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Searched refs:GROUP_EL (Results 1 – 18 of 18) sorted by relevance

/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/
H A DComponentProcessorTest.java33 Element group = new TokenEl(GROUP_EL); in testSubtractiveWithBiochemicalToAttachTo()
52 Element group1 = new TokenEl(GROUP_EL); in testSubtractiveRightMostPreferred()
59 Element group2 = new TokenEl(GROUP_EL); in testSubtractiveRightMostPreferred()
79 Element group1 = new TokenEl(GROUP_EL); in testSubtractiveBiochemicalPreferredToRightMost()
85 Element group2 = new TokenEl(GROUP_EL); in testSubtractiveBiochemicalPreferredToRightMost()
110 Element group = new TokenEl(GROUP_EL); in testSubtractiveWithMultiplierAndLocants()
126 Element aminoAcidEl = new TokenEl(GROUP_EL); in testDLStereochemistryLOnAminoAcid()
138 Element aminoAcidEl = new TokenEl(GROUP_EL); in testDLStereochemistryDOnAminoAcid()
150 Element aminoAcidEl = new TokenEl(GROUP_EL); in testDLStereochemistryDLOnAminoAcid()
161 Element aminoAcidEl = new TokenEl(GROUP_EL); in testDLStereochemistryDOnAchiralAminoAcid()
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H A DStructureBuildingMethodsTest.java63 Element amino = new TokenEl(GROUP_EL); in notPhosphoSubstitution()
69 Element methanol = new TokenEl(GROUP_EL); in notPhosphoSubstitution()
88 Element phospho = new TokenEl(GROUP_EL); in phosphoUnlocantedSubstitution()
95 Element methanol = new TokenEl(GROUP_EL); in phosphoUnlocantedSubstitution()
114 Element phospho = new TokenEl(GROUP_EL); in phosphoLocantedSubstitution()
122 Element methanol = new TokenEl(GROUP_EL); in phosphoLocantedSubstitution()
H A DComponentGeneration_MiscTest.java17 Element group = new TokenEl(GROUP_EL); in testRejectSingleComponentSaltComponent()
35 Element group = new TokenEl(GROUP_EL); in testNumericallyMultipliedSaltComponent()
H A DVerifyFragmentsTest.java66 if (tagname.equals(GROUP_EL) || in verifySmilesInTokenList()
78 TokenEl tokenEl = new TokenEl(GROUP_EL); in verifySmilesInTokenList()
H A DComponentGeneration_ProcesslocantsTest.java19 …substituent.addChild(new TokenEl(GROUP_EL));//a dummy element to give the locant a potential purpo… in setUpSubstituent()
273 assertEquals(group.getName(), GROUP_EL); in testCarbohydrateStyleLocants() local
290 assertEquals(group.getName(), GROUP_EL); in testCarbohydrateStyleLocantsNoNumericComponent() local
H A DComponentGeneration_StereochemistryTest.java325 Element group = new TokenEl(GROUP_EL); in testLocantedExoOn()
350 Element group = new TokenEl(GROUP_EL); in testLocantedExo()
571 Element naturalProduct = new TokenEl(GROUP_EL); in testBrackettedAlphaBeta()
617 Element naturalProduct = new TokenEl(GROUP_EL); in testAlphaBeta()
691 Element naturalProduct = new TokenEl(GROUP_EL); in testAlphaBetaNotDirectlyPrecedingANaturalProduct3()
/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/
H A DStereochemistryHandler.java163 Element nextGroup = OpsinTools.getNextSibling(carbohydrateStereoChemistryEl, GROUP_EL); in processCarbohydrateStereochemistry()
189 …> adjacentGroupEls = OpsinTools.getDescendantElementsWithTagName(parentSubBracketOrRoot, GROUP_EL); in assignStereoCentre()
206 List<Element> possibleGroups = OpsinTools.getDescendantElementsWithTagName(word, GROUP_EL); in assignStereoCentre()
284 …> adjacentGroupEls = OpsinTools.getDescendantElementsWithTagName(parentSubBracketOrRoot, GROUP_EL); in assignStereoBond()
315 List<Element> possibleGroups = OpsinTools.getDescendantElementsWithTagName(word, GROUP_EL); in assignStereoBond()
455 …> adjacentGroupEls = OpsinTools.getDescendantElementsWithTagName(parentSubBracketOrRoot, GROUP_EL); in assignCisTransOnRing()
470 List<Element> possibleGroups = OpsinTools.getDescendantElementsWithTagName(word, GROUP_EL); in assignCisTransOnRing()
