| /dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/ |
| H A D | FragmentTest.java | 196 frag = fm.buildSMILES("C(N)(=N)N-", NONCARBOXYLICACID_TYPE_VAL, NONE_LABELS_VAL); in testLabelCarbamimidamido()
205 frag = fm.buildSMILES("C(=NN)NN" , NONCARBOXYLICACID_TYPE_VAL, NONE_LABELS_VAL); in testLabelHydrazonoHydrazide()
216 frag = fm.buildSMILES("C(=N)" , ACIDSTEM_TYPE_VAL, NONE_LABELS_VAL); in testLabelCarbonimidoyl()
226 frag = fm.buildSMILES("C", ACIDSTEM_TYPE_VAL, NONE_LABELS_VAL); in testLabelHydrazonicAmide()
227 Fragment suffixfrag = fm.buildSMILES("[R](N)=NN", SUFFIX_TYPE_VAL, NONE_LABELS_VAL); in testLabelHydrazonicAmide()
241 frag = fm.buildSMILES("C", ACIDSTEM_TYPE_VAL, NONE_LABELS_VAL); in testLabelHydrazonate()
256 Fragment suffixfrag1 = fm.buildSMILES("[R]N", SUFFIX_TYPE_VAL, NONE_LABELS_VAL); in testLabelHexanDiamide()
257 Fragment suffixfrag2 = fm.buildSMILES("[R]N", SUFFIX_TYPE_VAL, NONE_LABELS_VAL); in testLabelHexanDiamide()
303 frag = fm.buildSMILES("C(=O)(NN)NN", NONCARBOXYLICACID_TYPE_VAL, NONE_LABELS_VAL); in testLabelCarbonicDihydrazide()
443 Fragment suffix = fm.buildSMILES("N", SUFFIX_TYPE_VAL, NONE_LABELS_VAL); in testIsCharacteristicAtomSuffix()
[all …]
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| H A D | FusedRingNumbererTest.java | 447 Fragment fusedRing = sBuilder.build(smiles, mock(Element.class), XmlDeclarations.NONE_LABELS_VAL); in compareNumbering()
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| H A D | SMILESWriterTest.java | 429 Fragment f = fm.buildSMILES("CCC", "", XmlDeclarations.NONE_LABELS_VAL); in testLabelling1()
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| /dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/ |
| H A D | FunctionalReplacement.java | 378 …placementFrag = state.fragManager.buildSMILES(replacementSMILES, SUFFIX_TYPE_VAL, NONE_LABELS_VAL); in processInfixFunctionalReplacementNomenclature()
542 …ager.buildSMILES(groupValue, SUFFIX_TYPE_VAL, labelsValue != null ? labelsValue : NONE_LABELS_VAL); in processAcidReplacingFunctionalClassNomenclatureFunctionalWord()
752 Fragment newOxygen = state.fragManager.buildSMILES("O", SUFFIX_TYPE_VAL, NONE_LABELS_VAL); in performPeroxyFunctionalReplacement()
761 … Fragment replacementFrag = state.fragManager.buildSMILES("OO", SUFFIX_TYPE_VAL, NONE_LABELS_VAL); in performPeroxyFunctionalReplacement()
851 ….fragManager.buildSMILES(replacementSmiles, atomToReplace.getFrag().getTokenEl(), NONE_LABELS_VAL); in performFunctionalReplacementOnAcid()
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| H A D | StructureBuilder.java | 344 …lentGroup =state.fragManager.buildSMILES(smilesOfGroup, FUNCTIONALCLASS_TYPE_VAL, NONE_LABELS_VAL); in buildDiValentFunctionalGroup()
389 …S(functionalGroups.get(0).getAttributeValue(VALUE_ATR), FUNCTIONALCLASS_TYPE_VAL, NONE_LABELS_VAL); in buildMonovalentFunctionalGroup()
539 …ildSMILES(smilesReplacement, FUNCTIONALCLASS_TYPE_VAL, labels != null ? labels : NONE_LABELS_VAL)); in buildOxide()
