Package org.jmol.modelset

Examples of org.jmol.modelset.Atom


    mat.setRow(2, m4.m20, m4.m21, m4.m22);
    matScreenToCartesian.invert(mat);

    Atom[] atoms = modelSet.atoms;
    for (int i = modelSet.getAtomCount(); --i >= 0;) {
      Atom atom = atoms[i];
      if (!atom.isVisible(myVisibilityFlag))
        continue;
      if (atom.screenZ <= 1)
        continue;
      Object[] ellipsoid = atom.getEllipsoid();
      if (ellipsoid == null)
        continue;
      colix = Shape.getColix(ellipsoids.colixes, i, atom);
      if (!g3d.setColix(colix))
        continue;
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          : ((Boolean) value).booleanValue() ? 1 : -1);
      if (mads == null)
        mads = new short[atomCount];
      for (int atomIndex = atomCount; --atomIndex >= 0;) {
        if (bsSelected.get(atomIndex)) {
          Atom atom = atoms[atomIndex];
          if (formats == null || atomIndex >= formats.length)
            formats = ArrayUtil.ensureLength(formats, atomIndex + 1);
          if (strings != null && strings.length > atomIndex
              && strings[atomIndex] != null) {
            mads[atomIndex] = (short) (mode == 0 && mads[atomIndex] <
                || mode == 1 ? 1 : -1);
          } else {
            if (bsSizeSet == null)
              bsSizeSet = new BitSet();
            String strLabel = viewer.getStandardLabelFormat();
            strings = ArrayUtil.ensureLength(strings, atomIndex + 1);
            strings[atomIndex] = LabelToken.formatLabel(viewer, atom, strLabel);
            formats[atomIndex] = strLabel;
            bsSizeSet.set(atomIndex);
            if ((bsBgColixSet == null || !bsBgColixSet.get(atomIndex))
                && defaultBgcolix != 0)
              setBgcolix(atomIndex, defaultBgcolix);
            mads[atomIndex] = (short) (mode >= 0 ? 1 : -1);
          }
          atom.setShapeVisibility(myVisibilityFlag, strings != null
              && atomIndex < strings.length && strings[atomIndex] != null
              && mads[atomIndex] >= 0);
          //        } else if (strings != null && atomIndex < strings.length) {
          //        strings[atomIndex] = null;         
        }
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