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Searched refs:cipOrderedAtoms (Results 1 – 3 of 3) sorted by relevance

/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/
H A DStereoAnalyser.java66 List<Atom> cipOrderedAtoms = new CipSequenceRules(stereoAtom).getNeighbouringAtomsInCipOrder(); in getCipOrderedAtoms() local
67 …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()
H A DStereochemistryHandler.java249 List<Atom> cipOrderedAtoms =stereoCentre.getCipOrderedAtoms(); in applyStereoChemistryToStereoCentre() local
250 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()
H A DFragmentManager.java743 List<Atom> cipOrderedAtoms = new CipSequenceRules(atom).getNeighbouringAtomsInCipOrder(); in modifyAtomParityToTakeIntoAccountExplicitHydrogen() local
745 if (cipOrderedAtoms.indexOf(neighbours.get(0)) > cipOrderedAtoms.indexOf(neighbours.get(1))) { in modifyAtomParityToTakeIntoAccountExplicitHydrogen()