Package org.jmol.api

Examples of org.jmol.api.AtomIndexIterator.foundDistance2()

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        if (!isNearInSetA && !isNearInSetB
            || !(isAtomInSetA && isNearInSetB || isAtomInSetB && isNearInSetA)
            || isFirstExcluded && bsExclude.get(atomIndexNear))
          continue;
        short order = getBondOrder(myBondingRadius, atomNear
            .getBondingRadiusFloat(), iter.foundDistance2(), minBondDistance2,
            bondTolerance);
        if (order > 0) {
          if (checkValencesAndBond(atom, atomNear, order, mad, bsBonds))
            nNew++;
        }
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      while (iter.hasNext()) {
        Atom atomNear = atoms[iter.next()];
        int elementNumberNear = atomNear.getElementNumber();
        if (atomNear == atom || !isH && elementNumberNear != 7
            && elementNumberNear != 8 || isH && elementNumberNear == 1
            || (d2 = iter.foundDistance2()) < min2 || d2 > max2 || firstIsCO
            && bsCO.get(atomNear.index) || atom.isBonded(atomNear)) {
          continue;
        }
        if (minAttachedAngle > 0) {
          v1.sub(atom, atomNear);
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