Searched refs:functionalAtom (Results 1 – 6 of 6) sorted by relevance
100 FunctionalAtom functionalAtom = functionalAtoms.get(i); in removeFunctionalAtom() local101 functionalAtom.getAtom().getFrag().removeFunctionalAtom(functionalAtom); in removeFunctionalAtom()
463 Atom functionalAtom; in buildFunctionalClassEster() local468 functionalAtom = acidBr.getFunctionalAtom(0); in buildFunctionalClassEster()475 if (functionalAtom.getCharge() == -1) { in buildFunctionalClassEster()476 functionalAtom.neutraliseCharge(); in buildFunctionalClassEster()949 oxygen1=functionalAtom; in buildAnhydride()959 oxygen2=functionalAtom; in buildAnhydride()1479 Atom functionalAtom = br.getFunctionalAtom(0); in buildAlcoholEster() local1481 functionalAtom.neutraliseCharge(); in buildAlcoholEster()1893 for (Atom functionalAtom : functionalAtoms) { in deprotonateAcidIfSaltWithMetal()1894 if (functionalAtom.getCharge() == 0 && functionalAtom.getIncomingValency() == 1){ in deprotonateAcidIfSaltWithMetal()[all …]
419 void removeFunctionalAtom(FunctionalAtom functionalAtom) { in removeFunctionalAtom() argument420 functionalAtoms.remove(functionalAtom); in removeFunctionalAtom()
953 FunctionalAtom functionalAtom = origFrag.getFunctionalAtom(i); in removeOrMoveObsoleteFunctionalAtoms() local954 if (atomToBeReplaced.equals(functionalAtom.getAtom())){ in removeOrMoveObsoleteFunctionalAtoms()992 FunctionalAtom functionalAtom = frag.getFunctionalAtom(i); in removeAssociatedFunctionalAtom() local993 if (atomWithFunctionalAtom.equals(functionalAtom.getAtom())){ in removeAssociatedFunctionalAtom()
460 FunctionalAtom functionalAtom = originalFragment.getFunctionalAtom(i); in copyAndRelabelFragment() local461 newFragment.addFunctionalAtom(oldToNewAtomMap.get(functionalAtom.getAtom())); in copyAndRelabelFragment()
2222 Atom functionalAtom = suffixableFragment.removeFunctionalAtom(0).getAtom();2223 functionalAtom.neutraliseCharge();