/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/ |
H A D | ComponentGeneration_StereochemistryTest.java | 24 assertEquals(null, newStereochemistryEl.getAttributeValue(LOCANT_ATR)); in testUnlocantedS() 41 assertEquals(null, newStereochemistryEl1.getAttributeValue(LOCANT_ATR)); in testMultipleUnLocanted() 47 assertEquals(null, newStereochemistryEl2.getAttributeValue(LOCANT_ATR)); in testMultipleUnLocanted() 64 assertEquals("1", newStereochemistryEl.getAttributeValue(LOCANT_ATR)); in testLocantedR() 87 assertEquals("3", newStereochemistryEl2.getAttributeValue(LOCANT_ATR)); in testMultipleRorSLocanted() 93 assertEquals("7'", newStereochemistryEl3.getAttributeValue(LOCANT_ATR)); in testMultipleRorSLocanted() 111 assertEquals(null, newStereochemistryEl.getAttributeValue(LOCANT_ATR)); in testUnLocantedE() 128 assertEquals("5", newStereochemistryEl.getAttributeValue(LOCANT_ATR)); in testLocantedZ() 145 assertEquals("N", newStereochemistryEl1.getAttributeValue(LOCANT_ATR)); in testMultipleRorSorEorZ() 151 assertEquals("2", newStereochemistryEl2.getAttributeValue(LOCANT_ATR)); in testMultipleRorSorEorZ() [all …]
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H A D | ComponentGeneration_ProcesslocantsTest.java | 144 assertEquals("5'", addedHydrogen.getAttributeValue(LOCANT_ATR)); in testAddedHydrogen() 156 assertEquals("7", addedHydrogen1.getAttributeValue(LOCANT_ATR)); in testAddedHydrogen2() 160 assertEquals("2", addedHydrogen2.getAttributeValue(LOCANT_ATR)); in testAddedHydrogen2() 256 assertEquals("5", addedHydrogen.getAttributeValue(LOCANT_ATR)); in testMultipleTypesTogether()
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H A D | StructureBuildingMethodsTest.java | 119 substituent.addAttribute(new Attribute(LOCANT_ATR, "4")); in phosphoLocantedSubstitution()
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/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/ |
H A D | WordRulesOmittedSpaceCorrector.java | 48 …if (firstSubOrbracket.getAttribute(LOCANT_ATR) == null && firstSubOrbracket.getAttribute(MULTIPLIE… in checkAndCorrectOmittedSpacesInDivalentFunctionalGroupRule() 97 if (firstChild.getAttribute(LOCANT_ATR) != null) { in checkAndCorrectOmittedSpaceEster() 102 if (subOrBracket.getAttribute(LOCANT_ATR) == null) { in checkAndCorrectOmittedSpaceEster() 143 if (substituentsAndBrackets.get(i).getAttribute(LOCANT_ATR)==null){ in allBarFirstSubstituentHaveLocants() 243 if (subOrBracket.getAttribute(LOCANT_ATR) != null){ in checkSuitabilityOfSubstituentForEsterFormation()
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H A D | ComponentProcessor.java | 2292 if (suffix.getAttribute(LOCANT_ATR)==null){ 2345 String locant = suffix.getAttributeValue(LOCANT_ATR); 2708 && previous.getAttribute(LOCANT_ATR) == null) { 2773 if(prev.getAttribute(LOCANT_ATR) != null) { 2872 String locant = heteroatom.getAttributeValue(LOCANT_ATR); 3847 if (lambdaConventionEl.getAttribute(LOCANT_ATR)!=null){ in applyLambdaConvention() 4627 suffix.getAttribute(LOCANT_ATR) == null && in isATerminalSuffix() 4725 if (substituent.getAttribute(LOCANT_ATR) != null) { in processBiochemicalLinkageDescriptors() 4739 if (elToAddAtrTo.getAttribute(LOCANT_ATR) !=null) { in processBiochemicalLinkageDescriptors() 4764 if (bracket.getAttribute(LOCANT_ATR) !=null){ in processBiochemicalLinkageDescriptors() [all …]
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H A D | StructureBuildingMethods.java | 241 if (subBracketOrRoot.getAttribute(LOCANT_ATR) != null){ in performUnLocantedSubstitutiveOperations() 372 currentElement.getAttribute(LOCANT_ATR).setValue(locants[i]); in multiplyOutAndSubstitute() 402 if (subBracketOrRoot.getAttribute(LOCANT_ATR) != null){ in performUnlocantedSubstitutiveOperations() 515 String locant = subtractivePrefix.getAttributeValue(LOCANT_ATR); in resolveLocantedFeatures() 597 String locant = hydrogen.getAttributeValue(LOCANT_ATR); in resolveLocantedFeatures() 615 String locant = unsaturator.getAttributeValue(LOCANT_ATR); in resolveLocantedFeatures() 642 String locant = heteroatomEl.getAttributeValue(LOCANT_ATR); in resolveLocantedFeatures() 674 String suffixLocant = suffix.getAttributeValue(LOCANT_ATR); in acdNameSpiroIndicatedHydrogenBug() 2244 if (bracketOrSubOrRoot.getAttribute(LOCANT_ATR) != null) { in findAlternativeGroups() 2528 if (stereoChemistryElement.getAttribute(LOCANT_ATR) != null){ in addPrimesToLocantedStereochemistryElements() [all …]
