/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/ |
H A D | ComponentProcessorTest.java | 33 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() [all …]
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H A D | StructureBuildingMethodsTest.java | 63 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()
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H A D | ComponentGeneration_MiscTest.java | 17 Element group = new TokenEl(GROUP_EL); in testRejectSingleComponentSaltComponent() 35 Element group = new TokenEl(GROUP_EL); in testNumericallyMultipliedSaltComponent()
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H A D | VerifyFragmentsTest.java | 66 if (tagname.equals(GROUP_EL) || in verifySmilesInTokenList() 78 TokenEl tokenEl = new TokenEl(GROUP_EL); in verifySmilesInTokenList()
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H A D | ComponentGeneration_ProcesslocantsTest.java | 19 …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
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H A D | ComponentGeneration_StereochemistryTest.java | 325 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()
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/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/ |
H A D | StereochemistryHandler.java | 163 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() [all …]
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H A D | ComponentProcessor.java | 154 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() [all …]
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H A D | ComponentGenerator.java | 201 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() [all …]
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H A D | WordRules.java | 359 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()
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H A D | StructureBuildingMethods.java | 166 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() [all …]
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H A D | OpsinTools.java | 87 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()
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H A D | FunctionalReplacement.java | 138 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()
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H A D | BuildResults.java | 33 …> groups = OpsinTools.getDescendantElementsWithTagName(wordSubOrBracket, XmlDeclarations.GROUP_EL); in BuildResults()
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H A D | FusedRingBuilder.java | 45 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()
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H A D | StructureBuilder.java | 56 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()
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H A D | XmlDeclarations.java | 101 static final String GROUP_EL ="group"; field in XmlDeclarations
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H A D | FragmentManager.java | 510 …lGroups = OpsinTools.getDescendantElementsWithTagName(elementToBeCloned, XmlDeclarations.GROUP_EL); in cloneElement() 511 …ment> clonedGroups = OpsinTools.getDescendantElementsWithTagName(clone, XmlDeclarations.GROUP_EL); in cloneElement()
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