Package org.openscience.cdk.interfaces

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

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          if(mol != null) {
            StructureConverter.configureMolecule(mol);         
            makeStructure = !MultiFragmentStructureDiagramGenerator.hasStructure(mol);
            if(mol.getAtomCount() == 1) makeStructure = true;
           
            for (Iterator<IAtom> iterator = mol.atoms(); iterator.hasNext();) {//remove explicit hydrogen and make hydrogens properties of atoms to make viewing easier
              IAtom a = iterator.next();
              int hydrogen =0;
              List<IAtom> neighbours = mol.getConnectedAtomsList(a);
              for (IAtom neighbour : neighbours) {
                if (neighbour.getAtomicNumber() ==1 ){
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