Searched refs:hasSpareValency (Results 1 – 15 of 15) sorted by relevance
| /dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/ |
| H A D | FragmentTools.java | 532 if(a.hasSpareValency()) { in convertSpareValenciesToDoubleBonds()
534 if(aa.hasSpareValency()) { in convertSpareValenciesToDoubleBonds()
608 if(a.hasSpareValency()) { in convertSpareValenciesToDoubleBonds()
611 if(aa.hasSpareValency()) { in convertSpareValenciesToDoubleBonds()
638 if(aa.hasSpareValency()) { in convertSpareValenciesToDoubleBonds()
659 if(a.hasSpareValency()) { in convertSpareValenciesToDoubleBonds()
661 if(aa.hasSpareValency()) { in convertSpareValenciesToDoubleBonds()
683 if(a.hasSpareValency()) { in findBestAtomToRemoveSpareValencyFrom()
686 if(aa.hasSpareValency()) { in findBestAtomToRemoveSpareValencyFrom()
696 if(a.hasSpareValency()) { in findBestAtomToRemoveSpareValencyFrom()
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| H A D | StructureBuildingMethods.java | 570 if (!a.hasSpareValency()){ in resolveLocantedFeatures()
580 boolean hasSpareValency =false; in resolveLocantedFeatures()
582 if (neighbour.hasSpareValency()){ in resolveLocantedFeatures()
583 hasSpareValency = true; in resolveLocantedFeatures()
587 if (!hasSpareValency){ in resolveLocantedFeatures()
600 if (a.hasSpareValency()){ in resolveLocantedFeatures()
883 if (atom.hasSpareValency()) { in applyUnlocantedHydro()
887 if (!atom.hasSpareValency()) { in applyUnlocantedHydro()
915 if(aa.hasSpareValency()) { in applyUnlocantedHydro()
1247 if (atom.hasSpareValency() != spareValency){ in casIsotopeAmbiguitySpecialCase()
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| H A D | AmbiguityChecker.java | 195 …ing s = a.getElement().toString() +"\t" + valency + "\t" + numOfBonds + "\t" + a.hasSpareValency(); in findPlausibleSubstitutionPatternUsingLocalEnvironment()
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| H A D | SMILESFragmentBuilder.java | 421 if (atom.hasSpareValency()) { in processBracketedAtom()
881 if (atom.hasSpareValency()) { in setupAtomValency()
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| H A D | Atom.java | 444 boolean hasSpareValency() { in hasSpareValency() method in Atom
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| H A D | WordRulesOmittedSpaceCorrector.java | 279 …int currentValency = (atom.getIncomingValency() + (atom.hasSpareValency() ? 1 : 0) + atom.getOutV… in getAtomForEachSubstitutableHydrogen()
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| H A D | StructureBuilder.java | 608 …if (fromAtom.hasSpareValency() && toAtom.hasSpareValency() &&fromAtom.getElement() == ChemEl.C && … in buildOxide()
2232 if ((incomingValency + connectedAtom.getOutValency()) ==3 && connectedAtom.hasSpareValency()){ in processSpecialCases()
2266 …if (atom.getElement() == ChemEl.N && atom.hasSpareValency() && atom.getBondCount() == 3 && atom.ge… in processSpecialCases()
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| H A D | SuffixApplier.java | 502 if (a.hasSpareValency() && !a.getFrag().getIndicatedHydrogen().contains(a)) { in applyUnlocantedChargeModification()
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| H A D | FragmentManager.java | 381 newAtom.setSpareValency(atom.hasSpareValency()); in copyAndRelabelFragment()
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| H A D | ValencyChecker.java | 364 valency +=a.hasSpareValency() ? 1 : 0; in checkValencyAvailableForReplacementByHeteroatom()
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| H A D | SMILESWriter.java | 596 …if (atom.hasSpareValency()) {//spare valency corresponds directly to lower case SMILES in OPSIN's … in atomToSmiles()
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| H A D | ComponentProcessor.java | 2803 if (a.hasSpareValency()){
3376 if (atomToBeReplaced.hasSpareValency()){ in processNonIdenticalPolyCyclicSpiro()
3483 if (atomToBeReplaced.hasSpareValency()){ in processOldMethodPolyCyclicSpiro()
3556 if (atomToBeReplaced.hasSpareValency()){ in processSpiroBiOrTer()
3595 if (atomToBeReplaced.hasSpareValency()){ in processDispiroter()
3603 if (atomToBeReplaced.hasSpareValency()){ in processDispiroter()
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| H A D | FusedRingBuilder.java | 868 if (childAtom.hasSpareValency()){ in fuseRings()
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| /dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/ |
| H A D | FragmentTest.java | 396 assertEquals("All atoms have sv", true, a.hasSpareValency()); in testSpareValenciesOnAromaticAtoms()
408 assertEquals("All atoms have no sv", false, a.hasSpareValency()); in testConvertSpareValenciesToDoubleBonds()
413 assertEquals("All atoms have no sv", false, a.hasSpareValency()); in testConvertSpareValenciesToDoubleBonds()
418 assertEquals("All atoms have no sv", false, a.hasSpareValency()); in testConvertSpareValenciesToDoubleBonds()
422 assertEquals("All atoms have sv", true, a.hasSpareValency()); in testConvertSpareValenciesToDoubleBonds()
426 assertEquals("All atoms have no sv", false, a.hasSpareValency()); in testConvertSpareValenciesToDoubleBonds()
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| H A D | SMILESFragmentBuilderTest.java | 94 assertEquals(false, atom.hasSpareValency()); in testSimple6()
105 assertEquals(true, atom.hasSpareValency()); in testSimple7()
496 assertEquals(true, atomList.get(0).hasSpareValency()); in hydrogenHandling21()
500 assertEquals(true, atomList.get(1).hasSpareValency()); in hydrogenHandling21()
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