710 …uildSMILES(smilesReplacement, FUNCTIONALCLASS_TYPE_VAL, labels != null ? labels : NONE_LABELS_VAL); in buildCarbonylDerivative()
1011 …ydride = state.fragManager.buildSMILES(anhydrideSmiles, FUNCTIONALCLASS_TYPE_VAL, NONE_LABELS_VAL); in formAnhydrideLink()
1039 …S(functionalGroups.get(0).getAttributeValue(VALUE_ATR), FUNCTIONALCLASS_TYPE_VAL, NONE_LABELS_VAL); in buildAcidHalideOrPseudoHalide()
1102 …buildSMILES(functionGroup.getAttributeValue(VALUE_ATR), FUNCTIONALCLASS_TYPE_VAL, NONE_LABELS_VAL); in buildAdditionCompound()
1220 …functionalClassEls.get(0).getAttributeValue(VALUE_ATR), FUNCTIONALCLASS_TYPE_VAL, NONE_LABELS_VAL); in buildGlycol()
1229 Fragment hydroxy =state.fragManager.buildSMILES("O", FUNCTIONALCLASS_TYPE_VAL, NONE_LABELS_VAL); in buildGlycol()
1393 …lFrag = state.fragManager.buildSMILES(StringTools.arrayToString(elements, "."),"",NONE_LABELS_VAL); in formAcetal()
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| H A D | XmlDeclarations.java | 527 static final String NONE_LABELS_VAL ="none"; field in XmlDeclarations
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| H A D | SMILESFragmentBuilder.java | 640 return build(smiles, "", NONE_LABELS_VAL); in build()
732 if (labelMapping.equals(NONE_LABELS_VAL) || labelMapping.length() == 0) { in processLabelling()
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| H A D | ComponentProcessor.java | 242 …te.fragManager.buildSMILES(groupValue, group, labelsValue != null ? labelsValue : NONE_LABELS_VAL); in resolveGroup()
339 fragToAdd = state.fragManager.buildSMILES(smiles, group, NONE_LABELS_VAL); in processXyleneLikeNomenclature()
1724 Fragment f = state.fragManager.buildSMILES("O", group, NONE_LABELS_VAL); in processAldoseDiSuffix()
1727 f = state.fragManager.buildSMILES("O", group, NONE_LABELS_VAL); in processAldoseDiSuffix()
1735 f = state.fragManager.buildSMILES("O", group, NONE_LABELS_VAL); in processAldoseDiSuffix()
1746 Fragment f = state.fragManager.buildSMILES("O", group, NONE_LABELS_VAL); in processAldoseDiSuffix()
2371 labels = NONE_LABELS_VAL;
2541 …gManager.buildSMILES(suffix.getAttributeValue(SUFFIXPREFIX_ATR), SUFFIX_TYPE_VAL, NONE_LABELS_VAL);
3774 …rag = state.fragManager.buildSMILES(bridge.getAttributeValue(VALUE_ATR), groupEl, NONE_LABELS_VAL); in processFusedRingBridges()
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| H A D | ComponentGenerator.java | 561 String labels = NONE_LABELS_VAL; in processAlkaneStemModifications()
2257 group.getAttribute(LABELS_ATR).setValue(NONE_LABELS_VAL); in handleGroupIrregularities()
2329 group.getAttribute(LABELS_ATR).setValue(NONE_LABELS_VAL); in handleGroupIrregularities()
2356 group.getAttribute(LABELS_ATR).setValue(NONE_LABELS_VAL); in handleGroupIrregularities()
2359 group.addAttribute(new Attribute(LABELS_ATR, NONE_LABELS_VAL)); in handleGroupIrregularities()
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| H A D | FragmentManager.java | 57 return buildSMILES(smiles, "", NONE_LABELS_VAL); in buildSMILES()
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