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H A D | StereochemistryHandler.java | 50 if (stereoChemistryElement.getAttributeValue(LOCANT_ATR)!=null){ in applyStereochemicalElements() 193 String locant = stereoChemistryEl.getAttributeValue(LOCANT_ATR); in assignStereoCentre() 288 String locant = stereoChemistryEl.getAttributeValue(LOCANT_ATR); in assignStereoBond() 450 if (stereoChemistryEl.getAttribute(LOCANT_ATR) != null) { in assignCisTransOnRing() 650 String locant = stereoChemistryEl.getAttributeValue(LOCANT_ATR); in assignAlphaBetaXiStereochem()
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H A D | StructureBuilder.java | 222 String locantForSubstituent = word.getAttributeValue(LOCANT_ATR); in buildEster() 462 String locantForSubstituent = currentWord.getAttributeValue(LOCANT_ATR); in buildFunctionalClassEster() 682 locantForFunctionalTerm.add(children.get(0).getAttributeValue(LOCANT_ATR)); in buildCarbonylDerivative() 684 else if (children.size()==2 && children.get(0).getAttribute(LOCANT_ATR)!=null ){ in buildCarbonylDerivative() 685 String locant =children.get(0).getAttributeValue(LOCANT_ATR); in buildCarbonylDerivative() 687 locantForFunctionalTerm.add(children.get(0).getAttributeValue(LOCANT_ATR)); in buildCarbonylDerivative() 688 children.get(0).removeAttribute(children.get(0).getAttribute(LOCANT_ATR)); in buildCarbonylDerivative() 1312 String locantForSubstituent = currentWord.getAttributeValue(LOCANT_ATR); in buildAcetal() 1425 String locant = ateWord.getAttributeValue(LOCANT_ATR); in buildAlcoholEster() 1509 String locant = word.getAttributeValue(LOCANT_ATR); in buildAmineDiConjunctiveSuffix() [all …]
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H A D | FusedRingBuilder.java | 330 …if (unsaturator.getAttribute(LOCANT_ATR)==null && unsaturator.getAttributeValue(VALUE_ATR).equals(… in processPartiallyUnsaturatedHWSystems() 365 else if (unsaturators.get(0).getAttribute(LOCANT_ATR)!=null){ in aromatiseCyclicAlkane() 376 if (value2 !=2 || unsaturators.get(1).getAttribute(LOCANT_ATR)!=null){ in aromatiseCyclicAlkane() 1004 if (suffix.getAttribute(LOCANT_ATR)==null){ in locantsCouldApplyToHeteroatomPositions()
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H A D | ComponentGenerator.java | 269 addedHydrogenElement.addAttribute(new Attribute(LOCANT_ATR, hydrogenLocant)); in processLocants() 831 indicatedHydrogenEl.addAttribute(new Attribute(LOCANT_ATR, locant)); in processIndicatedHydrogens() 915 …stereoChemEl.addAttribute(new Attribute(LOCANT_ATR, fixLocantCapitalisation(StringTools.removeDash… in processStereochemistryBracket() 996 stereoChemistryElement.addAttribute(new Attribute(LOCANT_ATR, possibleLocant.getValue())); in assignLocantUsingPreviousElementIfPresent() 1006 stereoChemistryElement.addAttribute(new Attribute(LOCANT_ATR, possibleLocant.getValue())); in processLocantAssigningForEndoExoSynAnti() 1032 stereoChemEl.addAttribute(new Attribute(LOCANT_ATR, locant)); in processUnbracketedAlphaBetaStereochemistry() 1125 locants.add(stereochemistryTerm.getAttributeValue(LOCANT_ATR)); in duplicateLocantFromStereoTermIfAdjacentToEneOrYlidene() 1340 heteroAtom.addAttribute(LOCANT_ATR, locant); in processLambdaConvention() 1347 newLambda.addAttribute(LOCANT_ATR, locant); in processLambdaConvention() 1362 heteroAtom.addAttribute(new Attribute(LOCANT_ATR, locant)); in processLambdaConvention() [all …]
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H A D | XmlDeclarations.java | 265 static final String LOCANT_ATR = "locant"; field in XmlDeclarations
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H A D | FunctionalReplacement.java | 437 String locant = acidReplacingWord.getAttributeValue(LOCANT_ATR); in processAcidReplacingFunctionalClassNomenclatureFullWord() 910 suffix.addAttribute(new Attribute(LOCANT_ATR, locants[0])); in disambiguateMultipliedInfixMeaning() 921 newSuffix.getAttribute(LOCANT_ATR).setValue(locants[j]); in disambiguateMultipliedInfixMeaning()
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H A D | SuffixApplier.java | 378 String locant = suffix.getAttributeValue(LOCANT_ATR); in processCycleFormingSuffix() 453 String locant = suffix.getAttributeValue(LOCANT_ATR); in getFragAtomToUse()
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