest - Class in uk.ac.cam.ch.wwmm.opsin
 
CMLFragmentBuilderTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.CMLFragmentBuilderTest
 
ComponentGeneration_AmbiguitiesAndIrregularitiesTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ComponentGeneration_AmbiguitiesAndIrregularitiesTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
ComponentGeneration_ProcesslocantsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ComponentGeneration_ProcesslocantsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
ComponentGeneration_StereochemistryTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ComponentGeneration_StereochemistryTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
ComponentProcessorTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ComponentProcessorTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
compoundWithInvalidUse1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
compoundWithInvalidUse2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
compoundWithValidUse() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
convertNonAsciiAndNormaliseRepresentation(String) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
Converts a unicode string into ISO-8859-1, converting greek letters to their names, and difficult characters to underscore.
coronene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
countNumberOfElementsAndNumberOfChildLessElements(Element) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
Finds and returns the number of elements and the number of elements with no children, that are descendants of the startingElement The 0th position of the returned array is the total number of elements The 1st position is the number of child less elements
countTerminalPrimes(String) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
Counts the number of primes at the end of a locant
CycleDetectorTest - Class in uk.ac.cam.ch.wwmm.opsin
 
CycleDetectorTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 

D

difficultChain() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
difficultChain2() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
doubleNegativeCharge1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
doubleNegativeCharge2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
doublePositiveCharge1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
doublePositiveCharge2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
DtdTest - Class in uk.ac.cam.ch.wwmm.opsin
 
DtdTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.DtdTest
 

E

elemToString(Element) - Method in class uk.ac.cam.ch.wwmm.opsin.XOMFormatter
Converts an Element to an indented string.
endsWithCaseInsensitive(String, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
Tests if this string ends with the specified suffix ignoring case.
equals(Object) - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
 
ethylChloride() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 

F

findStereoCentresBromoChloroFluoroMethane() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
findStereoCentresBut2ene() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
findStereoCentresNacetylleucine() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
FragmentManagerTest - Class in uk.ac.cam.ch.wwmm.opsin
 
FragmentManagerTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
FragmentTest - Class in uk.ac.cam.ch.wwmm.opsin
 
FragmentTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
FusedRingNumbererFunctionsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
FusedRingNumbererFunctionsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererFunctionsTest
 
FusedRingNumbererTest - Class in uk.ac.cam.ch.wwmm.opsin
Tests that fused ring numbering is working as expected.
FusedRingNumbererTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

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 frm
getChildElementsWithTagName(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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
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
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
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
Constructs a NameToStructureConfig with default settings: allowRadicals = false detailedFailureAnalysis = false
getDescendantElementsWithTagName(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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
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
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
 
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
getNext(Node) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
Gets the next node.
getNextAdjacentSiblingsOfType(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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
Gets the next sibling of a given node.
getNextSibling(Node, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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
Gets the next sibling element of the given element.
getNextSiblingsOfType(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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
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
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
getPrevious(Node) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
Gets the previous node.
getPreviousSibling(Node) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
Gets the previous sibling of a given node.
getPreviousSibling(Node, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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
Gets the previous sibling element of the given element.
getPreviousSiblingsOfType(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
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
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
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
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
 
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.

H

hashCode() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
 
HeteroAtomReplacementTest - Class in uk.ac.cam.ch.wwmm.opsin
 
HeteroAtomReplacementTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
hexachlorohexane() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
hexachlorohexaneeeeeee() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
hexane() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
hydrogenHandling1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling11() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling12() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling13() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling14() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling15() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling16() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling17() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling18() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling19() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling20() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling21() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
hydrogenHandling9() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 

I

indane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
indicatedHydrogen1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
indicatedHydrogen2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
insertAfter(Node, Node) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
Inserts a node so that it occurs after a reference node.
insertBefore(Node, Node) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
Inserts a node so that it occurs before a reference node.
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
isoarsindole() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isoarsinoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isophosphindole() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isophosphinoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
isotopeSpecified() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
isoviolanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

M

main(String[]) - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructure
Run OPSIN as a command-line application.
mercuranthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
methyl() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
multiplyString(String, int) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
Produce repetitions of a string.

