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Searched refs:OXIDATION_NUMBER (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 DFragmentManager.java423 Integer oxidationNumber = atom.getProperty(Atom.OXIDATION_NUMBER); in copyAndRelabelFragment()
425 oldToNewAtomMap.get(atom).setProperty(Atom.OXIDATION_NUMBER, oxidationNumber); in copyAndRelabelFragment()
H A DStructureBuilder.java524 else if (elementaryAtom.getProperty(Atom.OXIDATION_NUMBER)!=null){ in buildOxide()
525 …int valency = elementaryAtom.getProperty(Atom.OXIDATION_NUMBER) - elementaryAtom.getIncomingValenc… in buildOxide()
1123 if (elementaryAtom.getProperty(Atom.OXIDATION_NUMBER) != null) { in buildAdditionCompound()
1124 expectedValency = elementaryAtom.getProperty(Atom.OXIDATION_NUMBER); in buildAdditionCompound()
2001 …if (metalAtom.getCharge() == 0 && metalAtom.getProperty(Atom.OXIDATION_NUMBER) == null) {//if not … in getMetalsThatCanBeImplicitlyCations()
2308 if (atom.getProperty(Atom.OXIDATION_NUMBER)!=null){ in processOxidationNumbers()
2321 … atom.setCharge(atom.getProperty(Atom.OXIDATION_NUMBER)-chargeThatWouldFormIfLigandsWereRemoved); in processOxidationNumbers()
H A DAtom.java62 static final PropertyKey<Integer> OXIDATION_NUMBER = new PropertyKey<Integer>("oxidationNumber"); field in Atom
H A DFragmentTools.java1156 Integer oxidationNumber = atom.getProperty(Atom.OXIDATION_NUMBER);//explicitly set oxidation state in getTimesElementaryAtomCanBeSubstituted()
H A DComponentProcessor.java701 …frag.getFirstAtom().setProperty(Atom.OXIDATION_NUMBER, Integer.parseInt(nextEl.getAttributeValue(V… in processChargeAndOxidationNumberSpecification()