Package org.openscience.cdk.interfaces

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

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        a1E.setImplicitHydrogenCount(1);
        a2E.setImplicitHydrogenCount(1);
        acE.addAtom(a1E);
        acE.addAtom(a2E);
        acE.addAtom(a3E);
        acE.addAtom(a4E);

        acE.addBond(new Bond(a1E, a2E, CDKConstants.BONDORDER_DOUBLE));
        acE.addBond(new Bond(a1E, a3E, CDKConstants.BONDORDER_SINGLE));
        acE.addBond(new Bond(a2E, a4E, CDKConstants.BONDORDER_SINGLE));
       
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   */
  private Point2d getConnectedAtomsCenter(IAtomContainer sharedAtoms,
      IChemModel chemModel) {
    IAtomContainer conAtoms = sharedAtoms.getBuilder().newInstance(IAtomContainer.class);
    for (IAtom sharedAtom : sharedAtoms.atoms()) {
      conAtoms.addAtom(sharedAtom);
      IAtomContainer atomCon = ChemModelManipulator
          .getRelevantAtomContainer(chemModel, sharedAtom);
      for (IAtom atom : atomCon.getConnectedAtomsList(sharedAtom)) {
        conAtoms.addAtom(atom);
      }
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        IAtom a2Z = new Atom("C", new Point2d(3.732, 0.060));
        IAtom a3Z = new Atom("Cl", new Point2d(2.000, 0.060));
        IAtom a4Z = new Atom("Cl", new Point2d(3.732, 1.060));
        a1Z.setImplicitHydrogenCount(1);
        a2Z.setImplicitHydrogenCount(1);
        acZ.addAtom(a1Z);
        acZ.addAtom(a2Z);
        acZ.addAtom(a3Z);
        acZ.addAtom(a4Z);

        acZ.addBond(new Bond(a1Z, a2Z, CDKConstants.BONDORDER_DOUBLE));
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        IAtom a3Z = new Atom("Cl", new Point2d(2.000, 0.060));
        IAtom a4Z = new Atom("Cl", new Point2d(3.732, 1.060));
        a1Z.setImplicitHydrogenCount(1);
        a2Z.setImplicitHydrogenCount(1);
        acZ.addAtom(a1Z);
        acZ.addAtom(a2Z);
        acZ.addAtom(a3Z);
        acZ.addAtom(a4Z);

        acZ.addBond(new Bond(a1Z, a2Z, CDKConstants.BONDORDER_DOUBLE));
        acZ.addBond(new Bond(a1Z, a3Z, CDKConstants.BONDORDER_SINGLE));
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   */
  public IRing addRing(IBond bond, int size, boolean phantom) {
    IAtomContainer sharedAtoms = bond.getBuilder().newInstance(IAtomContainer.class);
    IAtom firstAtom = bond.getAtom(0); // Assumes two-atom bonds only
    IAtom secondAtom = bond.getAtom(1);
    sharedAtoms.addAtom(firstAtom);
    sharedAtoms.addAtom(secondAtom);
    sharedAtoms.addBond(bond);
    IAtomContainer sourceContainer = ChemModelManipulator
        .getRelevantAtomContainer(chemModel, firstAtom);

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        IAtom a4Z = new Atom("Cl", new Point2d(3.732, 1.060));
        a1Z.setImplicitHydrogenCount(1);
        a2Z.setImplicitHydrogenCount(1);
        acZ.addAtom(a1Z);
        acZ.addAtom(a2Z);
        acZ.addAtom(a3Z);
        acZ.addAtom(a4Z);

        acZ.addBond(new Bond(a1Z, a2Z, CDKConstants.BONDORDER_DOUBLE));
        acZ.addBond(new Bond(a1Z, a3Z, CDKConstants.BONDORDER_SINGLE));
        acZ.addBond(new Bond(a2Z, a4Z, CDKConstants.BONDORDER_SINGLE));
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        a1Z.setImplicitHydrogenCount(1);
        a2Z.setImplicitHydrogenCount(1);
        acZ.addAtom(a1Z);
        acZ.addAtom(a2Z);
        acZ.addAtom(a3Z);
        acZ.addAtom(a4Z);

        acZ.addBond(new Bond(a1Z, a2Z, CDKConstants.BONDORDER_DOUBLE));
        acZ.addBond(new Bond(a1Z, a3Z, CDKConstants.BONDORDER_SINGLE));
        acZ.addBond(new Bond(a2Z, a4Z, CDKConstants.BONDORDER_SINGLE));
       
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  public IRing addRing(IBond bond, int size, boolean phantom) {
    IAtomContainer sharedAtoms = bond.getBuilder().newInstance(IAtomContainer.class);
    IAtom firstAtom = bond.getAtom(0); // Assumes two-atom bonds only
    IAtom secondAtom = bond.getAtom(1);
    sharedAtoms.addAtom(firstAtom);
    sharedAtoms.addAtom(secondAtom);
    sharedAtoms.addBond(bond);
    IAtomContainer sourceContainer = ChemModelManipulator
        .getRelevantAtomContainer(chemModel, firstAtom);

    Point2d sharedAtomsCenter = GeometryTools.get2DCenter(sharedAtoms);
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    // decide on which side to draw the ring??
    IAtomContainer connectedAtoms = bond.getBuilder().newInstance(IAtomContainer.class);
    for (IAtom atom : sourceContainer.getConnectedAtomsList(firstAtom)) {
      if (atom != secondAtom)
        connectedAtoms.addAtom(atom);
    }
    for (IAtom atom : sourceContainer.getConnectedAtomsList(secondAtom)) {
      if (atom != firstAtom)
        connectedAtoms.addAtom(atom);
    }
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                    List<IAtom> l=container.getConnectedAtomsList(lastplaced);
                    for(int i=0;i<l.size();i++){
                        if(l.get(i).getPoint2d()!=null)
                            placedNeighbours.addAtom((IAtom)l.get(i));
                        else
                            unplacedNeighbours.addAtom((IAtom)l.get(i));
                    }
                    ap.distributePartners(lastplaced, placedNeighbours, GeometryTools.get2DCenter(placedNeighbours), unplacedNeighbours, 1.4);
                    IRingSet ringset=new SSSRFinder(container).findSSSR();
                    for(IAtomContainer ring:ringset.atomContainers()){
                        ringPlacer.placeRing((IRing)ring, GeometryTools.get2DCenter(container), chemModelRelay.getRenderer().getRenderer2DModel().getBondLength() / chemModelRelay.getRenderer().getRenderer2DModel().getScale());
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