N

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 detailedFailureAnalysis = false
NameToStructureConfigurationsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
NameToStructureConfigurationsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
NameToStructureException - Exception in uk.ac.cam.ch.wwmm.opsin
Thrown if OPSIN failed to initialise
NameToStructureTest - Class in uk.ac.cam.ch.wwmm.opsin
 
NameToStructureTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.NameToStructureTest
 
naphthotetraphene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
noIsotopeSpecified() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
notCas1() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
notCas2() - Method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 

O

octalenotetraphene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
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.
ovalene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
oxanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

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.
ParserTest - Class in uk.ac.cam.ch.wwmm.opsin
 
ParserTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
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
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
ParsingException - Exception in uk.ac.cam.ch.wwmm.opsin
Thrown during finite-state parsing.
partiallyInterpretatableLR() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
partiallyInterpretatableRL1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
partiallyInterpretatableRL2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
perylene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenanthridine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenarsazinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoarsazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenomercazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenomercurazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenomercurine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenophosphazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenophosphazinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoselenazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenotellurazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenothiarsine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenothiarsinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenothiazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxantimonine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxaphosphine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxaphosphinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxarsine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxarsinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxaselenine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxastibinine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxatellurine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxathiine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phenoxazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phosphanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phosphindole() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
phosphinoline() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
picene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
pleiadene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
PreProcessorTest - Class in uk.ac.cam.ch.wwmm.opsin
 
PreProcessorTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
pyranthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
pyrrolizine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

Q

quinolizine() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

R

RadixTrieTest - Class in uk.ac.cam.ch.wwmm.opsin
 
RadixTrieTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
removeDashIfPresent(String) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
If a dash is the last character it is removed
replaceChargedWithEquallyCharged() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
replaceChargedWithUnEquallyCharged() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
replaceNeutralWithCharged() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
ringClosureHandling1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
ringClosureHandling2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
ringClosureHandling3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
ringClosureHandling4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
ringSupportGreaterThan10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
rubicene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

S

selenanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
selenochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
selenochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
selenoisochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
selenoisochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
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
setTextChild(Element, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.XOMTools
Sets the first text child of the group to the newName Throws an exception if the first child is not a Text node
setUp() - Method in class uk.ac.cam.ch.wwmm.opsin.AtomTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.CASToolsTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.CMLFragmentBuilderTest
 
setup() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
setUp() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
setUp() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
setUp() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
setUp() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
setup() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
setup() - Static method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
setUp() - Static method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
setUpInstance() - Method in class uk.ac.cam.ch.wwmm.opsin.CMLFragmentBuilderTest
 
setUpSubstituent() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
silanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
SMILESFragmentBuilderTest - Class in uk.ac.cam.ch.wwmm.opsin
 
SMILESFragmentBuilderTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
SMILESWriterTest - Class in uk.ac.cam.ch.wwmm.opsin
 
SMILESWriterTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
SSSRTest - Class in uk.ac.cam.ch.wwmm.opsin
 
SSSRTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.SSSRTest
 
StereochemistryTest - Class in uk.ac.cam.ch.wwmm.opsin
 
StereochemistryTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
StreamSerializer - Class in uk.ac.cam.ch.wwmm.opsin
 
StreamSerializer(OutputStream) - Constructor for class uk.ac.cam.ch.wwmm.opsin.StreamSerializer
 
stringListToString(List<String>, String) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
Converts a list of strings into a single string delimited by the given separator
stringToList(String) - Static method in class uk.ac.cam.ch.wwmm.opsin.StringTools
Converts a string to a list of characters.
StringTools - Class in uk.ac.cam.ch.wwmm.opsin
Static routines for string manipulation.
StringTools() - Constructor for class uk.ac.cam.ch.wwmm.opsin.StringTools
 
StructureBuilderTest - Class in uk.ac.cam.ch.wwmm.opsin
 
StructureBuilderTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.StructureBuilderTest
 
sulfanida() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
sulfanuida() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
sulfanylia() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 

