Package org.jmol.modelset

Examples of org.jmol.modelset.Atom

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    xAxis1 += dxStep; yAxis1 += dyStep;
    xAxis2 += dxStep; yAxis2 += dyStep;
  }

  private int getAromaticDottedBondMask() {
    Atom atomC = atomB.findAromaticNeighbor(atomA.getIndex());
    if (atomC == null)
      return 1;
    int dxAC = atomC.screenX - xA;
    int dyAC = atomC.screenY - yA;
    return ((dx * dyAC - dy * dxAC) < 0 ? 2 : 1);
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    if (bsSizeSet == null)
      bsSizeSet = new BitSet();
    int bsLength = Math.min(atoms.length, bsSelected.length());
    for (int i = bsSelected.nextSetBit(0); i >= 0 && i < bsLength; i = bsSelected
        .nextSetBit(i + 1)) {
      Atom atom = atoms[i];
      atom.setMadAtom(viewer, rd);
      bsSizeSet.set(i);
    }
  }
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        colix = Graphics3D.USE_PALETTE;
      if (bsColixSet == null)
        bsColixSet = new BitSet();
      byte pid = JmolConstants.pidOf(value);
      for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
        Atom atom = atoms[i];
        atom.setColixAtom(setColix(colix, pid, atom));
        bsColixSet.set(i, colix != Graphics3D.USE_PALETTE
            || pid != JmolConstants.PALETTE_NONE);
        atom.setPaletteID(pid);
      }
      return;
    }
    if ("colorValues" == propertyName) {
      int[] values = (int[]) value;
      if (values.length == 0)
        return;
      if (bsColixSet == null)
        bsColixSet = new BitSet();
      int n = 0;
      Integer color = null;
      for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
        if (n >= values.length)
          return;
        color = new Integer(values[n++]);
        short colix = Graphics3D.getColix(color);
        if (colix == Graphics3D.INHERIT_ALL)
          colix = Graphics3D.USE_PALETTE;
        byte pid = JmolConstants.pidOf(color);
        Atom atom = atoms[i];
        atom.setColixAtom(setColix(colix, pid, atom));
        bsColixSet.set(i, colix != Graphics3D.USE_PALETTE
            || pid != JmolConstants.PALETTE_NONE);
        atom.setPaletteID(pid);
      }
      return;
    }
    if ("translucency" == propertyName) {
      boolean isTranslucent = (((String) value).equals("translucent"));
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public void setModelClickability() {
   BitSet bs = viewer.getDeletedAtoms();
   if (bs == null)
     bs = new BitSet();
   for (int i = atomCount; --i >= 0;) {
     Atom atom = atoms[i];
     atom.setClickable(0);
     if (bs.get(i) || (atom.getShapeVisibilityFlags() & myVisibilityFlag) == 0
         || modelSet.isAtomHidden(i))
       continue;
     atom.setClickable(myVisibilityFlag);
   }
}
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public void setVisibilityFlags(BitSet bs) {
    boolean showHydrogens = viewer.getShowHydrogens();
    BitSet bsDeleted = viewer.getDeletedAtoms();
    for (int i = atomCount; --i >= 0; ) {
      Atom atom = atoms[i];
      int flag = atom.getShapeVisibilityFlags();
      flag &= (~JmolConstants.ATOM_IN_FRAME & ~myVisibilityFlag);
      atom.setShapeVisibilityFlags(flag);
      if (bsDeleted != null && bsDeleted.get(i)
          || !showHydrogens && atom.getElementNumber() == 1)
        continue;
      int modelIndex = atom.getModelIndex();
      if (bs.get(modelIndex)) {
        atom.setShapeVisibility(JmolConstants.ATOM_IN_FRAME, true);
        if (atom.madAtom != 0 &&  !modelSet.isAtomHidden(i))
          atom.setShapeVisibility(myVisibilityFlag, true);
      }
    }
  }
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    }
    iter.release();
  }

  private Polyhedron constructBondsPolyhedron(int atomIndex) {
    Atom atom = atoms[atomIndex];
    Bond[] bonds = atom.getBonds();
    if (bonds == null)
      return null;
    int bondCount = 0;
    for (int i = bonds.length; --i >= 0;) {
      Bond bond = bonds[i];
      Atom otherAtom = bond.getAtom1() == atom ? bond.getAtom2() : bond
          .getAtom1();
      if (bsVertices != null && !bsVertices.get(otherAtom.getIndex()))
        continue;
      if (radius > 0f && bond.getAtom1().distance(bond.getAtom2()) > radius)
        continue;
      otherAtoms[bondCount++] = otherAtom;
      if (bondCount == MAX_VERTICES)
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      otherAtoms[otherAtomCount++] = atoms[i];
    return validatePolyhedronNew(atoms[atomIndex], otherAtomCount, otherAtoms);
  }

