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Searched refs:getLambdaConventionValency (Results 1 – 9 of 9) sorted by relevance

/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/
H A DSuffixApplier.java494 …tExpectedValency = (a.getLambdaConventionValency() ==null ? ValencyChecker.getDefaultValency(chemE… in applyUnlocantedChargeModification()
H A DValencyChecker.java317 if (a.getLambdaConventionValency() != null) { in getMaximumValency()
318 maxVal = a.getLambdaConventionValency() + a.getProtonsExplicitlyAddedOrRemoved(); in getMaximumValency()
H A DAtom.java493 Integer getLambdaConventionValency() { in getLambdaConventionValency() method in Atom
H A DFragmentTools.java941 if (atom.getLambdaConventionValency()!=null){//corrects valency for phosphin/arsin/stibin in removeTerminalOxygen()
942 atom.setLambdaConventionValency(atom.getLambdaConventionValency()-desiredBondOrder); in removeTerminalOxygen()
H A DFragmentManager.java383 newAtom.setLambdaConventionValency(atom.getLambdaConventionValency()); in copyAndRelabelFragment()
H A DSMILESFragmentBuilder.java723 …if (atom.getProperty(Atom.SMILES_HYDROGEN_COUNT) != null && atom.getLambdaConventionValency() == n… in build()
H A DStructureBuilder.java651 …if (atomToAddOxideTo.getLambdaConventionValency()==null || !ValencyChecker.checkValencyAvailableFo… in formAppropriateBondToOxideAndAdjustCharges()
2236 …if (connectedAtom.getLambdaConventionValency()!=null && connectedAtom.getLambdaConventionValency()… in processSpecialCases()
H A DStructureBuildingMethods.java1363 if (a.getLambdaConventionValency() != null) { in getLambdaValencyOrHwValencyOrMaxValIfCharged()
1364 return a.getLambdaConventionValency() + a.getProtonsExplicitlyAddedOrRemoved(); in getLambdaValencyOrHwValencyOrMaxValIfCharged()
/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/
H A DSMILESFragmentBuilderTest.java402 int lambdaConvent =atomList.get(0).getLambdaConventionValency(); in hydrogenHandling11()