Package org.openscience.cdk.interfaces

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

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        deletedAtoms.get(i).getPoint2d().x+=offset.x;
        deletedAtoms.get(i).getPoint2d().y+=offset.y;
        chemModelRelay.updateAtom(mergedPartnerAtoms.get(i));

        if (droppedContainer!=null) {
              for (IAtom mAt : droppedContainer.atoms()) {
                if (!containerWithMerge.contains(mAt)) {
                  containerWithMerge.addAtom(mAt);
                }
              }
              for (IBond mBond : droppedContainer.bonds()) {
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            chemModelRelay.updateAtom(mergedPartnerAtoms.get(i));

            if (droppedContainer!=null) {
             
              //remove from atc1 what was merged in from atc2
              for (IAtom mAt : droppedContainer.atoms()) {
                if (containerWithMerge.contains(mAt)) {
                  containerWithMerge.removeAtom(mAt);
                }
              }
              for (IBond mBond : droppedContainer.bonds()) {
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            // It could be that only a  selected bond is going to be moved.
            // So make sure that the attached atoms are included, otherwise
            // the undo will fail to place the atoms back where they were
           atomsToMove = new HashSet<IAtom>();

            for (IAtom atom : selectedAC.atoms()) {
                atomsToMove.add(atom);
            }
            for (IBond bond : selectedAC.bonds()) {
                for (IAtom atom : bond.atoms()){
                    atomsToMove.add(atom);
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   */
  public void mouseClickedDown(Point2d worldCoord) {
     
      IAtomContainer selectedAC = getSelectedAtomContainer( worldCoord );
      if(selectedAC == null) return;
      for(IAtom atom:selectedAC.atoms()) {
            if(add){
                chemModelRelay.addSingleElectron(atom);
            }else{
                chemModelRelay.removeSingleElectron(atom);
            }
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