T

telluranthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
tellurochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
tellurochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
telluroisochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
telluroisochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
testAchiralDueToResonance() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testAchiralDueToTautomerism() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testAddAtom() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testAddBond() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testAddedHydrogen() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testAddedHydrogen2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testAddLocantHasLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.AtomTest
 
testAddWithBranchFindPrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testAllowRadicals() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureConfigurationsTest
 
testAlphaBeta() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAlphaBetaNotDirectlyPrecedingANaturalProduct1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAlphaBetaNotDirectlyPrecedingANaturalProduct2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAlphaBetaNotDirectlyPrecedingANaturalProduct3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAlphaBetaStereoMixedWithNormalLocants() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testAminoAcidStyleLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testAssignCyclic1() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic2() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic3() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic4() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic5() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAssignCyclic6() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testAtom() - Method in class uk.ac.cam.ch.wwmm.opsin.AtomTest
 
testAtom() - Method in class uk.ac.cam.ch.wwmm.opsin.CMLFragmentBuilderTest
 
testAtomParityEquivalence1() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testAtomParityEquivalence2() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testBond() - Method in class uk.ac.cam.ch.wwmm.opsin.BondTest
 
testBracketedLocantedCisTrans() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testBracketedUnlocantedCisTrans() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testBrackettedAlphaBeta() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testBuild() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testBuilderFromName() - Method in class uk.ac.cam.ch.wwmm.opsin.StructureBuilderTest
 
testBuildStringString() - Method in class uk.ac.cam.ch.wwmm.opsin.CMLFragmentBuilderTest
 
testCarbohydrateStyleLocants() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCarbohydrateStyleLocantsCounterExample() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCarbohydrateStyleLocantsNoNumericComponent() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCardinalNumber() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCardinalNumberWithHyphen() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testCharged1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testCharged2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testCharged3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testCharged4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testChiralAtomWhichBecomesAchiral() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testChiralBondWhichBecomesAchiral() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority1() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority10() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority11() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority12() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority13() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority14() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority2() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority3() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority4() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority5() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority6() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority7() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority8() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCIPpriority9() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCis() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testCisTransAmbiguous() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCisTransUnambiguous() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testCloneFragment() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
testCompoundLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testConvertHighOrderBondsToSpareValencies() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testConvertSpareValenciesToDoubleBonds() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testConvertStringToComponentRatios1() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testConvertStringToComponentRatios2() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testConvertStringToComponentRatios3() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testCorrectlyTokenisedAlkane() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testCorrectlyTokenisedAlkane2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testCorrectlyTokenisedAlkane3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testDashInsteadOfComma() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testDLStereochemistryDLOnAminoAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryDOnAchiralAminoAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryDOnAminoAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryDOnCarbohydrate() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryDOnCarbohydratePrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryLOnAminoAcid() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDLStereochemistryLOnCarbohydrate() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testDoubleBondMultiStereo1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondMultiStereo2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondMultiStereo3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondMultiStereo4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoela() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelb() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelc() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoeld() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoele() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelf() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelg() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelLike1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondNoelLike2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo5a() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo5b() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondStereo6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testDoubleBondSupport1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDoubleBondSupport8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testDStereochemistryDOnCarbohydratePrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testEandZUnbrackettedLocanted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testElementSymbol() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testFindBond() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testFindPathBetweenAtoms1() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testFindPathBetweenAtoms2() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testFindPathBetweenAtoms3() - Method in class uk.ac.cam.ch.wwmm.opsin.CycleDetectorTest
 
testFindPseudoAsymmetricCarbon1() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testFindPseudoAsymmetricCarbon2() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testFindSSSR() - Method in class uk.ac.cam.ch.wwmm.opsin.SSSRTest
 
testFragment() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetAtomByID() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetAtomByLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetAtomNeighbours() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetChainLength() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetIDFromLocant() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testGetIncomingValency() - Method in class uk.ac.cam.ch.wwmm.opsin.AtomTest
 
