Package org.jmol.modelset

Examples of org.jmol.modelset.Bond$BondSet

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  public Point3fi checkObjectClicked(int x, int y, int modifiers,
                                    BitSet bsVisible) {
    Point3fi pt = new Point3fi();
    Bond bond = findPickedBond(x, y, bsVisible, pt);
    if (bond == null)
      return null;
    pt.index = bond.getIndex();
    viewer.setStatusAtomPicked(-3, "[\"bond\",\"" + bond.getIdentity() + "\"," + pt.x + "," + pt.y + "," + pt.z + "]");
    return pt;
  }
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    if (g3d.isAntialiased()) {
      x <<= 1;
      y <<= 1;
      dmin2 <<= 1;
    }
    Bond pickedBond = null;
    Point3f v = new Point3f();
    Bond[] bonds = modelSet.getBonds();
    for (int i = modelSet.getBondCount(); --i >= 0;) {
      Bond bond = bonds[i];
      if (bond.getShapeVisibilityFlags() == 0)
        continue;
      Atom atom1 = bond.getAtom1();
      Atom atom2 = bond.getAtom2();
      if (!atom1.isVisible(0) || !atom2.isVisible(0))
        continue;
      v.set(atom1);
      v.add(atom2);
      v.scale(0.5f);
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    if (partialCharges == null)
      return;
    clear(true);
    Bond[] bonds = modelSet.getBonds();
    for (int i = bonds.length; --i >= 0;) {
      Bond bond = bonds[i];
      if (!bond.isCovalent())
        continue;
      float c1 = partialCharges[bond.getAtomIndex1()];
      float c2 = partialCharges[bond.getAtomIndex2()];
      if (c1 != c2)
        setDipole(bond.getAtom1(), bond.getAtom2(), c1, c2);
    }
  }
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    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)
        break;
    }
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Related Classes of org.jmol.modelset.Bond$BondSet

  • org.jmol.script.ScriptEvaluator
  • org.jmol.shape.Sticks
  • org.jmol.shapespecial.Dipoles
  • org.jmol.shapespecial.Polyhedra
  • org.jmol.viewer.StateManager$Connections
  • org.jmol.viewer.Viewer
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