Package org.openscience.cdk.interfaces

Examples of org.openscience.cdk.interfaces.IAtomContainer.addAtom()

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        acD.addAtom(a1D);
        acD.addAtom(a2D);
        acD.addAtom(a3D);
        acD.addAtom(a4D);
        acD.addAtom(a5D);
        acD.addAtom(a6D);
       
        acD.addBond(new Bond(a1D, a2D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a1D, a3D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a1D, a4D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a2D, a5D, CDKConstants.BONDORDER_SINGLE));
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      newMoleculeSet.addAtomContainer(toPaste);
      moleculeToAddTo = toPaste;
    } else {
      IAtomContainer mol = chemModel.getBuilder().newInstance(IAtomContainer.class);
      for (IAtom atom: moleculeToAddTo.atoms())
        mol.addAtom(atom);
      for (IBond bond: moleculeToAddTo.bonds())
        mol.addBond(bond);
      oldMoleculeSet.addAtomContainer(mol);
      moleculeToAddTo.add(toPaste);
    }
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    if(rGroupHandler!=null && !rGroupHandler.checkRGroupOkayForDelete(selected, this))
      return removed;
   
    for (int i = 0; i < selected.getAtomCount(); i++) {
      IAtom atom = selected.getAtom(i);
      removed.addAtom(atom);
      Iterator<IBond> it = ChemModelManipulator.getRelevantAtomContainer(
          chemModel, atom).getConnectedBondsList(atom).iterator();
      IAtomContainer ac = selected.getBuilder().newInstance(IAtomContainer.class);
      while (it.hasNext()) {
        IBond bond = it.next();
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    for (int i = 0; i < containers.size(); i++) {
      IAtomContainer removeatoms = chemModel.getBuilder()
          .newInstance(IAtomContainer.class);
      for (IAtom atom : containers.get(i).atoms()) {
        if (atom.getSymbol().equals("H")) {
          removeatoms.addAtom(atom);
          removeatoms.addBond(containers.get(i)
              .getConnectedBondsList(atom).get(0));
          containers
              .get(i)
              .getConnectedAtomsList(atom)
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    if (container != null) {
      for (int i = 0; i < 2; i++) {
        if (container.getConnectedAtomsCount(bondToRemove.getAtom(i)) == 0) {
          removeAtomWithoutUndo(bondToRemove.getAtom(i));
          undoRedoContainer.addAtom(bondToRemove.getAtom(i));
        }
      }
    }
    removeEmptyContainers(chemModel);
    IUndoRedoable undoredo = getUndoRedoFactory()
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    if (totalmove != null && getUndoRedoFactory() != null
        && getUndoRedoHandler() != null) {
      IAtomContainer undoRedoContainer = chemModel.getBuilder()
          .newInstance(IAtomContainer.class);
      for (IAtom atom : atoms) {
        undoRedoContainer.addAtom(atom);
      }
      IUndoRedoable undoredo = getUndoRedoFactory().getMoveAtomEdit(
          undoRedoContainer, totalmove, "Move atom");
      getUndoRedoHandler().postEdit(undoredo);
    }
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        applet.button("C").click();
        applet.button("bondTool").click();
        applet.panel("renderpanel").robot.click(applet.panel("renderpanel").component(),new Point(100,100));
    IAtomContainer ethane = panel.getChemModel().getMoleculeSet().getAtomContainer(0);
    IAtomContainer selected = ethane.getBuilder().newInstance(IAtomContainer.class);
    selected.addAtom(ethane.getAtom(0));
    panel.getRenderPanel().getHub().deleteFragment(selected);
       
        /*
        applet.button("C").click();
        applet.button("bondTool").click();
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        applet.button("C").click();
        applet.button("bondTool").click();
        applet.panel("renderpanel").robot.click(applet.panel("renderpanel").component(),new Point(100,100));
    IAtomContainer ethane = panel.getChemModel().getMoleculeSet().getAtomContainer(0);
    IAtomContainer selected = ethane.getBuilder().newInstance(IAtomContainer.class);
    selected.addAtom(ethane.getAtom(0));
    panel.getRenderPanel().getHub().deleteFragment(selected);
       
        /*
        applet.button("C").click();
        applet.button("bondTool").click();
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   * @param hub
   * @return
   */
  public boolean checkRGroupOkayForDelete(IAtom at,IChemModelRelay hub ) {
    IAtomContainer tmp = at.getBuilder().newInstance(IAtomContainer.class);
    tmp.addAtom(at);
    return (checkRGroupOkayForDelete(tmp,hub));
  }

  /**
   * TODO
 
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        IAtomContainer ac = new AtomContainer();
        if (atoms.size() != 0) {
           ac = atoms.get(0).getBuilder().newInstance(IAtomContainer.class);
           for (IAtom atom : atoms) {
              ac.addAtom(atom);
           }
        }
       
        for (IBond bond : bonds) {
           ac.addBond(bond);
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