644 substituentGroup = parentSubBracketOrRoot.getFirstChildElement(GROUP_EL).getFrag(); in assignAlphaBetaXiStereochem()
646 …> adjacentGroupEls = OpsinTools.getDescendantElementsWithTagName(parentSubBracketOrRoot, GROUP_EL); in assignAlphaBetaXiStereochem()
826 && elementToApplyTo.getName().equals(GROUP_EL) in assignDlStereochem()
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H A DComponentProcessor.java154 if (substituent.getChildElements(GROUP_EL).size() == 0) { in processParse()
1198 Element group = finalSub.getFirstChildElement(GROUP_EL); in checkSpecialLocantUses()
1954 List<Element> groups = subOrRoot.getChildElements(GROUP_EL); in detectConjunctiveSuffixGroups()
2065 List<Element> groups = subOrRoot.getChildElements(GROUP_EL);
3164 if (currentEl.getName().equals(GROUP_EL)) { in determineElementsToResolveIntoRingAssembly()
3266 if (name.equals(GROUP_EL)) { in processNonIdenticalPolyCyclicSpiro()
3650 if (elName.equals(GROUP_EL)){ in resolveFeaturesOntoGroup()
3871 Element group =subOrRoot.getFirstChildElement(GROUP_EL); in handleMultiRadicals()
4445 Element group =subOrRoot.getFirstChildElement(GROUP_EL); in matchLocantsToIndirectFeatures()
4554 else if (el.getName().equals(GROUP_EL)){ in findLocantsThatCouldBeIndirectLocants()
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H A DComponentGenerator.java201 while(currentElem != null && !currentElem.getName().equals(GROUP_EL)){ in resolveAmbiguities()
481 if(elName.equals(GROUP_EL)){ in orthoMetaParaLocantIsTwoLocants()
515 Element alkaneStem = new TokenEl(GROUP_EL, alkaneName.toString()); in formAlkaneStemsFromComponents()
647 if(multipliedElem.getName().equals(GROUP_EL) && in processHeterogenousHydrides()
717 Element addedGroup = new TokenEl(GROUP_EL, newGroupName.toString()); in processHeterogenousHydrides()
1254 if (subOrRoot.getChildElements(GROUP_EL).size()>1){ in processLambdaConvention()
1487 Element group =new TokenEl(GROUP_EL, annulenValue); in processHydroCarbonRings()
1663 Element alk = OpsinTools.getPreviousSibling(suffix, GROUP_EL); in handleSuffixIrregularities()
1675 Element group = OpsinTools.getPreviousSibling(suffix, GROUP_EL); in handleSuffixIrregularities()
1695 Element precedingGroup = OpsinTools.getPreviousSibling(suffix, GROUP_EL); in handleSuffixIrregularities()
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H A DWordRules.java359 functionalGroups.get(0).setName(GROUP_EL); in matchWordRule()
368 …ntElementsWithTagNameAndAttribute(possibleElementaryAtomContainingWord, GROUP_EL, SUBTYPE_ATR, ELE… in matchWordRule()
542 else if (elName.equals(GROUP_EL)) { in endsWithGroupPredicateSatisfied()
549 if (elName.equals(GROUP_EL)) { in endsWithGroupPredicateSatisfied()
589 if (lastEl.getName().equals(GROUP_EL)) { in getLastGroupInWordRule()
593 List<Element> groups = lastEl.getParent().getChildElements(GROUP_EL); in getLastGroupInWordRule()
684 functionalGroup.setName(GROUP_EL); in convertFunctionalGroupIntoGroup()
H A DStructureBuildingMethods.java166 group = subBracketOrRoot.getFirstChildElement(GROUP_EL); in performLocantedSubstitutiveOperations()
234 group = subBracketOrRoot.getFirstChildElement(GROUP_EL); in performUnLocantedSubstitutiveOperations()
398 group = subBracketOrRoot.getFirstChildElement(GROUP_EL); in performUnlocantedSubstitutiveOperations()
445 group = subBracketOrRoot.getFirstChildElement(GROUP_EL); in performUnlocantedSubstitutiveOperations()
465 List<Element> groups = subOrRoot.getChildElements(GROUP_EL); in resolveLocantedFeatures()
806 List<Element> groups = subOrRoot.getChildElements(GROUP_EL); in resolveUnLocantedFeatures()
1383 group =subBracketOrRoot.getFirstChildElement(GROUP_EL); in performAdditiveOperations()
1563 group = currentElement.getFirstChildElement(GROUP_EL); in multiplyOutAndAdditivelyBond()
