Searched refs:getBondToAtom (Results 1 – 9 of 9) sorted by relevance
111 bonds.remove(atomList.get(4).getBondToAtom(atomList.get(9))); in testFindPathBetweenAtoms2()141 bonds.remove(atomList.get(0).getBondToAtom(atomList.get(1))); in testFindPathBetweenAtoms3()142 bonds.remove(atomList.get(6).getBondToAtom(atomList.get(7))); in testFindPathBetweenAtoms3()143 bonds.remove(atomList.get(5).getBondToAtom(atomList.get(11))); in testFindPathBetweenAtoms3()
118 Bond chiralBond = atom2.getBondToAtom(atom3); in applyStereochemistryLocantedZ()133 Bond chiralBond = atom2.getBondToAtom(atom3); in applyStereochemistryLocantedE()148 Bond chiralBond = atom2.getBondToAtom(atom3); in applyStereochemistryUnlocantedZ()163 Bond chiralBond = atom2.getBondToAtom(atom3); in applyStereochemistryUnlocantedE()178 Bond chiralBond = atom2.getBondToAtom(atom3); in applyStereochemistryCis()193 Bond chiralBond = atom2.getBondToAtom(atom3); in applyStereochemistryTrans()
173 fm.removeBond(a2.getBondToAtom(a4)); in testGetChainLength()
85 Bond bond = atom.getBondToAtom(atom1); in getAncestors1()107 Bond linkBond = atom.getBondToAtom(ligandAtom); in expand()
607 Bond getBondToAtom(Atom a) { in getBondToAtom() method in Atom624 Bond b = getBondToAtom(a); in getBondToAtomOrThrow()
374 if (possibleToAtom !=null && fromAtom.getBondToAtom(possibleToAtom)!=null){ in unsaturate()379 if (possibleToAtom !=null && fromAtom.getBondToAtom(possibleToAtom)!=null){ in unsaturate()387 …if (initialIndice +1 < atomList.size() && fromAtom.getBondToAtom(atomList.get(initialIndice +1))!=… in unsaturate()
379 Bond bond1 = atomRefs4[0].getBondToAtom(atomRefs4[1]); in assignDoubleBondStereochemistrySlashes()380 Bond bond2 = atomRefs4[2].getBondToAtom(atomRefs4[3]); in assignDoubleBondStereochemistrySlashes()
258 if (previous != null && previous.getBondToAtom(next) == null){ in getChainLength()
1810 if (previous != null && previous.getBondToAtom(next) == null){ in getLocantOfEndOfChainIfGreaterThan1()