testGetOppositeDirection() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererFunctionsTest
 
testGetUnifiedFrags() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
testGreek() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testHydrogenNotBondedToAnyNonHydrogen1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testHydrogenNotBondedToAnyNonHydrogen2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testHydrogenNotBondedToAnyNonHydrogen3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testHydrogenNotBondedToAnyNonHydrogen4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testImportFrag() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testIsotope() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testIsTetrahedral() - Method in class uk.ac.cam.ch.wwmm.opsin.StereochemistryTest
 
testIUPAC2004() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testLabelAcetoanilide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelCarbamimidamido() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelCarbonicDihydrazide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelCarbonimidoyl() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelCarboximidohydrazide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelDiimidooxalicDiamide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHexanDiamide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHydrazinecarbohydrazide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHydrazonate() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHydrazonicAmide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelHydrazonoHydrazide() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelPiperazine() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelPyridine() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLabelSulfonoThioate() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testLocantedCisTrans() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testLocantedR() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testLocantedZ() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testLocantsIndicatingTokenizationIsCorrect() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testLocantsIndicatingTokenizationIsIncorrect() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testLStereochemistryDOnCarbohydratePrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testMisTokenisedAlkane() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testMultipleCardinals() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testMultipleHits() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testMultipleHits2() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testMultipleParsesAmbiguousWordTokenisationTerminalFunctionalTerm() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testMultipleParsesTerminalFunctionalTerm() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testMultipleRorSLocanted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testMultipleRorSorEorZ() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testMultipleTypesTogether() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testMultipleUnLocanted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testNameToStructure() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureTest
 
testNormalCase() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testNormalCase2() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testNormalCase3() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testNormalCase4() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testNotlowercase1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testNotlowercase2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testOrganic1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testOrganic9() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testParseReturnsOneWordRuleForEachMixtureComponent() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testParseThrowsWhenNameIsSubstituentOnly() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testParseThrowsWhenNameIsUninterpretable() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testParseToCML() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureTest
 
testParseToSmiles() - Method in class uk.ac.cam.ch.wwmm.opsin.NameToStructureTest
 
testParseUninvertsCASNomenclature() - Method in class uk.ac.cam.ch.wwmm.opsin.ParserTest
 
testPickUpIndicatedHydrogen() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testPreProcessBlankThrows() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarA() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarB() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarD() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarE() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarG() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsDollarL() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsGreekLetterToWord() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testPreProcessConvertsSulphToSulf() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testRacemate1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate4() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRacemate5() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRegexes() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testRegexTokens() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testRelabelFusedRingSystem() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentManagerTest
 
testRelabelSuffixLocants() - Method in class uk.ac.cam.ch.wwmm.opsin.FragmentTest
 
testRelativeStereoChemistry1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRelativeStereoChemistry2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testRemovalOfDotsFromGreekWords1() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testRemovalOfDotsFromGreekWords2() - Method in class uk.ac.cam.ch.wwmm.opsin.PreProcessorTest
 
testReverseMatching() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testRGroup() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRingOpeningsGreaterThan10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip11() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip12() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testRoundTrip9() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testSimple1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple10() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple11() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple8() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimple9() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 
testSimpleAddFindPrefix() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testSimpleAddSimpleGet() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testStartingFunctionalTerm1() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testStartingFunctionalTerm2() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testStereochemistryInLocant1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testStereochemistryInLocant2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testStereochemistryInLocant3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSubtractiveBiochemicalPreferredToRightMost() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSubtractiveRightMostPreferred() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSubtractiveWithBiochemicalToAttachTo() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSubtractiveWithMultiplierAndLocants() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSubtractiveWithNoGroupToAttachTo() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentProcessorTest
 
testSuffixApplicability() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testSuffixRules() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testSuperscript1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript4() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript5() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testSuperscript6() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_ProcesslocantsTest
 
