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Searched refs:AMBIGUOUS_ELEMENT_ASSIGNMENT (Results 1 – 5 of 5) sorted by relevance

/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/
H A DFunctionalReplacement.java399 if (atomThatWillReplaceOxygen.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT)!=null){ in processInfixFunctionalReplacementNomenclature()
400 …guousElementAtoms.addAll(atomThatWillReplaceOxygen.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT)); in processInfixFunctionalReplacementNomenclature()
406 if (a.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT)!=null){ in processInfixFunctionalReplacementNomenclature()
407 ambiguousElementAtoms.addAll(a.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT)); in processInfixFunctionalReplacementNomenclature()
412 if (a.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT)!=null){ in processInfixFunctionalReplacementNomenclature()
413 ambiguousElementAtoms.addAll(a.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT)); in processInfixFunctionalReplacementNomenclature()
417 atom.setProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT, ambiguousElementAtoms); in processInfixFunctionalReplacementNomenclature()
710 atom.setProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT, ambiguousElementAtoms); in performChalcogenFunctionalReplacement()
H A DFragmentManager.java411 …Set<Atom> oldAmbiguousElementAssignmentAtoms = atom.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT); in copyAndRelabelFragment()
417 oldToNewAtomMap.get(atom).setProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT, newAtoms); in copyAndRelabelFragment()
659 Set<Atom> ambiguousElementAssignment = atom.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT); in removeAtomAndAssociatedBonds()
663 … ambiguousElementAssignment.iterator().next().setProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT, null); in removeAtomAndAssociatedBonds()
H A DAtom.java52 …static final PropertyKey<Set<Atom>> AMBIGUOUS_ELEMENT_ASSIGNMENT = new PropertyKey<Set<Atom>>("amb… field in Atom
H A DSuffixApplier.java567 Set<Atom> ambiguouslyElementedAtoms = atom.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT); in swapElementsSuchThatThisElementIsAcidic()
H A DStructureBuilder.java1704 Set<Atom> degenerateAtoms = possibleAtom.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT); in determineFunctionalAtomToUse()
1717 Set<Atom> degenerateAtoms = possibleAtom.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT); in determineFunctionalAtomToUse()
1736 Set<Atom> degenerateAtoms = possibleAtom.getProperty(Atom.AMBIGUOUS_ELEMENT_ASSIGNMENT); in determineFunctionalAtomToUse()