Searched refs:outAtom2 (Results 1 – 2 of 2) sorted by relevance
348 Atom outAtom2 = getOutAtomTakingIntoAccountWhetherSetExplicitly(substituent2, 0); in buildDiValentFunctionalGroup() local353 state.fragManager.createBond(outAtom2, diValentGroup.getFirstAtom(), 1); in buildDiValentFunctionalGroup()356 if (outAtom1 != outAtom2){//general case in buildDiValentFunctionalGroup()358 state.fragManager.createBond(outAtom2, diValentGroup.getFirstAtom(), 1); in buildDiValentFunctionalGroup()1227 OutAtom outAtom2 = theDiRadical.getOutAtom(1); in buildGlycol() local1228 …Atom chosenAtom2 = outAtom2.isSetExplicitly() ? outAtom2.getAtom() : findAtomForUnlocantedRadical(… in buildGlycol()1230 if (outAtom2.getValency() != 1){ in buildGlycol()1231 …eBuildingException("OutAtom has unexpected valency. Expected 1. Actual: " + outAtom2.getValency()); in buildGlycol()
2112 OutAtom outAtom2 = bridgingFragment.getOutAtom(0); in formEpoxide() local2114 if (outAtom1.getAtom().equals(outAtom2.getAtom()) && firstAtomToJoinTo == secondAtomToJoinTo){ in formEpoxide()2117 int bondValency = outAtom2.getValency(); in formEpoxide()2118 if (outAtom2.getAtom().hasSpareValency() && !secondAtomToJoinTo.hasSpareValency()) { in formEpoxide()2123 state.fragManager.createBond(outAtom2.getAtom(), secondAtomToJoinTo, bondValency); in formEpoxide()