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Reason for existence

The IMolecule represents a group of atoms (as in a molecule). The IMolecule holds and manages a list of child IAtomPositioneds and provides it on request in the form of an IAtomList.

Proposed Interface

interface IMolecule {

    attribute int index;

     * Adds the given Atom as a child of this IMolecule.  The given child IAtom
     * should be parentless when this method is called.
     * @throws IllegalArgumentException if the given atom already has a parent.
    void addChildAtom(in IAtomLeaf newChildAtom);

     * Removes the given child Atom from this IMolecule.
     * @throws IllegalArgumentException if the given atom is not a child.
    void removeChildAtom(in IAtomLeaf oldChildAtom);

     * Returns the IAtom children of this IMolecule as an IAtomList
    readonly attribute IAtomList childList;

    readonly attribute ISpecies getType();


IAtomGroup would be used for any multi-atom molecule.


mol-sim-api discussion of IMolecule