testTerminalFunctionalTerm() - Method in class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
testTetrahedralChirality1() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality2() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality3() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality4() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality5() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality6() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetrahedralChirality7() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESWriterTest
 
testTetraphenShouldBeTetra_Phen1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testTetraphenShouldBeTetra_Phen2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testTetraphenShouldBeTetraphen1() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testTetraphenShouldBeTetraphen2() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testTetraphenShouldBeTetraphen3() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_AmbiguitiesAndIrregularitiesTest
 
testToCMLAtom() - Method in class uk.ac.cam.ch.wwmm.opsin.AtomTest
 
testToCMLBond() - Method in class uk.ac.cam.ch.wwmm.opsin.BondTest
 
testTokenFiles() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testTokenFilesValueValidity() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testUnLocantedE() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testUnlocantedS() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
testWordRules() - Method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
testZeroLengthToken() - Method in class uk.ac.cam.ch.wwmm.opsin.RadixTrieTest
 
testZUnbracketted() - Method in class uk.ac.cam.ch.wwmm.opsin.ComponentGeneration_StereochemistryTest
 
thia() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
thianthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thiochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thiochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thioisochromane() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thioisochromene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 
thionia() - Method in class uk.ac.cam.ch.wwmm.opsin.HeteroAtomReplacementTest
 
tokenizeDoesNotTokenizeUnTokenizableName() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUninterpretableNameLR1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUninterpretableNameLR2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUninterpretableNameRL1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUninterpretableNameRL2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsableNameLR1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsableNameLR2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsableNameRL1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsableNameRL2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsedNameLR1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsedNameLR2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsedNameRL1() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
tokenizePreservesSpacesInUnparsedNameRL2() - Method in class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
TokenizerTest - Class in uk.ac.cam.ch.wwmm.opsin
 
TokenizerTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.TokenizerTest
 
toString() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseRulesResults
 
toString() - Method in class uk.ac.cam.ch.wwmm.opsin.ParseTokens
 
trindene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

U

uk.ac.cam.ch.wwmm.opsin - package uk.ac.cam.ch.wwmm.opsin
 
unterminatedRingOpening() - Method in class uk.ac.cam.ch.wwmm.opsin.SMILESFragmentBuilderTest
 

V

validate(URI) - Static method in class uk.ac.cam.ch.wwmm.opsin.DtdTest
 
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.
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.
verifyCML() - Method in class uk.ac.cam.ch.wwmm.opsin.VerifyFragmentsTest
 
VerifyFragmentsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
VerifyFragmentsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.VerifyFragmentsTest
 
verifySMILES() - Method in class uk.ac.cam.ch.wwmm.opsin.VerifyFragmentsTest
 
violanthrene() - Method in class uk.ac.cam.ch.wwmm.opsin.FusedRingNumbererTest
 

W

WordToolsTest - Class in uk.ac.cam.ch.wwmm.opsin
 
WordToolsTest() - Constructor for class uk.ac.cam.ch.wwmm.opsin.WordToolsTest
 
write(Element) - Method in class uk.ac.cam.ch.wwmm.opsin.StreamSerializer
 
writeEndTag(Element) - Method in class uk.ac.cam.ch.wwmm.opsin.StreamSerializer
 
writeStartTag(Element) - Method in class uk.ac.cam.ch.wwmm.opsin.StreamSerializer
 
writeXMLDeclaration() - Method in class uk.ac.cam.ch.wwmm.opsin.StreamSerializer
 

X

XOMFormatter - Class in uk.ac.cam.ch.wwmm.opsin
Turns a XOM Element into a pretty indented string.
XOMFormatter() - Constructor for class uk.ac.cam.ch.wwmm.opsin.XOMFormatter
Sets up a new XOMFormatter.
XOMTools - Class in uk.ac.cam.ch.wwmm.opsin
Accessory functions for the manipulation of XOM Nodes/Elements Only those that are necessary for OPSIN's execution
XOMTools() - Constructor for class uk.ac.cam.ch.wwmm.opsin.XOMTools
 
A B C D E F G H I M N O P Q R S T U V W X