  private Polyhedron constructRadiusPolyhedron(int atomIndex, AtomIndexIterator iter) {
    Atom atom = atoms[atomIndex];
    int otherAtomCount = 0;
    viewer.setIteratorForAtom(iter, atomIndex, radius);
    while (iter.hasNext()) {
      Atom other = atoms[iter.next()];
      if (bsVertices != null && !bsVertices.get(other.getIndex())
          || atom.distance(other) > radius)
        continue;
      if (other.getAlternateLocationID() != atom.getAlternateLocationID()
          && other.getAlternateLocationID() != 0
          && atom.getAlternateLocationID() != 0)
        continue;
      if (otherAtomCount == MAX_VERTICES)
        break;
      otherAtoms[otherAtomCount++] = other;
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      return;
    isAntialiased = g3d.isAntialiased();
    Atom[] atoms = modelSet.atoms;
    BitSet bsSelected = (selectDisplayTrue ? viewer.getSelectionSet(false) : null);
    for (int i = modelSet.getAtomCount(); --i >= 0;) {
      Atom atom = atoms[i];
      if ((atom.getShapeVisibilityFlags() & JmolConstants.ATOM_IN_FRAME) == 0)
        continue;
      boolean isHidden = modelSet.isAtomHidden(i);
      mad = (halos.mads == null ? 0 : halos.mads[i]);
      colix = (halos.colixes == null || i >= halos.colixes.length ? Graphics3D.INHERIT_ALL
          : halos.colixes[i]);
      if (selectDisplayTrue && bsSelected.get(i)) {
        if (isHidden && !showHiddenSelections)
          continue;
        if (mad == 0)
          mad = -1; // unsized
        if (colix == Graphics3D.INHERIT_ALL)
          colix = halos.colixSelection;
        if (colix == Graphics3D.USE_PALETTE)
          colix = Graphics3D.GOLD;
        else if (colix == Graphics3D.INHERIT_ALL)
          colix = Graphics3D.getColixInherited(colix, atom.getColix());
      } else if (isHidden) {
        continue;
      } else {
        colix = Graphics3D.getColixInherited(colix, atom.getColix());
      }
      if (mad != 0)
        render1(atom);
      if (!isHidden && halos.bsHighlight != null && halos.bsHighlight.get(i)) {
        mad = -2;
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    minAtoms = new MinAtom[atomCount];
    int elemnoMax = 0;
    BitSet bsElements = new BitSet();
    for (int i = bsAtoms.nextSetBit(0), pt = 0; i >= 0; i = bsAtoms
        .nextSetBit(i + 1), pt++) {
      Atom atom = atoms[i];
      atomMap[i] = pt;
      int atomicNo = atoms[i].getElementNumber();
      elemnoMax = Math.max(elemnoMax, atomicNo);
      bsElements.set(atomicNo);
      minAtoms[pt] = new MinAtom(pt, atom, new double[] { atom.x, atom.y,
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  void updateAtomXYZ() {
    if (steps <= 0)
      return;
    for (int i = 0; i < atomCount; i++) {
      MinAtom minAtom = minAtoms[i];
      Atom atom = minAtom.atom;
      atom.x = (float) minAtom.coord[0];
      atom.y = (float) minAtom.coord[1];
      atom.z = (float) minAtom.coord[2];
    }
    viewer.refreshMeasures(false);
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Related Classes of org.jmol.modelset.Atom

  • org.jmol.minimize.Minimizer
  • org.jmol.modelsetbio.AlphaMonomer
  • org.jmol.modelsetbio.AlphaPolymer
  • org.jmol.modelsetbio.AminoMonomer
  • org.jmol.modelsetbio.AminoPolymer
  • org.jmol.modelsetbio.BioPolymer
  • org.jmol.modelsetbio.CarbohydrateMonomer
  • org.jmol.modelsetbio.Monomer
  • org.jmol.modelsetbio.NucleicMonomer
  • org.jmol.modelsetbio.NucleicPolymer
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