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order = JmolEdge.BOND_H_MINUS_4; break; default: order = JmolEdge.BOND_H_CALC; } vHBonds.add(new HBond(nitrogen, oxygen, order, energy)); }
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String key = nitrogen.index + " " + oxygen.index; if (htTemp.containsKey(key)) return; htTemp.put(key, Boolean.TRUE); } vHBonds.add(new HBond(nitrogen, oxygen, type, iEnergy / 1000f)); }
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} static protected int addHydrogenBond(List vAtoms, Atom atom1, Atom atom2) { if (atom1 == null || atom2 == null) return 0; vAtoms.add(new HBond(atom1, atom2, JmolEdge.BOND_H_NUCLEOTIDE, 0)); return 1; }