Searched refs:cipOrderedAtoms (Results 1 – 3 of 3) sorted by relevance
66 List<Atom> cipOrderedAtoms = new CipSequenceRules(stereoAtom).getNeighbouringAtomsInCipOrder(); in getCipOrderedAtoms() local67 …if (cipOrderedAtoms.size()==3){//lone pair is the 4th. This is represented by the atom itself and … in getCipOrderedAtoms()68 cipOrderedAtoms.add(0, stereoAtom); in getCipOrderedAtoms()70 return cipOrderedAtoms; in getCipOrderedAtoms()
249 List<Atom> cipOrderedAtoms =stereoCentre.getCipOrderedAtoms(); in applyStereoChemistryToStereoCentre() local250 if (cipOrderedAtoms.size()!=4){ in applyStereoChemistryToStereoCentre()254 atomRefs4[0] = cipOrderedAtoms.get(cipOrderedAtoms.size()-1); in applyStereoChemistryToStereoCentre()255 …for (int i = 0; i < cipOrderedAtoms.size() -1; i++) {//from highest to lowest (true for S) hence a… in applyStereoChemistryToStereoCentre()256 atomRefs4[i+1] = cipOrderedAtoms.get(i); in applyStereoChemistryToStereoCentre()
743 List<Atom> cipOrderedAtoms = new CipSequenceRules(atom).getNeighbouringAtomsInCipOrder(); in modifyAtomParityToTakeIntoAccountExplicitHydrogen() local745 if (cipOrderedAtoms.indexOf(neighbours.get(0)) > cipOrderedAtoms.indexOf(neighbours.get(1))) { in modifyAtomParityToTakeIntoAccountExplicitHydrogen()