CMLTools

CMLTools add non-DOM functionality to CMLDOM

public interface MoleculeTool extends BaseTool {
    void   createCartesiansFromFractionals(RealSquareMatrix orthogonalMatrix);
    int    getCalculatedFormalCharge();
    CMLMolecule[] joinCoordinates();
    void   expandImplicitHydrogens(String control);
    void   contractExplicitHydrogens(String control);
    void   addCalculatedCoordinatesForHydrogens(String control);
    FormulaTool getCalculatedFormula(String control);
    void   setPreferredBondOrders();
    void   setBondOrders(String order);
    void   adjustHydrogenCountsToValency(String control);
    void   adjustBondOrdersToValency();
    void   reorderAtoms(int order[]);
    void   partitionIntoMolecules();
    void   add2DCoordinates();
    void   calculateBondedAtoms();
    void   deleteBond(CMLAtom atom1, CMLAtom atom2);
    void   transform(Transform3 transform);
    Vector getRingNuclei();
    Vector getMoleculesFromRingSetVector(Vector ringSetVector);
    Real2  getCentroid2D();
}