1859 Element group = descendantChild.getFirstChildElement(GROUP_EL); in getNextInScopeMultiValentFragment()
2218 if (currentElement.getName().equals(GROUP_EL)) { in findAlternativeGroups()
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H A DOpsinTools.java87 if (current.getName().equals(GROUP_EL)) {//can start with a group or the sub/root the group is in in getPreviousGroup()
102 List<Element> groups = previous.getParent().getChildElements(GROUP_EL); in getPreviousGroup()
117 if (current.getName().equals(GROUP_EL)) {//can start with a group or the sub/root the group is in in getNextGroup()
132 List<Element> groups = next.getParent().getChildElements(GROUP_EL); in getNextGroup()
H A DFunctionalReplacement.java138 Element groupToBeModified = nextSubOrBracket.getFirstChildElement(GROUP_EL); in processPrefixFunctionalReplacementNomenclature()
286 if (possibleAcidGroup !=null && possibleAcidGroup.getName().equals(GROUP_EL) && in processInfixFunctionalReplacementNomenclature()
448 Element groupToBeModified = acidContainingRoot.getFirstChildElement(GROUP_EL); in processAcidReplacingFunctionalClassNomenclatureFullWord()
460 …h " + functionalGroupName +"s in " + acidContainingRoot.getFirstChildElement(GROUP_EL).getValue()); in processAcidReplacingFunctionalClassNomenclatureFullWord()
517 Element groupToBeModified = acidContainingRoot.getFirstChildElement(GROUP_EL); in processAcidReplacingFunctionalClassNomenclatureFunctionalWord()
529 …ygen to replace with nitrogen in " + acidContainingRoot.getFirstChildElement(GROUP_EL).getValue()); in processAcidReplacingFunctionalClassNomenclatureFunctionalWord()
H A DBuildResults.java33 …> groups = OpsinTools.getDescendantElementsWithTagName(wordSubOrBracket, XmlDeclarations.GROUP_EL); in BuildResults()
H A DFusedRingBuilder.java45 List<Element> groups = subOrRoot.getChildElements(GROUP_EL); in processFusedRings()
123 if (ncIndice <0 || !nameComponents.get(ncIndice).getName().equals(GROUP_EL)){ in buildFusedRing()
279 if (currentEl.getName().equals(GROUP_EL) || currentEl.getName().equals(FUSION_EL)){ in formNameComponentList()
412 if (i <0 || !nameComponents.get(i).getName().equals(GROUP_EL)){ in processMultiParentSystem()
H A DStructureBuilder.java56 List<Element> groupElements = OpsinTools.getDescendantElementsWithTagName(molecule, GROUP_EL); in buildFragment()
369 List<Element> groups = OpsinTools.getDescendantElementsWithTagName(words.get(0), GROUP_EL); in buildMonovalentFunctionalGroup()
1175 Element group = root.getFirstChildElement(GROUP_EL); in applyAluminiumHydrideSpecialCase()
1371 if (currentEl.getName().equals(GROUP_EL)) { in replaceChalcogensInAcetal()
1647 …cids = OpsinTools.getDescendantElementsWithTagNameAndAttribute(peptide, GROUP_EL, TYPE_ATR, AMINOA… in buildCyclicPeptide()
1997 …oms = OpsinTools.getDescendantElementsWithTagNameAndAttribute(molecule, GROUP_EL, SUBTYPE_ATR, ELE… in getMetalsThatCanBeImplicitlyCations()
2049 …ist<Element> groups1 = OpsinTools.getDescendantElementsWithTagName(wordRule.getChild(0), GROUP_EL); in triHalideSpecialCase()
2050 …ist<Element> groups2 = OpsinTools.getDescendantElementsWithTagName(wordRule.getChild(1), GROUP_EL); in triHalideSpecialCase()
2051 …ist<Element> groups3 = OpsinTools.getDescendantElementsWithTagName(wordRule.getChild(2), GROUP_EL); in triHalideSpecialCase()
2073 List<Element> groups = OpsinTools.getDescendantElementsWithTagName(wordRule, GROUP_EL); in acetylideSpecialCase()
H A DXmlDeclarations.java101 static final String GROUP_EL ="group"; field in XmlDeclarations
H A DFragmentManager.java510 …lGroups = OpsinTools.getDescendantElementsWithTagName(elementToBeCloned, XmlDeclarations.GROUP_EL); in cloneElement()
511 …ment> clonedGroups = OpsinTools.getDescendantElementsWithTagName(clone, XmlDeclarations.GROUP_EL); in cloneElement()